title: control17_platelets

description: 20101122_RD_Lankenau_c17_Platelet_RNA_1ug_B1_T1.CEL

value: Blood

value: platelets

value: healthy control


title: control20_platelets

status: Public on Feb 21 2012

type: RNA

city: Santa Clara

first: Radha

last: Duttagupta

state: CA

address: 3450 Central Expressway

department: Applied Research

country: USA

institute: Affymetrix

description: 20101122_RD_Lankenau_c20_Platelet_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.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: platelets

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.

tag: tissue

tag: cell type

tag: disease status

tag: subject


title: KO_C226TG_rep2

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

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).

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 using GCRMA (v2.2.0) in Bioconductor, applying the emperical Bayes (EB) model for background estimation.

organism: Mus musculus

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.

tag: strain

tag: gender

value: male

tag: age

tag: genotype

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

tag: treatment

value: tridocosahexaenoin


title: KO_C226TG_rep1


title: control18_platelets

description: 20101122_RD_Lankenau_c18_Platelet_RNA_1ug_B1_T1.CEL


title: Fasting Insulin Resistant 21

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: Fasting Insulin Resistant

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

extract_protocol: 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: female

value: subcutaneous adipose

tag: stimulation

value: fasting

tag: resistance status

value: resistant


title: 129S6_BrainStem_Wild-type HSV-1_1d_m (251486827618_1_3)

city: Seattle

first: Michael

last: Katze

state: WA

address: Rosen Building 960 Republican St.

department: Microbiology

institute: University of Washington

description: US93503719_251486827618_S01_GE1-v5_95_Feb07_1_3.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 G2505C).

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: BrainStem

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

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.

tag: genotype/variation

value: Wild-type

value: BrainStem

value: m

tag: sample collection time post infection

tag: virus infection

value: Wild-type HSV-1


title: 129S6_BrainStem_mock_7d_f (251486827692_1_1)

description: US93503719_251486827692_S01_GE1-v5_95_Feb07_1_1.txt

value: f

value: mock


title: Fasting Insulin Resistant 14


title: Fasting Insulin Resistant 9


title: 129S6_BrainStem_mock_7d_m (251486827692_1_4)

description: US93503719_251486827692_S01_GE1-v5_95_Feb07_1_4.txt


title: Fasting Insulin Resistant 1


title: 129S6_BrainStem_mock_5d_m (251486827618_1_1)

description: US93503719_251486827618_S01_GE1-v5_95_Feb07_1_1.txt


title: control15_platelets

description: 20101122_RD_Lankenau_c15_Platelet_RNA_1ug_B1_T1.CEL


title: control13_platelets

description: 20101122_RD_Lankenau_c13_Platelet_RNA_1ug_B1_T1.CEL


title: control14_platelets

description: 20101122_RD_Lankenau_c14_Platelet_RNA_1ug_B1_T1.CEL


title: control16_platelets

description: 20101122_RD_Lankenau_c16_Platelet_RNA_1ug_B1_T1.CEL


title: KO_C181TG_rep2

value: triolein


title: KO_C181TG_rep4


title: KO_C181TG_rep3


title: KO_C181TG_rep1


title: control11_platelets

description: 20101122_RD_Lankenau_c11_Platelet_RNA_1ug_B1_T1.CEL

value: Blood


title: KO_C226TG_rep3


title: patient12_Microvesicles

description: 20101118_RD_Lankenau_p12_Microvesicles_RNA_3ug_B1_T1.CEL

source_name: Microvesicles

value: Microvesicles

value: ulcerative colitis


title: 129S6_BrainStem_mock_5d_f (251486827693_1_2)

description: US93503719_251486827693_S01_GE1-v5_95_Feb07_1_2.txt


title: 129S6_BrainStem_mock_3d_m (251486827141_1_4)

description: US93503719_251486827141_S01_GE1-v5_95_Feb07_1_4.txt


title: KO_C182TG_rep5

value: male

value: trilinolein


title: 129S6_BrainStem_mock_3d_f (251486827612_1_1)

description: US93503719_251486827612_S01_GE1-v5_95_Feb07_1_1.txt


title: KO_C182TG_rep3

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


title: 129S6_BrainStem_mock_1d_m (251486827617_1_4)

description: US93503719_251486827617_S01_GE1-v5_95_Feb07_1_4.txt


title: KO_C182TG_rep4


title: Muscle_Old_Men_22.0

city: Indianapolis

first: Shawn

middle: T.

last: Estrem

address: Lilly Corporate Center

institute: Eli Lilly and Company

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: Vastus lateralis muscle

value: Old

value: Male


title: Muscle_Old_Men_19.0


title: Muscle_Old_Men_15.0


title: control10_platelets

description: 20101122_RD_Lankenau_c10_Platelet_RNA_1ug_B1_T1.CEL

value: platelets

value: healthy control


title: control12_platelets

description: 20101122_RD_Lankenau_c12_Platelet_RNA_1ug_B1_T1.CEL


title: 129S6_BrainStem_mock_1d_m (251486827693_1_4)

description: US93503719_251486827693_S01_GE1-v5_95_Feb07_1_4.txt

value: Wild-type

value: BrainStem


title: control8_platelets

description: 20101122_RD_Lankenau_c8_Platelet_RNA_1ug_B1_T1.CEL


title: control6_platelets

description: 20101122_RD_Lankenau_c6_Platelet_RNA_1ug_B1_T1.CEL


title: Muscle_Old_Men_12.0


title: 129S6_BrainStem_vhs-null HSV-1_7d_m (251486827612_1_3)

description: US93503719_251486827612_S01_GE1-v5_95_Feb07_1_3.txt

value: m

value: vhs-null HSV-1


title: Muscle_Old_Men_33.0


title: 129S6_BrainStem_vhs-null HSV-1_5d_f (251486827696_1_1)

description: US93503719_251486827696_S01_GE1-v5_95_Feb07_1_1.txt

value: f


title: KO_C182TG_rep1


title: Muscle_Old_Men_5.0


title: KO_C182TG_rep2


title: 129S6_BrainStem_vhs-null HSV-1_3d_m (251486827142_1_2)

description: US93503719_251486827142_S01_GE1-v5_95_Feb07_1_2.txt


title: KO_C183TG_rep2

value: trilinolenin


title: 129S6_BrainStem_vhs-null HSV-1_5d_m (251486827693_1_3)

description: US93503719_251486827693_S01_GE1-v5_95_Feb07_1_3.txt


title: 129S6_Liver_Wild-type HSV-1_7d_m (251486831387_1_3)

description: US93503719_251486831387_S01_GE1-v5_95_Feb07_1_3.txt

source_name: Liver

value: Liver

value: Wild-type HSV-1


title: KO_C183TG_rep4


title: 129S6_BrainStem_vhs-null HSV-1_7d_f (251486827612_1_2)

description: US93503719_251486827612_S01_GE1-v5_95_Feb07_1_2.txt


title: Muscle_Young_Men_14.0

value: Young


title: Muscle_Old_Men_2.0


title: Muscle_Old_Men_25.0


title: Muscle_Young_Men_8.0


title: control7_platelets

description: 20101122_RD_Lankenau_c7_Platelet_RNA_1ug_B1_T1.CEL

value: Blood


title: KO_C183TG_rep3

value: male


title: 129S6_Liver_Wild-type HSV-1_7d_f (251486831368_1_3)

description: US93503719_251486831368_S01_GE1-v5_95_Feb07_1_3.txt


title: control2_platelets

description: 20101122_RD_Lankenau_c2_Platelet_RNA_1ug_B1_T1.CEL


title: Muscle_Old_Men_35.0


title: control5_platelets

description: 20101122_RD_Lankenau_c5_Platelet_RNA_1ug_B1_T1.CEL


title: control4_platelets

description: 20101122_RD_Lankenau_c4_Platelet_RNA_1ug_B1_T1.CEL


title: KO_C183TG_rep5

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


title: control1_platelets

description: 20101122_RD_Lankenau_c1_Platelet_RNA_1ug_B1_T1.CEL


title: KO_C183TG_rep1


title: KO_Control_rep5


title: control3_platelets

description: 20101122_RD_Lankenau_c3_Platelet_RNA_1ug_B1_T1.CEL


title: Muscle_Old_Men_32.0

value: Vastus lateralis muscle


title: 129S6_BrainStem_vhs-null HSV-1_3d_f (251486827121_1_4)

description: US93503719_251486827121_S01_GE1-v5_95_Feb07_1_4.txt


title: patient7c_platelets

description: 20101122_RD_Lankenau_p7c_Platelet_RNA_1ug_B1_T1.CEL

value: ulcerative colitis


title: patient7b_platelets

description: 20101122_RD_Lankenau_p7b_Platelet_RNA_1ug_B1_T1.CEL


title: 129S6_Liver_Wild-type HSV-1_5d_f (251486831258_1_2)

description: US93503719_251486831258_S01_GE1-v5_95_Feb07_1_2.txt


title: 129S6_Liver_Wild-type HSV-1_5d_m (251486831228_1_1)

description: US93503719_251486831228_S01_GE1-v5_95_Feb07_1_1.txt


title: Muscle_Young_Men_23.0

value: Male


title: Muscle_Young_Men_20.0


title: 129S6_Liver_Wild-type HSV-1_3d_f (251486831359_1_2)

description: US93503719_251486831359_S01_GE1-v5_95_Feb07_1_2.txt


title: KO_Control_rep3


title: 129S6_Liver_Wild-type HSV-1_3d_m (251486831226_1_1)

description: US93503719_251486831226_S01_GE1-v5_95_Feb07_1_1.txt


title: KO_Control_rep1


title: WT_WY_rep4

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


title: 129S6_Liver_Wild-type HSV-1_1d_m (251486831367_1_1)

description: US93503719_251486831367_S01_GE1-v5_95_Feb07_1_1.txt


title: Muscle_Young_Men_11.0


title: Muscle_Young_Men_1.0


title: patient7a_platelets

description: 20101122_RD_Lankenau_p7a_Platelet_RNA_1ug_B1_T1.CEL

value: platelets


title: KO_Control_rep2


title: KO_Control_rep4


title: 129S6_Liver_Wild-type HSV-1_1d_m (251486831126_1_4)

description: US93503719_251486831126_S01_GE1-v5_95_Feb07_1_4.txt

value: Wild-type


title: patient14_platelets

description: 20101208_RD_Lankenau_p14_Platelet_RNA_1ug_B2_T1.CEL


title: 129S6_Liver_mock_7d_m (251486831356_1_2)

description: US93503719_251486831356_S01_GE1-v5_95_Feb07_1_2.txt

value: mock


title: patient21_platelets

description: 20101122_RD_Lankenau_p21_Platelet_RNA_1ug_B1_T1.CEL


title: Muscle_Old_Female_31.0

value: Old

value: Female


title: patient19_platelets

description: 20101122_RD_Lankenau_p19_Platelet_RNA_1ug_B1_T1.CEL


title: Muscle_Young_Men_26.0


title: Muscle_Old_Female_17.0


title: patient20_platelets

description: 20101122_RD_Lankenau_p20_Platelet_RNA_1ug_B1_T1.CEL


title: patient18_platelets

description: 20101122_RD_Lankenau_p18_Platelet_RNA_1ug_B1_T1.CEL


title: WT_WY_rep2


title: Muscle_Old_Female_24.0


title: WT_WY_rep1


title: 129S6_Liver_mock_7d_f (251486831388_1_3)

description: US93503719_251486831388_S01_GE1-v5_95_Feb07_1_3.txt

value: f


title: patient17_platelets

description: 20101122_RD_Lankenau_p17_Platelet_RNA_1ug_B1_T1.CEL


title: WT_WY_rep3


title: Muscle_Old_Female_27.0


title: Muscle_Old_Female_34.0


title: 129S6_Liver_mock_5d_f (251486831357_1_2)

description: US93503719_251486831357_S01_GE1-v5_95_Feb07_1_2.txt


title: 129S6_Liver_mock_5d_m (251486831367_1_4)

description: US93503719_251486831367_S01_GE1-v5_95_Feb07_1_4.txt

value: m


title: patient16_platelets

description: 20101122_RD_Lankenau_p16_Platelet_RNA_1ug_B1_T1.CEL


title: patient15_platelets

description: 20101122_RD_Lankenau_p15_Platelet_RNA_1ug_B1_T1.CEL


title: 129S6_Liver_mock_3d_m (251486831228_1_3)

