title: Diet B. Biopsy sample collected 48 hours after exercice S9

city: Lausanne

first: Frederic

last: Raymond

address: Campus EPFL - Quartier de l'Innovation

department: Functional Genomics

country: Switzerland

institute: Nestle Institute of Health Sciences

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation in Genome Studio software

source_name: vastus lateralis (quadriceps femoris)

label_protocol: Biotinylated cRNA were prepared with the TotalPrep (Ambion) kit for Illumina arrays

extract_protocol: RNA was extracted with RNAdvance tissue kit from Agencourt (Beckman-Coulter) in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser 2100.

value: exercise for 1 h

tag: diet

value: Diet B - Protein enriched

tag: time

value: 48 hours after exercise

tag: subject id

value: vastus lateralis (quadriceps femoris)


title: 2A 96hr Replicate 1

status: Public on Nov 21 2011

type: RNA

city: Philadelphia

first: Michael

last: Slifker

state: PA

address: 333 Cottman Ave.

country: USA

institute: Fox Chase Cancer Center

description: E2 treated sample vs. time-matched control pool

hyb_protocol: Hybridizations were performed using the Agilent Gene Expression Hybridization Kit (Cat#5188-5242) and protocol. Fragmented samples in 1X Hi-RPM Hybridization Buffer were hybridized to 4X44K Agilent oligonicleotide arrays (Cat# G2534-60011) in Agilent Stainless Chamber slides (Cat# G2534A). Hybridizations were performed in an Agilent Microarray Hybridization Oven (Cat# G2545A) for 17h at 65°C at 10rpm. Slides were washed using Agilent's Gene Expression Wash Buffer Kit and Protocol in an ozone-controlled environment at 5ppb ozone or less. A maximum of 4 slides were washed at a time prior to immediate scaning.

scan_protocol: Slides were scanned using an Agilent Scanner (G2505C) in an ozone controlled environment (less than 5ppb ozone) at 5um resolution, Single Pass, eXtended Dynamic Range (XDR), Green and Red PMT: XDR Hi 100% and XDR Lo 10% Images were quantified using Agilent Feature Extraction Software (version 10.7).

data_processing: Agilent Feature Extraction v10.7 was used for background correction and dye-normalization

molecule: total RNA

organism: Homo sapiens

source_name: E2-treated 2A 96hr Replicate 1

label_protocol: 250 ng of total RNA from each E2-treated sample and 500ng of total RNA from each pooled reference sample were labeled using the protocol provided with the Agilent Quick Amp Labeling Kit (Cat# 5190-0447) using 1.2ul of T7 Promoter primer. Test samples were labeled with Cy3-dCTP (Perkin Elmer NEL580) and reference samples with Cy5-dCTP (Perkin Elmer NEL581). Labeled/amplified RNAs were purified using Qiaen's RNeasy spin columns (Qiagen# 74104). Purified cRNA was quantified on a Nanodrop ND-1000 Specrophotometer. 825 ng of each cRNA probe with a specific activity of at least 8.0 pmol Cy Dye per ug cRNA were used for hybridization.

growth_protocol:
Estrogen-dependent WS8 cells were maintained in fully-estrogenized media [phenol red-containing RPMI-1640 and 10% whole fetal bovine serum (FBS), supplemented with 6 ng/ml insulin, 2 mM glutamine, 100 μM non-essential amino acids, and 100 U of penicillin and streptomycin per ml], while 5C and 2A cells were maintained in estrogen-free medium (phenol red-free RPMI-1640 plus 10% dextran-coated charcoal-stripped FBS and the same supplements as for fully-estrogenized medium). Estrogen-dependent WS8 cells were switched to estrogen-free media for 3 days before all experiments.
MCF-7:WS8, MCF-7:2A, and MCF-7:5C cells were seeded at 2, 4, and 5 million cells per 15 cm plate, respectively, in estrogen-free RPMI-1640 + 10% dextran-coated charcoal-treated fetal bovine serum

extract_protocol:
Cells were harvested for RNA using TRIzol (Invitrogen) according to manufacturers instructions. RNA was further isolated using Total RNeasy purification columns (Qiagen).
RNA samples were controlled for purity and integrity using a Nanodrop 1000 spectrophotometer and an Agilent 2100 Bioanalyzer by requiring each sample to exhibit an RNA Integrity Number (RIN) of 9.8-10.0.

treatment_protocol: Cells were parsed into 2 groups of 6 replicate plates per treatment per time point, and then treated with either 0.1% ethanol (vehicle control) or 10-9 M E2 for 2, 6, 12, 24, 48, 72, and 96 h. At 48 h, media on the remaining cells was replenished.

tag: cell line

tag: treatment

tag: time (hr)

source_name: Control-treated RNA reference pool - 2A 96h

value: vehicle


title: S2 vs. S1 (H02)

city: Beijing

first: Zhengfan

last: Jiang

address: No.5 Yiheyuan Road, Haidian District

department: School of Life Sciences

country: China

institute: Peking University

hyb_protocol: HOA v4.3 arrays were pre-heat at 60℃ for 10 mins, rehydrated by 100% ethanol following with deionized water. The slides were pre-hybridized with 5x SSPE, 0.1% SDS and 1% BSA at 42℃ for 2 hour. After the pre-hybridization, 5 µg Cy5-labeled aRNA was hybridize on HOA in the presentation of the Phalanx OneArray hybridization buffer.

scan_protocol: The arrays were scanned by Axon GenePix 4000B scanner (635nm power 100 PMT 600~630 ; 532nm power 10, PMT 460) and quantify the fluoresence intensity.

data_processing: The raw data were adjust by Rosetta Resolver® error model calculation. The statistic values were calculated after the replicated probes squeezing and median scaling normalization.

source_name: S2: HEK293 control

label_protocol: 2.5 µg of total RNA was reverse-transcribed and amplified using MessageAmpTM aRNA Amplification Kit (Ambion).  Indirect labeling the aa-UTP whereon by NHS-CyDye (Cy5, Cy3; Amershan).

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions. RNA purity was checked by optical density of NanoDrop ND-1000 and agarose electrophoresis. RNA integrity was measured by Agilent RNA 6000 Nano Assay (RIN≧7).

value: HEK293 cells

value: control

source_name: S1: HEK293 cells transfected with Poly(I:C) for 16hours

value: poly(I:C) transfection for 16 hours


title: B cells WT vs CCR7-/- Replicate 1 (Pool1)

city: Hannover

first: Oliver

last: Dittrich-Breiholz

address: Carl-Neuberg-Str. 1

department: Research Core Unit Genomics

country: Germany

institute: Medical School Hannover

hyb_protocol: cRNA fragmentation, hybridization, and washing steps were carried out according to Agilent’s Two-Color Microarray-Based Gene Expression Analysis Protocol V5.7 (for details see http://www.agilent.com) except that 500ng of each labeled cRNA sample were used for hybridization. Microarrays were co-hybridized with differently-labeled material from CCR7 -/- versus wildtype animals in a dual-color setting.

scan_protocol: Slides were scanned on the Agilent Micro Array Scanner G2505 B at two different PMT settings (100 % and 5 %) to increase the dynamic range of the measurements (extended dynamic range mode).

data_processing: Data extraction and normalization were performed with the “Feature Extraction Software V9.5.3.1” by using the recommended default extraction protocol file: GE2-v5_95_Feb07.xml. To correct for systematic bias at the high end of the fluorescence intensity measurements, the highest ranking 2% of Processed Signals in the green channel (gPS) were further normalized according to an intensity-dependent, non-linear scaling strategy, to optimize fitting to their respective counterparts in the red channel.

organism: Mus musculus

source_name: B cells

label_protocol: 20ng of total RNA per condition were used to prepare Cy3-, or Cy5-labeled cRNA (Amino Allyl MessageAmp™ II Kit; Ambion) as directed by the company.

growth_protocol: The cells were not cultured after isolation.

extract_protocol: Total RNA from sorted cell samples was extracted by use of the Nucleospin RNA XS kit (Macherey & Nagel).

treatment_protocol: The cells were sorted on a FACSAria (BD Biosciences) and immediately subjected to total RNA isolation.

tag: strain

tag: genotype/variation

value: wildtype

tag: tissue

value: peripheral lymph nodes

value: Ccr7 knock-out


title: S3 vs. S4 (H03)

source_name: S3: HEK293-STAT6 stable cell line control

value: HEK293 stably expressing Stat6

source_name: S4: HEK293-STAT6 stable cell line transfected with Poly(I:C) for 16 hours


title: Diet B. Biopsy sample collected 48 hours after exercice S6

label: biotin


title: 2A 72hr Replicate 6

source_name: E2-treated 2A 72hr Replicate 6

source_name: Control-treated RNA reference pool - 2A 72h


title: 2A 96hr Replicate 2

source_name: E2-treated 2A 96hr Replicate 2


title: Diet B. Biopsy sample collected 48 hours after exercice S3


title: TES 2 4h

city: Tübingen

first: Gabriel

last: Willmann

address: Schleichstrasse 12-16

institute: University Eye Hospital and Centre for Ophthalmology Tübingen

hyb_protocol: 15 micrograms of labeled cRNA from retina was fragmented, and 10ug was hybridized to Affymetrix Rat Gene 1.0 ST Gene Chip arrays for 18-24h (Affymetrix Inc.). Gene chip was washed and stained with streptavidin-phycoerythrin.

scan_protocol: The chip was scanned at 6um resolution with Agilant model G2500A Gene Array scanner. A visual quality control measurement was performed to ensure proper hybridization after each chip was scanned.

data_processing: For statistical analysis of microarray data all .cel files were imported to GeneSpring GX software (Agilent Technologies Inc.) where GC-RMA algorithm was applied to yield log signal values on each probe set. All transcripts with a minimum change of 1.2 fold together with a p value less than 0.05 were selected using Significance Analysis of Microarray (SAM) (Tusher VG, 2001).

label: Biotin

organism: Rattus norvegicus

source_name: retina

label_protocol: Three microliter total RNA was used for each sample to obtain linearly amplified labeled cRNA by using GeneChip® One-Cycle Target Labeling kit (Affymetrix, Santa Clara, CA, USA) as described by manufacturer. Briefly, total RNA was used to generate double-stranded cDNA with the T7-oligo (dT) primer. This double-stranded cDNA was used in vitro transcription and biotin labeling steps. Labeled cRNA yield and purity were determined by measuring the absorbance at 260 and 280nm. All the cRNA 260/280 ratios were between 1.9 and 2.1. Quality control of the labeled cRNA products was assessed by performing 1µg labeled cRNA on 2% agarose gel to see similar RNA smear type.

extract_protocol: mRNA of retina was isolated 4h after transcornial electrical stimulation and compared to sham animals using RNAeasy Isolation Kit (Ambion, Austin, Texas, USA) according to manufacturers instructions.

value: Brown Norway Rat

tag: gender

value: male

tag: age

value: 8 weeks


title: 2A 96hr Replicate 4

source_name: E2-treated 2A 96hr Replicate 4


title: 2A 96hr Replicate 6

source_name: E2-treated 2A 96hr Replicate 6


title: 2A 72hr Replicate 4

source_name: E2-treated 2A 72hr Replicate 4


title: Diet B. Biopsy sample collected 48 hours after exercice S5


title: Diet B. Biopsy sample collected 48 hours after exercice S7


title: 2A 96hr Replicate 5

source_name: E2-treated 2A 96hr Replicate 5


title: Diet B. Biopsy sample collected 48 hours after exercice S2


title: TES Control 4 4h


title: 2A 72hr Replicate 5

source_name: E2-treated 2A 72hr Replicate 5


title: TES Control 3 4h


title: 2A 72hr Replicate 3

source_name: E2-treated 2A 72hr Replicate 3


title: Diet B. Biopsy sample collected 48 hours after exercice S1

source_name: vastus lateralis (quadriceps femoris)


