title: Normal colon tissue, NBRCCC012

value: 61 yr

value: recurrence-free


title: genomic DNA from primary UM F-1

status: Public on Feb 14 2013

type: genomic

city: Cleveland

first: Li

last: Zhang

state: OH

address: 9500 Euclid Ave, JJN3

department: Quantitative Health Sciences

country: USA

institute: CleveLAND CLINIC LERNER COL/MED-CWRU

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

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

data_processing: GenomeStudio software Methylation Module

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: primary uveal melanoma cells

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from primary UM, neural crest stem cell and embryonic stem cells using Qiagen DNeasy Kit according to standard instructions

tag: cell type

value: primary uveal melanoma cells

tag: gender

value: unknown

tag: survival (days)

tag: death with metastasis

tag: metastasis


title: Normal colon tissue, NBRCCC015

city: Seodaemun-gu

first: Park

last: Chan Hee

state: Seoul

address: Shinchondong 134

country: South Korea

institute: Cancer Metastasis Research Center

hyb_protocol: The labeled DNA was denatured and pre-annealed with Cot-1 DNA and Agilent blocking reagent and hybridized for 40 hours at 20 rpm in an Agilent hybridization oven.

scan_protocol: The arrays were scanned at 5-㎛ resolution using an Agilent scanner (Agilent), and the image was analyzed with Feature Extraction Software 9.1.1.1. Images were quantified using Agilent Feature Extraction Software.

data_processing: Agilent Feature Extraction Software was used for background subtraction and LOWESS normalization.

source_name: Normal colon tissue, recurrence-free group

label_protocol: Labeling was performed according to Agilent's recommended protocol. Briefly, 5 μg gDNA was digested with restriction enzymes Alu I (Promega) and Rsa I (Promega), and was labeled fluorescently using the Agilent DNA Labeling kit (Agilent). Patients' gDNAs were labeled with Cy5 and commercial gDNAs as a reference were labeled with Cy3 dUTP, respectively.

growth_protocol: Tissues were obtained and immediately snap-frozen in liquid nitrogen and stored.

extract_protocol: Genomic DNA (gDNA) was prepared using the phenol/chloroform/isoamyl alcohol method.

tag: tissue

value: normal colon adjacent to colon cancer

tag: age

value: 48 yr

tag: relapse status

source_name: Commerical gDNA

extract_protocol: Control DNA: Promega #G1471 (male) and #G1521 (female).

tag: sample type

value: reference


title: Oryzias latipes 7day 20ng/L rep2

type: RNA

city: Tsukuba

first: Katsuyuki

last: Kadota

state: Ibaraki

address: Tokodai 5-13-11

department: Research

country: Japan

institute: Japan pulp & Research Institute, Inc.

description: Gene expression after 7 day in 20 ng/L TB treated whole medaka

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60oC for 30 minutes in a reaction volume of 55ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Medaka Genome Oligo Microarrays (G2514F) for 17 hours at 65oC in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37oC GE Wash buffer 2 (Agilent), then dried immediately by N2 gas.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

molecule: total RNA

organism: Oryzias latipes

source_name: Oryzias latipes, 7 day, 20 ng/L, replicate 2

label_protocol: cRNA was prepared from the total RNA using the Quick Amp Labeling Kit (Agilent Technologies) following procedures recommended by the manufacturer. Briefly, 500 ng of the total RNA was reverse transcribed to cDNA followed by synthesis of cRNA incorporated with cyanine 3 (Cy3)-labeled nucleotide. cRNA was then purified using RNeasy mini columns (QIAGEN GmbH). The quality of the cRNA samples was verified by total yield of the cRNA and the incorporation rates of Cy3 calculated based on the spectrophotometric measurement using a NanoDrop ND 1000 spectrophotometer (Thermo Fisher Scientific Co., Ltd.).

growth_protocol: The experiment was performed in a climate chamber at 24±1oC and with 16 h light-8 h dark photoperiod. Each aquarium contained 90 medaka.

extract_protocol: Each frozen sample was ground with a mortar and pestle in liquid nitrogen. Total RNA was isolated from the homogeneous powder using the Qiagen RNeasy Lipid Tissue Midi Kit (QIAGEN GmbH) following procedures recommended by the manufacture. The quantity and purity of the total RNA were examined photometrically by 260nm/280nm and 260nm/230nm ratios using a NanoDrop ND1000 spectrophotometer (Thermo Fisher Scientific Co., Ltd., Wilmington, USA) and electrophoretically with RNA 6000 Nano LabChip Kit using Agilent Bioanalyzer 2100 (Agilent Technologies). Only RNA samples with RNA Integrity Number (RIN) values above 9.0 were used for further cRNA preparations.

treatment_protocol: Exposures of TB were carried out by a continuous flowthrough system, designed to maintain constant concentrations of TB throughout the exposure experiments. Briefly, the TB stock solution was delivered to a mixing glass chamber by a mini-chemical pump unit (Oriental Mortar Co., Ltd., Tokyo, Japan) and diluted with carbon-filtered tap water continuously delivered at a flow rate of 100 mL/min. The TB test solution overflowed the mixing chamber to enter each test glass aquaria containing 23L of the test solution. Larvae were exposed to TB for 7 days by the continuous flow-through system as for the chronic exposures except in 1L test chambers.   TB concentrations used were 0 (control), 2, 6, 20, 60, 100 and 200 ng/L for 7 days of exposure (dimethyl sulfoxide with a final concentration of 1:2,500 v/v water). Each TB treatment had 90 larvae for each chamber. At day 7 of the exposures, triplicate samples (30 larvae/sample) from each chamber respectively were collected, flash-frozen in liquid nitrogen, and stored in liquid nitrogen until RNA extraction. All experiments were conducted with a 16 h light-8 h dark photoperiod and at 24±1oC. The fish were fed Artemia nauplii (<24 h after hatching) twice a day.

value: whole body

value: 7 day

tag: dose

value: 20 ng/L


title: genomic DNA from primary UM 11M

value: M


title: Normal colon tissue, NBRCCC011

value: 58 yr


title: genomic DNA from primary UM 9M

value: F


title: Oryzias latipes 7day 6ng/L rep3

description: Gene expression after 7 day in 6 ng/L TB treated whole medaka

source_name: Oryzias latipes, 7 day, 6 ng/L, replicate 3

value: 6 ng/L


title: genomic DNA from NUM Asingh-660w_C05

hyb_protocol: RA1 resuspended DNA was loaded onto BeadChips arrays. After overnight incubation at 48¡C, single-base extension and allele-specific staining was performed on a Teflow chamber rack system (Tecan, Maennedorf, Switzerland).

scan_protocol: After allele-specific staining BeadChip arrays were coated with XC4/ethanol , dried for 1 hour and scanned on a BeadArray Reader (Illumina).

data_processing: Genomic DNA was genotyped using Infinium HumanHap66W-Quad v1.0 Genotyping BeadChips (Illumina).

label: C-Bio and A-DNP

source_name: Normal Uveal Melanocytes

label_protocol: 750ng of genomic DNA was whole-genome amplified in an overnight reaction at 37¡C using amplification master mix (WG-AMM) and primer/neutralization mix (WG-MP1). After incubation the amplified DNA was fragmented with fragmentation mix (WG-FRG), precipitated with isopropanol and precipitation mix (PA1) and resuspended in hybridization buffer (RA1).

extract_protocol: Extraction of genomic DNA from fresh frozen tissue was performed using proteinase K and repeated phenol-chloroform extraction.

value: Normal Uveal Melanocytes


title: genomic DNA from primary UM Asingh-660w_E05


title: genomic DNA from primary UM Asingh-660w_D05


title: Normal colon tissue, NBRCCC010

source_name: Normal colon tissue, relapse group

value: 26 yr

value: relapse


title: genomic DNA from primary UM 8


title: genomic DNA from primary UM Asingh-660w_F04


title: Oryzias latipes 7day 6ng/L rep2

source_name: Oryzias latipes, 7 day, 6 ng/L, replicate 2


title: genomic DNA from primary UM Asingh-660w_E04


title: genomic DNA from primary UM Asingh-660w_G04


title: genomic DNA from primary UM Asingh-660w_D04


title: Oryzias latipes 7day 2ng/L rep3

description: Gene expression after 7 day in 2 ng/L TB treated whole medaka

source_name: Oryzias latipes, 7 day, 2 ng/L, replicate 3

value: 2 ng/L


title: genomic DNA from primary UM Asingh-660w_H04


title: Normal colon tissue, NBRCCC008

value: 52 yr


title: Normal colon tissue, NBRCCC006

value: 63 yr

value: recurrence-free


title: genomic DNA from primary UM Asingh-660w_B04

value: primary uveal melanoma cells


title: Oryzias latipes 7day 6ng/L rep1

source_name: Oryzias latipes, 7 day, 6 ng/L, replicate 1


title: Oryzias latipes 7day 2ng/L rep1

source_name: Oryzias latipes, 7 day, 2 ng/L, replicate 1


title: Normal colon tissue, NBRCCC009

value: normal colon adjacent to colon cancer

value: 61 yr


title: Oryzias latipes 7day 0ng/L rep4

description: Gene expression after 7 day in 0 ng/L TB treated whole medaka

source_name: Oryzias latipes, 7 day, 0 ng/L, replicate 4

value: whole body

value: 0 ng/L


title: genomic DNA from primary UM 3M


title: Normal colon tissue, NBRCCC007

value: 66 yr

value: reference


title: genomic DNA from primary UM 7M

value: M


title: Normal colon tissue, NBRCCC005

value: 83 yr


title: Oryzias latipes 7day 2ng/L rep2

source_name: Oryzias latipes, 7 day, 2 ng/L, replicate 2

value: 7 day


title: genomic DNA from MUM2B MUM2B

source_name: MUM2B uveal melanoma cell line

tag: cell line

value: MUM2B uveal melanoma cell line

value: unknown


title: genomic DNA from OCM1A OCM1A

source_name: OCM1A uveal melanoma cell line

value: OCM1A uveal melanoma cell line


title: genomic DNA from primary UM Asingh-660w_C04


title: genomic DNA from primary UM Asingh-660w_A04


title: genomic DNA from primary UM 1


title: Normal colon tissue, NBRCCC004

value: 47 yr

value: relapse


title: Oryzias latipes 7day 0ng/L rep2

source_name: Oryzias latipes, 7 day, 0 ng/L, replicate 2


title: genomic DNA from primary UM Asingh-660w_E03

value: F


title: genomic DNA from ESC Asingh-660w_G03

source_name: Embryonic Stem Cells

value: Embryonic Stem Cells


title: genomic DNA from primary UM Asingh-660w_F03

source_name: primary uveal melanoma cells

value: primary uveal melanoma cells


title: genomic DNA from primary UM Asingh-660w_H03


title: ctsR mutant vs. wild type_bio rep 2 tech rep 2

city: Wyndmoor

first: yanhong

last: Liu

state: PA

address: 600 E. Mermaid Lane

institute: ERRS-ARS-USDA

hyb_protocol: according to CustomArray 12K microarray protocols provided by Combimatrix

scan_protocol: at 5-um resolutions by the ScanArray ExpressHT microarray scanner

data_processing: normalized using median over entire array,  log2 of Red signal/ Green signal. BRB-ArrayTools software was used.

organism: Listeria monocytogenes str. Scott A

source_name: ctsR mutant cells

label_protocol: dye swap labeling using Alexa 555(cy3)  and Alexa 647 (cy5)

growth_protocol: Listeria monocytogenes Scott A ctsR mutant and wild type grown to O.D.600 0.3 to 0.4

extract_protocol: Total RNA extracted using Ambion RiboPure-Bacterial Kit following manufacture's instructions

treatment_protocol: add nisin to the concentration of 20ug/ml, 37 ⁰C, 200 rpm, grew overnight (24 hours)

tag: genotype/variation

value: ctsR mutant

tag: agent

value: nisin

source_name: wild type cells

value: wild type


title: Normal colon tissue, NBRCCC002

value: normal colon adjacent to colon cancer

value: 68 yr

source_name: Commerical gDNA


title: Normal colon tissue, NBRCCC003

source_name: Normal colon tissue, recurrence-free group

value: 52 yr

value: recurrence-free

value: reference


title: Normal colon tissue, NBRCCC016

value: 65 yr


title: genomic DNA from primary UM Asingh-660w_D03


title: Oryzias latipes 7day 0ng/L rep1

source_name: Oryzias latipes, 7 day, 0 ng/L, replicate 1

value: whole body

value: 7 day

value: 0 ng/L


title: ctsR mutant vs. wild type_bio rep 2 tech rep 1


title: ctsR mutant vs. wild type_bio rep 1 tech rep 2


title: Normal colon tissue, NBRCCC001

value: 56 yr


title: 35S::gMtABI3 roots Replicate 3

city: BEAUCOUZE

first: Sandra

last: Pelletier

address: 42, rue Georges Morel - BP 60057

country: France

institute: INRA

hyb_protocol: The hybridization performed on a NimbleGen Hybridization System 4 (mix mode B) at 42° overnigth. Afterwards, the slide were washed, dried, and scanned.