description: US93503719_251486831228_S01_GE1-v5_95_Feb07_1_3.txt

value: Liver


title: 129S6_Liver_mock_3d_f (251486831388_1_1)

description: US93503719_251486831388_S01_GE1-v5_95_Feb07_1_1.txt


title: Muscle_Old_Female_7.0


title: WT_C226TG_rep2

value: tridocosahexaenoin


title: WT_C226TG_rep3


title: patient13_platelets

description: 20101122_RD_Lankenau_p13_Platelet_RNA_1ug_B1_T1.CEL


title: WT_C181TG_rep4

value: triolein


title: patient12_platelets

description: 20101122_RD_Lankenau_p12_Platelet_RNA_1ug_B1_T1.CEL

value: Blood


title: WT_C226TG_rep1

value: male


title: 129S6_Liver_vhs-null HSV-1_7d_m (251486831386_1_4)

description: US93503719_251486831386_S01_GE1-v5_95_Feb07_1_4.txt

value: vhs-null HSV-1


title: WT_C226TG_rep4


title: Muscle_Old_Female_10.0

value: Vastus lateralis muscle


title: 129S6_Liver_mock_1d_m (251486831359_1_3)

description: US93503719_251486831359_S01_GE1-v5_95_Feb07_1_3.txt


title: patient9_platelets

description: 20101122_RD_Lankenau_p9_Platelet_RNA_1ug_B1_T1.CEL

value: ulcerative colitis


title: WT_C181TG_rep3


title: 129S6_Liver_vhs-null HSV-1_7d_f (251486831128_1_1)

description: US93503719_251486831128_S01_GE1-v5_95_Feb07_1_1.txt


title: Muscle_Old_Female_13.0


title: Muscle_Old_Female_36.0


title: patient11_platelets

description: 20101122_RD_Lankenau_p11_Platelet_RNA_1ug_B1_T1.CEL


title: patient10_platelets

description: 20101122_RD_Lankenau_p10_Platelet_RNA_1ug_B1_T1.CEL


title: Muscle_Old_Female_4.0


title: Muscle_Old_Female_29.0


title: 129S6_Liver_mock_1d_m (251486831357_1_1)

description: US93503719_251486831357_S01_GE1-v5_95_Feb07_1_1.txt


title: 129S6_Liver_vhs-null HSV-1_5d_m (251486831368_1_1)

description: US93503719_251486831368_S01_GE1-v5_95_Feb07_1_1.txt


title: patient8_platelets

description: 20101122_RD_Lankenau_p8_Platelet_RNA_1ug_B1_T1.CEL


title: 129S6_Liver_vhs-null HSV-1_5d_f (251486831230_1_4)

description: US93503719_251486831230_S01_GE1-v5_95_Feb07_1_4.txt


title: patient6_platelets

description: 20101122_RD_Lankenau_p6_Platelet_RNA_1ug_B1_T1.CEL


title: Muscle_Young_Female_28.0

value: Young


title: WT_C181TG_rep2


title: WT_C182TG_rep5

value: trilinolein


title: WT_C181TG_rep1


title: patient5_platelets

description: 20101122_RD_Lankenau_p5_Platelet_RNA_1ug_B1_T1.CEL

value: platelets


title: 129S6_Liver_vhs-null HSV-1_3d_f (251486831356_1_1)

description: US93503719_251486831356_S01_GE1-v5_95_Feb07_1_1.txt

value: Wild-type


title: 129S6_Liver_vhs-null HSV-1_3d_m (251486831129_1_4)

description: US93503719_251486831129_S01_GE1-v5_95_Feb07_1_4.txt


title: WT_C182TG_rep3


title: WT_C182TG_rep4


title: Muscle_Young_Female_3.0


title: Muscle_Young_Female_30.0


title: Muscle_Young_Female_21.0


title: WT_C182TG_rep2


title: patient2_platelets

description: 20101122_RD_Lankenau_p2_Platelet_RNA_1ug_B1_T1.CEL


title: 129S6_Liver_vhs-null HSV-1_1d_m (251486831258_1_3)

description: US93503719_251486831258_S01_GE1-v5_95_Feb07_1_3.txt


title: patient4_platelets

description: 20101122_RD_Lankenau_p4_Platelet_RNA_1ug_B1_T1_2.CEL


title: 129S6_BrainStem_vhs-null HSV-1_1d_m (251486827662_1_4)

description: US93503719_251486827662_S01_GE1-v5_95_Feb07_1_4.txt

value: BrainStem


title: WT_C182TG_rep1


title: 129S6_Liver_vhs-null HSV-1_1d_m (251486831230_1_3)

description: US93503719_251486831230_S01_GE1-v5_95_Feb07_1_3.txt


title: Muscle_Young_Female_6.0


title: Muscle_Young_Female_18.0


title: patient3_platelets

description: 20101122_RD_Lankenau_p3_Platelet_RNA_1ug_B1_T1.CEL


title: 129S6_BrainStem_vhs-null HSV-1_1d_m (251486827662_1_1)

description: US93503719_251486827662_S01_GE1-v5_95_Feb07_1_1.txt


title: Muscle_Young_Female_9.0


title: Muscle_Young_Female_16.0


title: WT_C183TG_rep3

value: trilinolenin


title: Cell line ACC-LC319/bone2

city: Tokushima

first: Le

middle: Tan

last: Dat

state: Tokushima

address: 3-18-15, Kuramoto-cho

department: Genome center

country: Japan

institute: Tokushima university

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity in the range of 13-25 pmol Cy3/μg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 μl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer's protocol. When the fragmentation reaction completed, 55 μl of 2x Agilent's GEx hybridization buffer HI-RPM was added to the fragmentation mixture and hybridized to 4x44K Agilent Whole Human Genome Oligo Microarrays (G4112F) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed one minute at room temperature with  Agilent's GE Wash Buffer 1 (addition of Triton X-102 at 0.005%) and one minute with 37°C GE Wash buffer 2 (pre-warmed overnight at 37°C), dried the array slides at room temperature about 10 seconds, then scanned immediately using Tecan scanner. The procedures were performed in the ozone - protection hood as recommendation by Agilent manufacturer.

scan_protocol: Dried microarray slides were scanned immediately on the Agilent DNA Microarray Scanner using one color scan setting for 4x44K array formats (Scan area: 61x21.6 mm; Scan resolution: 5μm; Dye channel: Green; Green PMT: 100%).

data_processing: Features of the scanned images were extract with Feature Extraction version 10.7 (Agilent) using default parameters (protocol GE1-107_Sep09 and Grid template: 014850_D_F_20080627) to obtain background subtracted and spatially detrended Processed signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. The output files were processed for analysis of gene expression using GeneSpring version 11.5 and Microsoft Excel 2007.

source_name: Cell line ACC-LC319/bone2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng of total RNA using the Agilent's Low Input Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (Qiagen).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer. cRNA was used for hybridization immediately without freezing and thawing.

extract_protocol: RNA was prepared using the Qiagen RNeasy mini kit. DNase digestion were performed on-column. Eluted volume was minimized to get suitable concentration of total RNA (about 12ul). RNA was quantified using the NanoDrop-1000 Spectrophotometer and RNA quality was monitored using the Agilent 2100 Bioanalyzer (Agilent).

treatment_protocol: SCID mice were depleted NK T-cells by intraperitoneally injection of TM-β1(300μg/300 μl/mouse), and two days later mice were injected one million of ACC-LC319/bone 2 human lung cancer cells. The mice were sacrificed on day 34 after tumor inoculation. The metastatic tissues in lung, liver and bone of these SCID mice and the corresponding surrounding normal tissues were subjected to laser microdissection system (PALM) to collect pure population of the cells of interest. The in vitro monolayer culture of ACC-LC319/bone 2 cells were grown to 70-80 % confluent before harvested to purify RNA.

tag: tissue/cell type

value: ACC-LC319/bone2, in vitro monolayer cell culture


title: Mouse normal tissue_Lung

source_name: Mouse normal tissues in lung

value: Mouse normal tissue


title: Mouse normal tissue_Liver

source_name: Mouse normal tissues in liver


title: WT_Control_rep3


title: Hnf4aF/F;AlbCrePositive-4

city: Bethesda

first: Jessica

last: Bonzo

state: MD

address: 9000 Rockville Pike, Building 37, Rm3112

department: CCR

institute: NCI/NIH

hyb_protocol: Blocking buffer and Hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential.

scan_protocol: Scanned on an Agilent G2565AA scanner.

data_processing: mages were quantified using Agilent Feature Extraction Software. Agilent Feature Extraction Software was used for background subtraction and LOWESS normalization.

source_name: Liver-Hnf4alpha;Alb cre positive control diet (developmental liver knockout)

label_protocol: cDNA was generated with SuperScript® Indirect cDNA Labeling Core kit (Invitrogen) and labeled with Cy3/Cy5-mono reactive dye pack (GE healthcare), and the labeled cDNA was purified with Qiagen kit (#28004)

extract_protocol: Total RNA extracted using Trizol from liver and purified with QIAGEN kit (#74104) following manufacturer's instructions.

treatment_protocol: Control mice were fed a regular chow diet ad lib. Mice received tamoxifen containg chow (1g/kg diet) ad lib for 5 days at which time food was replaced with regular chow and mice euthanasized 14 days later.

value: Hnf4alpha; Alb cre positive

value: 8 weeks

value: liver

tag: diet

value: control diet

source_name: Ambion Mouse Assorted Total RNA

value: Swiss Webster

value: brain, embryo (10–12 days), heart, kidney, liver, lung, ovary, spleen, testicle, and thymus


title: WT_Control_rep2

value: male


title: WT_Control_rep1


title: Hnf4aF/F;AlbCrePositive-1


title: Mouse normal tissue_Bone

source_name: Mouse normal tissues in bone


title: Metastasis_Liver 5

source_name: Metastatic lesion in mouse liver

value: Metastatic tissue


title: Metastasis_Liver 4


title: Hnf4aF/F;AlbCreNegative-4

source_name: Liver-Hnf4alpha;Alb cre negative control diet (wild-type)

value: Hnf4alpha; Alb cre negative


title: Hnf4aF/F;AlbCrePositive-3


title: WT_C183TG_rep1


title: WT_C183TG_rep2


title: Hnf4aF/F;AlbCrePositive-2


title: WT_C226TG_rep5

value: tridocosahexaenoin


title: Metastasis_Liver 3


title: Hnf4aF/F;AlbCreNegative-3


title: Hnf4aF/F;AlbCreNegative-2


title: oviduct_genistein_ rep4

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description:
US22502532_251486821683_S01_H.tif
US22502532_251486821683_S01_L.tif
neonatal genistein oviduct

hyb_protocol: For each sample, 1.65ug of Cy3 labeled cRNA was fragmented and hybridized for 17 hours in a rotating hybridization oven.

scan_protocol: Slides were washed and then scanned with an Agilent Scanner.

data_processing: Data was obtained using the Agilent Feature Extraction software(v9.5), using the 1-color defaults for all parameters.

source_name: oviduct, pregnancy day 2, neonatal genistein

label_protocol: Starting with 500ng of total RNA, Cy3 labeled cRNA was produced according to manufacturer’s protocol.

