title: Newborn epidermis of ctrl biological replicate 3

city: Koln

first: Mehmet

middle: Deniz

last: Akyuz

state: NRW

address: Robert Koch Str.21

department: Dermatology

institute: Uni-Klinik Koln

description: Gene expression data from newborn mouse epidermis

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix 430-2.0 platform. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with MAS 5. The further-processed data are analyzed using Partek software.

source_name: Newborn epidermis

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

growth_protocol: Newborn mice were collected

treatment_protocol: Epidermis  was seperated from the dermis and RNA was isolated from control and dKO epidermis.


title: B6_NS_2

status: Public on May 18 2013

type: RNA

city: Edinburgh

first: Musa

last: Hassan

state: Scotland

address: Easter Bush

department: Roslin

country: United Kingdom

institute: University of Edinburgh

hyb_protocol: Followed Affymetrix instructions.

scan_protocol: Scanned using Affymetrix GeneChip Scanner 3000.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings. We normalized such that the median intensity value was 500. We then set the minimum intensity to be 50.

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: B6 Non_stimulated BMDMs plated for 18 hrs 20% L929 conditioned DMEM medium

label_protocol: biotin

growth_protocol: BMDMs were plated at 3x10^6 cells per well in 6-well plates. They were generated by incubating bonemarrow cells in 20% L929 medium for 6-7 days before harvesting.

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

treatment_protocol: Unstimulated or IFNγ/TNFα-stimulated BMDMs were infected with parasite strains at  an Multiplicity of Infection (MOI) of 1 for 18 hours, before RNA harvesting. IL-4, CCL22, LPS, and IFNγ/TNFα (100ng/ml) stimulation wasperformed individually for 18 hrs

tag: strain

tag: cell type

value: Bone marrow-derived macrophages (BMDMs)


title: Deletion of tR(CCU)J,  biological rep2

status: Public on May 17 2013

city: Rehovot

first: Zohar

last: Bloom-Ackermann

address: Hertzl

country: Israel

institute: Weizmann Institute of Science

description: Gene expression data from cells at mid log phase

data_processing: GC-RMA algorithm in the Matlab bioinformatix toolbox

organism: Saccharomyces cerevisiae

source_name: Haploid cells at mid log phase

label_protocol: cDNA was prepared using poly(T) primers, labeled cRNA was prepared using the GeneChip system according to manufacture instructions

growth_protocol: Cells were grown at 30°C in rich medium to mid log phase

extract_protocol: Total RNA using EPICENTER yeast RNA purification kit

treatment_protocol: Cells were centrifuged and frozen in liquid nitrogen

tag: genetic background

tag: genotype

value: Deletion of tR(CCU)J


title: Newborn epidermis of ctrl biological replicate 1

country: Germany

tag: genotype/variation

value: wild type


title: Deletion of tR(CCU)J,  biological rep1

hyb_protocol: GeneChip system according to manufacture instructions


title: Newborn epidermis of dKO biological replicate 2


title: Deletion of tM(CAU), biological rep2

scan_protocol: GeneChip system according to manufacture instructions

value: Deletion of tM(CAU)


title: AJ_NS_1

source_name: AJ Non_stimulated BMDMs plated for 18 hrs DMEM medium without 20% L929

value: AJ


title: Deletion of tL(GAG)G, biological rep2

value: Deletion of tL(GAG)G


title: Deletion of tL(GAG)G, biological rep1


title: Deletion of tM(CAU), biological rep1


title: Newborn epidermis of dKO biological replicate 4


title: B6_NS_1

source_name: B6 Non_stimulated BMDMs plated for 18 hrs DMEM medium without 20% L929


title: Wild type,  biological rep1

value: Wild type


title: Newborn epidermis of dKO biological replicate 3


title: Wild type,  biological rep3


title: Newborn epidermis of dKO biological replicate 1


title: Newborn epidermis of ctrl biological replicate 4


title: Wild type,  biological rep2


title: Deletion of tR(UCU)M2, biological rep1

value: Deletion of tR(UCU)M2


title: Newborn epidermis of ctrl biological replicate 2


title: genotype: CM82036 (resistant) - treatment: water - time: 24 hai - rep1

city: Ames

first: PLEXdb Curator

middle: Sudhansu

state: IA

address: 1023  Crop Genomes Informatics Lab (Iowa State University)