scan_protocol: Slides were scanned at 532/635nm at 2 μm resolution and high sensitivity with a Roche-NimbleGen MS200. NimbleScan Software v2.4 was used to extract pair-data files from the scanned images.

data_processing: All statistical analyses on the gene expression data were performed using the R language, version 2.5.1 (R Development Core Team, 2011) and the package LIMMA (Smyth G.K., 2005) from the Bioconductor project. For the processing step, data were normalized by the lowess method in LIMMA.

organism: Medicago truncatula

label_protocol: 400 ng of total RNAs were amplified using the Ambion messageAmp II (Ambion, Austin TX) following manufacturer's instructions. 5µg of each aRNAs were retrotranscribed with 400U of Superscript II reverse-transcriptase (Invitrogen Corp., Carlsbad, CA) and labelled with 1,5mmol of Cyanine-3 (Cy3) or Cyanine-5 (Cy5) (Interchim, France), then purified with NucleoSpin Gel and PCR Clean-up column kits (Macherey-Nagel, GmbH & Co. KG, Germany). Purified labeled cDNA were quantified using NanoDrop ND-1000 (Nanodrop Technologies, DE, USA). Labelled samples were combined as 30 pmol for each dye and co-hybridized to the Medtr_v1 12x135K arrays.

growth_protocol: Seeds were sterilized, grown and transformed according to Boisson-Dernier et al (2001). Germinated and transformed roots seeds were cultivated with Fahräeus medium, with appropriated antibiotics, with sixteen hours of photoperiod, at 20°C.

extract_protocol: Roots total RNA was extract with Macherey-Nagel's Nucleospin Plant II Kit according manufacturer's recommandations.

treatment_protocol: Binary vector pK7GW2D (Karimi et al, 2002) containing the full-lenght MtABI3 gene was introduced in Arqua1 strain of Agrobacterium rhizogenes by a freeze-thaw method. Thirty hours age old apex roots were cut and scrapped on fourty eight hours age old transformed ARqua1 culture before being placed on solid medium

tag: tissus

value: roots

tag: genetic background ecotype

tag: genotype

tag: phenotype

value: Wild-type

tag: treatment

value: 4 weeks

tag: harvest date


title: DKO5

city: Philadelphia

first: Tao

last: Gao

address: 421 Curie Blvd, BRB II/III, Room 527

institute: University of Pennsylvania

description: the hippo kinases Mst1 and Mst2 are specifically deleted in mouse pancreas

hyb_protocol: A total of 1.5 μg of biotinylated cDNA was hybridized to the moues Gene 1.0 ST microarray.

scan_protocol: Samples were scanned uing GCS3000 laser scanner, and data were collected.

data_processing: Array data was processed by Affymetrix Expression Console software.

label: biotin

organism: Mus musculus

source_name: pancreas

label_protocol: 500 ng of total RNA were used for the synthesis of cDNA, followed by amplification and biotin labeling.

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

tag: strain

value: mixed background


title: ctsR mutant vs. wild type_bio rep 1 tech rep 1

value: ctsR mutant


title: DKO4


title: genomic DNA from primary UM Asingh-660w_C03

tag: cell type

value: primary uveal melanoma cells

tag: gender

value: F

tag: survival (days)

tag: death with metastasis


title: 35S::gMtABI3 roots Replicate 1

tag: age


title: 35S::GUS roots Replicate 2

treatment_protocol: Binary vector pK7GW2D (Karimi et al, 2002) containing the full-lenght GUS gene was introduced in Arqua1 strain of Agrobacterium rhizogenes by a freeze-thaw method. Thirty hours age old apex roots were cut and scrapped on fourty eight hours age old transformed ARqua1 culture before being placed on solid medium

value: GUS


title: 35S::GUS roots Replicate 3


title: 35S::gMtABI3 roots Replicate 2


title: genomic DNA from primary UM Asingh-660w_B03

value: M

tag: metastasis


title: Listeria ctsR mutant ctsR mutant biological replicate 2

description: normalized log2 ratios of mutant under pressure/mutant under normal condition

scan_protocol: at 5-um resolutions by the ScanArray ExpressHT microarray scanner Images were quantified using Microarray_mager_5.9.3 (Combimatrix)

data_processing: median normalization by substracting out the median log-ratio for each array, so that each normalized array has a median log-ratio of 0.  BRB-ArrayTools software was used.

source_name: ctsR mutant 2-1 under normal condition (no pressure)

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

value: Listeria monocytogenes str. Scott A

value: ctsR mutant 2-1

value: control

source_name: ctsR mutant 2-1 under pressure

value: 450Mpa for 3min


title: genomic DNA from primary UM Asingh-660w_A03


title: Listeria ctsR mutant ctsR mutant biological replicate 1

treatment_protocol: ctsR mutant 2-1 under normal condition (no pressure)


title: Control5

value: Control


title: DKO1


title: 35S::GUS roots Replicate 1


title: Control4


title: Control3


title: Control2


title: Testis RNA of mouse 6 fed on High Fat diet

city: Nice

first: Valerie

last: Grandjean

address: Parc Valrose

department: University of Nice

institute: INSERM

description: W

hyb_protocol: Illumina Direct Hybridization Assay was used to hybridize the cRNA to MouseWG-6 v2 Expression BeadChips

scan_protocol: Illumina iScan system was used to scan the beadchip.

data_processing:
GenomeStudio was used to process the data generated from iScan system.
GeneSpring software computed normalized data generated from GenomeStudio.

source_name: Mouse testis

label_protocol: TargetAmp™ Nano-g™ Biotin-aRNA Labeling Kit for the Illumina® System  was used to label and amplify the RNA.

growth_protocol: Testis RNA of mice fed on High Fat and standard diets

extract_protocol: QIAGEN RNEasy Mini Kit was used to isolate total RNA.

value: 4 months

tag: tissue

value: testis

tag: diet

value: high fat


title: DKO2


title: genomic DNA from primary UM 4M


title: genomic DNA from primary UM Asingh-660w_G02


title: genomic DNA from NCSC Asingh-660w_F02

source_name: Neural Crest Stem Cells

value: neural crest stem cells

value: unknown


title: genomic DNA from primary UM Asingh-660w_H02


title: Testis RNA of mouse 5 fed on standard diet

description: N

value: standard


title: DKO3

value: mixed background


title: genomic DNA from primary UM Asingh-660w_D02


title: genomic DNA from primary UM Asingh-660w_C02


title: filgrastim + cyclophosphamide-2

status: Public on Feb 13 2013

city: New York

first: Maureen

middle: E

last: Lane

state: NY

address: 1300 York Avenue

department: Medicine

institute: Weill Cornell Medical College

description:
PB 3779
Amplified RNA.

hyb_protocol: Following fragmentation and labeling, 5 ug of labeled cDNA were hybridized for 16 hr at 45 degrees Celsius on the Affymetrix HG-U133 Plus 2.0 microarray chips (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip scanner (GCS); Scanner type = M10.

data_processing: GC-RMA normalization and baseline transformation were performed using GeneSpring 12.1 (Agilent Technologies and Strand Life Science) using default parameters. Data were analyzed in GeneSpring 12.1 using the following parameters: Filtered on expression (50), corrected p-value cutoff of 0.05, unpaired T-test between the 2 mobilization groups, p-value computation was asymptotic and Benjamini-Hochberg multiple test correction was applied. Differential expression between the DoVed and filgrastim + cyclophosphamide groups was further analyzed using a greater than 2.0-fold change in gene regulation.

label: Biotin

source_name: CD34+ cells from patients post-G-CSF+Cytoxan therapy

label_protocol: 25-250 ng of total RNA were reverse transcribed and amplified using the WT-Ovation Pico RNA amplification system (NuGEN Technologies, San Carlos, CA). 5 ug of amplified cDNA were fragmented and labeled with biotin using the FL-Ovation CDNA Biotin Module (Nugen Technologies, San Carlos, CA) version 2.

extract_protocol: RNeasy micro kit (Qiagen, Valencia, CA).

treatment_protocol: DoVeD induction: bortezomib-dexamethasone ± liposomal doxorubicin. Non-bortezomib induction: filgrastim + cyclophosphamide.

tag: disease state

value: multiple myeloma

value: non-bortezomib-based mobilization

value: blood (leukapheresis products)

value: CD34+ stem cells


title: genomic DNA from primary UM Asingh-660w_F01

value: primary uveal melanoma cells

value: M


title: DoVeD-4

description:
PB 4015
Amplified RNA.

source_name: CD34+ cells from patients post-DoVeD therapy

value: bortezomib-based mobilization


title: Testis RNA of mouse 2 fed on standard diet


title: filgrastim + cyclophosphamide-3

description:
PB 3334
Amplified RNA.


title: Testis RNA of mouse 3 fed on High Fat diet


title: DoVeD-2

description:
PB 3469
Amplified RNA.


title: DoVeD-3

description:
PB 3728
Amplified RNA.


title: Testis RNA of mouse 1 fed on standard diet


title: DoVeD-5

description:
PB 4370
Amplified RNA.


title: Testis RNA of mouse 4 fed on High Fat diet


title: genomic DNA from primary UM Asingh-660w_A02


title: Oryzias latipes 7day 0ng/L rep3

source_name: Oryzias latipes, 7 day, 0 ng/L, replicate 3

value: whole body

value: 7 day

tag: dose

value: 0 ng/L


title: genomic DNA from primary UM Asingh-660w_G01


title: DoVeD-1

description:
PB 3722
Amplified RNA.


title: genomic DNA from primary UM Asingh-660w_B02

value: F


title: genomic DNA from primary UM Asingh-660w_C01


title: genomic DNA from primary UM Asingh-660w_H01


title: genomic DNA from primary UM Asingh-660w_A01


title: genomic DNA from MUM2B Asingh-660w_B01

source_name: MUM2B uveal melanoma cell line

tag: cell line

value: MUM2B uveal melanoma cell line


title: genomic DNA from primary UM Asingh-660w_D01


title: Nephrectomy8_GSM880500 reanalysis

city: Edmonton

first: Jessica

last: Chang

address: 250 Heritage Medical Research Centre

country: Canada

institute: University of Alberta

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HGU133 Plus 2.0 Human Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using Gene Array Scanner (Affymetrix) and processed with GeneChip Operating Software Version 1.4.0 (Affynetrix).

data_processing: Microarray data files were preprocessed using robust multi-chip averaging (RMA) implemented in Bioconductor.

source_name: nephrectomy

label_protocol: RNA (1-2µg) was labeled using GeneChip HT One-Cycle Target Labeling and Control kit. Quality of labeled cRNA was assessed on an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA) before hybridization to HGU133Plus2.0. GeneChip (Affymetrix, Santa Clara, CA).

growth_protocol: All human renal allograft biopsies taken for clinical indication during the period specified above were included. Tissue was immediately placed in RNA later.

extract_protocol: Following homogenization of the tissue in 0.5ml of Trizol reagent (Invitrogen, Carlsbad, CA), total RNA was extracted and purified using the Rneasy Micro Kit (Quiagen, Ontario, Canada) (average yield 4µg/core, (RNA integrity number >7).

treatment_protocol: The immunosuppressive treatment of the patients before the biopsy was based on individual treatment regiments; the treatment after the biopsy was adjusted based on the histopathological diagnosis.

value: nephrectomy

tag: diagnosis (good,bad)

tag: dgf status

tag: geo sample


title: Nephrectomy3_GSM880299 reanalysis


title: genomic DNA from OCM1A Asingh-660w_E01

source_name: OCM1A uveal melanoma cell line

value: OCM1A uveal melanoma cell line


title: Nephrectomy5_GSM880318 reanalysis


title: Nephrectomy6_GSM880430 reanalysis


title: DD66

source_name: renal allograft biopsy

value: renal allograft biopsy

value: good

value: IGF

tag: remuzzi score (inadequate tissue for pathology interpretation)

tag: mapi (inadequate tissue for pathology interpretation)

tag: glomerulosclerosis  (inadequate tissue for pathology interpretation)

tag: irish score

tag: schold score

tag: kdri

tag: donor age


title: DD63


title: genomic DNA from primary UM Asingh-660w_E02

source_name: primary uveal melanoma cells

tag: cell type

tag: gender

tag: survival (days)

tag: death with metastasis


title: Nephrectomy4_GSM880311 reanalysis

tag: tissue


title: Nephrectomy7_GSM880447 reanalysis


title: DD69


title: DD64


title: DD65


title: DD62


title: DD70


title: DD68

value: bad


title: DD61


title: DD67

value: DGF


title: Nephrectomy2_GSM880246 reanalysis


title: DD59


title: Control1

tag: strain

value: mixed background

tag: genotype

value: Control


title: DD60

tag: diagnosis (good,bad)


title: DD47

tag: dgf status


title: DD58


title: DD57


title: DD51


title: DD54


title: DD49


title: DD48


title: DD55


title: DD52


title: DD45


title: DD37


title: DD44


title: DD56


title: DD50


title: DD34


title: DD40


title: DD42


title: DD43


title: DD41


title: DD39


title: DD53


title: DD33


title: DD46


title: DD35


title: DD36


title: DD38


title: DD31


title: filgrastim + cyclophosphamide-1

description:
PB 3924
Amplified RNA.