extract_protocol: RNA was isolated using Qiagen RNeasy kit and DNase I clean up kit following manufacturer's instructions

value: female


title: oviduct_control_rep4

description:
US22502532_251486820676_S01_H.tif
US22502532_251486820676_S01_L.tif
control oviduct

source_name: oviduct, pregnancy day 2, control


title: oviduct_genistein_ rep3


title: Hnf4aF/F;AlbERT2cre with Tamoxifen-4

source_name: Liver-Hnf4alpha;ErT2Alb cre positive tamoxifen diet (acute liver knockout)

value: Hnf4alpha; ErT2Alb cre positive

value: tamoxifen diet


title: oviduct_control_rep1


title: Metastasis_Liver 2


title: oviduct_genistein_ rep1


title: Hnf4aF/F;AlbERT2cre with Tamoxifen-1


title: Hnf4aF/F;AlbCreNegative-1


title: Metastasis_Lung 3

source_name: Metastatic lesion in mouse lung


title: Metastasis_Liver 1


title: oviduct_control_rep2


title: Hnf4aF/F;AlbERT2cre with Tamoxifen-3


title: Hnf4aF/F;AlbERT2cre-4

source_name: Liver-Hnf4alpha;ErT2Alb cre positive control diet (wild-type)


title: oviduct_genistein_ rep2


title: Hnf4aF/F;AlbERT2cre-3


title: Metastasis_Lung 1


title: Metastasis_Lung 4


title: Metastasis_Lung 5


title: Metastasis_Lung 2


title: Hnf4aF/F;AlbERT2cre with Tamoxifen-2


title: Hnf4aF/F;AlbERT2cre-2


title: Metastasis_Bone 2

source_name: Metastatic lesion in mouse bone


title: oviduct_control_rep3


title: Hnf4aF/F;AlbERT2cre-1


title: Metastasis_Bone 5


title: Hnf4aF/F with Tamoxifen-4

source_name: Liver-Hnf4alpha;ErT2Alb cre negative tamoxifen diet (wild-type, tamoxifen)

value: Hnf4alpha; ErT2Alb cre negative


title: Metastasis_Bone 4


title: Metastasis_Bone 1


title: Metastasis_Bone 3


title: B. breve UCC2003 delta-Bbr_0838 0.06 % cholic acid stress

status: Public on Feb 20 2012

city: Utrecht

first: Aldert

last: Zomer

address: Yalelaan 1

department: Department of Infectious Diseases and Immunology,Faculty of Veterinary Medicine

institute: Utrecht University

description: Generated scans were converted to data files with Agilent's Feature Extraction software (Version 9.5).

hyb_protocol: Labelled cDNA was hybridized using the Agilent Gene Expression hybridization kit (part number 5188-5242) as described in the Agilent Two-Color Microarray-Based Gene Expression Analysis v4.0 manual (G4140-90050).

scan_protocol: Following hybridization, all microarrays were washed in accordance with Agilent’s standard procedures and scanned using an Agilent DNA microarray scanner (model G2565A).

data_processing:
DNA-microarray data were processed as previously described (Garcia De La Nava, J., D. F. Santaella, J. C. Alba, J. M. Carazo, O. Trelles & A. Pascual-Montano, (2003) Engene: the processing and exploratory analysis of gene expression data. Bioinformatics 19: 657-658., van Hijum, S. A. F. T., J. Garcia De La Nava, O. Trelles, J. Kok & O. P. Kuipers, (2003) MicroPreP: a cDNA microarray data pre-processing framework. Appl. Bioinformatics. 2: 241-244., van Hijum, S. A. F. T., J. A. De, R. J. Baerends, H. A. Karsens, N. E. Kramer, R. Larsen, C. D. den Hengst, C. J. Albers, J. Kok & O. P. Kuipers, (2005) A generally applicable validation scheme for the assessment of factors involved in reproducibility and quality of DNA-microarray data. BMC.Genomics 6: 77). Data were Lowess normalized. The VALUE column contains normalized log10 ratios from a single array experiment.
Differential expression tests were performed with the Cyber-T implementation of a variant of the t-test (Long, A. D., H. J. Mangalam, B. Y. Chan, L. Tolleri, G. W. Hatfield & P. Baldi, (2001) Improved statistical inference from DNA microarray data using analysis of variance and a Bayesian statistical framework. Analysis of global gene expression in Escherichia coli K12. J. Biol. Chem. 276: 19937-19944.). A gene was considered differentially expressed when p < 0.001 and an expression ratio of >3 or <0.33 relative to the control.

organism: Bifidobacterium breve UCC2003

label_protocol: Labelling was performed as described previously (van Hijum, S. A. F. T., J. A. De, R. J. Baerends, H. A. Karsens, N. E. Kramer, R. Larsen, C. D. den Hengst, C. J. Albers, J. Kok & O. P. Kuipers, (2005) A generally applicable validation scheme for the assessment of factors involved in reproducibility and quality of DNA-microarray data. BMC.Genomics 6: 77).

growth_protocol: Bifidobacterium breve UCC2003 delta-Bbr_0838 was grown in MRS supplemented with 0.05% (w/v) L-cysteine-HCl (Sigma-Aldrich, Steinhein, Germany). Strain was grown under anaerobic conditions in a Modular Atmosphere Controlled System (Davidson & Hardy Ltd., Dublin, Ireland) till OD600 was 0.5. Sterile water was added with the same volume as the cholic acid in the target sample and growth was continued for 1 hr.

extract_protocol: RNA isolation, RNA quality control and complementary DNA synthesis was performed as described previously (van Hijum, S. A. F. T., J. A. De, R. J. Baerends, H. A. Karsens, N. E. Kramer, R. Larsen, C. D. den Hengst, C. J. Albers, J. Kok & O. P. Kuipers, (2005) A generally applicable validation scheme for the assessment of factors involved in reproducibility and quality of DNA-microarray data. BMC.Genomics 6: 77).

treatment_protocol: Method for cell disruption was performed as described previously (van Hijum, S. A. F. T., J. A. De, R. J. Baerends, H. A. Karsens, N. E. Kramer, R. Larsen, C. D. den Hengst, C. J. Albers, J. Kok & O. P. Kuipers, (2005) A generally applicable validation scheme for the assessment of factors involved in reproducibility and quality of DNA-microarray data. BMC.Genomics 6: 77).

value: UCC2003 delta Bbr_0838

tag: growth stage

value: exponential

source_name: Bifidobacterium breve UCC2003 delta-Bbr_0838 grown in MRS exposed to 0.06 % cholic acid

growth_protocol: Bifidobacterium breve UCC2003 delta-Bbr_0838 was grown in MRS supplemented with 0.05% (w/v) L-cysteine-HCl (Sigma-Aldrich, Steinhein, Germany). Strain was grown under anaerobic conditions in a Modular Atmosphere Controlled System (Davidson & Hardy Ltd., Dublin, Ireland) till OD600 was 0.5. Cholic acid was added at a concentration of 0.06 % and growth was continued for 1 hr.


title: Hnf4aF/F with Tamoxifen-3

tag: tissue


title: Hnf4aF/F with Tamoxifen-2


title: Hnf4aF/F-4

source_name: Liver-Hnf4alpha;ErT2Alb cre negative control diet (wild-type)


title: B. breve UCC2003 delta-Bbr_0838 0.06 % cholic acid stress dyeswap

source_name: Bifidobacterium breve UCC2003 delta-Bbr_0838 grown in MRS


title: B. breve UCC2003 delta-Bbr_0838 0.1 % cholic acid stress

source_name: Bifidobacterium breve UCC2003 delta-Bbr_0838 grown in MRS exposed to 0.1 % cholic acid

growth_protocol: Bifidobacterium breve UCC2003 delta-Bbr_0838 was grown in MRS supplemented with 0.05% (w/v) L-cysteine-HCl (Sigma-Aldrich, Steinhein, Germany). Strain was grown under anaerobic conditions in a Modular Atmosphere Controlled System (Davidson & Hardy Ltd., Dublin, Ireland) till OD600 was 0.5. Cholic acid  was added at a concentration of 0.15 % and growth was continued for 1 hr.


title: KO_WY_pool

source_name: heart

growth_protocol: Pure-bred wild type (129S1/SvImJ) and PPARα-/- (129S4/SvJae) mice, aged 2-3 months, were used. Animals were kept on a standard chow diet (RMH-B, AB Diets, Woerden, the Netherlands) until 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). For array hybridisation, pools were made by pooling equal amount of RNA from 4-5 hearts per experimental group.

treatment_protocol: Mice were fed a chow diet (RMH-B, AB Diets, Woerden, the Netherlands) containing 0.1 % Wy14643 or the control diet (non-supplemented RMH-B) for 5 days. Mice were then 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. RNA of

value: PPARalpha knockout

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


title: WT_WY_pool

value: wild type


title: B. breve UCC2003 vs delta-Bbr_0838 both exposed to 0.1 % cholic acid

source_name: Bifidobacterium breve UCC2003 grown in MRS exposed to 0.1% cholic acid

growth_protocol: Bifidobacterium breve UCC2003 was grown in MRS supplemented with 0.05% (w/v) L-cysteine-HCl (Sigma-Aldrich, Steinhein, Germany). Strain was grown under anaerobic conditions in a Modular Atmosphere Controlled System (Davidson & Hardy Ltd., Dublin, Ireland) till OD600 was 0.5. Cholic acid was added at a concentration of 0.1 % and growth was continued for 1 hr.

growth_protocol: Bifidobacterium breve UCC2003 delta-Bbr_0838 was grown in MRS supplemented with 0.05% (w/v) L-cysteine-HCl (Sigma-Aldrich, Steinhein, Germany). Strain was grown under anaerobic conditions in a Modular Atmosphere Controlled System (Davidson & Hardy Ltd., Dublin, Ireland) till OD600 was 0.5. Cholic acid was added at a concentration of 0.1 % and growth was continued for 1 hr.


type: genomic

city: London

first: Joanna

last: Zhuang

address: 74 Huntley Street

country: United Kingdom

institute: UCL

description: endometrium tissue samples were drawn from 18 metastatic endometrial cancers.

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner settings

data_processing: BeadStudio software v3.2

label: Biotin

molecule: genomic DNA

source_name: genomic DNA from endometrium tissues EndomMETA-621 T2 04 A

label_protocol: Standard Illumina Protocol for Infinium 27k Chip

extract_protocol: DNA was extracted from endometrium tissue samples using the Qiagen DNeasy Blood and Tissue kit (Qiagen Ltd, UK)

tag: sample type

value: bisulphite converted genomic DNA from endometrium tissues

tag: sampleID

tag: samplecode

tag: ChIP

tag: bsc


title: Hnf4aF/F-3

tag: strain

tag: gender

tag: age

value: 8 weeks

value: liver

value: control diet

source_name: Ambion Mouse Assorted Total RNA


title: KO_Control_pool

tag: genotype

value: male

tag: treatment


title: endometrium tissues EndomMETA-279 T2 A

source_name: genomic DNA from endometrium tissues EndomMETA-279 T2 A


title: endometrium tissues EndomMETA-816 Met A

source_name: genomic DNA from endometrium tissues EndomMETA-816 Met A

value: 816 Met A


source_name: genomic DNA from endometrium tissues EndomMETA-993 T2 08 C


source_name: genomic DNA from endometrium tissues EndomMETA-394 M 06 A


title: Hnf4aF/F-1

tag: genotype/variation

value: Swiss Webster

value: brain, embryo (10–12 days), heart, kidney, liver, lung, ovary, spleen, testicle, and thymus


title: Hnf4aF/F with Tamoxifen-1


title: WT_Control_pool


title: WT_C183TG_rep4

value: trilinolenin


source_name: genomic DNA from endometrium tissues EndomMETA-492 recidiv 04 A

value: 492 recidiv 04 A


source_name: genomic DNA from endometrium tissues EndomMETA-499 recidiv 06 A

value: 499 recidiv 06 A


source_name: genomic DNA from endometrium tissues EndomMETA-497 T2 03 B


source_name: genomic DNA from endometrium tissues EndomMETA-1749 T2 10 B


source_name: genomic DNA from endometrium tissues EndomMETA-1749 T3 10 A


title: B. breve UCC2003 delta-Bbr_0838 0.1 % cholic acid stress dyeswap

growth_protocol: Bifidobacterium breve UCC2003 delta-Bbr_0838 was grown in MRS supplemented with 0.05% (w/v) L-cysteine-HCl (Sigma-Aldrich, Steinhein, Germany). Strain was grown under anaerobic conditions in a Modular Atmosphere Controlled System (Davidson & Hardy Ltd., Dublin, Ireland) till OD600 was 0.5. Cholic acid  was added at a concentration of 0.1 % and growth was continued for 1 hr.


title: endometrium tissues EndomMETA-1495 T2 A

source_name: genomic DNA from endometrium tissues EndomMETA-1495 T2 A


source_name: genomic DNA from endometrium tissues EndomMETA-492 recidiv 09 A

value: 492 recidiv 09 A


title: Hnf4aF/F-2

source_name: Liver-Hnf4alpha;ErT2Alb cre negative control diet (wild-type)

value: Hnf4alpha; ErT2Alb cre negative


title: endometrium tissues EndomMETA-1495 T1 A

source_name: genomic DNA from endometrium tissues EndomMETA-1495 T1 A


title: White Blood Cells WB-T28

description: Whole blood samples were drawn from 30 BRCA1 mutation carriers (15 women with breast cancer and 15 healthy women) and 30 females without BRCA1 mutation (15 breast cancers and 15 healthy).