title: Diet A. Biopsy sample collected 48 hours after exercice S9

value: Diet A - Control


title: Diet A. Biopsy sample collected 48 hours after exercice S5


title: Diet A. Biopsy sample collected 48 hours after exercice S7


title: Diet A. Biopsy sample collected 48 hours after exercice S6


title: Diet A. Biopsy sample collected 48 hours after exercice S8


title: 2A 72hr Replicate 1

source_name: E2-treated 2A 72hr Replicate 1


title: 2A 48hr Replicate 5

source_name: E2-treated 2A 48hr Replicate 5

source_name: Control-treated RNA reference pool - 2A 48h


title: 2A 72hr Replicate 2

source_name: E2-treated 2A 72hr Replicate 2


title: 2A 48hr Replicate 2

source_name: E2-treated 2A 48hr Replicate 2


title: Diet B. Biopsy sample collected 3 hours after exercice S7

value: 3 hours after exercise


title: 2A 24hr Replicate 4

source_name: E2-treated 2A 24hr Replicate 4

source_name: Control-treated RNA reference pool - 2A 24h


title: Diet A. Biopsy sample collected 48 hours after exercice S2

value: exercise for 1 h


title: Diet A. Biopsy sample collected 48 hours after exercice S3


title: 2A 48hr Replicate 3

source_name: E2-treated 2A 48hr Replicate 3


title: 2A 48hr Replicate 4

source_name: E2-treated 2A 48hr Replicate 4


title: Diet B. Biopsy sample collected 3 hours after exercice S3

value: Diet B - Protein enriched


title: Diet B. Biopsy sample collected 3 hours after exercice S5


title: 2A 48hr Replicate 6

source_name: E2-treated 2A 48hr Replicate 6


title: 2A 24hr Replicate 2

source_name: E2-treated 2A 24hr Replicate 2


title: Diet A. Biopsy sample collected 48 hours after exercice S1

value: 48 hours after exercise


title: Diet B. Biopsy sample collected 3 hours after exercice S6

value: vastus lateralis (quadriceps femoris)


title: 2A 48hr Replicate 1

source_name: E2-treated 2A 48hr Replicate 1

value: vehicle


title: 2A 24hr Replicate 6

source_name: E2-treated 2A 24hr Replicate 6


title: 2A 24hr Replicate 5

source_name: E2-treated 2A 24hr Replicate 5


title: Diet B. Biopsy sample collected 3 hours after exercice S9


title: Diet B. Biopsy sample collected 3 hours after exercice S8


title: 2A 24hr Replicate 3

source_name: E2-treated 2A 24hr Replicate 3


title: 2A 24hr Replicate 1

source_name: E2-treated 2A 24hr Replicate 1


title: Diet B. Biopsy sample collected 3 hours after exercice S2

source_name: vastus lateralis (quadriceps femoris)


title: 2A 12hr Replicate 5

source_name: E2-treated 2A 12hr Replicate 5

source_name: Control-treated RNA reference pool - 2A 12h


title: Diet B. Biopsy sample collected 3 hours after exercice S1


title: 2A 12hr Replicate 6

source_name: E2-treated 2A 12hr Replicate 6


title: Diet A. Biopsy sample collected 3 hours after exercice S1


title: 2A 12hr Replicate 4

source_name: E2-treated 2A 12hr Replicate 4


title: Diet A. Biopsy sample collected 3 hours after exercice S6


title: Diet A. Biopsy sample collected 3 hours after exercice S9


title: Diet A. Biopsy sample collected 3 hours after exercice S7


title: 2A 6hr Replicate 2

source_name: E2-treated 2A 6hr Replicate 2

source_name: Control-treated RNA reference pool - 2A 6h


title: 2A 6hr Replicate 4

source_name: E2-treated 2A 6hr Replicate 4


title: Diet A. Biopsy sample collected 3 hours after exercice S2


title: Biopsy sample collected at rest after baseline exercise S9

value: baseline exercise

value: baseline


title: 2A 2hr Replicate 6

source_name: E2-treated 2A 2hr Replicate 6

source_name: Control-treated RNA reference pool - 2A 2h


title: 2A 12hr Replicate 3

source_name: E2-treated 2A 12hr Replicate 3


title: Biopsy sample collected at rest after baseline exercise S5


title: 2A 6hr Replicate 6

source_name: E2-treated 2A 6hr Replicate 6


title: 2A 12hr Replicate 2

source_name: E2-treated 2A 12hr Replicate 2


title: Diet A. Biopsy sample collected 3 hours after exercice S8


title: Biopsy sample collected at rest after baseline exercise S6


title: Biopsy sample collected at rest after baseline exercise S8


title: Biopsy sample collected at rest after baseline exercise S3


title: Diet A. Biopsy sample collected 3 hours after exercice S5


title: Diet A. Biopsy sample collected 3 hours after exercice S3


title: Biopsy sample collected at rest after baseline exercise S7


title: Biopsy sample collected at rest after baseline exercise S2


title: 2A 2hr Replicate 2

source_name: E2-treated 2A 2hr Replicate 2


title: 2A 6hr Replicate 1

source_name: E2-treated 2A 6hr Replicate 1


title: 2A 6hr Replicate 3

source_name: E2-treated 2A 6hr Replicate 3


title: 2A 2hr Replicate 5

source_name: E2-treated 2A 2hr Replicate 5


title: Biopsy sample collected at rest after baseline exercise S1

source_name: vastus lateralis (quadriceps femoris)


title: 2A 6hr Replicate 5

source_name: E2-treated 2A 6hr Replicate 5


title: 2A 12hr Replicate 1

source_name: E2-treated 2A 12hr Replicate 1

source_name: Control-treated RNA reference pool - 2A 12h


title: 5C 96hr Replicate 5

source_name: E2-treated 5C 96hr Replicate 5

source_name: Control-treated RNA reference pool - 5C 96h


title: 5C 96hr Replicate 1

source_name: E2-treated 5C 96hr Replicate 1


title: D18h4

city: Beaverton

first: Cecily

middle: Vauna

last: Bishop

state: OR

address: 505 NW 185th Ave

department: Division of Reproductive & Developmental Sciences

institute: Oregon National Primate Research Center

description: Simulated Early Pregnancy

hyb_protocol: Labeled target is fragmented at 95o C in the presence of high magnesium concentration. The fragmented material is combined with biotinylated hybridization control oligomer and biotinylated control cRNAs for BioB, BioC, BioD and CreX (Affymetrix) in hybridization buffer. Ten mg of target is hybridized with the GeneChip (insert array name) array (Affymetrix) overnight, followed by washing, staining with streptavidin-phycoerythrin (Molecular Probes), signal amplification with biotinylated anti-streptavidin antibody (Vector Labs), and a final staining step on the Fluidics Station 450 (Affymetrix).

scan_protocol: The distribution of fluorescent material on the processed array is determined using the Affymetrix 3000 GeneArray laser scanner with the 7G upgrade. Image inspection is performed manually immediately following each scan.

data_processing: All array scanning and data processing on the Affymetrix system is performed with GeneChip Operating System (GCOS) software.

label: biotin-CTP

organism: Macaca mulatta

source_name: D18 CL + hCG

label_protocol: Messenger RNA is amplified and labeled from 2 mg of total RNA in two steps. In the first step, mRNA is converted to double-stranded cDNA using Superscript Reverse Transcriptase (Invitrogen) and an oligo-dT primer linked to a T7 RNA polymerase binding site sequence (Affymetrix). In the second step, amplified and labeled cRNA (the target) is produced in an in vitro transcription reaction using T7 RNA polymerase and biotin-CTP (Affymetrix.). Following removal of free nucleotides, target yield is measured by UV260 absorbance.

extract_protocol: TRIzol® (Invitrogen) according to manufacturer's protocols

treatment_protocol: Simulated early pregnancy (SEP) treatment was begun on day 9 as [Duffy DM and Stouffer RL (1997) Biol Reprod 57, 1451-60] by treatment of females with recombinant human chorionic gonadotropin (hCG; Novarel™, Ferring Pharmaceuticals Inc. Parsippany, NJ, USA) in increasing dosages (15, 30,45,90,180,360,720,1440, and 2880 IU) twice daily by intramuscular injection. CL were collected by laparotomy on days 10, 12, 15, and 18, representing 1, 3, 6 and 9 days of hCG treatment (n=4 CL/day). Additionally, luteal day 10 untreated CL were collected to serve as baseline controls for SEP CL. All CL were dissected away from luteal tissue, sectioned, and snap-frozen in liquid nitrogen and stored at -80°C until RNA and protein isolation by TRIzol® extraction (Invitrogen, Carlsbad, CA, USA) according to manufacturer’s protocols.

value: female

value: Corpora Lutea

tag: day of tissue dissection


title: 5C 96hr Replicate 3

source_name: E2-treated 5C 96hr Replicate 3


title: D18h3

description: Simulated Early Pregnancy


title: D18h2

description: Simulated Early Pregnancy


title: 5C 96hr Replicate 4

source_name: E2-treated 5C 96hr Replicate 4


title: 5C 96hr Replicate 6

source_name: E2-treated 5C 96hr Replicate 6


title: 5C 96hr Replicate 2

source_name: E2-treated 5C 96hr Replicate 2


title: 5C 72hr Replicate 6

source_name: E2-treated 5C 72hr Replicate 6

source_name: Control-treated RNA reference pool - 5C 72h


title: 2A 2hr Replicate 3

source_name: E2-treated 2A 2hr Replicate 3

source_name: Control-treated RNA reference pool - 2A 2h


title: D18h1

description: Simulated Early Pregnancy


title: D12h4

description: Simulated Early Pregnancy

source_name: D12 CL + hCG


title: D15h4

description: Simulated Early Pregnancy

source_name: D15 CL + hCG


title: 5C 72hr Replicate 3

source_name: E2-treated 5C 72hr Replicate 3


title: 5C 72hr Replicate 4

source_name: E2-treated 5C 72hr Replicate 4


title: D15h3

description: Simulated Early Pregnancy


title: D15h2

description: Simulated Early Pregnancy


title: 5C 72hr Replicate 5

source_name: E2-treated 5C 72hr Replicate 5


title: D15h1

description: Simulated Early Pregnancy


title: 5C 72hr Replicate 2

source_name: E2-treated 5C 72hr Replicate 2


title: 5C 72hr Replicate 1

source_name: E2-treated 5C 72hr Replicate 1


title: 5C 48hr Replicate 5

source_name: E2-treated 5C 48hr Replicate 5

source_name: Control-treated RNA reference pool - 5C 48h


title: 5C 48hr Replicate 1

source_name: E2-treated 5C 48hr Replicate 1


title: D10h4

description: Simulated Early Pregnancy

source_name: D10 CL + hCG


title: D12h2

description: Simulated Early Pregnancy


title: D12h3

description: Simulated Early Pregnancy


title: D12h1

description: Simulated Early Pregnancy


title: 5C 48hr Replicate 6

source_name: E2-treated 5C 48hr Replicate 6


title: 5C 24hr Replicate 5

source_name: E2-treated 5C 24hr Replicate 5

source_name: Control-treated RNA reference pool - 5C 24h


title: D10h3

description: Simulated Early Pregnancy


title: D10 4

description: Mid late/ Late Luteal Phase

source_name: D10 Control corpora lutea


title: SAH108_R2

city: Princeton

first: Alison

last: Hottes

state: NJ

address: 220 Carl Icahn Lab Washington Road

department: Lewis-Sigler Institute for Integrative Genomics

institute: Princeton University

description:
Gene expression data from PA3726::ISlacZ/hah MPAO1 cells
Tav_AH_20100527_PA108_R2.CEL

hyb_protocol: Following fragmentation, 4 ug of cDNA were hybridized for 16 hr at 50C on Affymetrix GeneChip P. aeruginosa Genome Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using an Affymetrix GeneGhip Scanner 3000.

data_processing:
The data were analyzed using GeneChip Operating Software (Version 1.3) with default settings.
MAS5.0 signal intensity; also given are the values sum-normalized so the average signal from each array is 500.

organism: Pseudomonas aeruginosa

source_name: UW-14479 from University of Washington mutant collection (Jacobs et al., PNAS, 2003)

label_protocol: The RNA was converted to cDNA, fragmented, and end-labeled with biotin.

growth_protocol: PA3726 and wild type cells were grown to mid-exponential phase (OD600 =0.3 on an Ultraspec 3100 pro) in M63 minimal media + 0.5% casamino acids and 0.3% glucose

extract_protocol: 2 ml of culture was added to 4 ml of RNAprotect Bacteria Reagent (Qiagen).  The mixture was incubated at room temperature for 5 min and then centrifuged at 5000 g for 10 min.  The supernatant was removed and the pellets were stored at -80°C.  RNA was isolated using the RNeasy Mini Kit and an initial incubation with 5 mg/ml lysozyme in TE and an on-column DNA digestion

treatment_protocol: No special treatment was carried out.