tag: disease state

value: multiple myeloma

tag: treatment

value: non-bortezomib-based mobilization

value: blood (leukapheresis products)

value: CD34+ stem cells


title: DD32

tag: remuzzi score (inadequate tissue for pathology interpretation)

tag: mapi (inadequate tissue for pathology interpretation)


title: DD27

tag: glomerulosclerosis  (inadequate tissue for pathology interpretation)

tag: irish score


title: DD26

tag: schold score

tag: kdri


title: DD24

tag: donor age


title: DD23


title: DD28


title: DD29


title: DD25


title: DD22


title: Nephrectomy1_GSM880245 reanalysis

tag: geo sample


title: DD21


title: DD20


title: DD16


title: DD30


title: DD19


title: DD11


title: DD10


title: DD12


title: DD9


title: DD17


title: DD7


title: DD14


title: DD6


title: DD18


title: DD8


title: DD15


title: DD2


title: DD4


title: DD5


title: DD1


title: DD3


title: DD13


title: MM_#44

city: Saint Herblain

first: Wilfried

last: Gouraud

address: bd Jacques Monod

department: Integrated Center of Oncology René Gauducheau

institute: ICO (Integrated Center of Oncology Nantes)

description: Diagnosis

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

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

data_processing: Affymetrix Genotyping Console 4.0 for processing SNPs, detecting copy number abnormalities with default parameters and 270 HapMap reference samples.

source_name: Bone marrow and/or blood

label_protocol: According to manufacturer protocol

extract_protocol: DNA was extracted using the DNA AllPrep DNA/RNA MiniKit (Qiagen, Valencia, CA). Matched germline DNA from 17 patients was extracted from buffy coat and purified using Nucleon BACC Genomic DNA Extraction Kit (GE Healthcare Life Sciences Piscataway, NJ). DNA quality and quantity were assessed using the Nanodrop Spectrophotometer (NanoDrop Technologies, Inc. Wilmington, DE).

tag: patient id

tag: tumor

value: bone marrow

tag: cells

value: purified CD138+ plasma cells

tag: sample type

value: Diagnosis


title: MOSAIC_000

description: Mosaic

tag: tissue

value: bone marrow and blood

value: purified CD138+ plasma cells & blood

value: Mosaic


title: MOSAIC_005

description: Mosaic


title: MM_#41R

description: Relapse

value: Relapse


title: MM_#42R_blood

description: Blood

value: blood


title: MM_#44R

description: Relapse


title: MM_#44_blood

description: Blood


title: MM_#43

description: Diagnosis


title: MOSAIC_100

description: Mosaic


title: MOSAIC_080

description: Mosaic


title: MM_#43R

description: Relapse


title: MOSAIC_020

description: Mosaic


title: MM_#41_blood

description: Blood


title: MM_#41

description: Diagnosis


title: MM_#43_blood

description: Blood


title: KMS-28PE

description: Cell line

source_name: Bone marrow cell line

value: multiple myeloma cell line

tag: cell line

value: bone marrow cell line

value: Cell line


title: MOSAIC_040

description: Mosaic


title: RPMI-8226

description: Cell line


title: MM_#40R1

description: Relapse


title: MM_#42

description: Diagnosis


title: MM_#40R2

description: Relapse


title: MM_#42R

description: Relapse


title: MOSAIC_060

description: Mosaic


title: MM_#40_blood

description: Blood


title: MM_#39R

description: Relapse


title: MM_#38R

description: Relapse


title: MM_#39

description: Diagnosis


title: MM_#40

description: Diagnosis


title: MM_#39_blood

description: Blood


title: MM_#38_blood

description: Blood


title: MM_#37

description: Diagnosis


title: MM_#38

description: Diagnosis


title: MM_#37R

description: Relapse


title: MM_#33R

description: Relapse


title: MM_#32

description: Diagnosis


title: MM_#32R

description: Relapse


title: MM_#31R

description: Relapse


title: MM_#25R_blood

description: Blood


title: MM_#25

description: Diagnosis


title: MM_#36_blood

description: Blood


title: MM_#27R_blood

description: Blood


title: MM_#24R

description: Diagnosis


title: MM_#17R

description: Relapse


title: MM_#16

description: Diagnosis


title: MM_#31

description: Diagnosis


title: MM_#27R

description: Relapse


title: MM_#36

description: Diagnosis


title: MM_#13R

description: Relapse


title: MM_#12

description: Diagnosis


title: MM_#16R

description: Relapse


title: MM_#11R

description: Relapse


title: MM_#16R_blood

description: Blood


title: MM_#10R

description: Relapse


title: MM_#25R

description: Relapse


title: MM_#12R

description: Relapse


title: MM_#17

description: Diagnosis


title: MM_#37_blood

description: Blood


title: Clinical strain #7, biological rep2

city: Yongin

first: yuna

middle: sophia

last: yun

address: Yonggu St. 1920

institute: AmorePacific Co.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45℃ on Affymetrix GeneChip® GeneChip S. aureus Genome Array.

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

data_processing: The data were analyzed using Affymetrix Command Console, R affy-package (v.2.8.1), Expression Console (v.1.1) DAVID.

organism: Staphylococcus aureus

source_name: clinical strain isolated from human skin

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2005, Affymetrix).

growth_protocol: The four isolates were cultured in TSB with 1% glucose for 24 h at 32°C to a concentration of about 10^9 cfu/mL

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

treatment_protocol: The bacteria from 1 mL of each culture were harvested by centrifugation and the pellet stored in -70~80℃

tag: strain

value: Clinical strain #7

tag: strain phenotype

value: biofilm-negative

tag: donor group

value: LSG

tag: tissue source

value: human skin


title: Clinical strain #10, biological rep1

value: Clinical strain #10

value: biofilm-positive

value: HSG


title: Clinical strain #7, biological rep1


title: MM_#10_blood

description: Blood

value: multiple myeloma

value: purified CD138+ plasma cells


title: MM_#13

description: Diagnosis

value: bone marrow

value: Diagnosis


title: Clinical strain #33, biological rep1

value: Clinical strain #33


title: Clinical strain #33, biological rep2


title: Clinical strain #10, biological rep2


title: Clinical strain #2, biological rep2

value: Clinical strain #2


title: MM_#36R

description: Relapse

value: Relapse


title: Clinical strain #2, biological rep1


title: MM_#33R_blood

description: Blood

value: blood


title: 211At_thryoid_0_Gy_#2

city: Göteborg

first: Nils

last: Rudqvist

state: VG

address: Gula stråket 2b

country: Sweden

institute: Gothenburg university

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Data preprocessing and quantile normalization were applied to the raw signal intensities using BASE. Further data processing was done in Nexus Expression 2.0 (BioDiscovery).

source_name: Mouse thyroid, 0 Gy, 24h

label_protocol: Standard Illumina labeling protocol

extract_protocol: Total RNA was extracted with RNeasy Lipid Tissue Mini Kit according to the manufacturer’s instructions. Quality control was performed with Agilent Bioanalyzer.

value: BALB/c

value: thyroid

tag: absorbed dose

value: 0 Gy


title: MM_#11

description: Diagnosis


title: C2

city: Syracuse

first: Jiachuan

last: Pan

address: 121 Link Hall

institute: Syracuse Unievrsity

description:
Ren_2-F 11-12-12_(E_coli_2)
Control

hyb_protocol: Fragmented cDNA was hybridized on the Affymetrix E. coli Genome 2.0 Array for 16 h at 45oC. Arrays were washed and stained in an Affymetrix Fluidics Station 450 using the FS450_0006 fluidics protocol

scan_protocol: Arrays were scanned with an Affymetrix GeneChip Scanner 7G Plus

data_processing: GeneChip Operating Software (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method, genes with a p-value of less than 0.0025 or greater than 0.9975 were considered statistically significant based on Wilcoxon signed rank test and Tukey Byweight, labeled as I and D in the attached txt file. To ensure the significance of microarray data, an additional criterion was applied to only select the genes with an expression ratio of 2 or high from this group as induced and repressed genes.

organism: Escherichia coli

source_name: furanone-free control

label_protocol: Biotinylated cDNA was prepared from 10 ug total RNA using the Prokaryotic Target Preparation protocol in the Affymetrix Expression Analysis Technical Manual

growth_protocol: RP437 was inoculated in 100 mL LB and grown for 18 h (200 rpm, 37oC). Persister cells were isolated by lysing the normal cells with 5 µg/mL Ofloxacin (3.5h, 200 rpm, 37oC), followed by centrifugation and washing with 0.85% NaCl solution.

extract_protocol: RNeasy Mini Kit (Qiagen, Austin, TX, USA) with on-column DNase treatment (RNase-Free DNase Set, Qiagen).

treatment_protocol: The isolated persisters were incubated in 0.85% NaCl solution for 1 h (200 rpm, 37oC) with or without 5 µg/mL BF8.

value: E. coli RP437

tag: cell type

value: Persister cells


title: F2

description:
Ren_2-C 11-12-12_(E_coli_2)
Gene expression data from persister cells treated by BF8

source_name: RP437 persisters treated with BF8 at 5 µg/mL for 1 hour


title: MM_#10

description: Diagnosis


title: MM_#24_Sty

description: Diagnosis


title: 211At_thyroid_32.4_Gy_#2

source_name: Mouse thyroid, 32.4 Gy, 24h


title: MM_#09R_blood

description: Blood


title: 211At_thyroid_11.2_Gy_#3

source_name: Mouse thyroid, 11.2 Gy, 24h


title: F1

description:
Ren_C 11-1-12_(E_coli_2)
Gene expression data from persister cells treated by BF8


title: 211At_thyroid_32.4_Gy_#3


title: 211At_thryoid_0_Gy_#1


title: 211At_thyroid_32.4_Gy_#1


title: C1

description:
Ren_F 11-1-12_(E_coli_2)
Control


title: 211At_thryoid_0_Gy_#3


title: 211At_thyroid_11.2_Gy_#2


title: MM_#07_blood

description: Blood


title: CLL_79_L

city: Vienna

first: Stefanie

last: Tauber

address: Dr. Bohr-Gasse 9

department: CIBIV

country: Austria

institute: MFPL

hyb_protocol: Affymetrix GeneChip® Human Gene 1.0 ST arrays were washed, stained and scanned according to the protocol described in WT Sense Target Labeling Assay Manual (Fluidics Protocol FS450_0007).

scan_protocol: Scanning was done on an Affymetrix GeneChip Scanner 7G.

data_processing: Data processing was done with R 2.11, and, respectively BioConductor 2.6.

source_name: Prim. CLL

label_protocol: 100ng of total RNA were amplified and labeled with biotin using the Whole Transcript (WT) Sense Target Labeling Protocol.

growth_protocol: Primary CLL cells were kept at 37°C in RPMI 1640 (phenol red free) containing 10% foetal calf serum, 1% L-glutamine, and 1ng/mlphorbol-12-myristate-13-acetate for 1 hour before siRNA transfection.

extract_protocol: Trizol followed by purifiaction using Rneasy Minelute kit (QIAGEN)

treatment_protocol: LPL specific and scrambled siRNA, respectively, were mixed with Lipofectamine2000 reagent and diluted in Opti-MEM. RNAi-Lipofectamine complexes were added to each experiment at final siRNA concentration of 60 pmol/ml. Transfections were done in duplicate and incubated for 48h before harvesting cells.