source_name: genomic DNA from white blood cells WB-T28

extract_protocol: DNA was extracted from white blood cell samples using the Qiagen DNeasy Blood and Tissue kit (Qiagen Ltd, UK)

value: bisulphite converted genomic DNA from white blood cells

tag: sentrixpos

value: E

tag: beadchipid

tag: agegrp


title: White Blood Cells WB-T12

source_name: genomic DNA from white blood cells WB-T12

value: H


title: White Blood Cells WB-T29

source_name: genomic DNA from white blood cells WB-T29

value: L


title: White Blood Cells WB-T60

source_name: genomic DNA from white blood cells WB-T60

value: F


title: White Blood Cells WB-T13

source_name: genomic DNA from white blood cells WB-T13

value: C


title: White Blood Cells WB-T43

source_name: genomic DNA from white blood cells WB-T43

value: G


title: White Blood Cells WB-T15

source_name: genomic DNA from white blood cells WB-T15


title: White Blood Cells WB-T30

source_name: genomic DNA from white blood cells WB-T30

value: B


title: White Blood Cells WB-T41

source_name: genomic DNA from white blood cells WB-T41


title: White Blood Cells WB-T14

source_name: genomic DNA from white blood cells WB-T14

value: K


title: White Blood Cells WB-T31

source_name: genomic DNA from white blood cells WB-T31

value: J


title: White Blood Cells WB-T51

source_name: genomic DNA from white blood cells WB-T51


source_name: genomic DNA from endometrium tissues EndomMETA-1749 T1 10 A

value: bisulphite converted genomic DNA from endometrium tissues


title: endometrium tissues EndomMETA-1406 T2 A

source_name: genomic DNA from endometrium tissues EndomMETA-1406 T2 A


title: White Blood Cells WB-T22

source_name: genomic DNA from white blood cells WB-T22


title: White Blood Cells WB-T24

source_name: genomic DNA from white blood cells WB-T24


title: White Blood Cells WB-T39

source_name: genomic DNA from white blood cells WB-T39

value: D


title: White Blood Cells WB-T59

source_name: genomic DNA from white blood cells WB-T59

value: I


title: White Blood Cells WB-T56

source_name: genomic DNA from white blood cells WB-T56

value: A


title: White Blood Cells WB-T44

source_name: genomic DNA from white blood cells WB-T44


title: endometrium tissues EndomMETA-1406 T3 A

source_name: genomic DNA from endometrium tissues EndomMETA-1406 T3 A


source_name: genomic DNA from endometrium tissues EndomMETA-1495 Met A

value: 1495 Met A


title: White Blood Cells WB-T54

source_name: genomic DNA from white blood cells WB-T54


title: White Blood Cells WB-T26

source_name: genomic DNA from white blood cells WB-T26


title: White Blood Cells WB-T03

source_name: genomic DNA from white blood cells WB-T03


title: White Blood Cells WB-T05

source_name: genomic DNA from white blood cells WB-T05


source_name: genomic DNA from endometrium tissues EndomMETA-1393 T2 08 A


title: White Blood Cells WB-T42

source_name: genomic DNA from white blood cells WB-T42


title: White Blood Cells WB-T45

source_name: genomic DNA from white blood cells WB-T45


title: White Blood Cells WB-T25

source_name: genomic DNA from white blood cells WB-T25


title: White Blood Cells WB-T55

source_name: genomic DNA from white blood cells WB-T55


title: White Blood Cells WB-T09

source_name: genomic DNA from white blood cells WB-T09


title: White Blood Cells WB-T58

source_name: genomic DNA from white blood cells WB-T58


title: White Blood Cells WB-T19

source_name: genomic DNA from white blood cells WB-T19


title: White Blood Cells WB-T38

source_name: genomic DNA from white blood cells WB-T38


title: White Blood Cells WB-T48

source_name: genomic DNA from white blood cells WB-T48


title: White Blood Cells WB-T20

source_name: genomic DNA from white blood cells WB-T20


title: White Blood Cells WB-T35

source_name: genomic DNA from white blood cells WB-T35


title: White Blood Cells WB-T07

source_name: genomic DNA from white blood cells WB-T07


title: White Blood Cells WB-T52

source_name: genomic DNA from white blood cells WB-T52


title: White Blood Cells WB-T11

source_name: genomic DNA from white blood cells WB-T11


title: White Blood Cells WB-T33

source_name: genomic DNA from white blood cells WB-T33


title: White Blood Cells WB-T36

source_name: genomic DNA from white blood cells WB-T36


title: White Blood Cells WB-T23

source_name: genomic DNA from white blood cells WB-T23


title: White Blood Cells WB-T02

source_name: genomic DNA from white blood cells WB-T02


title: White Blood Cells WB-T47

source_name: genomic DNA from white blood cells WB-T47


title: White Blood Cells WB-T53

source_name: genomic DNA from white blood cells WB-T53


title: White Blood Cells WB-T06

source_name: genomic DNA from white blood cells WB-T06


title: White Blood Cells WB-T10

source_name: genomic DNA from white blood cells WB-T10


title: White Blood Cells WB-T27

source_name: genomic DNA from white blood cells WB-T27


title: White Blood Cells WB-T46

source_name: genomic DNA from white blood cells WB-T46


title: White Blood Cells WB-T18

source_name: genomic DNA from white blood cells WB-T18


title: White Blood Cells WB-T49

source_name: genomic DNA from white blood cells WB-T49


title: White Blood Cells WB-T34

source_name: genomic DNA from white blood cells WB-T34


title: White Blood Cells WB-T37

source_name: genomic DNA from white blood cells WB-T37


title: White Blood Cells WB-T16

source_name: genomic DNA from white blood cells WB-T16


title: White Blood Cells WB-T01

source_name: genomic DNA from white blood cells WB-T01


title: White Blood Cells WB-T50

source_name: genomic DNA from white blood cells WB-T50


title: White Blood Cells WB-T32

source_name: genomic DNA from white blood cells WB-T32


title: White Blood Cells WB-T57

source_name: genomic DNA from white blood cells WB-T57


title: White Blood Cells WB-T04

source_name: genomic DNA from white blood cells WB-T04


title: Breast Tissues BC-972

description: Breast tissue samples were drawn from 114 breast cancers and 23 non-neoplastic breast tissues.

source_name: genomic DNA from breast tissues BC-972

extract_protocol: DNA was extracted from breast tissue samples using the Qiagen DNeasy Blood and Tissue kit (Qiagen Ltd, UK)

value: bisulphite converted genomic DNA from breast tissues

tag: dataid

tag: Stage

tag: grade

tag: histology(1=invasive ductal(idc),2=invasive lobular(ilc),3=mucinous or medullary,4=others)