value: MPAO1 PA3726::ISlacZ/hah

tag: growth state

value: planktonic


title: 5C 24hr Replicate 6

source_name: E2-treated 5C 24hr Replicate 6


title: D10 3

description: Mid late/ Late Luteal Phase


title: 5C 12hr Replicate 5

source_name: E2-treated 5C 12hr Replicate 5

source_name: Control-treated RNA reference pool - 5C 12h


title: SAH087

description:
Gene expression data from MPAO1 cells
Tav_AH_20100527_SAH087.CEL

source_name: This Study (Transpon sequence and its flanking region in UW-18931 (PA4854::lacZ) was replaced with original MPAO1 DNA)

value: wild-type, reference


title: SAH084

description:
Gene expression data from MPAO1 cells
Tav_AH_20100312_SAH084.CEL

source_name: UW-50363 from University of Washington mutant collection (Jacobs et al., PNAS, 2003)

value: MPAO1 PA0311::ISphoA/hah


title: SAH502

description:
Gene expression data from MPAO1 cells
Tav_AH_20100527_SAH502.CEL

source_name: This Study (Transpon sequence and its flanking region in UW-31715 (PA0035::phoA) was replaced with original MPAO1 DNA)


title: 5C 24hr Replicate 4

source_name: E2-treated 5C 24hr Replicate 4


title: 5C 24hr Replicate 1

source_name: E2-treated 5C 24hr Replicate 1


title: D10h2

description: Simulated Early Pregnancy


title: 5C 24hr Replicate 2

source_name: E2-treated 5C 24hr Replicate 2


title: 5C 12hr Replicate 6

source_name: E2-treated 5C 12hr Replicate 6


title: 5C 12hr Replicate 3

source_name: E2-treated 5C 12hr Replicate 3


title: 5C 6hr Replicate 6

source_name: E2-treated 5C 6hr Replicate 6

source_name: Control-treated RNA reference pool - 5C 6h


title: 5C 12hr Replicate 2

source_name: E2-treated 5C 12hr Replicate 2


title: D10 1

description: Mid late/ Late Luteal Phase


title: 5C 24hr Replicate 3

source_name: E2-treated 5C 24hr Replicate 3

source_name: Control-treated RNA reference pool - 5C 24h


title: 5C 48hr Replicate 3

source_name: E2-treated 5C 48hr Replicate 3

source_name: Control-treated RNA reference pool - 5C 48h


title: D10 2

description: Mid late/ Late Luteal Phase

source_name: D10 Control corpora lutea


title: D10h1

description: Simulated Early Pregnancy

source_name: D10 CL + hCG


title: SAH108_R1

description:
Gene expression data from PA3726::ISlacZ/hah MPAO1 cells
Tav_AH_20100312_SAH108_R1.CEL

source_name: UW-14479 from University of Washington mutant collection (Jacobs et al., PNAS, 2003)


title: FOLFOX non-responder test, #1137

city: Meguro-ku

first: Shingo

last: Tsuji

state: Tokyo

address: 4-6-1 Komaba

department: Research Center for Advanced Science and Technology

country: Japan

institute: The University of Tokyo

hyb_protocol: Hybridization was performed according to standard protocols for Affymetrix HG-U133 plus 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Affymetrix Power Tools (APT version:1.12.0). The apt-probeset-summarize command were used with -a plier-mm-sketch option.

source_name: tumor sample of patients with unresectable CRC before mFOLFOX6 therapy

label_protocol: Experimental procedures for GeneChip(TM) were performed in accordance with the GeneChip Expression Analysis Technical Manual (Affymetrix, Santa Clara, CA), using 3 µg of total RNA.

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

treatment_protocol: Surgical specimens were immediately cut into small pieces after resection, snap frozen in liquid nitrogen, and stored at –80°C

tag: lesion

value: Metastasis

tag: location

value: Liver

value: non-responder

value: F

tag: type

value: test


title: 5C 6hr Replicate 5

source_name: E2-treated 5C 6hr Replicate 5


title: 5C 6hr Replicate 3

source_name: E2-treated 5C 6hr Replicate 3


title: FOLFOX non-responder test, #1358

value: Primary

value: Ascending

value: M


title: FOLFOX non-responder test, #1326

value: Cecum


title: FOLFOX non-responder test, #1136


title: 5C 2hr Replicate 4

source_name: E2-treated 5C 2hr Replicate 4

source_name: Control-treated RNA reference pool - 5C 2h

value: vehicle


title: FOLFOX non-responder test, #1110


title: FOLFOX non-responder test, #1126


title: 5C 6hr Replicate 1

source_name: E2-treated 5C 6hr Replicate 1


title: 5C 2hr Replicate 5

source_name: E2-treated 5C 2hr Replicate 5


title: 5C 6hr Replicate 2

source_name: E2-treated 5C 6hr Replicate 2


title: 5C 2hr Replicate 6

source_name: E2-treated 5C 2hr Replicate 6


title: FOLFOX non-responder test, #1308

value: Sigmoid


title: 5C 2hr Replicate 3

source_name: E2-treated 5C 2hr Replicate 3


title: FOLFOX non-responder test, #1301

value: Rectum


title: 5C 2hr Replicate 2

source_name: E2-treated 5C 2hr Replicate 2


title: 5C 6hr Replicate 4

source_name: E2-treated 5C 6hr Replicate 4

source_name: Control-treated RNA reference pool - 5C 6h


title: WS8 96hr Replicate 5

source_name: E2-treated WS8 96hr Replicate 5

source_name: Control-treated RNA reference pool - WS8 96h


title: WS8 96hr Replicate 4

source_name: E2-treated WS8 96hr Replicate 4


title: WS8 96hr Replicate 6

source_name: E2-treated WS8 96hr Replicate 6


title: FOLFOX non-responder test, #1078

source_name: tumor sample of patients with unresectable CRC before mFOLFOX6 therapy


title: FOLFOX non-responder test, #1093


title: FOLFOX non-responder test, #1025


title: FOLFOX non-responder test, #1336


title: FOLFOX responder test, #1357

value: responder


title: 5C 2hr Replicate 1

source_name: E2-treated 5C 2hr Replicate 1


title: FOLFOX non-responder test, #1071


title: WS8 96hr Replicate 3

source_name: E2-treated WS8 96hr Replicate 3


title: FOLFOX responder test, #1319


title: FOLFOX responder test, #1335


title: FOLFOX non-responder test, #1323


title: WS8 72hr Replicate 3

source_name: E2-treated WS8 72hr Replicate 3

source_name: Control-treated RNA reference pool - WS8 72h


title: WS8 72hr Replicate 6

source_name: E2-treated WS8 72hr Replicate 6


title: FOLFOX responder test, #1235


title: FOLFOX responder test, #1233

value: Descending


title: FOLFOX responder test, #1057


title: WS8 72hr Replicate 5

source_name: E2-treated WS8 72hr Replicate 5


title: FOLFOX responder test, #1234


title: FOLFOX responder test, #1334


title: WS8 72hr Replicate 4

source_name: E2-treated WS8 72hr Replicate 4


title: FOLFOX responder test, #1058


title: WS8 96hr Replicate 2

source_name: E2-treated WS8 96hr Replicate 2


title: FOLFOX responder test, #1232


title: WS8 96hr Replicate 1

source_name: E2-treated WS8 96hr Replicate 1


title: WS8 72hr Replicate 1

source_name: E2-treated WS8 72hr Replicate 1


title: FOLFOX responder test, #1343


title: WS8 72hr Replicate 2

source_name: E2-treated WS8 72hr Replicate 2


title: WS8 48hr Replicate 3

source_name: E2-treated WS8 48hr Replicate 3

source_name: Control-treated RNA reference pool - WS8 48h


title: WS8 48hr Replicate 6

source_name: E2-treated WS8 48hr Replicate 6


title: WS8 48hr Replicate 2

source_name: E2-treated WS8 48hr Replicate 2


title: FOLFOX responder test, #1134


title: WS8 48hr Replicate 5

source_name: E2-treated WS8 48hr Replicate 5


title: FOLFOX responder test, #1141

source_name: tumor sample of patients with unresectable CRC before mFOLFOX6 therapy


title: WS8 48hr Replicate 4

source_name: E2-treated WS8 48hr Replicate 4


title: FOLFOX responder test, #1354


title: FOLFOX responder test, #1035


title: FOLFOX non-responder training, #1329

value: training


title: WS8 48hr Replicate 1

source_name: E2-treated WS8 48hr Replicate 1


title: WS8 24hr Replicate 6

source_name: E2-treated WS8 24hr Replicate 6

source_name: Control-treated RNA reference pool - WS8 24h


title: WS8 24hr Replicate 3

source_name: E2-treated WS8 24hr Replicate 3


title: WS8 24hr Replicate 5

source_name: E2-treated WS8 24hr Replicate 5


title: FOLFOX non-responder training, #1315


title: FOLFOX non-responder training, #1313


title: FOLFOX non-responder training, #1210


title: FOLFOX non-responder training, #1322


title: FOLFOX non-responder training, #1303


title: WS8 12hr Replicate 5

source_name: E2-treated WS8 12hr Replicate 5

source_name: Control-treated RNA reference pool - WS8 12h


title: FOLFOX non-responder training, #1140


title: FOLFOX non-responder training, #1213


title: FOLFOX non-responder training, #1125


title: WS8 24hr Replicate 1

source_name: E2-treated WS8 24hr Replicate 1


title: WS8 12hr Replicate 4

source_name: E2-treated WS8 12hr Replicate 4


title: FOLFOX non-responder training, #1119


title: FOLFOX non-responder training, #1117


title: WS8 12hr Replicate 6

source_name: E2-treated WS8 12hr Replicate 6


title: WS8 12hr Replicate 2

source_name: E2-treated WS8 12hr Replicate 2


title: WS8 12hr Replicate 3

source_name: E2-treated WS8 12hr Replicate 3


title: FOLFOX non-responder training, #1120


title: WS8 24hr Replicate 2

source_name: E2-treated WS8 24hr Replicate 2


title: FOLFOX non-responder training, #1115

value: Lung


title: WS8 6hr Replicate 6

source_name: E2-treated WS8 6hr Replicate 6

source_name: Control-treated RNA reference pool - WS8 6h


title: WS8 24hr Replicate 4

source_name: E2-treated WS8 24hr Replicate 4


title: WS8 6hr Replicate 4

source_name: E2-treated WS8 6hr Replicate 4


title: WS8 6hr Replicate 5

source_name: E2-treated WS8 6hr Replicate 5


title: FOLFOX non-responder training, #1111

source_name: tumor sample of patients with unresectable CRC before mFOLFOX6 therapy


title: WS8 6hr Replicate 3

source_name: E2-treated WS8 6hr Replicate 3


title: WS8 12hr Replicate 1

source_name: E2-treated WS8 12hr Replicate 1


title: FOLFOX non-responder training, #1139


title: FOLFOX non-responder training, #1109


title: FOLFOX non-responder training, #1087


title: WS8 6hr Replicate 2

source_name: E2-treated WS8 6hr Replicate 2


title: FOLFOX non-responder training, #1103


title: WS8 2hr Replicate 5

source_name: E2-treated WS8 2hr Replicate 5

source_name: Control-treated RNA reference pool - WS8 2h


title: FOLFOX non-responder training, #1090


title: FOLFOX non-responder training, #225


title: FOLFOX non-responder training, #1048


title: WS8 2hr Replicate 4

source_name: E2-treated WS8 2hr Replicate 4


title: WS8 2hr Replicate 6

source_name: E2-treated WS8 2hr Replicate 6


title: FOLFOX non-responder training, #241


title: WS8 2hr Replicate 1

source_name: E2-treated WS8 2hr Replicate 1


title: FOLFOX non-responder training, #1046


title: FOLFOX non-responder training, #1074


title: FOLFOX non-responder training, #1052


title: FOLFOX non-responder training, #1008


title: FOLFOX responder training, #1218


title: FOLFOX responder training, #1219


title: FOLFOX non-responder training, #1033


title: FOLFOX responder training, #1216


title: WS8 2hr Replicate 3

source_name: E2-treated WS8 2hr Replicate 3


title: FOLFOX responder training, #1221


title: FOLFOX responder training, #1209


title: KO-1

city: Saint Louis

first: David

middle: Michael

last: Alvarado

state: MO

address: 660 South Euclid

department: Orthopaedic Surgery

institute: Washington University in St. Louis

description: replicate 1

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

source_name: E12.5 hindlimb bud

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: genotype

value: Hindlimb bud


title: FOLFOX responder training, #1212


title: FACS-sorted embryonic trachea, midline cells ttk overexpression in trachea, midline 2: btl-GAL4 UAS-ttk btl-enh-RFPmoe

city: Cambridge

first: Boris

last: Adryan

address: Tennis Court Road

department: Cambridge Systems Biology Centre & Department of Genetics

country: United Kingdom

institute: University of Cambridge

hyb_protocol: 2.2 µg of cDNA was hybridized per microarray for 16 hours of hybridization at 45C, washing and staining of microarrays was performed using a Fluidics Station 450 (Affymetrix, Santa Clara, CA)

scan_protocol: GeneChips were scanned in a GeneChip Scanner 3000 (Affymetrix, Santa Clara, CA)

data_processing: Data from ttk mutants and ttk overexpression were pre-processed separately. Data was processed using ENSEMBL gene-specific Custom CDF V12 (brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/genomic_curated_CDF.asp), quantile normalized and RMA summarized using Bioconductor.