department: Virtual Reality Application Center

country: USA

institute: Iowa State University

description: genotype=CM82036 (resistant)|treatment=water|time=24 hai rep 1 (May still include original submitter created erros/discrepancies)

hyb_protocol: Affymetrix Basic Protocol

scan_protocol: Affymetrix (AGRF)

data_processing: The MAS5.0 Normalization was performed using the justMAS function in the simpleaffy package of Bioconductor (www.bioconductor.org, Version: 2.12.1). The target value is 500 for all cases. The code was developed using R2.4.1 to 2.13.0, Bioconductor 1.9 to 2.12.1, and simpleaffy 2.8.0. to 2.28.0 The CDF files were downloaded from the Bioconductor website at http://www.bioconductor.org/packages/release/AffymetrixChip.html.

organism: Triticum aestivum

source_name: Spike (genotype: CM82036 (resistant) - treatment: water - time: 24 hai)

label_protocol: Affy-Eukaryotic Target Preparation

extract_protocol: RNA Isolation Using Trizol And Qiagen RNAeasy Columns

value: CM82036 (resistant)

tag: treatment

value: water

tag: time

value: 24 hai

tag: germplasm name

value: Remus,  CM82036

tag: tissue

value: Spike

tag: development stage

value: Anthesis

tag: growth media

value: garden soil


title: genotype: CM82036 (resistant) - treatment: water - time: 24 hai - rep2

description: genotype=CM82036 (resistant)|treatment=water|time=24 hai rep 2 (May still include original submitter created erros/discrepancies)


title: genotype: CM82036 (resistant) - treatment: water - time: 72 hai - rep3

description: genotype=CM82036 (resistant)|treatment=water|time=72 hai rep 3 (May still include original submitter created erros/discrepancies)

source_name: Spike (genotype: CM82036 (resistant) - treatment: water - time: 72 hai)

value: 72 hai


title: genotype: CM82036 (resistant) - treatment: water - time: 8 hai - rep3

description: genotype=CM82036 (resistant)|treatment=water|time=8 hai rep 3 (May still include original submitter created erros/discrepancies)

source_name: Spike (genotype: CM82036 (resistant) - treatment: water - time: 8 hai)

value: 8 hai


title: genotype: CM82036 (resistant) - treatment: water - time: 8 hai - rep1

description: genotype=CM82036 (resistant)|treatment=water|time=8 hai rep 1 (May still include original submitter created erros/discrepancies)


title: genotype: CM82036 (resistant) - treatment: Fusarium graminearum strain IFA-65 - time: 72 hai - rep2

description: genotype=CM82036 (resistant)|treatment=Fusarium graminearum strain IFA-65|time=72 hai rep 2 (May still include original submitter created erros/discrepancies)

source_name: Spike (genotype: CM82036 (resistant) - treatment: Fusarium graminearum strain IFA-65 - time: 72 hai)

value: Fusarium graminearum strain IFA-65


title: genotype: CM82036 (resistant) - treatment: water - time: 24 hai - rep3

description: genotype=CM82036 (resistant)|treatment=water|time=24 hai rep 3 (May still include original submitter created erros/discrepancies)


title: genotype: CM82036 (resistant) - treatment: Fusarium graminearum strain IFA-65 - time: 24 hai - rep3

description: genotype=CM82036 (resistant)|treatment=Fusarium graminearum strain IFA-65|time=24 hai rep 3 (May still include original submitter created erros/discrepancies)

source_name: Spike (genotype: CM82036 (resistant) - treatment: Fusarium graminearum strain IFA-65 - time: 24 hai)


title: genotype: CM82036 (resistant) - treatment: Fusarium graminearum strain IFA-65 - time: 24 hai - rep2

description: genotype=CM82036 (resistant)|treatment=Fusarium graminearum strain IFA-65|time=24 hai rep 2 (May still include original submitter created erros/discrepancies)


title: genotype: CM82036 (resistant) - treatment: water - time: 72 hai - rep2

description: genotype=CM82036 (resistant)|treatment=water|time=72 hai rep 2 (May still include original submitter created erros/discrepancies)