tag: ostime

tag: relapse

tag: rstime


title: Breast Tissues BC-821

source_name: genomic DNA from breast tissues BC-821

tag: sample type

tag: bsc


title: Breast Tissues BC-996

source_name: genomic DNA from breast tissues BC-996


title: Breast Tissues BC-905

source_name: genomic DNA from breast tissues BC-905


title: Breast Tissues BC-793

source_name: genomic DNA from breast tissues BC-793


title: White Blood Cells WB-T17

source_name: genomic DNA from white blood cells WB-T17


title: Breast Tissues BC-818

source_name: genomic DNA from breast tissues BC-818


title: White Blood Cells WB-T08

source_name: genomic DNA from white blood cells WB-T08


title: White Blood Cells WB-T40

source_name: genomic DNA from white blood cells WB-T40


title: Breast Tissues BC-782

source_name: genomic DNA from breast tissues BC-782


title: Breast Tissues BC-883

source_name: genomic DNA from breast tissues BC-883


title: White Blood Cells WB-T21

source_name: genomic DNA from white blood cells WB-T21


title: Breast Tissues BC-786

source_name: genomic DNA from breast tissues BC-786


title: Breast Tissues BC-732

source_name: genomic DNA from breast tissues BC-732


title: Breast Tissues BC-656

source_name: genomic DNA from breast tissues BC-656


title: Breast Tissues BC-623

source_name: genomic DNA from breast tissues BC-623


title: Breast Tissues BC-4443

source_name: genomic DNA from breast tissues BC-4443


title: Breast Tissues BC-622

source_name: genomic DNA from breast tissues BC-622


title: Breast Tissues BC-655

source_name: genomic DNA from breast tissues BC-655


title: Breast Tissues BC-618

source_name: genomic DNA from breast tissues BC-618


title: Breast Tissues BC-4248

source_name: genomic DNA from breast tissues BC-4248


title: Breast Tissues BC-443

source_name: genomic DNA from breast tissues BC-443


title: Breast Tissues BC-4073

source_name: genomic DNA from breast tissues BC-4073


title: Breast Tissues BC-4022

source_name: genomic DNA from breast tissues BC-4022


title: Breast Tissues BC-4023

source_name: genomic DNA from breast tissues BC-4023


title: Breast Tissues BC-4145

source_name: genomic DNA from breast tissues BC-4145


title: Breast Tissues BC-519

source_name: genomic DNA from breast tissues BC-519


title: Breast Tissues BC-4264

source_name: genomic DNA from breast tissues BC-4264


title: Breast Tissues BC-426

source_name: genomic DNA from breast tissues BC-426


title: Breast Tissues BC-4767

source_name: genomic DNA from breast tissues BC-4767


title: Breast Tissues BC-4119

source_name: genomic DNA from breast tissues BC-4119


title: Breast Tissues BC-3839

source_name: genomic DNA from breast tissues BC-3839


title: Breast Tissues BC-4294

source_name: genomic DNA from breast tissues BC-4294


title: Breast Tissues BC-3881

source_name: genomic DNA from breast tissues BC-3881


title: Breast Tissues BC-385

source_name: genomic DNA from breast tissues BC-385


title: Breast Tissues BC-4133

source_name: genomic DNA from breast tissues BC-4133


title: Breast Tissues BC-3974

source_name: genomic DNA from breast tissues BC-3974


title: Breast Tissues BC-3821

source_name: genomic DNA from breast tissues BC-3821


title: Breast Tissues BC-3672

source_name: genomic DNA from breast tissues BC-3672


title: Breast Tissues BC-3279

source_name: genomic DNA from breast tissues BC-3279


title: Breast Tissues BC-3151

source_name: genomic DNA from breast tissues BC-3151


title: Breast Tissues BC-3573

source_name: genomic DNA from breast tissues BC-3573


title: Breast Tissues BC-3650

source_name: genomic DNA from breast tissues BC-3650


title: Breast Tissues BC-3621

source_name: genomic DNA from breast tissues BC-3621


title: Breast Tissues BC-3485

source_name: genomic DNA from breast tissues BC-3485


title: Breast Tissues BC-3613

source_name: genomic DNA from breast tissues BC-3613


title: Breast Tissues BC-3322

source_name: genomic DNA from breast tissues BC-3322


title: Breast Tissues BC-3311

source_name: genomic DNA from breast tissues BC-3311


title: Breast Tissues BC-3424

source_name: genomic DNA from breast tissues BC-3424


title: Breast Tissues BC-3059

source_name: genomic DNA from breast tissues BC-3059


title: Breast Tissues BC-319

source_name: genomic DNA from breast tissues BC-319


title: Breast Tissues BC-318

source_name: genomic DNA from breast tissues BC-318


title: Breast Tissues BC-3193

source_name: genomic DNA from breast tissues BC-3193


title: Breast Tissues BC-3100

source_name: genomic DNA from breast tissues BC-3100


title: Breast Tissues BC-3166

source_name: genomic DNA from breast tissues BC-3166


title: Breast Tissues BC-3023

source_name: genomic DNA from breast tissues BC-3023


title: Breast Tissues BC-2992

source_name: genomic DNA from breast tissues BC-2992


title: Breast Tissues BC-3062

source_name: genomic DNA from breast tissues BC-3062


title: Breast Tissues BC-3057

source_name: genomic DNA from breast tissues BC-3057


title: Breast Tissues BC-3605

source_name: genomic DNA from breast tissues BC-3605


title: Breast Tissues BC-2800

source_name: genomic DNA from breast tissues BC-2800


title: Breast Tissues BC-2898

source_name: genomic DNA from breast tissues BC-2898


title: Breast Tissues BC-3025

source_name: genomic DNA from breast tissues BC-3025


title: Breast Tissues BC-2902

source_name: genomic DNA from breast tissues BC-2902


title: Breast Tissues BC-270

source_name: genomic DNA from breast tissues BC-270


title: Breast Tissues BC-2946

source_name: genomic DNA from breast tissues BC-2946


title: Breast Tissues BC-27

source_name: genomic DNA from breast tissues BC-27


title: Breast Tissues BC-26

source_name: genomic DNA from breast tissues BC-26


title: Breast Tissues BC-2500

source_name: genomic DNA from breast tissues BC-2500


title: Breast Tissues BC-2995

source_name: genomic DNA from breast tissues BC-2995


title: Breast Tissues BC-2516

source_name: genomic DNA from breast tissues BC-2516


title: Breast Tissues BC-2409

source_name: genomic DNA from breast tissues BC-2409


title: Breast Tissues BC-2448

source_name: genomic DNA from breast tissues BC-2448


title: Breast Tissues BC-2678

source_name: genomic DNA from breast tissues BC-2678


title: Breast Tissues BC-2544

source_name: genomic DNA from breast tissues BC-2544


title: Breast Tissues BC-3028

source_name: genomic DNA from breast tissues BC-3028


title: Breast Tissues BC-2783

source_name: genomic DNA from breast tissues BC-2783


title: Breast Tissues BC-2597

source_name: genomic DNA from breast tissues BC-2597


title: Breast Tissues BC-2499

source_name: genomic DNA from breast tissues BC-2499


title: Breast Tissues BC-2365

source_name: genomic DNA from breast tissues BC-2365


title: Breast Tissues BC-2747

source_name: genomic DNA from breast tissues BC-2747


title: Breast Tissues BC-2640

source_name: genomic DNA from breast tissues BC-2640


title: Breast Tissues BC-2602

source_name: genomic DNA from breast tissues BC-2602


title: Breast Tissues BC-2360

source_name: genomic DNA from breast tissues BC-2360


title: Breast Tissues BC-2771

source_name: genomic DNA from breast tissues BC-2771


title: Breast Tissues BC-2347

source_name: genomic DNA from breast tissues BC-2347


title: Breast Tissues BC-2322

source_name: genomic DNA from breast tissues BC-2322


title: Breast Tissues BC-2385

source_name: genomic DNA from breast tissues BC-2385


title: Breast Tissues BC-2495

source_name: genomic DNA from breast tissues BC-2495


title: Breast Tissues BC-2307

source_name: genomic DNA from breast tissues BC-2307


title: Breast Tissues BC-2506

source_name: genomic DNA from breast tissues BC-2506


title: Breast Tissues BC-2293

source_name: genomic DNA from breast tissues BC-2293


title: Breast Tissues BC-2017

source_name: genomic DNA from breast tissues BC-2017


title: Breast Tissues BC-2175

source_name: genomic DNA from breast tissues BC-2175


title: Breast Tissues BC-2181

source_name: genomic DNA from breast tissues BC-2181


title: Breast Tissues BC-2013

source_name: genomic DNA from breast tissues BC-2013


title: Breast Tissues BC-1975

source_name: genomic DNA from breast tissues BC-1975


title: Breast Tissues BC-2634

source_name: genomic DNA from breast tissues BC-2634


title: Breast Tissues BC-1942

source_name: genomic DNA from breast tissues BC-1942


title: Breast Tissues BC-2305

source_name: genomic DNA from breast tissues BC-2305


title: Breast Tissues BC-2316

source_name: genomic DNA from breast tissues BC-2316


title: Breast Tissues BC-1858

source_name: genomic DNA from breast tissues BC-1858


title: Breast Tissues BC-2270

source_name: genomic DNA from breast tissues BC-2270


title: Breast Tissues BC-2220

source_name: genomic DNA from breast tissues BC-2220


title: Breast Tissues BC-1657

source_name: genomic DNA from breast tissues BC-1657


title: Breast Tissues BC-2130

source_name: genomic DNA from breast tissues BC-2130


title: Breast Tissues BC-1718

source_name: genomic DNA from breast tissues BC-1718


title: Breast Tissues BC-1661

source_name: genomic DNA from breast tissues BC-1661


title: Breast Tissues BC-2158

source_name: genomic DNA from breast tissues BC-2158


title: Breast Tissues BC-1506

source_name: genomic DNA from breast tissues BC-1506


title: Breast Tissues BC-1484

source_name: genomic DNA from breast tissues BC-1484


title: Breast Tissues BC-206

source_name: genomic DNA from breast tissues BC-206


title: Breast Tissues BC-1959

source_name: genomic DNA from breast tissues BC-1959


title: Breast Tissues BC-1956

source_name: genomic DNA from breast tissues BC-1956


title: Breast Tissues BC-2164

source_name: genomic DNA from breast tissues BC-2164


title: Breast Tissues BC-1991

source_name: genomic DNA from breast tissues BC-1991


title: Breast Tissues BC-2265

source_name: genomic DNA from breast tissues BC-2265


title: Breast Tissues BC-1490

source_name: genomic DNA from breast tissues BC-1490


title: Breast Tissues BC-1926

source_name: genomic DNA from breast tissues BC-1926


title: Breast Tissues BC-1857

source_name: genomic DNA from breast tissues BC-1857


title: Breast Tissues BC-136

source_name: genomic DNA from breast tissues BC-136


title: Breast Tissues BC-1371

source_name: genomic DNA from breast tissues BC-1371


title: Breast Tissues BC-1797

source_name: genomic DNA from breast tissues BC-1797


title: Breast Tissues BC-1733

source_name: genomic DNA from breast tissues BC-1733


title: Breast Tissues BC-1312

source_name: genomic DNA from breast tissues BC-1312


title: Breast Tissues BC-1711

source_name: genomic DNA from breast tissues BC-1711


title: Breast Tissues BC-1684

source_name: genomic DNA from breast tissues BC-1684


title: Breast Tissues BC-1760

source_name: genomic DNA from breast tissues BC-1760


title: Breast Tissues BC-1119

source_name: genomic DNA from breast tissues BC-1119


title: Breast Tissues BC-1244

source_name: genomic DNA from breast tissues BC-1244


title: Breast Tissues BC-1579

source_name: genomic DNA from breast tissues BC-1579


title: Breast Tissues BC-1071

source_name: genomic DNA from breast tissues BC-1071


title: Breast Tissues BC-1526

source_name: genomic DNA from breast tissues BC-1526


title: Uterine Cervix 954

first: Andrew

middle: E

last: Teschendorff

address: 72 Huntley Street

department: UCL Cancer Institute/Institute for Women's Health

institute: University College London

description: A total of 63 samples, 15 of normal histology and 48 cervical cancers. The normal cervical samples were from women who underwent a hysterectomy for uterine fibroids. The 48 cervical cancers were from women who were treated at the Innsbruck Medical University between 1990 and 2006.

source_name: genomic DNA from cells of the uterine cervix 954

extract_protocol: DNA was extracted using the Qiagen DNeasy Blood and Tissue kit (Qiagen Ltd, UK)

tag: cell type

value: cells of the uterine cervix 954

value: bisulphite converted genomic DNA from  Cervical Cancer

tag: surgery

tag: radiation

tag: chemotherapy

tag: survival time (years)

tag: death status

tag: recurrence free survival (years)

tag: sentrix position

tag: sentrix id

tag: bisulphite conversion efficiency (log-scale)


title: Uterine Cervix 929

source_name: genomic DNA from cells of the uterine cervix 929

value: cells of the uterine cervix 929

tag: age

tag: Stage

tag: grade


title: Breast Tissues BC-1503

source_name: genomic DNA from breast tissues BC-1503

tag: sentrixpos

value: E

tag: beadchipid

tag: dataid

tag: histology(1=invasive ductal(idc),2=invasive lobular(ilc),3=mucinous or medullary,4=others)

tag: ostime

tag: relapse


title: Uterine Cervix 610

source_name: genomic DNA from cells of the uterine cervix 610

tag: cell type

value: cells of the uterine cervix 610

tag: sample type

tag: surgery

tag: radiation


title: Uterine Cervix 570

source_name: genomic DNA from cells of the uterine cervix 570

value: cells of the uterine cervix 570

tag: chemotherapy

tag: survival time (years)

tag: death status

tag: recurrence free survival (years)


title: Uterine Cervix 563

source_name: genomic DNA from cells of the uterine cervix 563

value: cells of the uterine cervix 563

tag: age

tag: sentrix position

tag: sentrix id

tag: bisulphite conversion efficiency (log-scale)


title: Breast Tissues BC-1492

source_name: genomic DNA from breast tissues BC-1492

tag: sentrixpos

tag: beadchipid

tag: bsc

tag: Stage

tag: grade

tag: rstime


title: Uterine Cervix 500

source_name: genomic DNA from cells of the uterine cervix 500

tag: cell type

value: cells of the uterine cervix 500

tag: sample type

tag: relapse


title: Breast Tissues BC-1459

source_name: genomic DNA from breast tissues BC-1459

tag: dataid

tag: histology(1=invasive ductal(idc),2=invasive lobular(ilc),3=mucinous or medullary,4=others)

tag: ostime


title: Uterine Cervix 5272

source_name: genomic DNA from cells of the uterine cervix 5272

value: cells of the uterine cervix 5272

tag: surgery

tag: radiation

tag: chemotherapy

tag: survival time (years)

tag: death status

tag: recurrence free survival (years)

value: G


title: Uterine Cervix 5211

source_name: genomic DNA from cells of the uterine cervix 5211

value: cells of the uterine cervix 5211

tag: age

tag: sentrix position

value: L

tag: sentrix id

tag: bisulphite conversion efficiency (log-scale)


title: Breast Tissues BC-1366

source_name: genomic DNA from breast tissues BC-1366

tag: sentrixpos

tag: beadchipid

tag: bsc

tag: Stage

tag: grade

tag: rstime


title: Breast Tissues BC-1276

source_name: genomic DNA from breast tissues BC-1276

tag: sample type

tag: dataid

tag: histology(1=invasive ductal(idc),2=invasive lobular(ilc),3=mucinous or medullary,4=others)

tag: ostime

tag: relapse


title: Uterine Cervix 440

source_name: genomic DNA from cells of the uterine cervix 440

tag: cell type

value: cells of the uterine cervix 440

tag: surgery

tag: radiation

tag: chemotherapy

tag: survival time (years)

tag: death status


title: Breast Tissues BC-1237

source_name: genomic DNA from breast tissues BC-1237

tag: sentrixpos

tag: age


title: Breast Tissues BC-1287

source_name: genomic DNA from breast tissues BC-1287

value: J

tag: beadchipid

tag: bsc


title: Uterine Cervix 792

source_name: genomic DNA from cells of the uterine cervix 792

value: cells of the uterine cervix 792

tag: Stage

tag: grade

tag: recurrence free survival (years)

tag: sentrix position

value: I

tag: sentrix id

tag: bisulphite conversion efficiency (log-scale)


title: Uterine Cervix 902

source_name: genomic DNA from cells of the uterine cervix 902

value: cells of the uterine cervix 902

tag: sample type

tag: relapse

value: D


title: Uterine Cervix 401

source_name: genomic DNA from cells of the uterine cervix 401

tag: cell type

value: cells of the uterine cervix 401

value: bisulphite converted genomic DNA from  Cervical Cancer

tag: surgery


title: Uterine Cervix 3892

source_name: genomic DNA from cells of the uterine cervix 3892

value: cells of the uterine cervix 3892

tag: radiation

tag: chemotherapy

value: H


title: Uterine Cervix 617

source_name: genomic DNA from cells of the uterine cervix 617

value: cells of the uterine cervix 617

tag: survival time (years)

tag: death status


title: Uterine Cervix 3418

source_name: genomic DNA from cells of the uterine cervix 3418

value: cells of the uterine cervix 3418

value: bisulphite converted genomic DNA from  Normal Cervix

tag: age


title: Breast Tissues BC-1196

source_name: genomic DNA from breast tissues BC-1196

value: bisulphite converted genomic DNA from breast tissues

tag: sentrixpos

tag: beadchipid

tag: dataid

tag: histology(1=invasive ductal(idc),2=invasive lobular(ilc),3=mucinous or medullary,4=others)