organism: Drosophila melanogaster

source_name: btl-enhancer embryonic expression domain, FACS-sorted

label_protocol: 25 ng total RNA per sample was processed using isothermal amplification SPIA Biotin System (NuGEN Technologies, Inc.)

growth_protocol: Embryos btl RFP moe ttk/twi GFP and btl RFP moe/twi GFP were grown at 25C for 7:40 hrs and then age for 5:20 hr more. The overexpression condiiton stock UAS ttk btl RFP moe x Btl Gal4 UAS tau GFP and its control stock UAS ttk RPF moe were grown at 29C.

extract_protocol: RNA was extracted with a combination of Trizol (for the whole embryo condition) and RNeasy minikit (Qiagen)(for the btl RFP positive cells)

treatment_protocol: For each condition, 100.000 btl RFP moe positive cells sorted out by fluorescence activated cell sorting were used to extract their RNA.

value: btl-GAL4 UAS-ttk btl-enh-RFPmoe

value: Tracheal system, midline


title: KO-3

description: replicate 3


title: KO-2

description: replicate 2


title: M-IPS cell transcription level

city: MARSEILLE CEDEX 09

first: Christelle

last: Cayrou

address: 27 Boulevard Lei Roure

country: France

institute: CRCM

hyb_protocol: Performed according to NimbleGen protocols

data_processing: Data was processed by performing background correction, quantile normalization, and calculation of expression set summaries using the Robust Multichip Average (RMA) protocol (Irizarry et al. (2003)).

source_name: mouse M-iPS cell

growth_protocol: M-iPS cells were grown on 0.1% gelatin without feeders. They were cultured at 37°C in 5% CO2 in ES medium: GMEM supplemented with 10% fetal calf serum, 0.1mM β- mercaptoethanol, 1mM sodium pyruvate, 1% non-essential amino acids (Gibco), 2 mM L-glutamine, in the presence of 1000 U/ml LIF (ES-GRO).

extract_protocol: Total RNA was obtained by using RNeasy kit (invitrogen) according to the manufacturer's instructions.

treatment_protocol: Constructs in pMXs retroviral vectors encoding Oct4, Sox2, Klf4 and c-Myc (obtained from Addgene) were transfected in Platinum HEK cells using the Lipofectamine 2000 transfection reagent (Invitrogen), according to the manufacturer's recommendations. 30 μl of Lipofectamine 2000 were added to 750 μl OPTIMEM and mixed with 12 μg DNA that had been diluted into 750 μl OPTIMEM and incubated for 5 min. After 20 min incubation at 20°C, the DNA/Lipofectamine 2000 mixture was added drop by drop to Platinum HEK cells. 48h after transfection, supernatants were collected, filtered through 0.45 μm Millex-HV (Millipore) filters and supplemented with 12 μg/ml polybrene. OCT4-GFP MEFs were seeded on 0.1% gelatin at a density of 8.105 cells in 56 cm2 Petri dishes and the four virus containing supernatants were pooled in equal amounts and added to the MEFs. 18 hours later, supernatants were removed and cells cultured in complete ES medium. Five-six hours later, cells were trypsinized and permeabilized with SLO as described above and then incubated either in mock buffer (HBSS) or in Xenopus M phase egg extracts for 40 min. After treatment, cells were washed twice and plated (8.105 cells per 56 cm2) in gelatin-covered dishes with ES medium supplemented with 2 mM CaCl2. After 2 hours, medium was removed and replaced by complete ES medium until appearance of OCT4-GFP positive colonies. M phase extract-treated OCT4-GFP positive colonies were mechanically isolated, individual cells dissociated and plated onto feeders for analysis that was performed after at least 15 passages on feeders.

tag: cell type

value: Xenopus M phase treated induced pluripotent stem cells


title: WT-2

description: replicate 2


title: FACS-sorted embryonic trachea, midline cells ttk overexpression control 2: btl-GAL4 btl-enh-RFPmoe

value: ttk2D50 btl-enh-RFPmoe


title: FOLFOX responder training, #1128

value: Metastasis

value: Liver


title: ES cell transcription level

description: experiment done in triplicates

scan_protocol: Performed according to NimbleGen protocols

source_name: mouse ES cell CGR8

growth_protocol: The ES cell line CGR8 was obtained from Dr C. Crozet (Institut de Génétique Humaine, Montpellier). ES cells were grown on 0.1% gelatin without feeders. They were cultured at 37°C in 5% CO2 in ES medium: GMEM (Glasgow Minimum Essential Medium) supplemented with 10% fetal calf serum, 0.1mM β- mercaptoethanol, 1mM sodium pyruvate, 1% non-essential amino acids (Gibco), 2 mM L-glutamine, in the presence of 1000 U/ml LIF (ES-GRO).

treatment_protocol: Asynchronous cells without treatment

value: embryonic stem cells


title: FOLFOX responder training, #1122

value: F


title: FOLFOX responder training, #1129


title: MEF cell transcription level

source_name: MEF cell

label_protocol: Performed according to NimbleGen protocols

growth_protocol: MEFs were then expanded in high-glucose DMEM (Invitrogen) supplemented with 10% ES-tested fetal bovine serum (cat N° S1810, Biowest), 2mM L-glutamine (Invitrogen), 1 mM sodium pyruvate (Sigma). MEFs were used up to passage 5.

treatment_protocol:
MEFs were derived from 13.5E wild type mouse embryos or from C57BL/6J-JF1 embryos hemizygous for the OCT4-GFP transgenic allele. Gonads, internal organs and heads were removed before MEF isolation.
cells were untreated

value: Murine Embryonic fibroblasts (MEF)


title: FOLFOX responder training, #1207

value: Primary

value: M


title: FOLFOX responder training, #1104


title: FACS-sorted embryonic trachea, midline cells ttk overexpression in trachea, midline 1: btl-GAL4 UAS-ttk btl-enh-RFPmoe


title: WT-3

description: replicate 3


title: FOLFOX responder training, #1105

value: Peritoneum


title: WT-1

description: replicate 1


title: FACS-sorted embryonic trachea, midline cells ttk overexpression control 1: btl-GAL4 btl-enh-RFPmoe


title: lymphoma3802_ADR_rep1

city: Berlin

first: Maja

last: Milanovic

address: Augustenburgerplatz 1

department: Hematology and Oncology

institute: Charite University Medicine, Berlin

description:
Primary lymphoma cells, isolated from lymph nodes of Emu-myc transgenic mice and retrovirally transduced by Bcl2 overexpression; treated 5 days in vitro with 0.05µg/ml Adriamycin.
3802_DOX.CEL

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45°C on MOE430 2.0 Arrays (Affymetrix). GeneChips were washed and stained with standard protocols in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Scanner G3000

data_processing: Affymetrix CEL files were imported into Partek Genomic Suite Software (Version 6.5, Partek Inc., St. Louis, USA) and processed by the implemented RMA workflow (median polish probe set summarization, RMA background correction, quantile normalization).

source_name: primary lymphoma cells, isolated from lymph nodes of Emu-myc transgenic mice with palpable lymphadenopathy

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol (One Cycle Target labeling protocol) from 3 ug total RNA.

growth_protocol: Primary Emu-myc lymphoma cells were cultivated in B-cell medium (DMEM and IMDM in 1:1 ratio, 10%FBS, 4mM L-glutamine, 25µM beta-mercaptoethanol, 100U/ml penicilin/streptamycin) on gamma-irradiated (20Gy) NIH 3T3 cells as feeder.

extract_protocol: The total RNA from untreated or 5 days ADR treated Myc;Bcl2 lymphomas was prepared using an RNeasy Mini kit (QIAGEN, Valencia, California) according to the manufacturer's instruction.

treatment_protocol: Freshly isolated lymphoma cells were retrovirally transduced by Bcl2 (MSCVpuro) and selected with Puromycin for 48h. These Myc;Bcl2 cells were either left untreated or treated in vitro with 0.05µg/ml Adriamycin for 5 days

tag: senescence induction

value: TIS


title: FOLFOX responder training, #1102

value: responder


title: FOLFOX responder training, #1116

value: training


title: Whole-embryo, ttk overexpression in trachea, midline 3: btl-GAL4 UAS-ttk btl-enh-RFPmoe

source_name: whole embryo

value: whole embryo


title: Whole-embryo, ttk overexpression in trachea, midline 2: btl-GAL4 UAS-ttk btl-enh-RFPmoe


title: Whole-embryo, ttk overexpression control 3: btl-GAL4 btl-enh-RFPmoe

value: btl-GAL4 btl-enh-RFPmoe


title: Whole-embryo, ttk overexpression in trachea, midline 1: btl-GAL4 UAS-ttk btl-enh-RFPmoe

value: btl-GAL4 UAS-ttk btl-enh-RFPmoe


title: 3sp_P79_b

city: Vienna

first: Martin

last: Bilban

country: Austria

institute: Medical University of Vienna

description: hepatocellular carcinoma cell lines hcc-1.2 and hcc-1.1 cells, referred to as 3p and 3sp cells, respectively, were isolated from one hcc patient as described ( sagmeister s, eisenbauer m, pirker c, et al. new cellular tools reveal complex epithelial-mesenchymal interactions in hepatocarcinogenesis. br j cancer 2008;99(1): 151-9.). 3p cells of passages 10 to 12 and 3sp cells of passages 7 to 13 are termed 3p early and 3sp early, respectively. 3p cells between passage 71 and 76 and 3sp from passage 72 to 87 were termed 3p late and 3sp late, respectively

hyb_protocol: Affymetrix

scan_protocol: Affymetrix

data_processing: RMA

source_name: liver cancer cell

label_protocol: Affymetrix

extract_protocol: RNeasy mini kit

tag: passage


title: FOLFOX responder training, #1101

source_name: tumor sample of patients with unresectable CRC before mFOLFOX6 therapy


title: 3sp_P79_a

tag: cell line


title: FOLFOX responder training, #1085

value: Rectum


title: Whole-embryo, ttk overexpression control 2: btl-GAL4 btl-enh-RFPmoe


title: FOLFOX responder training, #1084

value: Sigmoid


title: 3p_P68_a

source_name: hepatocellular carcinoma cell lines

extract_protocol: RNeasy Mini kit


title: FACS-sorted embryonic trachea, midline cells, ttk mutant 1: ttk2D50 btl-enh-RFPmoe

value: ttk2D50 btl-enh-RFPmoe

value: Tracheal system, midline


title: lymphoma3802_untreated_rep1

description:
Primary lymphoma cells, isolated from lymph nodes of Emu-myc transgenic mice and retrovirally transduced by Bcl2 overexpression; untreated.
3802.CEL

value: no


title: Whole-embryo, ttk overexpression control 1: btl-GAL4 btl-enh-RFPmoe


title: FOLFOX responder training, #1072


title: FACS-sorted embryonic trachea, midline cells, ttk mutant 2: ttk2D50 btl-enh-RFPmoe


title: 3p_P68_b

source_name: hepatocellular carcinoma cell


title: FOLFOX responder training, #1068


title: 3sp_P7_b


title: 3p_P10_b


title: 3sp_P7_a


title: FACS-sorted embryonic trachea, midline cells ttk mutant control 1: btl-enh-RFPmoe

value: btl-enh-RFPmoe


title: FOLFOX responder training, #1066

value: Cecum

value: F


title: FACS-sorted embryonic trachea, midline cells ttk mutant control 2: btl-enh-RFPmoe


title: 3p_P10_a


title: Whole-embryo, ttk mutant control 2: btl-enh-RFPmoe


title: myb46-2 plants vs wild type (Col0) REP3

city: Valencia

first: Pablo

last: Vera

email: vera@ibmcp.upv.es, oliveros@cnb.csic.es

state: Valencia

address: Camino de Vera s/n

country: Spain

institute: Instituto de Biología Molecular y Celular de Plantas (IBMCP) UPV-CSIC

description: Biological replicate 3 of 3: wild type plants versus myb46-2 plants

hyb_protocol: Amplifed and labeled aRNA (Cy3 and Cy5) was hybridized and washed following the Two-Color Microarray-Based Gene Expression Analysis (Quick Amp Labeling) protocol.The slides were then drained with a 2000-rpm spin for 2 min and stored in darkness until they were scanned.

scan_protocol: Images from Cy3 and Cy5 channels were equilibrated and captured with a GenePix 4000B (Molecular Devices) and spots quantified using GenPix 5.1 software (Molecular Devices).

data_processing: Local background was corrected by normexp method with an offset of 50. Background corrected intensities were transformed to log scale (base 2) and normalized by loess for each array (Smyth and Speed, 2003). Finally, to have similar intensity distribution across all arrays, loess-normalized-intensity values were scaled by adjusting their quantiles (Bolstad et al., 2003).