value: primary chronic lymphocytic leukemia

tag: treatment

value: LPL silencing siRNA


title: MM_#07R

description: Relapse


title: 211At_thyroid_11.2_Gy_#1


title: CLL_118_S

value: Non-targeting olico


title: MM_#09R

description: Relapse


title: MM_#07

description: Diagnosis


title: CLL_118_L


title: 211At_thyroid_1.4_Gy_#3

source_name: Mouse thyroid, 1.4 Gy, 24h


title: MM_#27

description: Diagnosis


title: MM_#03R_blood

description: Blood


title: MM_#03R

description: Relapse


title: CLL_79_S


title: CLL_128_L


title: MM_#44__Exon1.0ST

description: Myeloma

hyb_protocol: Following fragmentation, 5 µg of ST-cDNA were hybridized for 16-20 hours at 45°C on GeneChip Human Exon 1.0 ST array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

data_processing: Affymetrix Expression Console 1.1.2 using RMA Gene core analysis with default parameters.

source_name: Bone marrow

extract_protocol:
Total RNA extraction was performed according to the manufacturer's instructions using kit:
RLT

value: diagnosis


title: MM_#43__Exon1.0ST

description: Myeloma

value: multiple myeloma


title: MM_#03

description: Diagnosis

value: purified CD138+ plasma cells


title: 211At_thyroid_1.4_Gy_#1


title: CLL_128_S


title: 211At_thyroid_0.5_Gy_#3

source_name: Mouse thyroid, 0.5 Gy, 24h


title: 211At_thyroid_0.05_Gy_#3

source_name: Mouse thyroid, 0.05 Gy, 24h


title: CLL_80_S


title: MM_#42R_Exon1.0ST

description: Myeloma

extract_protocol:
Total RNA extraction was performed according to the manufacturer's instructions using kit:
RLT+

value: bone marrow

value: relapse


title: MM_#41R_Exon1.0ST

description: Myeloma


title: 211At_thyroid_1.4_Gy_#2


title: CLL_99_L


title: CLL_99_S


title: MM_#42__Exon1.0ST

description: Myeloma


title: 211At_thyroid_0.5_Gy_#1


title: MM_#33

description: Diagnosis

value: Diagnosis


title: MM_#09

description: Diagnosis


title: MM_#40R1_Exon1.0ST

description: Myeloma


title: CLL_69_L


title: MM_#40R2_Exon1.0ST

description: Myeloma


title: 211At_thyroid_0.05_Gy_#2


title: MM_#39R_Exon1.0ST

description: Myeloma


title: MM_#39__Exon1.0ST

description: Myeloma


title: 211At_thyroid_0.05_Gy_#1


title: MM_#38R_Exon1.0ST

description: Myeloma


title: IL7-3 6 2008 low pmt

city: Portici (NA)

first: Antonio

last: Di Matteo

address: Via Universita' 100 - Parco Gussone - Edificio 75

department: DiSSPAPA

country: Italy

institute: University of Naples Federico II

hyb_protocol: Prehybridization was performed by incubating the arrays with prehybridization solution (6X SSPE, 0.05% Tween-20, 20mM EDTA, 5x Denhardt's solution, 100 ng/ul Salmon Sperm DNA, 0.05% SDS) for 60 minutes at 45 °C.  5 ug of Labeled aRNA were fragmented by incubation with Fragmentation Solution (40mM Tris Acetate pH 8.1, 100 mM KOAc, 30 mM MgOAc) for 20' at 95 °C  Hybridization was performed at 45°C for 16 hours in hybridization solution (6X SSPE, 0.05% Tween-20, 20mM EDTA, 25% DiFormamide, 100 ng/ul Salmon Sperm DNA, 0.04% SDS).  Hybridization washings were performed as following:  - wash with 6X SSPET wash solution (6X SSPE, 0.05% Tween-20).  - wash with 3X SSPET wash solution (3X SSPE, 0.05% Tween-20).  - wash with 0.5X SSPET wash solution (0.5X SSPE, 0.05% Tween-20).  - wash with PBST was solution (2X PBS, 0.1% Tween-20).  - 2 washes with 2X PBS

scan_protocol: After hybridization and washing, the microarray was dipped in imaging solution, covered with LifterSlip™, and then scanned using a Perkin Elmer ScanArray 4000XL and the accompanying acquisition software (ScanArray Express Microarray Analysis System v4.0). Multiple scanning at different PMT was provided for each hybridization.

data_processing: Data extraction was carried out using CombiMatrix Microarray Imager software and a median normalization of raw medians and log2 transformation were performed using SPSS v.15.0 software. Further statistical processing was performed using the two-factor ANOVA module in the TIGR Multiple Experiment Viewer Software v4.0 (http://www.tigr.org/software/tm4/).

label: Alexa Fluor 647

organism: Solanum lycopersicum

source_name: Red ripe fruit from tomato IL7-3 variety, biological replica 6, trial 2008

label_protocol: Total RNA (1μg) was used as a template to synthesize antisense RNA (aRNA) with the SuperScript™ Indirect RNA Amplification System Kit (Invitrogen) incorporating  Alexa Fluor 647 Reactive Dye according to manifacturer instructions.

growth_protocol: The introgression line 7-3 (IL7-3) and its parental genotypes (cv. M82) were cultivated over consecutive years in a greenhouse at the Department of Soil, Plant, Environmental and Animal Production Sciences at the University of Naples (Portici, Italy). Six plants from IL 7-3 and from the parental cv. M82 were transferred into 20-cm pots containing a 1:1 mixture of medium sandy soil and compost at the beginning of March. Pots were distributed randomly 15 cm apart in rows 1 separated by a 50-cm 2 channel, and were supplemented with Nitrophoska Blu Spezial 12-12-17 (+2+20) (Compu) slow release fertilizer (5 g). Plants were watered twice daily using an automated irrigation device with 4 individual drip lines. Prior to flowering, the plants were supplied every two weeks with 30-10-10 liquid fertilizer (Grow More, USA). Fruits were collected at red-ripe stage.

extract_protocol: Total RNA was extracted from frozen, homogenized and powdered tomato fruit tissue using the CTAB (hexadecyltrimethylammonium bromide) method (Griffiths et al. J Exp Bot 50: 793–798 1999). Samples were taken from IL7-3 and M82 using three plants per genotype in the 2007 and 2008 growing trials.

treatment_protocol: Fruits were collected from IL 7-3 and its cultivated parent when 75% were full sized and red-ripe, softening had increased and the inside of the columella was completely red. Samples were generated by pooling ripe fruit from the same plant and discarding the seeds, jelly parenchyma, columella and placenta tissues. Samples were frozen under liquid nitrogen and stored at –80°C prior to homogenization in a Waring blender and processing for the extraction of ascorbic acid and total RNA.

tag: line

value: Introgression Line 7-3

value: epicarp and mesocarp

tag: trial

tag: plant replica


title: MM_#41__Exon1.0ST

description: Myeloma


title: CLL_13_L


title: CLL_69_S


title: IL7-3 6 2008 high pmt


title: IL7-3 4 2008 low pmt

source_name: Red ripe fruit from tomato IL7-3 variety, biological replica 4, trial 2008


title: CLL_13_S


title: MM_#40__Exon1.0ST

description: Myeloma


title: IL7-3 5 2008 low pmt

source_name: Red ripe fruit from tomato IL7-3 variety, biological replica 5, trial 2008


title: MM_#38__Exon1.0ST

description: Myeloma


title: IL7-3 5 2008 high pmt


title: KO CD8 T cells at T6, biological rep1

city: Los Angeles

first: Yoko

last: Kidani

state: CA

address: 650 Charles E Young Drive

institute: UCLA

description: Gene expression data from Scap deficient mouse CD8 T cells after 6h activation in vitro

hyb_protocol: Affymetrix standard hybridization protocol

scan_protocol: Affymetrix standard scanning protocol

data_processing: The data were analyzed with transformation algorithm GCOS and scaling parameter 500.

molecule: polyA RNA

source_name: 6 h activated mouse CD8 T cells purified from T cell specific Scap deficient mouse spleen

label_protocol: Affymetrix standard label protocol

growth_protocol: CD8 T cells were purified from spleens using Cd8 T cell enrichment kit. Plate-bound anti-CD3 and soluble anti-CD28 were used for activation.

extract_protocol: Qiagen RNeasy kit

tag: genotype

tag: gender

value: Male

value: Spleen


title: KO CD8 T cells at T6, biological rep3


title: KO CD8 T cells at T6, biological rep2


title: CLL_7_L


title: CLL_6_S


title: CLL_6_L


title: IL7-3 4 2008 high pmt


title: M82 6 2008 low pmt

source_name: Red ripe fruit from tomato M82 variety, biological replica 6, trial 2008

value: var. M82


title: MM_#36R_Exon1.0ST

description: Myeloma

tag: tumor


title: MM_#36__Exon1.0ST

description: Myeloma


title: KO CD8 T cells at T0, biological rep3

description: Gene expression data from Scap deficient mouse CD8 T cells at quiescence

source_name: Quiescent mouse CD8 T cells purified from T cell specific Scap deficient mouse spleen


title: MM_#13R_Exon1.0ST

description: Myeloma


title: CLL_80_L


title: KO CD8 T cells at T0, biological rep2


title: M82 5 2008 low pmt

source_name: Red ripe fruit from tomato M82 variety, biological replica 5, trial 2008


title: CLL_15_S


title: M82 5 2008 high pmt


title: MM_#33__Exon1.0ST

description: Myeloma


title: WT CD8 T cells at T6, biological rep3

description: Gene expression data from WT mouse CD8 T cells after 6h activation in vitro

source_name: 6 h activated mouse CD8 T cells purified from WT control mouse spleen


title: 211At_thyroid_0.5_Gy_#2

value: BALB/c

value: thyroid


title: M82 6 2008 high pmt


title: MM_#03__Exon1.0ST

description: Myeloma


title: CLL_7_S


title: MM_#03R_Exon1.0ST

description: Myeloma


title: MM_#13__Exon1.0ST

description: Myeloma


title: KO CD8 T cells at T0, biological rep1


title: MM_#33R_Exon1.0ST

description: Myeloma


title: M82 4 2008 low pmt

source_name: Red ripe fruit from tomato M82 variety, biological replica 4, trial 2008


title: CLL_15_L


title: WT CD8 T cells at T6, biological rep1


title: M82 4 2008 high pmt


title: IL7-3 2 2007 low pmt

source_name: Red ripe fruit from tomato IL7-3 variety, biological replica 2, trial 2007


title: WT CD8 T cells at T0, biological rep3

description: Gene expression data from WT mouse CD8 T cells at quiescence

source_name: Quiescent mouse CD8 T cells purified from WT control mouse spleen


title: WT CD8 T cells at T0, biological rep1


title: IL7-3 2 2007 high pmt


title: IL7-3 1 2007 high pmt

source_name: Red ripe fruit from tomato IL7-3 variety, biological replica 1, trial 2007


title: WT CD8 T cells at T0, biological rep2


title: IL7-3 1 2007 low pmt


title: Oct4_shutdown_Day4

city: Cambridge

first: Richard

middle: A

last: Young

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

hyb_protocol: Agilent (mouse 4x44k) expression arrays were hybridized according to our lab’s method, which differs slightly from the Agilent standard hybridization protocol. The hybridization cocktail consisted of 825 ng / 1.65 ug cy-dye labeled cRNA for each sample, Agilent hybridization blocking components, and fragmentation buffer. The hybridization cocktails were fragmented at 60°C for 30 minutes, and then Agilent 2X hybridization buffer was added to the cocktail prior to application to the array. The arrays were then hybridized for 16 hours at 60°C in an Agilent rotor oven set to maximum speed.

scan_protocol: Arrays were scanned using an Agilent scanner G2565BA and the data was extracted using Agilent’s Feature Extraction software v10.1.1.1.

data_processing: Data was extracted using Agilent’s Feature Extraction software v10.1.1.1 set to the default two-color gene expression protocol.

label_protocol: Cy-dye labeled cRNA samples were prepared using Agilent’s QuickAmp sample labeling kit. Input was 1 µg total RNA. Briefly, first and second strand cDNA are generated using MMLV-RT enzyme and an oligo-dT based primer. In vitro transcription is performed using T7 RNA polymerase and either cyanine 3-CTP or cyanine 5-CTP, creating a direct incorporation of dye into the cRNA.

growth_protocol: V6.5 (C57BL/6-129) murine ES cells were grown under typical ES conditions on irradiated mouse embryonic fibroblasts (MEFs). For location analysis, cells were grown for two passages off of MEFs, on gelatinized tissue-culture plates.

value: V6.5 embryonic stem cells

tag: background strain

value: shRNA knockdown of Oct4

source_name: Embyonic stem cells


title: M82 2 2007 low pmt

source_name: Red ripe fruit from tomato M82 variety, biological replica 2, trial 2007


title: M82 3 2007 low pmt

source_name: Red ripe fruit from tomato M82 variety, biological replica 3, trial 2007


title: M18: Primary oral squamous cell carcinoma tissue

city: Baltimore

first: Rafael

last: Guerrero-Preston

state: MD

address: 1550 Orleans Street, CRBII, Rm 5M

institute: Johns Hopkins School of Medicine

description: Provided by Hospital Gregorio Marañón, Madrid, Spain

hyb_protocol: Hybridization was performed at 48oC in a incubition oven for 16-20 hours. Chips were washed with wash buffers provided in the kit and assembled and placed into a fluid flow-through station for primer-extension reaction and staining with reagents and buffers provided in the kit.