tag: ostime

tag: rstime


title: Uterine Cervix 55

source_name: genomic DNA from cells of the uterine cervix 55

value: cells of the uterine cervix 55

tag: Stage

tag: grade

tag: recurrence free survival (years)

tag: sentrix position

tag: sentrix id


title: Uterine Cervix 524

source_name: genomic DNA from cells of the uterine cervix 524

tag: cell type

value: cells of the uterine cervix 524

tag: sample type

tag: surgery

tag: relapse

value: B

tag: bisulphite conversion efficiency (log-scale)


title: Uterine Cervix 3356

source_name: genomic DNA from cells of the uterine cervix 3356

value: cells of the uterine cervix 3356

tag: age

tag: radiation

tag: chemotherapy

tag: survival time (years)

tag: death status

value: C


title: Uterine Cervix 3358

source_name: genomic DNA from cells of the uterine cervix 3358

value: cells of the uterine cervix 3358

value: F


title: Uterine Cervix 5226

source_name: genomic DNA from cells of the uterine cervix 5226

value: cells of the uterine cervix 5226

value: A


title: Uterine Cervix 3016

source_name: genomic DNA from cells of the uterine cervix 3016

value: cells of the uterine cervix 3016

value: J


title: Uterine Cervix 4268

source_name: genomic DNA from cells of the uterine cervix 4268

value: cells of the uterine cervix 4268

value: bisulphite converted genomic DNA from  Cervical Cancer

value: E


title: Uterine Cervix 4900

source_name: genomic DNA from cells of the uterine cervix 4900

value: cells of the uterine cervix 4900


title: Uterine Cervix 4144

source_name: genomic DNA from cells of the uterine cervix 4144

value: cells of the uterine cervix 4144

value: I


title: Uterine Cervix 3461

source_name: genomic DNA from cells of the uterine cervix 3461

value: cells of the uterine cervix 3461

value: bisulphite converted genomic DNA from  Normal Cervix

value: L


title: Uterine Cervix 2295

source_name: genomic DNA from cells of the uterine cervix 2295

value: cells of the uterine cervix 2295


title: Uterine Cervix 2571

source_name: genomic DNA from cells of the uterine cervix 2571

value: cells of the uterine cervix 2571

value: G


title: Uterine Cervix 3446

source_name: genomic DNA from cells of the uterine cervix 3446

value: cells of the uterine cervix 3446

value: F


title: Uterine Cervix 4489

source_name: genomic DNA from cells of the uterine cervix 4489

value: cells of the uterine cervix 4489


title: Uterine Cervix 3366

source_name: genomic DNA from cells of the uterine cervix 3366

value: cells of the uterine cervix 3366

value: B


title: Uterine Cervix 2173

source_name: genomic DNA from cells of the uterine cervix 2173

value: cells of the uterine cervix 2173


title: Uterine Cervix 3998

source_name: genomic DNA from cells of the uterine cervix 3998

value: cells of the uterine cervix 3998

value: bisulphite converted genomic DNA from  Cervical Cancer

value: C


title: Uterine Cervix 337

source_name: genomic DNA from cells of the uterine cervix 337

value: cells of the uterine cervix 337

value: E


title: Uterine Cervix 303

source_name: genomic DNA from cells of the uterine cervix 303

value: cells of the uterine cervix 303


title: Uterine Cervix 3334

source_name: genomic DNA from cells of the uterine cervix 3334

value: cells of the uterine cervix 3334

value: bisulphite converted genomic DNA from  Normal Cervix


title: Uterine Cervix 1867

source_name: genomic DNA from cells of the uterine cervix 1867

value: cells of the uterine cervix 1867

value: K


title: Uterine Cervix 2780

source_name: genomic DNA from cells of the uterine cervix 2780

value: cells of the uterine cervix 2780

value: J


title: Uterine Cervix 3319

source_name: genomic DNA from cells of the uterine cervix 3319

value: cells of the uterine cervix 3319

value: H


title: Uterine Cervix 2424

source_name: genomic DNA from cells of the uterine cervix 2424

value: cells of the uterine cervix 2424


title: Uterine Cervix 2607

source_name: genomic DNA from cells of the uterine cervix 2607

value: cells of the uterine cervix 2607

value: L


title: Uterine Cervix 2520

source_name: genomic DNA from cells of the uterine cervix 2520

value: cells of the uterine cervix 2520


title: Uterine Cervix 1483

source_name: genomic DNA from cells of the uterine cervix 1483

value: cells of the uterine cervix 1483

value: bisulphite converted genomic DNA from  Cervical Cancer


title: Uterine Cervix 2227

source_name: genomic DNA from cells of the uterine cervix 2227

value: cells of the uterine cervix 2227

value: G


title: Uterine Cervix 1839

source_name: genomic DNA from cells of the uterine cervix 1839

value: cells of the uterine cervix 1839

value: D


title: Uterine Cervix 1823

source_name: genomic DNA from cells of the uterine cervix 1823

value: cells of the uterine cervix 1823

value: bisulphite converted genomic DNA from  Normal Cervix


title: Uterine Cervix 2007

source_name: genomic DNA from cells of the uterine cervix 2007

value: cells of the uterine cervix 2007

value: E


title: Uterine Cervix 1671

source_name: genomic DNA from cells of the uterine cervix 1671

value: cells of the uterine cervix 1671

value: J


title: Uterine Cervix 1456

source_name: genomic DNA from cells of the uterine cervix 1456

value: cells of the uterine cervix 1456


title: Uterine Cervix 1392

source_name: genomic DNA from cells of the uterine cervix 1392

value: cells of the uterine cervix 1392

value: F


title: Uterine Cervix 1342

source_name: genomic DNA from cells of the uterine cervix 1342

value: cells of the uterine cervix 1342


title: Uterine Cervix 1447

source_name: genomic DNA from cells of the uterine cervix 1447

value: cells of the uterine cervix 1447

value: H


title: Uterine Cervix 2706

source_name: genomic DNA from cells of the uterine cervix 2706

value: cells of the uterine cervix 2706

value: bisulphite converted genomic DNA from  Cervical Cancer


title: Uterine Cervix 2123

source_name: genomic DNA from cells of the uterine cervix 2123

value: cells of the uterine cervix 2123


title: Uterine Cervix 1934

source_name: genomic DNA from cells of the uterine cervix 1934

value: cells of the uterine cervix 1934


title: Uterine Cervix 1935

source_name: genomic DNA from cells of the uterine cervix 1935

value: cells of the uterine cervix 1935


title: Normal Uterine Cervix ART18761

description: Liquid Based Cytology samples from the uterine cervix were collected from 152 women as part of the ARTISTIC trial (A Randomised Trial in Screening to Improve Cytology). All samples were of normal histology at time of sample draw, but 75 women developed a CIN2+ within 3 years of sample collection.

source_name: genomic DNA from normal cells of the uterine cervix ART18761

extract_protocol: DNA was extracted from liquid based cytology samples of women using the Qiagen DNeasy Blood and Tissue kit (Qiagen Ltd, UK)

value: bisulphite converted genomic DNA from a prospective CIN2+

tag: outcome

tag: hpv status

tag: pcr

value: Round2Cyt 0

value: A

tag: bisulphite 1

value: BS conversion C1 Grn 2747

tag: bisulphite 2

value: BS conversion C2 Grn 1792


title: Uterine Cervix 1853

source_name: genomic DNA from cells of the uterine cervix 1853

value: cells of the uterine cervix 1853

value: bisulphite converted genomic DNA from  Normal Cervix

tag: Stage

tag: grade

tag: recurrence free survival (years)

tag: sentrix position

value: K


title: Normal Uterine Cervix ART18886

source_name: genomic DNA from normal cells of the uterine cervix ART18886

tag: cell type

tag: sample type

value: bisulphite converted genomic DNA from a prospective CIN2-

value: Round2Cyt 1

tag: sentrix id

value: E

value: BS conversion C1 Grn 3006

value: BS conversion C2 Grn 2159


title: Uterine Cervix 1826

source_name: genomic DNA from cells of the uterine cervix 1826

value: cells of the uterine cervix 1826

tag: age

tag: surgery

tag: relapse

tag: bisulphite conversion efficiency (log-scale)


title: Normal Uterine Cervix ART12459

source_name: genomic DNA from normal cells of the uterine cervix ART12459

value: I

value: BS conversion C1 Grn 3215

value: BS conversion C2 Grn 2687


title: Uterine Cervix 1656

source_name: genomic DNA from cells of the uterine cervix 1656

value: cells of the uterine cervix 1656

value: bisulphite converted genomic DNA from  Cervical Cancer

tag: radiation

tag: chemotherapy

tag: survival time (years)

tag: death status

value: J


title: Normal Uterine Cervix ART13254

source_name: genomic DNA from normal cells of the uterine cervix ART13254

value: bisulphite converted genomic DNA from a prospective CIN2+

tag: outcome

tag: hpv status

tag: pcr

value: Round2Cyt 0

tag: bisulphite 1

value: BS conversion C1 Grn 2846

value: BS conversion C2 Grn 1830


title: Normal Uterine Cervix ART10550

source_name: genomic DNA from normal cells of the uterine cervix ART10550

value: BS conversion C1 Grn 2530

tag: bisulphite 2

value: BS conversion C2 Grn 2041


title: Uterine Cervix 1445

source_name: genomic DNA from cells of the uterine cervix 1445

value: cells of the uterine cervix 1445

tag: Stage

tag: grade

tag: recurrence free survival (years)

tag: sentrix position

value: B


title: Normal Uterine Cervix ART20198

source_name: genomic DNA from normal cells of the uterine cervix ART20198

tag: cell type

tag: sample type

value: bisulphite converted genomic DNA from a prospective CIN2-

tag: age

tag: sentrix id

value: F

value: BS conversion C1 Grn 3359

value: BS conversion C2 Grn 2127


title: Normal Uterine Cervix ART8984

source_name: genomic DNA from normal cells of the uterine cervix ART8984

value: C

value: BS conversion C1 Grn 2834

value: BS conversion C2 Grn 1974


title: Normal Uterine Cervix ART11801

source_name: genomic DNA from normal cells of the uterine cervix ART11801

value: G

value: BS conversion C1 Grn 2510

value: BS conversion C2 Grn 2540


title: Normal Uterine Cervix ART2572

source_name: genomic DNA from normal cells of the uterine cervix ART2572

value: bisulphite converted genomic DNA from a prospective CIN2+

value: Round2Cyt 0

value: K

value: BS conversion C1 Grn 1746

value: BS conversion C2 Grn 1330


title: Normal Uterine Cervix ART10872

source_name: genomic DNA from normal cells of the uterine cervix ART10872

value: BS conversion C1 Grn 2711

value: BS conversion C2 Grn 1867


title: Uterine Cervix 1408

source_name: genomic DNA from cells of the uterine cervix 1408

value: cells of the uterine cervix 1408

value: bisulphite converted genomic DNA from  Cervical Cancer

tag: surgery

tag: radiation

tag: relapse

tag: bisulphite conversion efficiency (log-scale)


title: Normal Uterine Cervix ART4820

source_name: genomic DNA from normal cells of the uterine cervix ART4820

value: bisulphite converted genomic DNA from a prospective CIN2-

tag: outcome

value: BS conversion C1 Grn 3260

value: BS conversion C2 Grn 2113


title: Uterine Cervix 1227

source_name: genomic DNA from cells of the uterine cervix 1227

value: cells of the uterine cervix 1227

tag: chemotherapy

tag: survival time (years)

tag: death status

value: A


title: Normal Uterine Cervix ART14845

source_name: genomic DNA from normal cells of the uterine cervix ART14845

tag: hpv status

tag: pcr

value: C

tag: bisulphite 1

value: BS conversion C1 Grn 2657

tag: bisulphite 2

value: BS conversion C2 Grn 1984


title: Uterine Cervix 1279

source_name: genomic DNA from cells of the uterine cervix 1279

value: cells of the uterine cervix 1279

tag: Stage

tag: grade

tag: recurrence free survival (years)