organism: Arabidopsis thaliana

source_name: 10-15 days old Col-0 plants (Wild Type)

label_protocol: RNA was amplified with the MessageAmp aRNA amplification kit from Ambion following the instruction manual. To allow later labeling with Cy fluorophores, aminoallyl UTP (Ambion) was added to the mix of the T7 RNA polymerase-driven aRNA amplification reaction. The amount and quality of aRNA obtained was assessed as before. The aminoallyl-labeled aRNA (10 µg) was incubated in 1 M Na2CO3 with 8 nmol of dye monofunctional NHS ester (Cy3/Cy5) RPN 5661 (Amersham Biosciences) at room temperature in the dark for 1 h. Then, 35 µL of 0.1 M sodium acetate, pH 5.2, was added and incubated for a further 5 min in the dark. The Cy-labeled aRNA was purified with the Megaclear kit from Ambion and measured with the Nanodrop ND-100 spectrophotometer.

growth_protocol: Seeds previously surface-sterilized, were sown in round Petri dishes containing 2.2 g/L MS (Duchefa Biochemie), 5 g/L sucrose, 6 g/L Agargel (Sigma), and transferred to a phytochamber with a light intensity of approximately 150-200 µE m-2s-1 at 23°C under 10 h light/14 h dark cycles and for 14 days.

extract_protocol: RNA was isolated with Tri-Reagent (Invitrogen) following manufacture´s instructions. High-quality RNA was obtained by using RNeasy Plant Mini Kit (Qiagen).

value: Col-0 (wild type)

value: whole plant

source_name: 10-15 days old Col-0 plants (myb46-2)

value: myb46-2 mutant


title: Whole-embryo, ttk mutant 2: ttk2D50 btl-enh-RFPmoe


title: FOLFOX responder training, #1050

value: Primary

value: M


title: FOLFOX responder training, #1067

value: Ascending

value: responder

value: training


title: myb46-2 plants vs wild type (Col0) REP2

description: Biological replicate 2 of 3: wild type plants versus myb46-2 plants


title: myb46-2 plants vs wild type (Col0) REP1

description: Biological replicate 1 of 3: wild type plants versus myb46-2 plants


title: FOLFOX responder training, #1027

value: Transverse


title: FOLFOX responder training, #1015

value: Rectum


title: Whole-embryo, ttk mutant 1: ttk2D50 btl-enh-RFPmoe

value: whole embryo


title: FOLFOX responder training, #1022

value: Descending


title: FOLFOX responder training, #1073

value: Sigmoid


title: FACS-sorted embryonic trachea, midline cells ttk mutant control 3: btl-enh-RFPmoe

value: Tracheal system, midline


title: Whole-embryo, ttk mutant control 1: btl-enh-RFPmoe

value: btl-enh-RFPmoe


title: FOLFOX responder training, #211

value: Metastasis

value: Liver


title: C.tr. serD + IWP2 17.9 vs C.tr. serD 22.9

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

institute: Max-Planck-Institute for Infection Biology

hyb_protocol: After precipitation, purification and quantification of labeled samples, 1.25 µg of each labeled cRNA was fragmented and hybridized to whole human genome 4x44k multipack microarrays (AMADID 014850) according to the supplier’s protocol (Agilent Technologies).

scan_protocol: Scanning of microarrays was performed with 5 µm resolution and extended range using a G2565CA high resolution laser microarray scanner (Agilent Technologies).

data_processing:
Raw microarray image data were analyzed with the Image Analysis / Feature Extraction software G2567AA (Version A.10.5.1, Agilent Technologies) using default settings and the GE2_105_Jan09 FE protocol. The extracted MAGE-ML files were further analyzed with the Rosetta Resolver Biosoftware, Build 7.2.2 SP1.31 (Rosetta Biosoftware). Ratio profiles comprising single hybridizations were combined in an error-weighted fashion to create ratio experiments. A 1.5–fold change expression cut-off for ratio experiments was applied together with anti-correlation of ratio profiles rendering the microarray analysis highly significant (P-value > 0.01), robust and reproducible.
The normalized ratio provided in the data table below is always cy5/cy3 "log(REDsignal/GREENsignal) per feature (processed signals used)." Color swap arrays comprise either test/ref for positive polarity and ref/test for negative polarity.

source_name: C.tr. serD + IWP2 17.9

label_protocol: RNA labeling was performed with the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)

extract_protocol: Fallopain tube pieces were transferred into 2 ml tubes on ice with 0.4 ml ice-cold RLT buffer (RNeasy Mini Kit, Qiagen) and homogenized by three 20 sec pulses of an Ultra-turrax (IKA) at maximum speed on ice. Lysates were centrifuged for 10 min at 20,000 xg at 4 °C and RNA isolated from resulting supernatants, according to the manufacturer’s protocol (Qiagen)

value: fallopian tube sample 17.9 Chlamydia trachomatis serovar D infected + IWP2 inhibitor Porcupine (Porcn, 5µM) treatment

source_name: C.tr. serD 22.9

value: fallopian tube sample 22.9 Chlamydia trachomatis serovar D infected


title: cisplatin 24h rep 1

status: Public on Nov 20 2011

city: Torino

first: Raffaele

middle: A

last: Calogero

state: To

address: Via Nizza 52

department: Molecular Biotechnology Center

country: Italy

institute: University of Torino

hyb_protocol: Hybridization was done using Affymetrix kit and following manufacturer indications

scan_protocol: scanner procedures were done using a Genechip Affymetrix station (FS 450, Scanner 3000)  following manufacturer indications

data_processing: Microarray quality control and statistical validation were performed using oneChannelGUI Bioconductor package. Intensity summarization was done with GCRMA and quantile normalization

source_name: Cisplatin 24h

label_protocol: Biotinylated cRNA target preparation was done using Affymetrix kit and following manufacturer indications

growth_protocol: Cells were cultured as monolayers in flasks using American Type Culture Collection complete growth medium in a humidified atmosphere containing 5% CO2 at 37°C.

extract_protocol: Total RNA was extracted and purified using the RNeasy Midi kit (Qiagen, Valencia, CA, USA)

treatment_protocol: drug treatments, cells were seeded in complete growth medium 16 hours before the experiments, in order to allow attachment but not cell-doubling. Then cells were treated with piroxicam (760 microM) and cisplatin (4.5 microg/mL) alone or in combination for 8 or 24 hours. Controls samples were untreated.

tag: agent

value: Cisplatin

tag: time point

value: mesothelioma cell


title: piroxicam 24h rep 3

source_name: Piroxicam 24h

value: Piroxicam


title: piroxicam 24h rep 2


title: cisplatin 24h rep 3


title: piroxicam/cisplatin 24h rep 1

source_name: Piroxicam/Cisplatin 24h

value: Piroxicam/Cisplatin


title: cisplatin 24h rep 2


title: untreated 24h rep 1

source_name: untreated 24h

value: untreated


title: IWP2 17.9 vs ni 22.9

value: fallopian tube sample 17.9  IWP2 inhibitor Porcupine (Porcn, 5µM)

value: fallopian tube sample 22.9 uninfected


title: piroxicam 24h rep 1


title: untreated 24h rep 2


title: piroxicam/cisplatin 8h rep 3

source_name: Piroxicam/Cisplatin 8h


title: ni 17.9 vs C.tr. serD + IWP2 22.9

value: fallopian tube sample 17.9 uninfected

source_name: C.tr. serD + IWP2 22.9

value: fallopian tube sample 22.9 Chlamydia trachomatis serovar D infected + IWP2 inhibitor Porcupine (Porcn, 5 µM) treatment


title: HF24

city: Norfolk

first: yumi

last: imai

state: VA

address: 799W Olney Road, LH 2156

institute: Eastern Virginia Medical School

description: Expression values calculated from probe intensity data (cel files) with ArrayAssist Lite version 3.4 (Stratagene, La Jolla, CA) using GCRMA

hyb_protocol: Samples were hybridized with MOE430v2 Arrays (Affymetrix) according to Affymetrix GeneChips Expression Analysis Technical Manual.

scan_protocol: Scanning was performed at the University of Pennsylvania Microarray Core Facility following Affymetrix GeneChips Expression Analysis Technical Manual.

data_processing: For data analyses, probe intensity data (cel files) were input into ArrayAssist Lite version 3.4 (Stratagene, La Jolla, CA), and expression values for the probe sets were calculated using GCRMA. Affymetrix “present” or “absent” “marginal” flags were also calculated. Subsequently intensity and flag data were imported into GeneSpring GX version 7.3.1 (Agilent Technologies, Palo Alto, CA) and filtered to retain probe sets flagged as “present” in at least three out of eight samples.

source_name: high fat diet

label_protocol: 5 μg of total RNA from each sample was converted to first-strand cDNA by using reverse transcriptase (Superscript II; Invitrogen). Second-strand cDNA synthesis was followed by in vitro transcription for linear amplification of each transcript and incorporation of biotinylated CTP and UTP.

growth_protocol: Male C57Bl/6J were fed 45%kcal fat diet (HF) or regular rodent chow (NC) for 12 weeks after weaning at 4 weeks of age.

extract_protocol: RNA was isolated from pancreatic islets with the RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions.

treatment_protocol: Pancreas was digested with collagenase to release islets. Digests were separated by Ficoll density gradient centrifugation and pancreatic islets were hand picked under dissecting microscope.

value: Pancreatic islets

tag: strain


title: NC4

source_name: regular rodent chow


title: cisplatin 8h rep 3

source_name: Cisplatin 8h


title: ni 17.9 vs C.tr. serD 22.9


title: HF23


title: cisplatin 8h rep 1


title: ni 17.9 vs IWP2 22.9

value: fallopian tube sample 22.9  IWP2 inhibitor Porcupine (Porcn, 5 ÂµM) treatment


title: C.tr. serD 17.9 vs C.tr. serD + IWP2 22.9

source_name: C.tr. serD 17.9

value: fallopian tube sample 17.9 Chlamydia trachomatis serovar D infected

value: fallopian tube sample 22.9 Chlamydia trachomatis serovar D infected + IWP2 inhibitor Porcupine (Porcn, 5µM) treatment


title: NC2


title: piroxicam/cisplatin 8h rep 1


title: piroxicam 8h rep 3

source_name: Piroxicam 8h


title: piroxicam 8h rep 1


title: untreated 8h rep 3

source_name: untreated 8h


title: NC1


title: HF21


title: Mc-myc ChIP in  wild-type

type: genomic

city: Bethesda

first: Shiv

last: Grewal

state: MD

address: NCI bldg 37 Rm 6068 9000 Rockville Pike

department: LBMB

institute: NCI

hyb_protocol: Equal amounts of Cy5-labeled ChIP DNA and Cy3-labeled  whole-cell extract DNA were mixed and combined with human Cot1 DNA, Agilent Blocking Agent and Agilent Hybridization buffer, and hybridized to high-density  microarrays in Agilent SureHyb hybridization chamber for 17 hours at 60˚C, 10 rpm. After hybridization, slides were washed according to Agilent protocol.

scan_protocol: Scanned on an Agilent G2505B scanner.

data_processing: Data were extracted using Agilent Feature Extraction Software (CHIP-v1_95_Feb07 protocol). Signal was normalized by combined rank consistency filtering with LOWES intensity normalization.

molecule: genomic DNA

organism: Schizosaccharomyces pombe

source_name: Mc-myc immunoprecipitated ChIP DNA, log. growing cells

label_protocol: ChIP and whole-cell extract DNA was amplified by random-primed PCR and conjugated with Cy5 (ChIP DNA) or Cy3 (whole-cell extract DNA).

growth_protocol: Standard conditions were used to produce logarithmically growing cultures in rich media (YEA) at 30˚C.

extract_protocol: Fixed cells were lysed with glass-beads, DNA sheared by sonication to 500-1000bp fragments and immunoprecipitated by anti Myc antibody (A14 Santa Cruz). Immunoprecipitated DNA was recovered by incubation with protein A slurry and reversed-crosslinked at 65˚C.

treatment_protocol: Exponentially growing cells were fixed in 3% paraformaldehyde at 18 ˚C and in 10mM dimethyl adipimidate dihydrochloride at room tempreture

tag: genotype/variation

value: wild type

tag: chip antibody

value: anti Myc antibody (A14 Santa Cruz)

source_name: Whole-cell extract DNA, log. growing cells


title: Bead-induced deciduoma tissue, mouse 2

city: CARBONDALE

first: BRENT

last: BANY

state: ILLINOIS

address: 1135 LINCOLN DRIVE

department: PHYSIOLOGY

institute: SOUTHERN ILLINOIS UNIVERSITY SCHOOL OF MEDICINE

description:
BID2
Replicate 2 of 3 pseudopregnant tissue.