scan_protocol: Polymer-coated chips were image- processed in Illumina’s iScan scanner.

data_processing: Data were extracted and analyzed using GenomeStudio v1.0 software.

source_name: surgical biopsy

label_protocol: Sample processing was performed by using reagents provided in the Illumina HumanMethylation27 kit and following manufacturer’s manual. Briefly, 4 microlittersl of bisulfite-converted genomic DNA was added to a 0.8 ml 96-well storage plate (Thermo Scientific), denatured in 0.014N sodium hydroxide, neutralized and amplified with kit-provided reagents and buffer for 20-24 hours at 37oC. Samples were fragmented using a kit-provided reagents and buffer at 37oC for one hour and precipitated by adding 2-propanol. Re-suspended samples were denatured in a 96-well plate heat block at 95oC for 20 minutes. 12 microlitters of each sample was loaded onto a 12-sample chip and the chips were assembled into hybridization chamber as instructed in the manual.

growth_protocol: None, biopsies were frozen directly

extract_protocol: Tissue  samples were digested with 1% SDS and 50 μg/mL proteinase K (Boehringer Mannheim) at 48°C overnight, followed by phenol/chloroform extraction and ethanol precipitation of DNA.

treatment_protocol: Frozen in liquid nitrogen and stored at -80° C

value: female

tag: smoker

value: no

tag: disease state

value: oral squamous cell carcinoma


title: Oct4_shutdown_Day5


title: WT CD8 T cells at T6, biological rep2

tag: tissue


title: MM_#44R_Exon1.0ST

description: Myeloma

source_name: Bone marrow

value: multiple myeloma

tag: sample type


title: M4: Oral leukoplakia tissue

value: yes

value: Oral leukoplakia


title: M82 3 2007 high pmt


title: M35: Primary oral squamous cell carcinoma tissue


title: Oct4_shutdown_Day3


title: Med12_KD_Day4

value: shRNA knockdown of Med12


title: M9: Oral leukoplakia tissue

value: male


title: M41: Primary oral squamous cell carcinoma tissue


title: MM_#43R_Exon1.0ST

description: Myeloma

value: bone marrow

value: purified CD138+ plasma cells

value: relapse


title: M8: Oral leukoplakia tissue


title: Med12_KD_Day3


title: M82 1 2007 high pmt

source_name: Red ripe fruit from tomato M82 variety, biological replica 1, trial 2007

value: epicarp and mesocarp


title: M82 1 2007 low pmt

value: var. M82


title: M82 2 2007 high pmt


title: Gox_phase_II_vs_phase_I__exp_III

city: Juelich

first: Tino

last: Polen

state: NRW

address: Wilhelm-Johnen-Str 1

department: IBG-1: Biotechnology

country: Germany

institute: Forschungszentrum Jülich GmbH

hyb_protocol: Preparation of the slides was performed in 50 ml Falcon tubes. All reagents were from the OpArray system from Eurofins MWG Operon. Slides were incubated at 42°C in Pre-Hyb solution for 1 h, then the slides were transferred to Wash 1 solution (1.25 ml Wash B and 48.75 ml H2O) and incubated for 5 min at 37°C. Slides were washed with H2O and dried in a centrifuge (Sigma Laboratory Centrifuge 4K15C, 5 min, 521 x g). Hybridization was carried out for 16–18 h at 42°C using a MAUI hybridization system (BioMicro Systems, Salt Lake City, USA).

scan_protocol: For post-hybridization, slides were washed at 37°C in Wash 2 solution (5 ml Wash A, 2.5 ml Wash B and 42.5 ml H2O) and Wash 3 solution (5 ml Wash A and 45 ml H2O) for 10 minutes each. Slides were rotated in Wash 4 solution (1 ml Wash A and 49 ml H2O) for 5 min at room temperature. Finally, the slides were dried by centrifugation (Sigma Laboratory Centrifuge 4K15C, 5 min, 521 x g). Fluorescence of the hybridized DNA microarrays was determined at 532 nm (Cy3-dUTP) and 635 nm (Cy5-dUTP) at 10 µm resolution with a GenePix 4000B laser scanner (Molecular Devices, Sunnyvale, CA, USA).

data_processing: Quantitative image analysis was carried out using GenePix image analysis software and results were saved as GPR-file (GenePix Pro 6.0). For data normalization, GPR-files were processed using the BioConductor/R-packages limma and marray (http://www.bioconductor.org). For further analysis, the processed and loess-normalized data as well as detailed experimental information according to MIAME (Brazma et al., 2001) were stored in the in-house microarray database (Polen and Wendisch, 2004). DNA microarray experiments for growth phase II versus phase I were repeated independently in three biological replicates. To filter for differentially expressed genes, the following criteria had to be fulfilled: (i) flags ≥0 (GenePix Pro 6.0), (ii) signal/noise≥5 for Cy5 (F635Median/B635Median, GenePix Pro 6.0) or Cy3 (F532Median/B532Median, GenePix Pro 6.0), (iii) mRNA ratio≥2.0 (lower ones allowed in the case of operons) or≤0.5 (higher ones allowed in the case of operons), (iv) in a paired Student’s t-test, relative RNA levels had to be significantly different from all spots(p < 0.05).

organism: Gluconobacter oxydans 621H

label_protocol: cDNA synthesis for DNA microarray analysis was performed as described (Polen et al., 2007). 25 µg RNA was used for random hexamer-primed synthesis of fluorescently-labeled cDNA with the fluorescent nucleotide analogues Cy3-dUTP and Cy5-dUTP (GE Healthcare, Freiburg, Germany). The mixture contained 3 µl 1 mM Cy3-dUTP or Cy5-dUTP, 3 µl 0.1 M DTT, 6 µl 5x first strand buffer (Invitrogen, Karlsruhe, Germany), 0.6 µl dNTP-mix (25 mM each of dATP, dCTP, and dGTP and 10 mM dTTP) and 2 µl Superscript II reverse transcriptase (Invitrogen, Darmstadt, Germany). The mixture was incubated for 10 min at room temperature and 110 min at 42 °C, stopped by addition of 10 μl 0.1 N NaOH, incubated for 10 min at 70 °C, and then neutralized by addition of 10 μl 0.1 N HCl. The sensors were purified by washing three times with water on a Microcon column (Millipore, YM-30).

growth_protocol: For comparing genome-wide mRNA levels and in vitro activities of selected enzymes in the first and second growth phase, cells were harvested for RNA isolation and preparation of cell-free extracts after 6.5 h (OD600 = 2.2, sample point I) and after 14 h (OD600 = 6.0, sample point II), respectively.  Gluconobacter oxydans DSM 2343 (ATCC 621H) was obtained from the Deutsche Sammlung von Mikroorganismen und Zellkulturen (Braunschweig, Germany). Precultures of the strain were cultivated on complex medium containing 5 g l-1 yeast extract, 2.5 g l-1 MgSO4 x 7 H20, 1 g l-1 (NH4)2SO4, 1 g l-1 KH2PO4, 0.5 g l-1 glycerol and 8% (w/v) sorbitol. The initial pH value of the medium was 6.0. G. oxydans possesses a natural resistance towards cefoxitin; as a precaution to prevent bacterial contaminations, cefoxitin was added to the media at a concentration of 50 μg ml-1. Precultures were grown in baffled shaking flasks at 30°C and 140 rpm. For DNA microarray analysis and enzyme activity measurements, cells were cultivated in 250 ml of the same medium containing 8% glucose instead of sorbitol in a bioreactor system (DASGIP, Jülich, Germany) composed of four 400-ml vessels, each equipped with electrodes for measuring the dissolved oxygen concentration (DO) and the pH value. The system allows to constantly control these two parameters. The pH was kept at pH 6.0 by automatic titration of 2 M NaOH. The oxygen availability was kept constant at 15% DO by mixing air, O2 and N2.

extract_protocol: 25 ml of a G. oxydans culture was added to 25 g of crushed ice in a Falcon tube which had been pre-cooled in liquid nitrogen. The cells were sedimented by centrifugation for 3 min at 4 °C and 10,397 x g and after removal of the supernatant the tube with the cell pellet was immersed in liquid nitrogen and then stored at -70°C. For total RNA preparation, the RNeasy system (Qiagen, Hilden, Germany) was used. The cell pellet was resuspended in 700 µl of RLT buffer containing 7 µl ß-mercaptoethanol and transferred to two vials each containing 0.5 g of 0.1-mm diameter zirconium silica beads (Roth, Karlsruhe, Germany). Cells were disrupted by 4 x 30 s bead beating using a Silamat S5 (Ivoclar Vivadent, Ellwangen, Germany). The lysate was centrifuged at 8,000 x g for 2 min and the supernatant was mixed with 250 µl ethanol (-20 °C). RNA was extracted with two RNeasy mini-columns following the manufacturer’s instructions. DNA digestion was performed for 20 min on column by adding 30 Kuniz U RNase-free DNase. RNA concentration and quality were checked photometrically and on formaldehyde gels according to standard procedures (Sambrook and Russell, 2001).

tag: phase


title: M16: Normal oral mucosa

label_protocol: Sample processing was performed by using reagents provided in the Illumina HumanMethylation27 kit and following manufacturer’s manual. Briefly, 4 micro liters of bisulfite-converted genomic DNA was added to a 0.8 ml 96-well storage plate (Thermo Scientific), denatured in 0.014N sodium hydroxide, neutralized and amplified with kit-provided reagents and buffer for 20-24 hours at 37°C. Samples were fragmented using a kit-provided reagents and buffer at 37°C for one hour and precipitated by adding 2-propanol. Re-suspended samples were denatured in a 96-well plate heat block at 95oC for 20 minutes. 12 microlitters of each sample was loaded onto a 12-sample chip and the chips were assembled into hybridization chamber as instructed in the manual.

value: normal


title: M38: Normal oral mucosa


title: Gox_phase_II_vs_phase_I__exp_I


title: M6: Oral leukoplakia tissue


title: MM_#24_Nsp

description: Diagnosis

source_name: Bone marrow and/or blood

tag: patient id

tag: cells

value: Diagnosis


title: M5: Primary oral squamous cell carcinoma tissue


title: Gox_phase_II_vs_phase_I__exp_II


title: M12: Normal oral mucosa


title: M10: Normal oral mucosa


title: Cybrid cells_Wild_rep2_norm1

status: Public on Feb 12 2013

city: Pohang, Gyungbuk

first: Sehyun

last: Chae

address: San 31, Hyoja-Dong, Nam-Gu

department: Department of Interdisciplinary Bioscience and Bioengineering(I-BIO)

institute: POSTECH

description:
wild
SAMPLE 2 (4616443114_E)

scan_protocol: BeadStation 500 System (Illumina, San Diego, CA)

data_processing: The data were normalised using quantile normalization method with beadarray version 1.10 and lumi version 1.8.3 in R/Bioconductor package. The three replicates of the wild type and mutant cybrid cell Samples were normalized twice. Therefore, the 11 Samples of non-normalized data resulted in 17 normlalized data VALUES.

source_name: Cybrid cells_Wild

label_protocol: Refer to the Illumina Gene Expression System Manual

growth_protocol: Media: DMEM and 10% Fetal Bovine Serum

extract_protocol: RNA was extracted with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Mutant cells (sample 10,11) were treated with 9-cis retinoic acid for 12 hrs

tag: cell line

value: cybrid cell line with 3243A homoplasmy (Wild)


title: Blood, Subject 34350054, 1204.5 hours since injury

city: Boston

first: Wenzhong Xiao

address: 55 Fruit Street, GRV 1302

department: Department of Surgery

institute: Massachusetts General Hospital

hyb_protocol: Following fragmentation, 10 ug of cRNA was hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station FS 4500, and used the standard solutions recommended by Affymetrix

scan_protocol: GeneChips were scanned using the Affymetrix Scanner G3000

data_processing: Affymetrix Power Tools version 1.8.6 RMA model

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 2 ug RNA (Expression Analysis Technical Manual rev 3, 2002, Affymetrix)

extract_protocol: Total RNA was purified using the Rneasy RNA Isolation kit standard protocol (Qiagen, Valencia, CA)

treatment_protocol: White blood cells were separated using a modified buffy coat isolation and red blood cell lysis method. This protocol recovers the plasma fraction, lyses RBCs, and allows recovery of the white blood cell fraction, eliminating the need to recover the buffy coat interfacial layer.