tag: sentrix position

value: F


title: Normal Uterine Cervix ART609

source_name: genomic DNA from normal cells of the uterine cervix ART609

tag: cell type

tag: sample type

value: bisulphite converted genomic DNA from a prospective CIN2+

tag: age

value: Round2Cyt 0

tag: sentrix id

value: J

value: BS conversion C1 Grn 1855

value: BS conversion C2 Grn 1562


title: Normal Uterine Cervix ART23651

source_name: genomic DNA from normal cells of the uterine cervix ART23651

value: BS conversion C1 Grn 2045

value: BS conversion C2 Grn 1838


title: Uterine Cervix 1215

source_name: genomic DNA from cells of the uterine cervix 1215

value: cells of the uterine cervix 1215

value: bisulphite converted genomic DNA from  Cervical Cancer

tag: surgery

tag: radiation

tag: relapse

tag: bisulphite conversion efficiency (log-scale)


title: Normal Uterine Cervix ART6079

source_name: genomic DNA from normal cells of the uterine cervix ART6079

value: bisulphite converted genomic DNA from a prospective CIN2-

tag: outcome

value: Round2Cyt 1

value: E

value: BS conversion C1 Grn 1870

value: BS conversion C2 Grn 1385


title: Normal Uterine Cervix ART4249

source_name: genomic DNA from normal cells of the uterine cervix ART4249

tag: hpv status

value: C

value: BS conversion C1 Grn 2207

value: BS conversion C2 Grn 1788


title: Normal Uterine Cervix ART18949

source_name: genomic DNA from normal cells of the uterine cervix ART18949

value: bisulphite converted genomic DNA from a prospective CIN2+

tag: pcr

value: L

value: BS conversion C1 Grn 2706

value: BS conversion C2 Grn 1754


title: Normal Uterine Cervix ART14891

source_name: genomic DNA from normal cells of the uterine cervix ART14891

value: Round2Cyt 0

value: K

tag: bisulphite 1

value: BS conversion C1 Grn 3364

value: BS conversion C2 Grn 2250


title: Normal Uterine Cervix ART9887

source_name: genomic DNA from normal cells of the uterine cervix ART9887

value: I

value: BS conversion C1 Grn 1473

tag: bisulphite 2

value: BS conversion C2 Grn 1179


title: Normal Uterine Cervix ART4084

source_name: genomic DNA from normal cells of the uterine cervix ART4084

value: bisulphite converted genomic DNA from a prospective CIN2-

value: Round2Cyt 1

value: D

value: BS conversion C1 Grn 3381

value: BS conversion C2 Grn 2059


title: Normal Uterine Cervix ART9553

source_name: genomic DNA from normal cells of the uterine cervix ART9553

value: H

value: BS conversion C1 Grn 3571

value: BS conversion C2 Grn 3252


title: Normal Uterine Cervix ART23729

source_name: genomic DNA from normal cells of the uterine cervix ART23729

value: BS conversion C1 Grn 2492

value: BS conversion C2 Grn 1713


title: ∆med31 (replicate 4)

city: Montreal

first: Andre

last: Nantel

state: QC

address: 6100 Royalmount

department: Biotechnology Research Institute

country: Canada

institute: National Research Council of Canada

hyb_protocol: The microarray slides were pre-hybridized for 2 hours at 42°C with DIGeasy hybridization buffer (Roche) containing 0.5 ug/ul of yeast tRNA (Roche) and 0.5 ug/ul of salmon sperm DNA (Invitrogen) and subsequently washed with 0.1X SSC and air dried. The slides were then hybridized with labeled cDNAs overnight at 42°C in DIGeasy hybridization buffer with yeast tRNA and salmon sperm DNA. Hybridization was done with an Advalytix SlideBooster. The slides were washed twice with SSC-0.2% SDS, once with 0.1X SSC-0.2% SDS and 3 times with 0.1X SSC. A final wash with isopropanol was performed and slides were air-dried.

scan_protocol: Slides were scanned with a ScanArray 5000 scanner (Perkin Elmer) at 10-µm resolution.

data_processing: Signal intensity was quantified with QuantArray software (Perkin Elmer) and final Lowess normalization and inspection of the data was done with the GeneSpring package GX v.7.3 (Agilent Technologies).

organism: Candida albicans

source_name: ∆med31/MED31 complemented strain

label_protocol: 20 µg of total RNA was reverse transcribed using oligo(dT)21 in the presence of Cy5-dCTP (Perkin-Elmer-Cetus/NEN) and Superscript III reverse transcriptase (Invitrogen). Thereafter, template RNA was degraded by adding 2.5 units of RNase H (USB) and 1 ug of RNase A (Pharmacia) followed by incubation for 15 min at 37°C. The labeled cDNAs were purified with QIAquick PCR Purification Kit (Qiagen).

extract_protocol: Total RNA was isolated from quadruplicate independent biological samples using the RNeasy mini kit (Qiagen). Briefly, frozen cells were thawed out in RNeasy buffer RLT at a ratio of 3:1 [vol/vol] buffer/pellet. Resuspended cells were divided into 1 ml aliquots in 2 ml screw cap microcentrifuge tubes containing 0.6 ml of 0.5 mm diameter acid-washed glass beads. Samples were homogenized 6 times, for 5 minutes each, in a BeadBeater set at maximum speed.

treatment_protocol: Cells from an overnight culture were diluted to OD600 = 0.1 in 100 ml of YPD and grown to OD600 = 1.0.

tag: strain

value: ∆med31/MED31 complemented strain

source_name: ∆med31 strain

value: ∆med31 strain


title: Normal Uterine Cervix ART60709

source_name: genomic DNA from normal cells of the uterine cervix ART60709

value: J

value: BS conversion C1 Grn 2533

value: BS conversion C2 Grn 1830


title: Normal Uterine Cervix ART17049

source_name: genomic DNA from normal cells of the uterine cervix ART17049

value: bisulphite converted genomic DNA from a prospective CIN2+

value: Round2Cyt 0

value: C

value: BS conversion C1 Grn 1937

value: BS conversion C2 Grn 1426


title: Normal Uterine Cervix ART4423

source_name: genomic DNA from normal cells of the uterine cervix ART4423

value: F

value: BS conversion C1 Grn 2106

value: BS conversion C2 Grn 2436


title: Normal Uterine Cervix ART20151

source_name: genomic DNA from normal cells of the uterine cervix ART20151

value: I

value: BS conversion C1 Grn 2350

value: BS conversion C2 Grn 1810


title: ∆med31 (replicate 3)


title: Normal Uterine Cervix ART10658

source_name: genomic DNA from normal cells of the uterine cervix ART10658

value: D

value: BS conversion C1 Grn 2330

value: BS conversion C2 Grn 1601


title: Normal Uterine Cervix ART17144

source_name: genomic DNA from normal cells of the uterine cervix ART17144

value: G

value: BS conversion C1 Grn 1857

value: BS conversion C2 Grn 1349


title: Normal Uterine Cervix ART9369

source_name: genomic DNA from normal cells of the uterine cervix ART9369

value: bisulphite converted genomic DNA from a prospective CIN2+

value: A

value: BS conversion C1 Grn 3478

value: BS conversion C2 Grn 2670


title: ∆med31 (replicate 2)

value: ∆med31/MED31 complemented strain

value: ∆med31 strain


title: Normal Uterine Cervix ART12722

source_name: genomic DNA from normal cells of the uterine cervix ART12722

value: Round2Cyt 0

value: H

value: BS conversion C1 Grn 1832

value: BS conversion C2 Grn 1258


title: ∆med31 (replicate 1)