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: The data were normalised using the scale normalisation function of Chipster software.

source_name: mouse uterus, pseudopregnant

label_protocol: Biotin-labeled cRNA was prepared exactly as recommended by the manufacturer.

extract_protocol: Trizol extraction. Rnase-free DNAse treatment followed by re-extraction with Trizol.

tag: tissue

value: uterus

tag: condition

value: pseudopregnant


title: Bead-induced deciduoma tissue, mouse 3

description:
BID3
Replicate 3 of 3 pseudopregnant tissue.


title: C.tr. serD 17.9 vs ni 22.9


title: M833 / Reference_13431197

city: Grand Rapids

first: Karl

last: Dykema

state: MI

address: 333 Bostwick Ave. NE

institute: Van Andel Institute

description: Gene expression data from cell type: M833

hyb_protocol: Hybridization was performed at 50C and 35% formamide for 16 hours.

scan_protocol: Microarrays were scanned using the Agilent G2505B scanner.

data_processing: Image files were analyzed by use of GenePix Pro 4 image analysis software (Axon Instruments). The raw data was preprocessed using a pin-tip dependent normalization method as implemented in the limma package within Bioconductor. Calculated log2 ratio of Cy5/Cy3. VALUE column represents log2(test/ref) ratios.

label_protocol: Direct incorporation of CyDye labeled dCTP by reverse transcription.

extract_protocol: Trizol

source_name: ref

tag: ref


title: M833 / Reference_13431199


title: M833 / Reference_13431198


title: M833 / Reference_13425475


title: WT / Reference_13425476

description: Gene expression data from cell type: WT

source_name: WT

tag: WT


title: WT / Reference_13425630

description: Gene expression data from cell type: WT


title: WT / Reference_13425478

description: Gene expression data from cell type: WT


title: Bead-induced deciduoma tissue, mouse 1

description:
BID1
Replicate 1 of 3 pseudopregnant tissue.


title: WT / Reference_13425477

description: Gene expression data from cell type: WT


title: implantation segment tissue, mouse 3

description:
IS3
Replicate 3 of 3 pregnant tissue.

source_name: mouse uterus, pregnant

value: pregnant


title: M833 / Reference_13425673


title: M833 / Reference_13425520


title: M833 / Reference_13425519


title: WT / Reference_13425675

description: Gene expression data from cell type: WT


title: WT / Reference_13425676

description: Gene expression data from cell type: WT


title: C.tr. serD + IWP2 17.9 vs ni 22.9

source_name: C.tr. serD + IWP2 17.9

value: fallopian tube sample 17.9 Chlamydia trachomatis serovar D infected + IWP2 inhibitor Porcupine (Porcn, 5 µM) treatment


title: M833 / Reference_13425521


title: untreated 8h rep 1

value: mesothelioma cell


title: WT / Reference_13425560

description: Gene expression data from cell type: WT


title: WT / Reference_13425561

description: Gene expression data from cell type: WT


title: implantation segment tissue, mouse 1

description:
IS1
Replicate 1 of 3 pregnant tissue.


title: NC5


title: Forebrain_B6_Veh_BB707_1.1

status: Public on Nov 19 2011

city: Chapel Hill

first: Vasyl

last: Zhabotynsky

state: NC

address: 120 Mason Farm Road   5000 D, Genetic Medicine Building

institute: University of North Carolina at Chapel Hill

hyb_protocol: All samples were processed with the GeneChip WT terminal labeling and hybridization protocol in conjunction with the Ambion WT expression kit according the manufacturers instructions.

scan_protocol: Affymetrics GeneChip

data_processing: Affymetrics Expression Console V1.1

extract_protocol: Total RNA was isolated from frozen brains using a Biopulverizer (Biospec). Pulverized samples were placed in tubes containing 1ml Trizol reagent (Invitrogen) and a stainless steel bead. Samples were shaken for 5 minutes on a Tissuelyzer apparatus (Mixer Mill 300, Qiagen) and incubated at room temperature for 5 minutes. We added 200 µl chloroform (Fisher) and then samples were sequentially shaken for 15 seconds on a Tissuelyzer, incubated at room temperature for 3 minutes, and centrifuged at 10,000 rpm for 15 min at 4°C. The supernatant was transferred to a gDNA Eliminator spin column (RNeasy plus mini kit, Qiagen) and processed according to the manufacturer instructions.

tag: treatment

value: vehicle

tag: part of brain

value: Forebrain

tag: body wt (g)

tag: dob

tag: weaned

tag: litter size

tag: mouse id

tag: time inject

tag: time sac


title: Forebrain_NOD_Cloz_DD658_1.1

source_name: brain,Forebrain,NOD,Cloz

label_protocol: All samples were processed with the GeneChip WT terminal labeling and hybridization protocol in conjunction with the Ambion WT expression kit according the manufacturers instructions.

value: NOD

value: clozapine


title: Forebrain_NOD_Veh_DD657_1.1

source_name: brain,Forebrain,NOD,Veh


title: implantation segment tissue, mouse 2

description:
IS2
Replicate 2 of 3 pregnant tissue.


title: HF22


title: Wholebrain_NOD_Veh_DD656_1.1

source_name: brain,Wholebrain,NOD,Veh

value: Wholebrain


title: Wholebrain_NOD_Veh_DD657_1.1


title: Wholebrain_B6_Veh_BB687_1.1


title: Hindbrain_NOD_Veh_DD657_1.1

source_name: brain,Hindbrain,NOD,Veh

value: Hindbrain


title: Wholebrain_B6_Veh_BB707_1.1


title: Forebrain_NOD_Cloz_DD675_1.1


title: Wholebrain_B6_Veh_BB686_1.1


title: Forebrain_B6_Cloz_BB703_1.1


title: Forebrain_NOD_Veh_DD677_1.1


title: Forebrain_B6_Veh_BB687_1.1


title: Hindbrain_NOD_Veh_DD656_1.1


title: Hindbrain_NOD_Cloz_DD658_1.1

source_name: brain,Hindbrain,NOD,Cloz


title: Hindbrain_B6_Cloz_BB702_1.1


title: Hindbrain_NOD_Cloz_DD678_1.1


title: Wholebrain_B6_Cloz_BB685_1.1


title: Wholebrain_NOD_Veh_DD659_1.1


title: Forebrain_NOD_Veh_DD656_1.1


title: piroxicam/cisplatin 24h rep 3

source_name: Piroxicam/Cisplatin 24h

tag: cell line

tag: agent

value: Piroxicam/Cisplatin

tag: time point

tag: cell type


title: Forebrain_B6_Veh_BB708_1.1

tag: strain


title: Wholebrain_B6_Veh_BB708_1.1


title: Hindbrain_NOD_Cloz_DD676_1.1


title: Forebrain_B6_Cloz_BB685_1.1


title: Forebrain_NOD_Cloz_DD676_1.1


title: Hindbrain_B6_Cloz_BB703_1.1


title: Wholebrain_NOD_Veh_DD677_1.1


title: Forebrain_B6_Cloz_BB701_1.1


title: Hindbrain_B6_Veh_BB707_1.1


title: Hindbrain_B6_Cloz_BB685_1.1


title: Hindbrain_NOD_Cloz_DD675_1.1


title: Forebrain_NOD_Veh_DD659_1.1


title: Forebrain_B6_Cloz_BB702_1.1


title: Wholebrain_B6_Cloz_BB701_1.1


title: Wholebrain_NOD_Cloz_DD676_1.1

source_name: brain,Wholebrain,NOD,Cloz


title: Hindbrain_NOD_Veh_DD677_1.1


title: Wholebrain_NOD_Cloz_DD678_1.1


title: Hindbrain_NOD_Veh_DD659_1.1


title: Hindbrain_B6_Cloz_BB701_1.1


title: Wholebrain_NOD_Cloz_DD658_1.1


title: Hindbrain_B6_Veh_BB687_1.1


title: Wholebrain_B6_Cloz_BB703_1.1


title: Wholebrain_NOD_Cloz_DD675_1.1


title: Wholebrain_NOD_Veh_DD656_1.0


title: Forebrain_B6_Veh_BB686_1.1


title: Forebrain_NOD_Veh_DD656_1.0


title: Hindbrain_B6_Veh_BB686_1.1


title: Wholebrain_B6_Cloz_BB702_1.1


title: Forebrain_NOD_Cloz_DD678_1.1


title: Wholebrain_B6_Veh_BB687_1.0


title: Forebrain_B6_Veh_BB707_1.0


title: Wholebrain_B6_Veh_BB707_1.0


title: Hindbrain_B6_Veh_BB708_1.1


title: Hindbrain_NOD_Veh_DD657_1.0


title: Forebrain_NOD_Veh_DD677_1.0


title: Forebrain_B6_Veh_BB687_1.0


title: Forebrain_NOD_Cloz_DD675_1.0


title: Forebrain_NOD_Cloz_DD658_1.0


title: Hindbrain_NOD_Cloz_DD678_1.0


title: Hindbrain_NOD_Cloz_DD676_1.0


title: Forebrain_B6_Cloz_BB685_1.0


title: Hindbrain_B6_Cloz_BB702_1.0


title: Hindbrain_NOD_Cloz_DD658_1.0


title: Forebrain_NOD_Veh_DD657_1.0


title: Wholebrain_NOD_Veh_DD659_1.0


title: Forebrain_B6_Cloz_BB703_1.0


title: Hindbrain_NOD_Veh_DD656_1.0


title: Wholebrain_NOD_Veh_DD657_1.0


title: Wholebrain_B6_Cloz_BB685_1.0


title: Wholebrain_B6_Veh_BB708_1.0


title: Forebrain_NOD_Cloz_DD676_1.0


title: Wholebrain_B6_Cloz_BB701_1.0


title: Forebrain_B6_Veh_BB708_1.0


title: Hindbrain_B6_Veh_BB707_1.0


title: Hindbrain_NOD_Veh_DD659_1.0


title: Forebrain_B6_Cloz_BB701_1.0


title: Wholebrain_B6_Veh_BB686_1.0


title: Wholebrain_NOD_Veh_DD677_1.0


title: Forebrain_NOD_Veh_DD659_1.0


title: Hindbrain_B6_Veh_BB687_1.0


title: Wholebrain_NOD_Cloz_DD676_1.0


title: Hindbrain_B6_Cloz_BB703_1.0


title: Hindbrain_B6_Cloz_BB685_1.0


title: Wholebrain_B6_Cloz_BB703_1.0


title: Forebrain_B6_Cloz_BB702_1.0


title: Hindbrain_NOD_Cloz_DD675_1.0


title: MSC from patient B312

city: Taichung

first: Kuan-Chih

last: Chow

address: 250 Kuo Kuang Road

department: Graduate Institute of Biomedical Sciences

country: Taiwan

institute: National Chung Hsing University

description:
SAA B312
MSC from pediatric SAA patient vs. pooled MSC from healthy donors.

hyb_protocol: The fragmented Cy-labeled cRNA was pooled, and oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added. The samples were applied to Agilent Whole Human Genome 4x44k oligo microarrays (Agilent Technologies, Santa Clara, CA) enclosed in Agilent SureHyb-enabled hybridization chambers and hybridized at 60°C for 17 h. After hybridization, slides were washed sequentially to remove non-specifically binding residues.

scan_protocol: The hybridized microarrays were scanned with an Agilent microarray scanner (Agilent Technologies, Santa Clara, CA) at OD535 for Cy3 and OD625 for Cy5.

data_processing: Scanned images were analyzed by Feature extraction software 8.1 (Agilent Technologies, Santa Clara, CA). After image analysis, the data were normalized by a rank-consistency-filtering LOWESS method, which was included in the package software of Feature extraction software 10.5.1.1 (Agilent Technologies, Santa Clara, CA).

source_name: MSC from pediatric patient B312

label_protocol: cRNA was synthesized from 0.5 μg of total RNA, and the RNA was amplified (Fluorescent Linear Amplification Kit, Agilent Technologies, Santa Clara, CA) and labeled with Cy3-CTP or Cy5-CTP (PerkinElmer, Waltham, MA). The cRNA of MSC from SAA patients was labeled with Cy5 and the cRNA from the control group was labeled with Cy3. The Cy-labeled cRNA was fragmented to about 50-100 nucleotides long by incubation with fragmentation buffer (Agilent Technologies, Santa Clara, CA) at 60°C for 30 minutes.

growth_protocol: Mesenchymal stem cells (MSCs) were kept in an undifferentiated, pluripotent state by growing in DMEM with low glucose concentration.

extract_protocol: Total RNA was extracted using Trizol following the manufacturer's instructions.

treatment_protocol: Patients who had appropriate donors were having a bone transplantation; otherwise, they received anti-thymocyte immunoglobulins.