value: White blood cells

tag: Sex

value: M

tag: age


title: Blood, Subject 34350054, 73.1 hours since injury


title: Cybrid cells_Hetero_rep1_norm1

description:
hetero
SAMPLE 4 (4616443114_G)

source_name: Cybrid cells_Hetero

value: cybrid cell line with 3243A/G heteroplasmy (Hetero)


title: Cybrid cells_Wild_rep3_norm1

description:
wild
SAMPLE 3 (4616443114_F)


title: Cybrid cells_Mutant_rep2_norm2

description:
mutant
SAMPLE 8 (4616443114_K)

source_name: Cybrid cells_Mutant

value: cybrid cell line with 3243G homoplasmy (Mutant)


title: Blood, Subject 34195320, 417.3 hours since injury


title: Cybrid cells_Hetero_rep3_norm1

description:
hetero
SAMPLE 6 (4616443114_I)


title: Blood, Subject 34195320, 86.2 hours since injury


title: Blood, Subject 33846557, 41.2 hours since injury

value: F


title: Cybrid cells_Mutant_rep1_norm2

description:
mutant
SAMPLE 7 (4616443114_J)


title: Cybrid cells_Hetero_rep2_norm1

description:
hetero
SAMPLE 5 (4616443114_H)


title: Blood, Subject 34099766, 26.2 hours since injury


title: Cybrid cells_Mutant_rep3_norm2

description:
mutant
SAMPLE 9 (4616443114_L)


title: Blood, Subject 34264195, 42 hours since injury

source_name: Subject 34264195, 42 hours since injury


title: Cybrid cells_Mutant_rep2_norm1

description:
mutant
SAMPLE 8 (4616443114_K)


title: Cybrid cells_Wild_rep1_norm2

description:
wild
SAMPLE 1 (4616443114_D)


title: Blood, Subject 34099766, 169.1 hours since injury


title: Cybrid cells_Wild_rep3_norm2

description:
wild
SAMPLE 3 (4616443114_F)


title: Cybrid cells_Mutant_RA treat_rep2_norm2

description:
Mutant cells were treated with 9-cis retinoic acid for 12 hrs
SAMPLE 11 (5139124007_L)

source_name: Cybrid cells_Mutant_RA treat


title: Blood, Subject 34195320, 226.3 hours since injury


title: Blood, Subject 34568138, 42.8 hours since injury


title: Blood, Subject 33713774, 62.9 hours since injury


title: Cybrid cells_Mutant_rep3_norm1

description:
mutant
SAMPLE 9 (4616443114_L)


title: Cybrid cells_Mutant_RA treat_rep1_norm2

description:
Mutant cells were treated with 9-cis retinoic acid for 12 hrs
SAMPLE 10 (5139124007_J)


title: Cybrid cells_Wild_rep2_norm2

description:
wild
SAMPLE 2 (4616443114_E)


title: Blood, Subject 33632584, 68.1 hours since injury


title: Cybrid cells_Mutant_rep1_norm1

description:
mutant
SAMPLE 7 (4616443114_J)


title: Cybrid cells_Wild_rep1_norm1

description:
wild
SAMPLE 1 (4616443114_D)