title: Normal Uterine Cervix ART13193

source_name: genomic DNA from normal cells of the uterine cervix ART13193

value: bisulphite converted genomic DNA from a prospective CIN2-

value: Round2Cyt 1

value: BS conversion C1 Grn 2068

value: BS conversion C2 Grn 1495


title: Normal Uterine Cervix ART11513

source_name: genomic DNA from normal cells of the uterine cervix ART11513

value: BS conversion C1 Grn 1885

value: BS conversion C2 Grn 1507


title: Normal Uterine Cervix ART19417

source_name: genomic DNA from normal cells of the uterine cervix ART19417

value: L

value: BS conversion C1 Grn 2287

value: BS conversion C2 Grn 1553


title: Normal Uterine Cervix ART6530

source_name: genomic DNA from normal cells of the uterine cervix ART6530

value: G

value: BS conversion C1 Grn 2170

value: BS conversion C2 Grn 2096


title: Normal Uterine Cervix ART60561

source_name: genomic DNA from normal cells of the uterine cervix ART60561

value: F

value: BS conversion C1 Grn 1932

value: BS conversion C2 Grn 1713


title: Normal Uterine Cervix ART2167

source_name: genomic DNA from normal cells of the uterine cervix ART2167

value: bisulphite converted genomic DNA from a prospective CIN2+

value: Round2Cyt 0

value: B

value: BS conversion C1 Grn 2330

value: BS conversion C2 Grn 1574


title: Normal Uterine Cervix ART5066

source_name: genomic DNA from normal cells of the uterine cervix ART5066

value: bisulphite converted genomic DNA from a prospective CIN2-

value: Round2Cyt 1

value: BS conversion C1 Grn 1594

value: BS conversion C2 Grn 1649


title: Normal Uterine Cervix ART4259

source_name: genomic DNA from normal cells of the uterine cervix ART4259

value: C

value: BS conversion C1 Grn 1707

value: BS conversion C2 Grn 1230


title: Normal Uterine Cervix ART2367

source_name: genomic DNA from normal cells of the uterine cervix ART2367

value: J

value: BS conversion C1 Grn 2224

value: BS conversion C2 Grn 1983


title: Normal Uterine Cervix ART17029

source_name: genomic DNA from normal cells of the uterine cervix ART17029

value: E

value: BS conversion C1 Grn 2190

value: BS conversion C2 Grn 1322


title: Normal Uterine Cervix ART9933

source_name: genomic DNA from normal cells of the uterine cervix ART9933

value: A

value: BS conversion C1 Grn 1648

value: BS conversion C2 Grn 1766


title: Normal Uterine Cervix ART778

source_name: genomic DNA from normal cells of the uterine cervix ART778

value: bisulphite converted genomic DNA from a prospective CIN2+

value: Round2Cyt 0

value: L

value: BS conversion C1 Grn 2014

value: BS conversion C2 Grn 1145


title: Normal Uterine Cervix ART2133

source_name: genomic DNA from normal cells of the uterine cervix ART2133

value: H

value: BS conversion C1 Grn 1998

value: BS conversion C2 Grn 1311


title: Normal Uterine Cervix ART2604

source_name: genomic DNA from normal cells of the uterine cervix ART2604

value: I

value: BS conversion C1 Grn 2206

value: BS conversion C2 Grn 1354


title: Normal Uterine Cervix ART23786

source_name: genomic DNA from normal cells of the uterine cervix ART23786

value: F

value: BS conversion C1 Grn 1941

value: BS conversion C2 Grn 1608


title: Normal Uterine Cervix ART15717

source_name: genomic DNA from normal cells of the uterine cervix ART15717

value: bisulphite converted genomic DNA from a prospective CIN2-

value: Round2Cyt 1

value: BS conversion C1 Grn 1942

value: BS conversion C2 Grn 1609


title: Normal Uterine Cervix ART945

source_name: genomic DNA from normal cells of the uterine cervix ART945

value: B

value: BS conversion C1 Grn 2235

value: BS conversion C2 Grn 1889


title: Normal Uterine Cervix ART4895

source_name: genomic DNA from normal cells of the uterine cervix ART4895

value: D

value: BS conversion C1 Grn 1826

value: BS conversion C2 Grn 1668


title: Normal Uterine Cervix ART13004

source_name: genomic DNA from normal cells of the uterine cervix ART13004

value: Round2Cyt 0

value: A

value: BS conversion C1 Grn 1558

value: BS conversion C2 Grn 1554


title: Normal Uterine Cervix ART19141

source_name: genomic DNA from normal cells of the uterine cervix ART19141

value: bisulphite converted genomic DNA from a prospective CIN2+

value: K

value: BS conversion C1 Grn 2489

value: BS conversion C2 Grn 1813


title: Normal Uterine Cervix ART14472

source_name: genomic DNA from normal cells of the uterine cervix ART14472

value: BS conversion C1 Grn 1816

value: BS conversion C2 Grn 1390


title: Normal Uterine Cervix ART966

source_name: genomic DNA from normal cells of the uterine cervix ART966

value: J

value: BS conversion C1 Grn 1117

value: BS conversion C2 Grn 1041


title: Normal Uterine Cervix ART13446

source_name: genomic DNA from normal cells of the uterine cervix ART13446

value: H

value: BS conversion C1 Grn 1025

value: BS conversion C2 Grn 959


title: Normal Uterine Cervix ART2036

source_name: genomic DNA from normal cells of the uterine cervix ART2036

value: L

value: BS conversion C1 Grn 2299

value: BS conversion C2 Grn 1769


title: Normal Uterine Cervix ART11608

source_name: genomic DNA from normal cells of the uterine cervix ART11608

value: bisulphite converted genomic DNA from a prospective CIN2-

value: Round2Cyt 1

value: B

value: BS conversion C1 Grn 1813

value: BS conversion C2 Grn 1452


title: Normal Uterine Cervix ART10417

source_name: genomic DNA from normal cells of the uterine cervix ART10417

value: G

value: BS conversion C1 Grn 990

value: BS conversion C2 Grn 1188


title: Normal Uterine Cervix ART7029

source_name: genomic DNA from normal cells of the uterine cervix ART7029

value: Round2Cyt 0

value: K

value: BS conversion C1 Grn 2336

value: BS conversion C2 Grn 1548


title: Normal Uterine Cervix ART5723

source_name: genomic DNA from normal cells of the uterine cervix ART5723

value: I

value: BS conversion C1 Grn 1042

value: BS conversion C2 Grn 936


title: Normal Uterine Cervix ART23545

source_name: genomic DNA from normal cells of the uterine cervix ART23545

value: BS conversion C1 Grn 1754

value: BS conversion C2 Grn 1247


title: Normal Uterine Cervix ART2092

source_name: genomic DNA from normal cells of the uterine cervix ART2092

value: bisulphite converted genomic DNA from a prospective CIN2+

value: J

value: BS conversion C1 Grn 1948

value: BS conversion C2 Grn 1296


title: Normal Uterine Cervix ART14569

source_name: genomic DNA from normal cells of the uterine cervix ART14569

value: bisulphite converted genomic DNA from a prospective CIN2-

value: Round2Cyt 1

value: F

value: BS conversion C1 Grn 1955

value: BS conversion C2 Grn 1700


title: Normal Uterine Cervix ART23158

source_name: genomic DNA from normal cells of the uterine cervix ART23158

value: Round2Cyt 0

value: H

value: BS conversion C1 Grn 2035

value: BS conversion C2 Grn 1845


title: Normal Uterine Cervix ART8159

source_name: genomic DNA from normal cells of the uterine cervix ART8159

value: C

value: BS conversion C1 Grn 899

value: BS conversion C2 Grn 821


title: Normal Uterine Cervix ART14457

source_name: genomic DNA from normal cells of the uterine cervix ART14457

value: E

value: BS conversion C1 Grn 1468

value: BS conversion C2 Grn 785


title: Normal Uterine Cervix ART7211

source_name: genomic DNA from normal cells of the uterine cervix ART7211

value: J

value: BS conversion C1 Grn 1000

value: BS conversion C2 Grn 936


title: Normal Uterine Cervix ART28530

source_name: genomic DNA from normal cells of the uterine cervix ART28530

value: bisulphite converted genomic DNA from a prospective CIN2-

value: Round2Cyt 1

value: I

value: BS conversion C1 Grn 993

value: BS conversion C2 Grn 1020


title: Normal Uterine Cervix ART8132

source_name: genomic DNA from normal cells of the uterine cervix ART8132

value: B

value: BS conversion C1 Grn 896

value: BS conversion C2 Grn 991


title: Normal Uterine Cervix ART8406

source_name: genomic DNA from normal cells of the uterine cervix ART8406

value: bisulphite converted genomic DNA from a prospective CIN2+

value: Round2Cyt 0

value: G

value: BS conversion C1 Grn 1050

value: BS conversion C2 Grn 984


title: Normal Uterine Cervix ART7570

source_name: genomic DNA from normal cells of the uterine cervix ART7570

value: E

value: BS conversion C1 Grn 981

value: BS conversion C2 Grn 1093


title: Normal Uterine Cervix ART276

source_name: genomic DNA from normal cells of the uterine cervix ART276

value: L

value: BS conversion C1 Grn 689

value: BS conversion C2 Grn 789


title: Normal Uterine Cervix ART4817

source_name: genomic DNA from normal cells of the uterine cervix ART4817

value: bisulphite converted genomic DNA from a prospective CIN2-

value: C

value: BS conversion C1 Grn 2182

value: BS conversion C2 Grn 1628


title: Normal Uterine Cervix ART4486

source_name: genomic DNA from normal cells of the uterine cervix ART4486

value: BS conversion C1 Grn 836

value: BS conversion C2 Grn 896


title: IRT8712_T00320426

city: College Station

first: Youngmi

last: Cho

state: TX

address: 2253 TAMU

department: Faculty of Nutrition

institute: Texas A&M University

description: T00320426_2011-2-1_IRT 8712 28WK

hyb_protocol: Codelink Gene Expression System: Single-Assay Bioarray Hybridization and Detection according to manufacturer's instructions http://www.appliedmicroarrays.com/pdf/codelink_bioarray_processing_protocol.pdf

scan_protocol: Codelink Gene Expression System: Single-Assay Bioarray Hybridization and Detection according to manufacturer's instructions http://www.appliedmicroarrays.com/application_notes/63005079.pdf

data_processing: Median normalized values derived from Codelink Expression Analysis Version 5.0

organism: Rattus norvegicus

source_name: Exfoliated colonocytes

label_protocol: Ambion MessageAmp II aRNA Amplification and Biotin Enhanced kits:  Manual Labelled cRNA Target preparation following manufacturer's instructions http://www.ambion.com/techlib/prot/fm_1751.pdf and http://www.ambion.com/techlib/prot/fm_1791.pdf

growth_protocol: Rats were housed individually in a temperature and humidity controlled animal facility with a 12 h light/dark cycle.

extract_protocol: To enrich the level of eukaryotic mRNA in the fecal samples, poly (A)+ RNA was isolated from total RNA using oligo dT cellulose micro spin columns and the mTRAP Maxi kit.

treatment_protocol: Rats consumed diets containing FO/P or CO/C and were injected with azoxymethane (AOM, 2x, 15 mg/kg BW, s.c.).

value: Sprague Dawley

tag: diet

value: CO/C

tag: injection

value: AOM

tag: time

value: 28 wk after AOM injection


title: Normal Uterine Cervix ART11205

source_name: genomic DNA from normal cells of the uterine cervix ART11205

tag: cell type

value: Round2Cyt 1

tag: sentrix position

value: K

value: BS conversion C1 Grn 1054

value: BS conversion C2 Grn 1107


title: IRT8915_T00320417

description: T00320417_2011-2-1_IRT 8915 28WK


title: Normal Uterine Cervix ART17559

source_name: genomic DNA from normal cells of the uterine cervix ART17559

tag: sample type

tag: age

value: BS conversion C1 Grn 980

value: BS conversion C2 Grn 989


title: Normal Uterine Cervix ART28927

source_name: genomic DNA from normal cells of the uterine cervix ART28927

value: bisulphite converted genomic DNA from a prospective CIN2+

value: Round2Cyt 0

tag: sentrix id

value: L

value: BS conversion C1 Grn 808

value: BS conversion C2 Grn 812


title: IRT8813_T00244967

description: T00244967_2011-2-2_IRT 8813 28WK


title: Normal Uterine Cervix ART16545

source_name: genomic DNA from normal cells of the uterine cervix ART16545

value: bisulphite converted genomic DNA from a prospective CIN2-

value: F

value: BS conversion C1 Grn 998

value: BS conversion C2 Grn 987


title: IRT8403_T00320422

description: T00320422_2011-2-1_IRT 8403 28WK

value: Sprague Dawley

value: CO/C

value: AOM


title: IRT8814_T00245021

description: T00245021_2011-2-2_IRT 8814 29WK

value: 28 wk after AOM injection


title: Normal Uterine Cervix ART12751

source_name: genomic DNA from normal cells of the uterine cervix ART12751

value: Round2Cyt 1

value: B

value: BS conversion C1 Grn 753

value: BS conversion C2 Grn 727


title: IRT6713_T00320427

description: T00320427_2011-2-1_IRT 6713 28WK

value: FO/P


title: Normal Uterine Cervix ART4319

source_name: genomic DNA from normal cells of the uterine cervix ART4319

value: bisulphite converted genomic DNA from a prospective CIN2+

value: Round2Cyt 0

value: E

value: BS conversion C1 Grn 787

value: BS conversion C2 Grn 1032


title: Normal Uterine Cervix ART4706

source_name: genomic DNA from normal cells of the uterine cervix ART4706

value: bisulphite converted genomic DNA from a prospective CIN2-

value: D

value: BS conversion C1 Grn 814

value: BS conversion C2 Grn 1077


title: IRT5913_T00245607

description: T00245607_2011-2-2_IRT 5913 28WK

value: Sprague Dawley


title: Normal Uterine Cervix ART10395

source_name: genomic DNA from normal cells of the uterine cervix ART10395

value: J

value: BS conversion C1 Grn 945

value: BS conversion C2 Grn 975


title: Normal Uterine Cervix ART19707

source_name: genomic DNA from normal cells of the uterine cervix ART19707

value: BS conversion C1 Grn 876

value: BS conversion C2 Grn 1090


title: IRT5913_T00245585

description: T00245585_2011-2-2_IRT 5913 28WK

value: AOM

value: 28 wk after AOM injection


title: Normal Uterine Cervix ART20542

source_name: genomic DNA from normal cells of the uterine cervix ART20542

value: bisulphite converted genomic DNA from a prospective CIN2+

value: H

value: BS conversion C1 Grn 850

value: BS conversion C2 Grn 846


title: Normal Uterine Cervix ART10037

source_name: genomic DNA from normal cells of the uterine cervix ART10037

value: Round2Cyt 1

value: K

value: BS conversion C1 Grn 1007

value: BS conversion C2 Grn 942


title: IRT5914_T00244968

description: T00244968_2011-2-2_IRT 5914 29WK

value: FO/P


title: Normal Uterine Cervix ART12863

source_name: genomic DNA from normal cells of the uterine cervix ART12863

value: bisulphite converted genomic DNA from a prospective CIN2-

value: F

value: BS conversion C1 Grn 903


title: Normal Uterine Cervix ART11874

source_name: genomic DNA from normal cells of the uterine cervix ART11874

value: Round2Cyt 0

value: A

value: BS conversion C1 Grn 920

value: BS conversion C2 Grn 849


title: Normal Uterine Cervix ART22647

source_name: genomic DNA from normal cells of the uterine cervix ART22647

value: BS conversion C2 Grn 961


title: Normal Uterine Cervix ART8610

source_name: genomic DNA from normal cells of the uterine cervix ART8610

value: bisulphite converted genomic DNA from a prospective CIN2+

value: BS conversion C1 Grn 1128

value: BS conversion C2 Grn 1070


title: IRT5911_T00244965

description: T00244965_2011-2-2_IRT 5911 28WK

value: Sprague Dawley

value: AOM

value: 28 wk after AOM injection


title: Normal Uterine Cervix ART6406

source_name: genomic DNA from normal cells of the uterine cervix ART6406

value: L

value: BS conversion C1 Grn 1053

value: BS conversion C2 Grn 981


title: Normal Uterine Cervix ART15027

source_name: genomic DNA from normal cells of the uterine cervix ART15027

value: bisulphite converted genomic DNA from a prospective CIN2-

value: Round2Cyt 1

value: G

value: BS conversion C1 Grn 978

value: BS conversion C2 Grn 986


title: Normal Uterine Cervix ART723

source_name: genomic DNA from normal cells of the uterine cervix ART723

value: Round2Cyt 0

value: I

value: BS conversion C1 Grn 744

value: BS conversion C2 Grn 840


title: Normal Uterine Cervix ART27142

source_name: genomic DNA from normal cells of the uterine cervix ART27142

value: D

value: BS conversion C1 Grn 917

value: BS conversion C2 Grn 951


title: Normal Uterine Cervix ART17167

source_name: genomic DNA from normal cells of the uterine cervix ART17167

value: E

value: BS conversion C1 Grn 1009

value: BS conversion C2 Grn 959


title: Normal Uterine Cervix ART60089

source_name: genomic DNA from normal cells of the uterine cervix ART60089

value: B

value: BS conversion C1 Grn 752

value: BS conversion C2 Grn 757