value: mesenchymal stem cell (MSC)

tag: disease state

value: pediatric severe aplastic anemia (SAA)

tag: patient identifier

source_name: Pooled MSC from healthy donors

value: healthy

tag: sample type

value: reference


title: Hindbrain_NOD_Veh_DD677_1.0

tag: treatment


title: Wholebrain_NOD_Cloz_DD678_1.0

tag: part of brain


title: AB086N

status: Public on Nov 18 2011

city: San Francisco

first: Taku

last: Tokuyasu

state: CA

address: 1450 3rd Street, HD555

institute: UCSF

description:
normal tissue adjacent to tumor
DNA isolated from banked blood (buffy coat)

hyb_protocol: Labeled test (600ng) and reference (600ng) DNA was hybridized with human Cot-1 DNA for ~ 48 hours at 37°C to arrays of 2464 BAC clones spotted in triplicate (HumArray3.2, UCSF Helen Diller Family Comprehensive Cancer Center Microarray Core). Slides were washed with 50% formamide, 2X SSC for 15 minutes at 45°C followed by a 15 minute wash in PN buffer (0.1M phosphate buffer in 0.1% Nonidet P40) at room temperature. Slides were mounted in a DAPI solution to stain the array spots (90% glycerol, 10% PBS, 1μM DAPI) and imaged.

scan_protocol: DAPI, Cy3 and Cy5 images were acquired using a custom CCD camera system

data_processing:
Array image quantitation was done with UCSF Spot. After quality filtering on spots and clones, an in-house SpotCorrection algorithm was used to remove systematic geometric and GC content effects.  Replicate spot averaging and median centering were then performed.  A remaining 'paraffin-embedded effect' was removed as follows.  For tumor profiles with paired normals, we applied noise reduction using the normal sample as template.  The magnitude of the effect was estimated using the derivative log ratio spread (DLRS) [Agilent].  For the two tumor profiles without a paired normal (and AB029 and AB067), we employed the per-probe median of the normal profiles as a normal template, with DLRS scaling as above. Clones without mapping information were excluded. Also, clones of possibly poor quality where more than 50% of the samples had missing data were excluded. Then replicate clones were averaged.
The paired normals for the tumor samples did not have processed normalized data; therefore, these Samples are tableless. The paired normal data only played a role in the pre-processing stage that generated the processed tumor data.

source_name: Genomic DNA from normal adjacent to tumor

label_protocol: Test and reference samples labeled with Cy3 and Cy5 respectively using a random priming reaction in a 25 μL reaction to label genomic DNA

extract_protocol: Total DNA extracted from microdissected formalin fixed paraffin embedded tissue sections by digestion with proteinase K followed by a phenol chloroform extraction

tag: age

tag: gender

value: M

tag: site

value: Floor of Mouth

tag: tumor size (cm)

tag: tumor thickness

tag: node status (clinical)

tag: histology

value: WD

tag: recurrence

tag: follow up months

tag: vital status

value: Alive

tag: tumor status

value: Free

tag: node status (path)

tag: tobacco use

value: Current

tag: alcohol use

value: Previous

source_name: Normal human genomic DNA

value: Male


title: AB085N

department: Helen Diller Family Comprehensive Cancer Center

data_processing:
Array image quantitation was done with UCSF Spot. After quality filtering on spots and clones, an in-house SpotCorrection algorithm was used to remove systematic geometric and GC content effects.  Replicate spot averaging and median centering were then performed.  A remaining 'paraffin-embedded effect' was removed as follows.  For tumor profiles with paired normals, we applied noise reduction using the normal sample as template.  The magnitude of the effect was estimated using the derivative log ratio spread (DLRS) [Agilent].  For the two tumor profiles without a paired normal (and AB029 and AB067), we employed the per-probe median of the normal profiles as a normal template, with DLRS scaling as above. Clones without mapping information were excluded. Also, clones of possibly poor quality where more than 50% of the samples had missing data were excluded. Then replicate clones were averaged.
The paired normals for the tumor samples did not have processed normalized data; therefore, these Samples are tableless. The normal data only played a role in the pre-processing stage that generated the processed tumor data.

value: F

value: Tongue

value: X

value: MD

value: Dead

value: Unknown


title: AB083N

value: Floor of Mouth, tongue, gingiva

value: Not free


title: AB082N


title: AB084N

value: Gingiva


title: AB080N

value: PD


title: AB081N


title: Forebrain_NOD_Cloz_DD678_1.0

tag: strain

value: NOD

value: clozapine

value: Forebrain

tag: body wt (g)

tag: dob

tag: weaned

tag: litter size

tag: mouse id

tag: time inject

tag: time sac


title: Wholebrain_B6_Cloz_BB702_1.0

tag: treatment

tag: part of brain

value: Wholebrain


title: Wholebrain_NOD_Cloz_DD658_1.0


title: MSC from patient B216

description:
SAA B216
MSC from pediatric SAA patient vs. pooled MSC from healthy donors.

source_name: MSC from pediatric patient B216

tag: cell type

value: mesenchymal stem cell (MSC)

tag: disease state

value: pediatric severe aplastic anemia (SAA)

tag: patient identifier

value: healthy

tag: sample type

value: reference


title: Hindbrain_B6_Veh_BB708_1.0

value: vehicle

value: Hindbrain


title: Hindbrain_B6_Veh_BB686_1.0


title: AB085

description:
oral SCC
DNA isolated from banked blood (buffy coat)

source_name: Genomic DNA from tumor

tag: age

tag: gender

value: F

tag: site

value: Tongue

tag: tumor size (cm)

tag: tumor thickness

tag: node status (clinical)

value: X

tag: histology

value: MD

tag: recurrence

tag: follow up months

tag: vital status

tag: tumor status

value: Free

tag: node status (path)

value: Male


title: AB082

value: M

value: Floor of Mouth

value: Dead

tag: tobacco use

value: Unknown

tag: alcohol use


title: AB081

value: Gingiva

value: Current

value: Previous


title: AB083

value: Floor of Mouth, tongue, gingiva

value: Not free


title: MSC from patient B240

description:
SAA B240
MSC from pediatric SAA patient vs. pooled MSC from healthy donors.

source_name: MSC from pediatric patient B240

tag: cell type

value: mesenchymal stem cell (MSC)

tag: disease state

value: pediatric severe aplastic anemia (SAA)

value: healthy

value: reference


title: Forebrain_B6_Veh_BB686_1.0

tag: strain

tag: treatment

value: vehicle

tag: part of brain

value: Forebrain

tag: body wt (g)

tag: dob

tag: weaned

tag: litter size

tag: mouse id

tag: time inject

tag: time sac


title: AB084

tag: age

tag: gender

value: F

tag: site

tag: tumor size (cm)

tag: tumor thickness

tag: node status (clinical)

tag: histology

value: MD

tag: recurrence

tag: follow up months

tag: vital status

value: Alive

value: Free


title: Wholebrain_NOD_Cloz_DD675_1.0

tag: strain

value: NOD

tag: treatment

value: clozapine

tag: part of brain

value: Wholebrain

tag: body wt (g)


title: MSC from patient B256

description:
SAA B256
MSC from pediatric SAA patient vs. pooled MSC from healthy donors.

source_name: MSC from pediatric patient B256

tag: cell type

tag: disease state

tag: patient identifier

tag: sample type


title: AB079N

tag: age

tag: gender

value: Tongue

value: WD

value: Dead

tag: tumor status

tag: node status (path)

tag: tobacco use

tag: alcohol use

value: Male


title: Hindbrain_B6_Cloz_BB701_1.0

value: Hindbrain

tag: dob

tag: weaned

tag: litter size

tag: mouse id

tag: time inject

tag: time sac


title: Non-tumor tissue of esophagus

city: Hong Kong

first: Grace

last: Fu

address: 21 Sassoon Road

department: Clinical Oncology

country: Hong Kong

institute: The University of Hong Kong

description: Gene expression data from non-tumor tissues of patients with ESCC

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized on Affymetrix Human Genome U133 Plus 2.0 GeneChip. GeneChips were washed and stained.

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

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.

source_name: non-tumor tissue RNA from ESCC patient

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA

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

tag: tissue

value: esophageal tissue


title: MSC from patient B226

description:
SAA B226
MSC from pediatric SAA patient vs. pooled MSC from healthy donors.

source_name: MSC from pediatric patient B226

tag: cell type

value: mesenchymal stem cell (MSC)

value: pediatric severe aplastic anemia (SAA)

value: healthy


title: AB080

tag: site

tag: tumor size (cm)

tag: tumor thickness

tag: node status (clinical)

tag: histology

value: PD

tag: recurrence

tag: follow up months

tag: vital status

value: Current

value: Previous


title: AB086

tag: age

tag: gender

value: M

value: Floor of Mouth

value: Alive

tag: tumor status

tag: node status (path)

tag: tobacco use

tag: alcohol use


title: AB076N

value: F

value: Gingiva

value: not reported

value: MD

value: Free


title: AB077N

value: Male


title: Tumor tissue of esophagus

description: Gene expression data from tumor tissues of patients with ESCC

source_name: tumor tissue RNA from ESCC patient


title: AB071N

value: Hard Palate

value: Dead

value: Unknown


title: AB073N

value: x

value: Not free


title: AB079

value: Tongue

value: WD


title: AB077

value: Current


title: AB076

value: Previous


title: AB073


title: AB071


title: AB069N

value: M

value: Buccal Mucosa

value: NR


title: AB067N

value: F

value: Floor of Mouth

value: MD to PD


title: AB068N

value: Gingiva

value: X

value: Distant met

value: Alive


title: AB065N

value: MD

value: Dead

value: Free

value: Male


title: AB061N

value: WD

value: Unknown


title: AB064N

value: Current


title: AB062N

value: M


title: AB063N

value: Tongue

value: Previous


title: AB066N


title: AB069

value: Buccal Mucosa

value: NR


title: AB070

value: Floor of Mouth

value: Not free

value: Past


title: AB068

value: F

value: Gingiva

value: X

value: Distant met


title: AB067

value: not reported

value: MD to PD

value: Dead

value: Free


title: AB070N

value: WD

value: Male


title: AB061

value: M

value: Unknown

value: Alive

value: Current


title: AB060N

value: Tongue, Floor of Mouth

value: MD

value: Previous


title: AB059N

value: F

value: Tongue


title: AB055N

value: Floor of Mouth

value: X

value: LN met

value: Not free

value: Past


title: AB062

value: Gingiva

value: NR

value: Dead

value: Free


title: AB064

value: M

value: Buccal Mucosa

value: Male


title: AB063

value: Alive

value: Current


title: AB065

value: MD


title: AB066


title: AB054N

value: F

value: PD


title: AB052N

value: Tongue

value: MD to WD

value: Local


title: AB051N

value: Not free


title: AB060

value: Tongue, Floor of Mouth

value: Unknown

value: Previous


title: AB059


title: AB056

value: Retromolar area

value: Dead


title: AB055

value: M

value: Floor of Mouth

value: X

value: LN met

value: Past


title: AB056N

value: MD

value: Free

value: Current

value: Male


title: AB049

value: Tongue

value: Alive


title: AB051

value: Local

value: Not free


title: AB054

value: F

value: Buccal Mucosa

value: PD


title: AB042N

value: Previous


title: AB048N

value: M


title: AB045N

value: Gingiva

value: WD

value: Dead


title: AB041N

value: NR

value: not reported


title: AB039N

value: MD

value: Past


title: AB045

value: Free

value: Male


title: AB047

value: Never

value: Unknown


title: AB048

value: Tongue

value: X

value: Alive


title: AB038N


title: AB037N

value: Floor of Mouth

value: Current


title: AB049N

value: M


title: AB042

value: Previous


title: AB047N

value: F

value: Buccal Mucosa

value: Not free


title: AB052

value: MD to WD

value: Local

value: Dead


title: AB041

value: NR

value: not reported

value: MD

value: Free


title: AB039

value: Gingiva

value: Past

value: Male


title: AB034N

value: WD

value: Unknown


title: AB037

value: M

value: Floor of Mouth

value: Current


title: AB038

value: Tongue

value: Previous


title: AB032N

value: Buccal Mucosa


title: AB035


title: AB034


title: AB031N

value: F


title: AB030N

value: X

value: Alive


title: AB029N

value: Floor of Mouth, tongue, buccal mucosa

value: PD

value: Local


title: AB035N

value: MD

value: Dead

value: Free


title: AB032

value: not reported

value: NR

value: Male


title: AB033

value: Retromolar area

value: Not free


title: AB025N

value: Gingiva

value: Current

value: Unknown


title: AB033N

value: F


title: AB031

value: Tongue

value: WD


title: AB026N

value: MD to PD


title: AB022N

value: M

value: Floor of Mouth

value: X

value: Alive


title: AB023N

value: Local

value: Free


title: AB030

value: not reported

value: MD


title: AB027N

value: tongue

value: Dead

value: Male


title: AB021N

value: Not free


title: AB020N

value: Hard Palate


title: AB022

value: Current


title: AB027


title: AB023

value: Tongue


title: AB026

value: F

value: Retromolar area


title: AB019N

value: Floor of Mouth, tongue


title: AB025

value: Gingiva

value: Unknown


title: AB029

value: Floor of Mouth, tongue, buccal mucosa

value: PD

value: Alive


title: AB020

value: not reported

value: WD


title: AB018N

value: M

value: Floor of Mouth

value: MD

value: Free

value: Previous


title: X6686

description: DNA isolated from banked blood (buffy coat)

source_name: Genomic DNA from oral dysplasia

value: buccal mucosa

value: mild

tag: prior cancer

tag: cancer progression

tag: sample type

value: reference


title: X6689

tag: site

value: severe


title: qin ovary 3

city: Worcester

first: Zhao

last: Zhang

state: MA

address: LRB-870N, 364 Plantation Street

department: BMP

institute: UMass Medical School

hyb_protocol: Recommended Affymetrix protocol

scan_protocol: The tiling arrays were scanned using an Affymetrix GeneChip Scanner 3000 7G according to manufacturer's instruction.