title: Blood, Subject 33595468, 277.8 hours since injury


title: Blood, Subject 33557829, 46 hours since injury

source_name: Subject 33557829, 46 hours since injury


title: Blood, Subject 33104028, 6391.8 hours since injury


title: Blood, Subject 33167119, 6452 hours since injury


title: Blood, Subject 33091416, 499.6 hours since injury


title: Blood, Subject 33091416, 10081.5 hours since injury


title: Blood, Subject 33167119, 906.1 hours since injury


title: Blood, Subject 33104028, 464.8 hours since injury


title: Blood, Subject 33104028, 175.8 hours since injury


title: Blood, Subject 33167119, 40.6 hours since injury


title: Blood, Subject 33595468, 38.1 hours since injury


title: Blood, Subject 33091416, 43.8 hours since injury


title: Blood, Subject 34330981, 67.3 hours since injury


title: Blood, Subject 32424115, 18.6 hours since injury


title: Blood, Subject 33104028, 80.4 hours since injury


title: Blood, Subject 32815928, 288.1 hours since injury


title: Blood, Subject 33167119, 329.3 hours since injury


title: Blood, Subject 33091416, 1676.8 hours since injury


title: Blood, Subject 32441607, 295.8 hours since injury


title: Blood, Subject 32424115, 161.7 hours since injury


title: Blood, Subject 32424115, 378 hours since injury


title: Blood, Subject 32815928, 745.1 hours since injury


title: Blood, Subject 32424115, 858 hours since injury


title: Blood, Subject 33392968, 15.5 hours since injury


title: Blood, Subject 33104028, 799.4 hours since injury


title: Blood, Subject 32441607, 59.9 hours since injury


title: Blood, Subject 33069778, 46.5 hours since injury


title: Blood, Subject 32378805, 36.1 hours since injury


title: Blood, Subject 32136361, 44.4 hours since injury


title: Blood, Subject 31922467, 760.6 hours since injury


title: Blood, Subject 33167119, 666 hours since injury


title: Blood, Subject 31702260, 477.9 hours since injury


title: Blood, Subject 33104028, 32.7 hours since injury


title: Blood, Subject 31922467, 5.2 hours since injury


title: Blood, Subject 30522507, 42 hours since injury

source_name: Subject 30522507, 42 hours since injury


title: Blood, Subject 31922467, 62 hours since injury

source_name: Subject 31922467, 62 hours since injury


title: Blood, Subject 31889359, 21 hours since injury

source_name: Subject 31889359, 21 hours since injury


title: Blood, Subject 31702260, 815.7 hours since injury


title: Blood, Subject 31702260, 141.6 hours since injury


title: Blood, Subject 30284407, 26.5 hours since injury


title: Blood, Subject 31889359, 13.1 hours since injury


title: Blood, Subject 30349701, 9.8 hours since injury


title: Blood, Subject 31448162, 49.7 hours since injury


title: Blood, Subject 31702260, 645.9 hours since injury


title: Blood, Subject 30530860, 7.2 hours since injury


title: Blood, Subject 30349701, 325.7 hours since injury


title: Blood, Subject 30530860, 121.8 hours since injury


title: Blood, Subject 31702260, 310.3 hours since injury


title: Blood, Subject 30594569, 60.4 hours since injury


title: Blood, Subject 30530860, 505.3 hours since injury


title: Blood, Subject 31922467, 136.3 hours since injury


title: Blood, Subject 30840607, 1121.3 hours since injury


title: Blood, Subject 30349701, 84.1 hours since injury


title: Blood, Subject 30284407, 315 hours since injury


title: Blood, Subject 29019013, 420.5 hours since injury


title: Blood, Subject 30840607, 776.9 hours since injury


title: Blood, Subject 30840607, 104.8 hours since injury


title: Blood, Subject 29019013, 997.7 hours since injury


title: Blood, Subject 31922467, 254.9 hours since injury


title: Blood, Subject 29607776, 10202.3 hours since injury


title: Blood, Subject 28985434, 308.2 hours since injury


title: Blood, Subject 29538118, 52.9 hours since injury


title: Blood, Subject 28985434, 142.7 hours since injury


title: Blood, Subject 29019013, 15 hours since injury

source_name: Subject 29019013, 15 hours since injury


title: Blood, Subject 28943649, 24.8 hours since injury


title: Blood, Subject 28985434, 46.9 hours since injury


title: Blood, Subject 28943649, 452.6 hours since injury


title: Blood, Subject 28943649, 1028.5 hours since injury


title: Blood, Subject 28789224, 11174.7 hours since injury


title: Blood, Subject 28746981, 1440.3 hours since injury


title: Blood, Subject 28943649, 190.1 hours since injury


title: Blood, Subject 28406401, 440 hours since injury


title: Blood, Subject 28406401, 271.2 hours since injury


title: Blood, Subject 27544607, 43.3 hours since injury


title: Blood, Subject 28943649, 620.9 hours since injury


title: Blood, Subject 28746981, 43 hours since injury

source_name: Subject 28746981, 43 hours since injury


title: Blood, Subject 28789224, 324.3 hours since injury


title: Blood, Subject 28182892, 85.3 hours since injury


title: Blood, Subject 28789224, 4643.3 hours since injury


title: Blood, Subject 27660480, 68.5 hours since injury


title: Blood, Subject 27251796, 90.8 hours since injury


title: Blood, Subject 28789224, 12.8 hours since injury


title: Blood, Subject 27660480, 91.9 hours since injury


title: Blood, Subject 27660480, 17.3 hours since injury


title: Blood, Subject 28182892, 348.9 hours since injury


title: Blood, Subject 27544607, 549.2 hours since injury


title: Blood, Subject 27251796, 498.6 hours since injury


title: Blood, Subject 27217023, 69 hours since injury

source_name: Subject 27217023, 69 hours since injury


title: Blood, Subject 27660480, 305 hours since injury


title: Blood, Subject 27110791, 30.3 hours since injury


title: Blood, Subject 27116902, 64.5 hours since injury


title: Blood, Subject 27036689, 451.6 hours since injury


title: Blood, Subject 27110791, 1111.7 hours since injury


title: Blood, Subject 26380544, 9501.8 hours since injury


title: Blood, Subject 26085918, 225.9 hours since injury


title: Blood, Subject 27036689, 21 hours since injury

source_name: Subject 27036689, 21 hours since injury


title: Blood, Subject 27110791, 12 hours since injury

source_name: Subject 27110791, 12 hours since injury


title: Blood, Subject 25942786, 673.6 hours since injury


title: Blood, Subject 26697942, 325.4 hours since injury


title: Blood, Subject 26697942, 3806.7 hours since injury


title: Blood, Subject 25911536, 37.4 hours since injury


title: Blood, Subject 25911536, 1550.6 hours since injury


title: Blood, Subject 26110157, 473.4 hours since injury


title: Blood, Subject 26697942, 6498.3 hours since injury


title: Blood, Subject 25636027, 49.1 hours since injury


title: Blood, Subject 26380544, 71.3 hours since injury


title: Blood, Subject 25880698, 41.3 hours since injury


title: Blood, Subject 26110157, 18.4 hours since injury


title: Blood, Subject 27036689, 266.8 hours since injury


title: Blood, Subject 25911536, 7124 hours since injury


title: Blood, Subject 25942786, 72.7 hours since injury


title: Blood, Subject 25749143, 179.4 hours since injury


title: Blood, Subject 26085918, 730 hours since injury


title: Blood, Subject 25942786, 334.6 hours since injury


title: Blood, Subject 25394925, 9 hours since injury

source_name: Subject 25394925, 9 hours since injury


title: Blood, Subject 26351698, 61.9 hours since injury


title: Blood, Subject 25911536, 302.4 hours since injury


title: Blood, Subject 25747339, 69.1 hours since injury


title: Blood, Subject 26697942, 86.6 hours since injury


title: Blood, Subject 25372351, 1005.3 hours since injury


title: Blood, Subject 24999077, 43.9 hours since injury


title: Blood, Subject 25372351, 694.5 hours since injury


title: Blood, Subject 25036359, 60 hours since injury

source_name: Subject 25036359, 60 hours since injury


title: Blood, Subject 24871077, 58.4 hours since injury


title: Blood, Subject 25036359, 1205.5 hours since injury


title: Blood, Subject 25372351, 454.9 hours since injury


title: Blood, Subject 24892946, 317.5 hours since injury


title: Blood, Subject 24892946, 84.1 hours since injury


title: Blood, Subject 25372351, 23 hours since injury

source_name: Subject 25372351, 23 hours since injury


title: Blood, Subject 24918152, 35 hours since injury

source_name: Subject 24918152, 35 hours since injury


title: Blood, Subject 25036359, 4829.2 hours since injury


title: Blood, Subject 25033914, 61.8 hours since injury


title: Blood, Subject 24570957, 61 hours since injury

source_name: Subject 24570957, 61 hours since injury


title: Blood, Subject 25036359, 12.3 hours since injury


title: Blood, Subject 25036359, 556.8 hours since injury


title: Blood, Subject 24570957, 296.6 hours since injury


title: Blood, Subject 24892946, 11.3 hours since injury


title: Blood, Subject 25033914, 512.3 hours since injury


title: Blood, Subject 24062138, 137.3 hours since injury


title: Blood, Subject 24062138, 951.1 hours since injury


title: Blood, Subject 24062138, 15.4 hours since injury


title: Blood, Subject 24062138, 2875.1 hours since injury


title: Blood, Subject 24062138, 448.9 hours since injury


title: Blood, Subject 25372351, 285.7 hours since injury


title: Blood, Subject 24918152, 440.8 hours since injury


title: Blood, Subject 24892946, 389.3 hours since injury


title: Blood, Subject 24148923, 441.7 hours since injury


title: Blood, Subject 24696536, 53.8 hours since injury


title: Blood, Subject 24838215, 11.8 hours since injury


title: Blood, Subject 23512129, 90.7 hours since injury


title: Blood, Subject 23696249, 309.3 hours since injury


title: Blood, Subject 23456434, 1.7 hours since injury


title: Blood, Subject 23480950, 43 hours since injury

source_name: Subject 23480950, 43 hours since injury


title: Blood, Subject 23512129, 522.4 hours since injury


title: Blood, Subject 24012372, 46 hours since injury

source_name: Subject 24012372, 46 hours since injury


title: Blood, Subject 23924385, 60.2 hours since injury


title: Blood, Subject 23924385, 465.7 hours since injury


title: Blood, Subject 23435653, 20.3 hours since injury


title: Blood, Subject 23720011, 236.8 hours since injury


title: Blood, Subject 23924385, 12.7 hours since injury


title: Blood, Subject 23720011, 68.3 hours since injury


title: Blood, Subject 23480950, 111.2 hours since injury


title: Blood, Subject 23924385, 224.3 hours since injury


title: Blood, Subject 23696249, 525.2 hours since injury


title: Blood, Subject 23456434, 288.7 hours since injury


title: Blood, Subject 23479588, 29.8 hours since injury


title: Blood, Subject 23040658, 4430.3 hours since injury


title: Blood, Subject 23040658, 1196.8 hours since injury


title: Blood, Subject 22756017, 486.2 hours since injury


title: Blood, Subject 22988589, 616.3 hours since injury


title: Blood, Subject 23040658, 2563.9 hours since injury


title: Blood, Subject 23040658, 39.3 hours since injury


title: Blood, Subject 22730579, 41.3 hours since injury


title: Blood, Subject 22756017, 31 hours since injury

source_name: Subject 22756017, 31 hours since injury


title: Blood, Subject 22369005, 1208.3 hours since injury


title: Blood, Subject 23357070, 64.5 hours since injury


title: Blood, Subject 22756017, 126.3 hours since injury


title: Blood, Subject 22988589, 277 hours since injury


title: Blood, Subject 22369005, 536.3 hours since injury


title: Blood, Subject 23357070, 23 hours since injury

source_name: Subject 23357070, 23 hours since injury


title: Blood, Subject 22242375, 70 hours since injury

source_name: Subject 22242375, 70 hours since injury


title: Blood, Subject 22029401, 8683.2 hours since injury


title: Blood, Subject 22242375, 309 hours since injury


title: Blood, Subject 22076971, 23.8 hours since injury


title: Blood, Subject 22016242, 641.7 hours since injury


title: Blood, Subject 22029401, 1602.8 hours since injury


title: Blood, Subject 22016242, 1313.8 hours since injury


title: Blood, Subject 22016242, 22 hours since injury

source_name: Subject 22016242, 22 hours since injury


title: Blood, Subject 22016242, 88.2 hours since injury


title: Blood, Subject 22029401, 426.8 hours since injury


title: Blood, Subject 22076971, 257.9 hours since injury


title: Blood, Subject 25749143, 36.2 hours since injury


title: Blood, Subject 22242375, 46 hours since injury

source_name: Subject 22242375, 46 hours since injury


title: Blood, Subject 21278752, 904.2 hours since injury


title: Blood, Subject 22016242, 329.7 hours since injury


title: Blood, Subject 22988589, 17.4 hours since injury


title: Blood, Subject 21278752, 70.7 hours since injury


title: Blood, Subject 21471206, 230 hours since injury


title: Blood, Subject 21278752, 567.4 hours since injury


title: Blood, Subject 21278752, 22.8 hours since injury


title: Blood, Subject 21146063, 470.6 hours since injury


title: Blood, Subject 20577644, 347.2 hours since injury


title: Blood, Subject 20966598, 1288.5 hours since injury


title: Blood, Subject 20966598, 9258.8 hours since injury


title: Blood, Subject 20966598, 87 hours since injury

source_name: Subject 20966598, 87 hours since injury


title: Blood, Subject 21278752, 14.9 hours since injury


title: Blood, Subject 21146063, 86.2 hours since injury


title: Blood, Subject 20577644, 11.8 hours since injury


title: Blood, Subject 20528565, 1455.8 hours since injury


title: Blood, Subject 20475144, 473.9 hours since injury


title: Blood, Subject 20225565, 241.5 hours since injury


title: Blood, Subject 20528565, 7075.9 hours since injury


title: Blood, Subject 20475144, 65.9 hours since injury


title: Blood, Subject 20312203, 546.5 hours since injury


title: Blood, Subject 20966598, 3546.9 hours since injury


title: Blood, Subject 20225565, 52.2 hours since injury


title: Blood, Subject 20528565, 280 hours since injury


title: Blood, Subject 20304154, 53.2 hours since injury


title: Blood, Subject 20225565, 33.3 hours since injury


title: Blood, Subject 19627978, 151 hours since injury


title: Blood, Subject 19705244, 4.8 hours since injury


title: Blood, Subject 19627978, 13.6 hours since injury


title: Blood, Subject 19495512, 773.1 hours since injury


title: Blood, Subject 19627978, 486.4 hours since injury


title: Blood, Subject 19582126, 54.4 hours since injury


title: Blood, Subject 20225565, 1153.4 hours since injury


title: Blood, Subject 19630206, 64.3 hours since injury


title: Blood, Subject 19107943, 593.8 hours since injury


title: Blood, Subject 19495512, 79.2 hours since injury


title: Blood, Subject 19705244, 603.1 hours since injury


title: Blood, Subject 18715343, 9.4 hours since injury


title: Blood, Subject 18593696, 257.7 hours since injury


title: Blood, Subject 19705244, 214.7 hours since injury


title: Blood, Subject 17790776, 19 hours since injury

source_name: Subject 17790776, 19 hours since injury


title: Blood, Subject 19495512, 2623 hours since injury


title: Blood, Subject 17790776, 108.5 hours since injury


title: Blood, Subject 22369005, 32.3 hours since injury


title: Blood, Subject 18191545, 13.8 hours since injury


title: Blood, Subject 19107943, 284.3 hours since injury


title: Blood, Subject 18593696, 18.1 hours since injury


title: Blood, Subject 17525509, 712 hours since injury


title: Blood, Subject 18238815, 75.8 hours since injury


title: Blood, Subject 18191545, 347 hours since injury


title: Blood, Subject 17525509, 7101.8 hours since injury


title: Blood, Subject 18252404, 9765.8 hours since injury


title: Blood, Subject 17525509, 4220 hours since injury


title: Blood, Subject 18252404, 1515 hours since injury


title: Blood, Subject 17149385, 1289.5 hours since injury


title: Blood, Subject 16984675, 82 hours since injury

source_name: Subject 16984675, 82 hours since injury


title: Blood, Subject 17149385, 41.9 hours since injury


title: Blood, Subject 17525509, 88 hours since injury

source_name: Subject 17525509, 88 hours since injury


title: Blood, Subject 16855123, 1697.1 hours since injury


title: Blood, Subject 16984675, 62.9 hours since injury


title: Blood, Subject 17149385, 8874.6 hours since injury


title: Blood, Subject 16984675, 16.8 hours since injury


title: Blood, Subject 17149385, 282.3 hours since injury


title: Blood, Subject 16855123, 37.8 hours since injury


title: Blood, Subject 16164355, 32 hours since injury

source_name: Subject 16164355, 32 hours since injury


title: Blood, Subject 16159507, 26.7 hours since injury


title: Blood, Subject 16164355, 655.1 hours since injury


title: Blood, Subject 15859222, 31 hours since injury

source_name: Subject 15859222, 31 hours since injury


title: Blood, Subject 16669591, 221.2 hours since injury


title: Blood, Subject 16855123, 613.6 hours since injury


title: Blood, Subject 16669591, 29.3 hours since injury


title: Blood, Subject 15431623, 8750.4 hours since injury


title: Blood, Subject 15431623, 38.5 hours since injury


title: Blood, Subject 15431623, 3324.8 hours since injury


title: Blood, Subject 15998431, 38.2 hours since injury


title: Blood, Subject 14583689, 27.5 hours since injury


title: Blood, Subject 16435116, 67.8 hours since injury


title: Blood, Subject 15770499, 500.5 hours since injury


title: Blood, Subject 14570191, 14 hours since injury

source_name: Subject 14570191, 14 hours since injury


title: Blood, Subject 15770499, 358.8 hours since injury


title: Blood, Subject 14550002, 418.7 hours since injury


title: Blood, Subject 14570191, 205.4 hours since injury


title: Blood, Subject 15770499, 22.1 hours since injury


title: Blood, Subject 15431623, 349.8 hours since injury


title: Blood, Subject 15770499, 717.1 hours since injury


title: Blood, Subject 15474671, 9087.3 hours since injury


title: Blood, Subject 21471206, 62.5 hours since injury


title: Blood, Subject 14412351, 381.3 hours since injury


title: Blood, Subject 14412351, 1943.3 hours since injury


title: Blood, Subject 14412351, 6528.3 hours since injury


title: Blood, Subject 14550002, 57.8 hours since injury


title: Blood, Subject 14347553, 443.5 hours since injury


title: Blood, Subject 14307976, 16.6 hours since injury


title: Blood, Subject 14347553, 35.3 hours since injury


title: Blood, Subject 14101191, 49.7 hours since injury


title: Blood, Subject 13973468, 57.5 hours since injury


title: Blood, Subject 13760816, 65.2 hours since injury


title: Blood, Subject 13951326, 18.6 hours since injury


title: Blood, Subject 13387725, 655 hours since injury


title: Blood, Subject 13578460, 16.8 hours since injury


title: Blood, Subject 13627200, 71.5 hours since injury


title: Blood, Subject 13339157, 11.9 hours since injury


title: Blood, Subject 13209373, 48.2 hours since injury


title: Blood, Subject 13919177, 1022.3 hours since injury


title: Blood, Subject 13627200, 47 hours since injury

source_name: Subject 13627200, 47 hours since injury


title: Blood, Subject 13132431, 834 hours since injury


title: Blood, Subject 13132431, 1001.9 hours since injury


title: Blood, Subject 13341861, 37.3 hours since injury


title: Blood, Subject 13627200, 22.8 hours since injury


title: Blood, Subject 13919177, 17.7 hours since injury


title: Blood, Subject 13919177, 686.8 hours since injury


title: Blood, Subject 12892719, 41.8 hours since injury


title: Blood, Subject 13216633, 24.7 hours since injury


title: Blood, Subject 12823756, 488.6 hours since injury


title: Blood, Subject 13387725, 77.7 hours since injury


title: Blood, Subject 12823756, 4.9 hours since injury


title: Blood, Subject 12823756, 50.5 hours since injury


title: Blood, Subject 12747936, 137.1 hours since injury


title: Blood, Subject 13216633, 360.6 hours since injury


title: Blood, Subject 13009418, 419 hours since injury


title: Blood, Subject 12823756, 319.9 hours since injury


title: Blood, Subject 13951326, 251.9 hours since injury


title: Blood, Subject 12747936, 113.2 hours since injury


title: Blood, Subject 12627768, 41.1 hours since injury


title: Blood, Subject 12747936, 89.6 hours since injury


title: Blood, Subject 12286546, 3974.3 hours since injury


title: Blood, Subject 12286546, 449.8 hours since injury


title: Blood, Subject 12576618, 386.8 hours since injury


title: Blood, Subject 12627768, 448.7 hours since injury


title: Blood, Subject 12286546, 1526.3 hours since injury


title: Blood, Subject 12286546, 110.5 hours since injury


title: Blood, Subject 12627768, 136 hours since injury


title: Blood, Subject 12286546, 19.5 hours since injury


title: Blood, Subject 12228679, 7647.3 hours since injury


title: Blood, Subject 12097532, 1230.3 hours since injury


title: Blood, Subject 12286546, 280 hours since injury


title: Blood, Subject 12097532, 705.3 hours since injury


title: Blood, Subject 12097532, 78.8 hours since injury


title: Blood, Subject 11916003, 14.3 hours since injury


title: Blood, Subject 11878509, 461.4 hours since injury


title: Mature leaf 8WAT, severe water deficit, PD inoculated, biological rep 2 [27ID2L]

city: Davis

first: Douglas

middle: R

last: Cook

state: California

address: One Shields Aave

institute: University of California-Davis

hyb_protocol: Conducted at UC-Davis Genome Center according to Affymetrix protocol

data_processing: Probe signal intensities in *.DAT files were processed with the Affymetrix GCOS version 1.2 software package. Resulting *.CEL files were imported into the Bioconductor software suite (http://www.bioconductor.org, Gentleman et al., 2004) in R (Ihaka and Gentleman, 1996) for data quality control. Files were then analyzed using the AffylmGUI package procedure for time course experiments as described by Smyth (2005). The GC Robust Multichip Analysis (RMA) (Wu et al., 2004) in AffylmGUI was used for background adjustment, cross-chip quantile normalization and median polish summarization of probe level expression data using probe affinity data. Differentially expressed genes were identified using a moderated t-test with Benjamini-Hochberg adjustment for false discovery rate (Smyth, 2004). A standard linear model of the expression data for Limma was created and all possible contrasts within an irrigation treatment were calculated to identify differentially expressed genes. Two different sets of cut-offs were set to identify two distinct sets of differentially expressed genes. Genes in the first group have a log2 ratio (M) greater than or equal to 1 and a p-adjusted by false discovery rate (P) smaller than or equal to 0.05. Genes passing the more stringent cut-offs of the second group have an M smaller than 1, a P value smaller or equal to 0.01. Genes in both groups must have an empirical Bayes log odds of differential expression (B) greater than or equal to 0. Finally, a core set of differentially expressed genes was created by pulling together genes that were identified as differentially expressed in at least one of the performed contrasts. This final core set was used for subsequent expression analysis and interpretation.

organism: Vitis vinifera

source_name: Mature leaf from 2 year old-vine 8WAT, severe water deficit, PD inoculated

label_protocol: Four ug of total RNA was used to make biotin-labeled cRNA targets using the One-Cycle cDNA Synthesis Kit (Affymetrix, Santa Clara, CA) followed by cDNA cleanup, biotin labeling and fragmentation according to Affymetrix’s instructions.

growth_protocol: Two-year-old vines (Vitis vinifera L. cv. Cabernet sauvignon clone 8 on Freedom rootstock) were grown for one year under greenhouse conditions in 10” pots containing 50% by volume of Turface fritted clay (Profile products LLC, Buffalo Grove, USA) and 50% Pro-Mix BX peat moss (Premier Tech Ltd, Quebec, Canada) amended with 0.2 Kg per vine of 18-6-12 Multicote fertilizer (N-P-K; Schultz Co., Bridgeton, USA). Prior to bud break, plants were moved to growth chambers with a 14/10 hr light/dark period at a PPFD intensity of approximately 1000 mmol photons m-2 s-1; a 25/20 oC daily air temperature regime; and a 50/80% relative humidity for the photo and nictoperiod, respectively. Plants were organized in a block design of three rows with all treatments randomized in each row. Subsequent to a 4-week acclimation period, grapevines were pruned to produce a uniform shoot architecture consisting of two shoots per plant and ten leaves per shoot. Approximately two weeks after full bloom, the shoot apical meristems were removed to prevent further growth. Laterals were removed throughout the season to contain growth and ensure a uniform light environment. Vines were watered on a daily basis with nutrient solution (0.11 g/L of GrowMore 4-18-38, boron removed) using pressure compensated drip emitters, with watering rates depending on imposed treatment. Daily water uptake was calculated using a mini-lysimeter on plants watered to field capacity (100% water usage).

extract_protocol: Four weeks after the initiation of treatment, the third and fourth leaves were harvested from three plants of each treatment type and used for pre-symptomatic transcriptional analysis. At eight weeks following the treatments, when symptoms were evident on infected individuals, the 5th and 6th leaves from the same grapevines were harvested for the post-symptomatic transcriptional analysis. Total RNA was isolated as described in Iandolino et al (2004).

treatment_protocol: The estimated 100% water usage was used to establish treatment watering rates: 100% (water sufficient), 50% (moderate stress) and 25% (severe stress). Two different growth chambers were used to house the two different irrigation level experiments: a moderate water deficit (MD, vines irrigated at 50% of estimated daily vine water use) and a severe water deficit (SD, vines irrigated at 25% of estimated daily vine water use). Five different treatments were imposed in each chamber: a non-inoculated control (N), a mock inoculated control (vines inoculated with deionized water, M) and a PD inoculated treatment (I), all of them irrigated at a 100% of estimated daily vine water use. In addition, a PD inoculated (ID) and a non-inoculated (D) treatment was irrigated at the pre-established fraction of full daily water use. Each treatment was replicated 4 times. X. fastidiosa strain Fetzer was grown at 28 C on PD3 agar medium for two weeks (Davis et al. 1981), at which point bacterial cells were harvested into 2 ml of sterile water and adjusted to OD600=0.25 (108 cells/ml). Five µl of bacterial suspension was placed in triplicate on the basal internode of each shoot and a 27 gauge hypodermic needle pushed through the inoculum droplet into the stem to facilitate uptake into the vascular system.

tag: organ

value: Mature leaf

tag: cultivar

value: Cabernet sauvignon clone 8

tag: plant age

value: 2-year old vine

value: 8 weeks after inoculation treatment (WAT)


title: Blood, Subject 11898826, 55.1 hours since injury


title: Mature leaf 8WAT, severe water deficit, PD inoculated, biological rep 1 [27ID1L]

scan_protocol: Conducted at UC-Davis Genome Center according to Affymetrix protocol


title: Blood, Subject 11878509, 798.8 hours since injury


title: Blood, Subject 11710452, 69 hours since injury

source_name: Subject 11710452, 69 hours since injury


title: Mature leaf 4WAT, severe water deficit, PD inoculated, biological rep 3 [27ID4E]

source_name: Mature leaf from 2 year old-vine 4WAT, severe water deficit, PD inoculated

value: 4 weeks after inoculation treatment (WAT)


title: HuRef lymphoblastoid cell line, NimbleGen42M_60

city: Toronto

first: Andy

last: Pang

state: ON

address: MaRS Centre - East Tower, 101 College Street, Room 14-701

institute: The Centre for Applied Genomics

description: Competitively hybridized to NimbleGen 42M CGH array.

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to the array according to the manufacturer's instructions.

scan_protocol: Arrays were scanned per the manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

data_processing: Data were normalized by custom programs, and variants were called by the program GADA. The GFF file (linked to the Series record) includes the genomic coordinates and direction of calls (i.e., gain or loss).

source_name: HuRef lymphoblastoid cell line

label_protocol: As per the manufacturer's (NimbleGen) instructions.

extract_protocol: Genomic DNA was extracted from lymphoblastoid cell lines. DNA quality and quantity were assessed using a NanoDrop Spectrophotometer.

value: HuRef

tag: cell type

value: lymphoblastoid

value: male

source_name: NA15510 lymphoblastoid cell line

value: female

value: reference


title: HuRef lymphoblastoid cell line, NimbleGen42M_59

tag: gender


title: Blood, Subject 11430614, 882.1 hours since injury


title: Blood, Subject 11878509, 7.4 hours since injury


title: Mature leaf 4WAT, severe water deficit, PD inoculated, biological rep 2 [27ID2E]


title: Mature leaf 8WAT, no water deficit, PD inoculated, biological rep 2 [27I4L]

source_name: Mature leaf from 2 year old-vine 8WAT, no water deficit, PD inoculated


title: Mature leaf 4WAT, severe water deficit, PD inoculated, biological rep 1 [27ID1E]


title: Mature leaf 4WAT, no water deficit, PD inoculated, biological rep 3 [27I4E]

source_name: Mature leaf from 2 year old-vine 4WAT, no water deficit, PD inoculated


title: Mature leaf 4WAT, no water deficit, PD inoculated, biological rep 2 [27I3E]


title: Blood, Subject 11243166, 1177.3 hours since injury


title: Mature leaf 8WAT, severe water deficit, mock inoculated, biological rep 2 [27D2L]

source_name: Mature leaf from 2 year old-vine 8WAT, severe water deficit, mock inoculated


title: Blood, Subject 11243166, 27.9 hours since injury


title: Mature leaf 4WAT, no water deficit, PD inoculated, biological rep 1 [27I1E]


title: HuRef lymphoblastoid cell line, NimbleGen42M_57


title: HuRef lymphoblastoid cell line, NimbleGen42M_40


title: Mature leaf 8WAT, severe water deficit, PD inoculated, biological rep 3 [27ID4L]


title: Blood, Subject 11430614, 18.1 hours since injury


title: Blood, Subject 10974188, 486.5 hours since injury


title: Blood, Subject 10974188, 294.3 hours since injury


title: Blood, Subject 11287081, 19.5 hours since injury


title: Mature leaf 8WAT, no water deficit, PD inoculated, biological rep 1 [27I1L]


title: HuRef lymphoblastoid cell line, NimbleGen42M_42


title: HuRef lymphoblastoid cell line, NimbleGen42M_58


title: HuRef lymphoblastoid cell line, NimbleGen42M_26


title: HuRef lymphoblastoid cell line, NimbleGen42M_23


title: HuRef lymphoblastoid cell line, NimbleGen42M_43


title: HuRef lymphoblastoid cell line, NimbleGen42M_25


title: HuRef lymphoblastoid cell line, NimbleGen42M_24


title: Blood, Subject 10733971, 60 hours since injury

source_name: Subject 10733971, 60 hours since injury


title: Mature leaf 4WAT, severe water deficit, mock inoculated, biological rep 2 [27D2E]

source_name: Mature leaf from 2 year old-vine 4WAT, severe water deficit, mock inoculated


title: Blood, Subject 10974188, 149.9 hours since injury


title: Blood, Subject 10554016, 71.6 hours since injury


title: HuRef lymphoblastoid cell line, NimbleGen42M_56


title: Mature leaf 4WAT, severe water deficit, mock inoculated, biological rep 3 [27D4E]


title: Blood, Subject 10733971, 12.2 hours since injury


title: Mature leaf 8WAT, no water deficit, mock inoculated, biological rep 2 [27N3L]

source_name: Mature leaf from 2 year old-vine 8WAT, no water deficit, mock inoculated


title: Mature leaf 8WAT, no water deficit, mock inoculated, biological rep 1 [27N2L]


title: Mature leaf 4WAT, severe water deficit, mock inoculated, biological rep 1 [27D1E]


title: HuRef lymphoblastoid cell line, NimbleGen42M_09


title: Mature leaf 8WAT, severe water deficit, mock inoculated, biological rep 1 [27D1L]

description: Technical rep values for each probe were averaged to have a mean value for the biological rep in the Matrix Template


title: Blood, Subject 10974188, 78.6 hours since injury


title: HuRef lymphoblastoid cell line, NimbleGen42M_41


title: Blood, Subject 10488200, 292.7 hours since injury


title: Blood, Subject 10488200, 75.4 hours since injury


title: Blood, Subject 11430614, 306.1 hours since injury


title: Mature leaf 4WAT, no water deficit, mock inoculated, biological rep 2 [27N2E]

source_name: Mature leaf from 2 year old-vine 4WAT, no water deficit, mock inoculated


title: Mature leaf 4WAT, no water deficit, mock inoculated, biological rep 1 [27N1E]


title: Mature leaf 4WAT, no water deficit, mock inoculated, biological rep 3 [27N3E]


title: Blood, Subject 10488200, 61.9 hours since injury


title: Blood, Subject 10340666, 271.3 hours since injury


title: HuRef lymphoblastoid cell line, NimbleGen42M_07


title: HuRef lymphoblastoid cell line, NimbleGen42M_08


title: HuRef lymphoblastoid cell line, NimbleGen42M_06


title: Mature leaf 8WAT, moderate water deficit, PD inoculated, biological rep 2 [4ID2L]

source_name: Mature leaf from 2 year old-vine 8WAT, moderate water deficit, PD inoculated


title: Mature leaf 4WAT, moderate water deficit, PD inoculated, biological rep 2 [4ID2E]

source_name: Mature leaf from 2 year old-vine 4WAT, moderate water deficit, PD inoculated


title: Blood, Subject 10078209, 805.5 hours since injury


title: Mature leaf 8WAT, moderate water deficit, PD inoculated, biological rep 3 [4ID3L]


title: Blood, Subject 10078209, 16664.2 hours since injury


title: Mature leaf 4WAT, moderate water deficit, PD inoculated, biological rep 3 [4ID3E]


title: Mature leaf 8WAT, moderate water deficit, PD inoculated, biological rep 1 [4ID1L]


title: Mature leaf 8WAT, no water deficit, PD inoculated, biological rep 3 [4I4L]


title: Blood, Subject 10078209, 151.7 hours since injury


title: Mature leaf 8WAT, no water deficit, PD inoculated, biological rep 2 [4I2L]


title: Blood, Subject 10078209, 439.4 hours since injury


title: Mature leaf 4WAT, no water deficit, PD inoculated, biological rep 3 [4I4E]


title: Blood, Subject 10340666, 6.9 hours since injury


title: Blood, Subject 10017187, 538.3 hours since injury