data_processing: Since transposons account for more than 10% of the probes on the tiling array, a special normalization workflow has been taken to avoid over-normalization of signals. Coordinates and raw signal values for Drosophila tiling 2.0R array probes were extracted from Affymetrix Tiling Array Software. Then probes mapped to transposon regions were identified. The remaining non-transposon probes were quantile-normalized across qin mutant replicates based on the assumption that the overall signal distribution of these probes should remain the same across the different strains. Then the signals for transposon probes were calculated by looking up the normalized values of non-transposon probes at same raw signal level. To summarize the signal for each transposon element, probes mapped to any copy of the element were grouped together and Hodges-Lehmann estimator (ref1) was used to calculate the pseudomedian of their normalized signals. We used pseudomedian as it is less sensitive to the large number of outlier probes (probes with value of 1) in the tiling array experiments. Differentially expressed transposon elements were identified by contrasting their pseudomeidan values in three mutant replicates against three wild type replicates (Klattenhoff et al., 2009, Cell, 138,1137-49. ( accession number: GSE14307)). To correct for multiple testing, Express changed more than 3–fold and False Discovery Rates (FDRs) were calculated from t-test P-values. FDR<0.1 were used to call significantly changed transposons. Transposons with average expression value less than a minimal expression threshold of 149 (the 50th percentile expression value of RefSeq mRNAs) in both wild type and mutants were flagged as they are at the detection limit of the tiling array. Expression values of mRNAs were summarized by calculating the pseudomedian of probes mapped to each of the RefSeq mRNA transcripts. Differentially expressed transcripts were identified using FDR<0.1 cutoff.

label_protocol: Biotin

growth_protocol: Adult 2-4 day old female flies were fed yeast paste and maintained at 25ºC.

extract_protocol: The RNA was purified using Qiagen RNAeasy kit following the manufacturer's protocol(Qiagen)

tag: genotype

tag: tissue

value: ovary


title: X6690

value: tongue


title: X6889

value: Yes


title: X6695

value: Unknown


title: X6756

value: F


title: AB018

tag: tumor size (cm)

tag: tumor thickness

tag: node status (clinical)

value: Alive

value: Current

value: Male


title: AB019

value: Floor of Mouth, tongue

tag: histology

tag: recurrence

tag: follow up months

value: Dead


title: AB021

tag: age

tag: gender

value: Tongue

value: not reported

value: X

value: MD

value: Local

tag: vital status

value: Not free


title: X6419

value: M

value: severe

value: reference


title: qin ovary 2

value: ovary


title: X6464

value: Unknown


title: X6463

value: tongue


title: X6486

value: FOM

value: mild


title: qin ovary 1


title: X6418


title: X6402


title: wt ovary 3

source_name: wild-type

value: wild-type


title: AB017

value: Buccal Mucosa

value: WD

tag: tumor status

value: Free

tag: node status (path)

tag: tobacco use

value: Current

value: Male


title: X6475

value: F

value: palate

tag: prior cancer

tag: cancer progression


title: X6390

tag: site

value: moderate

tag: sample type


title: X6367

value: M

value: retromolar trigone

value: Yes


title: wt ovary 2

tag: genotype

tag: tissue

value: ovary


title: wt ovary 1


title: AB017N

tag: tumor size (cm)

tag: tumor thickness

value: not reported

value: Dead

tag: alcohol use


title: AB014N

value: Retromolar area

tag: node status (clinical)

tag: histology

value: MD

tag: recurrence

value: Alive


title: X6044

tag: age

value: Unknown

tag: gender

value: reference


title: AB016N

value: Buccal Mucosa

value: X

value: PD

tag: follow up months

tag: vital status

tag: tumor status

value: Past


title: X6162

value: F

value: tongue

value: mild

tag: prior cancer


title: X5952

value: M

value: FOM

value: moderate

tag: cancer progression


title: X6427

tag: site


title: X6201

value: gingiva

tag: sample type


title: X5922

value: Yes


title: X5905


title: AB010N

value: Tongue

value: Free

tag: node status (path)

tag: tobacco use

value: Male


title: X5823

value: Unknown


title: AB015

tag: tumor size (cm)

value: MD

value: Distant mets

value: Dead

value: Not free


title: X5914

value: reference


title: AB014

value: Retromolar area

tag: tumor thickness

value: Alive


title: X5824

value: tongue

value: severe


title: AB011

value: M

value: Current

tag: alcohol use

value: Previous


title: X5807

value: mild


title: AB011N

value: Tongue

tag: node status (clinical)


title: X5809

data_processing:
Array image quantitation was done with UCSF Spot. After quality filtering on spots and clones, an in-house SpotCorrection algorithm was used to remove systematic geometric and GC content effects.  Replicate spot averaging and median centering were then performed.  A remaining 'paraffin-embedded effect' was removed as follows.  For tumor profiles with paired normals, we applied noise reduction using the normal sample as template.  The magnitude of the effect was estimated using the derivative log ratio spread (DLRS) [Agilent].  For the two tumor profiles without a paired normal (and AB029 and AB067), we employed the per-probe median of the normal profiles as a normal template, with DLRS scaling as above. Clones without mapping information were excluded. Also, clones of possibly poor quality where more than 50% of the samples had missing data were excluded. Then replicate clones were averaged.
The paired normals for the tumor samples did not have processed normalized data; therefore, these Samples are tableless. The normal data only played a role in the pre-processing stage that generated the processed tumor data.
The paired normals for the tumor samples did not have processed normalized data; therefore, these Samples are tableless. The normal data only played a role in the pre-processing stage that generated the processed tumor data.

value: lower lip

tag: histology

value: Yes


title: AB007N

value: Floor of Mouth

value: WD

tag: recurrence

value: Regional

value: Male


title: AB016

tag: age

value: Buccal Mucosa

value: X

value: PD

value: Dead

value: Unknown

value: Past


title: X5806

tag: gender

value: reference


title: AB010

value: M

value: MD

tag: follow up months

value: Alive

value: Free


title: X5779

value: F

value: tongue

value: moderate


title: AB003N

value: Retromolar area

value: Local

tag: vital status

value: Previous


title: normal whole colon A

city: Edinburgh

first: Colm

middle: E

last: Nestor

address: Western General Hospital, Crewe Road

department: MRC Human Genetics Unit

institute: Univeristy of Edinburgh

description: normal whole colon genomic DNA

hyb_protocol: Labelled samples were applied to an 'Human DNA Methylation 4x72K ENCODE HG17 Targeted Tiling Array' which tiles the biologically significant ENCODE regions (EN001 - EN014) and hybridised overnight at 42degrees C.

scan_protocol: Arrays were scanned on a NimbleGen MS200 scanner per manufacturer's protocol (http://www.nimblegen.com/).

data_processing: Images  were processed using Nimblegen's standard protocol for Nimblescan DNA methylation DNA extraction.

source_name: normal whole colon

label_protocol: Amplified DNA samples were Cy5- (IP) or Cy3- (Input) labelled by random priming using the Dual-Color DNA Labeling Kit (NimbleGen, Iceland).

growth_protocol: normal human tissue

extract_protocol: Genomic DNA (5hmC-IP - 2.5 µg in 450 µl TE), sonicated to yield a fragment distribution of approximately 300-1000 bp, was denatured by incubation at 100 degrees C for 10 min. Samples were rapidly chilled on wet-ice. At this point, 45 µl (10%) of denatured sample was removed and saved as input, and 45 µl of 10X IP buffer (100 mM Na-Phosphate pH 7.0  (mono and dibasic), 1.4 M NaCl, 0.5 % Triton X-100) and 1 µg of 5hmC (ActiveMotif; #39769) antibody were added to the remaining sample. Samples were incubated at 4 degrees C with gentle agitation overnight. Then, 40 µl of magnetic beads (Dynabeads® Protein G, Invitrogen, UK) in 1X IP buffer were added to each sample to allow magnetic separation of the antibody from the unbound DNA using a magnetic tube rack. Samples were incubated at 4 degrees C for 1 hr with gentle agitation. Beads were collected with a magnetic rack and washed with 1000 µl of 1X IP buffer at RT for 10 min with gentle agitation; washing was repeated three times. Beads were collected with a magnetic rack and re-suspended in 250 µl of digestion buffer (50 mM Tris pH 8.0, 10 mM EDTA , 0.5 % SDS) followed by addition of 10 µl of proteinase K  (20 mg/ml; Roche Applied Science, Mannheim, Germany) and incubation at 52degrees C for 1.5 hr with constant shaking (≥800 rpm). Finally, beads were removed using a magnetic rack and DNA was purified from the remaining sample using a QIAquick PCR Purification Kit (QIAGEN,CA, USA), eluting in a final volume of 40 µl dH2O. Inputs were also purified using a QIAquick PCR Purification Kit and eluted in 40 µl dH2O. Subsequently, 10 ng of input and IP DNA was subjected to whole genome amplification (WGA) using the GenomePlex® Complete Whole Genome Amplification Kit (Sigma-Aldrich, UK) as per the manufacturer's instructions. Amplified DNA was run on a 1.2% agarose gel to confirm consistency of fragment size between samples.

treatment_protocol: genomic DNA extracted from normal human tissues, purchased from a commercial supplier

tag: antibody

tag: antibody manufacturer

value: Active Motif

tag: antibody catalog #

tag: tissue

value: normal whole colon

value: input DNA


title: AB004

tag: site

value: Gingiva

value: X

value: Dead

tag: tumor status

value: Current

value: Male


title: normal whole testis B

description: normal whole testis genomic DNA

source_name: normal whole testis

value: M

value: normal whole testis


title: normal whole colon B

description: normal whole colon genomic DNA


title: normal whole testis A

description: normal whole testis genomic DNA


title: X5724

value: mild

tag: prior cancer

value: Unknown

tag: cancer progression

tag: sample type

value: reference


title: X5749

value: tongue

value: severe


title: AB003

value: Retromolar area

tag: tumor size (cm)

tag: tumor thickness

value: MD

value: Local

tag: node status (path)

tag: tobacco use

tag: alcohol use


title: X5707

tag: age

tag: gender

tag: histology


title: X5653

value: F

value: Yes


title: X5769


title: X8444


title: X5681

value: gingiva

value: moderate


title: X7618


title: AB007

value: Floor of Mouth

tag: node status (clinical)

value: WD

tag: recurrence

value: Regional

tag: follow up months

tag: vital status

value: Dead

value: Not free


title: X0149

tag: site

value: yes


title: X8417

value: Unknown


title: X7646

value: M

value: reference


title: X8292

value: tongue

value: severe


title: normal whole liver B

description: normal whole liver genomic DNA

source_name: normal whole liver

tag: antibody

tag: antibody manufacturer

value: Active Motif

tag: antibody catalog #

tag: tissue

value: normal whole liver

value: input DNA


title: normal whole liver A

description: normal whole liver genomic DNA


title: normal whole breast B

description: normal whole breast genomic DNA

source_name: normal whole breast

value: F

value: normal whole breast


title: normal whole breast C

description: normal whole breast genomic DNA


title: normal whole breast A

description: normal whole breast genomic DNA


title: normal whole placenta C

description: normal whole placenta genomic DNA

source_name: normal whole placenta

value: normal whole placenta


title: normal whole placenta B

description: normal whole placenta genomic DNA


title: normal whole placenta A

description: normal whole placenta genomic DNA


title: X7694

value: moderate

tag: prior cancer

tag: cancer progression

tag: sample type


title: X7678

value: buccal mucosa


title: X7453