title: genotype: NIL4 (susceptible) - treatment: water - time: 24 hai - rep2

description: genotype=NIL4 (susceptible)|treatment=water|time=24 hai rep 2 (May still include original submitter created erros/discrepancies)

source_name: Spike (genotype: NIL4 (susceptible) - treatment: water - time: 24 hai)

value: NIL4 (susceptible)


title: genotype: CM82036 (resistant) - treatment: Fusarium graminearum strain IFA-65 - time: 8 hai - rep2

description: genotype=CM82036 (resistant)|treatment=Fusarium graminearum strain IFA-65|time=8 hai rep 2 (May still include original submitter created erros/discrepancies)

source_name: Spike (genotype: CM82036 (resistant) - treatment: Fusarium graminearum strain IFA-65 - time: 8 hai)


title: genotype: CM82036 (resistant) - treatment: Fusarium graminearum strain IFA-65 - time: 8 hai - rep1

description: genotype=CM82036 (resistant)|treatment=Fusarium graminearum strain IFA-65|time=8 hai rep 1 (May still include original submitter created erros/discrepancies)


title: genotype: CM82036 (resistant) - treatment: Fusarium graminearum strain IFA-65 - time: 72 hai - rep3

description: genotype=CM82036 (resistant)|treatment=Fusarium graminearum strain IFA-65|time=72 hai rep 3 (May still include original submitter created erros/discrepancies)


title: genotype: CM82036 (resistant) - treatment: water - time: 72 hai - rep1

description: genotype=CM82036 (resistant)|treatment=water|time=72 hai rep 1 (May still include original submitter created erros/discrepancies)


title: genotype: NIL4 (susceptible) - treatment: water - time: 24 hai - rep3

description: genotype=NIL4 (susceptible)|treatment=water|time=24 hai rep 3 (May still include original submitter created erros/discrepancies)


title: genotype: CM82036 (resistant) - treatment: Fusarium graminearum strain IFA-65 - time: 72 hai - rep1

description: genotype=CM82036 (resistant)|treatment=Fusarium graminearum strain IFA-65|time=72 hai rep 1 (May still include original submitter created erros/discrepancies)


title: genotype: NIL4 (susceptible) - treatment: water - time: 8 hai - rep1

description: genotype=NIL4 (susceptible)|treatment=water|time=8 hai rep 1 (May still include original submitter created erros/discrepancies)

source_name: Spike (genotype: NIL4 (susceptible) - treatment: water - time: 8 hai)


title: genotype: CM82036 (resistant) - treatment: Fusarium graminearum strain IFA-65 - time: 24 hai - rep1

description: genotype=CM82036 (resistant)|treatment=Fusarium graminearum strain IFA-65|time=24 hai rep 1 (May still include original submitter created erros/discrepancies)


title: genotype: NIL4 (susceptible) - treatment: water - time: 8 hai - rep2

description: genotype=NIL4 (susceptible)|treatment=water|time=8 hai rep 2 (May still include original submitter created erros/discrepancies)


title: genotype: NIL4 (susceptible) - treatment: water - time: 72 hai - rep2

description: genotype=NIL4 (susceptible)|treatment=water|time=72 hai rep 2 (May still include original submitter created erros/discrepancies)

source_name: Spike (genotype: NIL4 (susceptible) - treatment: water - time: 72 hai)


title: genotype: NIL4 (susceptible) - treatment: Fusarium graminearum strain IFA-65 - time: 72 hai - rep3

description: genotype=NIL4 (susceptible)|treatment=Fusarium graminearum strain IFA-65|time=72 hai rep 3 (May still include original submitter created erros/discrepancies)

source_name: Spike (genotype: NIL4 (susceptible) - treatment: Fusarium graminearum strain IFA-65 - time: 72 hai)


title: genotype: NIL4 (susceptible) - treatment: water - time: 8 hai - rep3

description: genotype=NIL4 (susceptible)|treatment=water|time=8 hai rep 3 (May still include original submitter created erros/discrepancies)


title: genotype: CM82036 (resistant) - treatment: Fusarium graminearum strain IFA-65 - time: 8 hai - rep3

description: genotype=CM82036 (resistant)|treatment=Fusarium graminearum strain IFA-65|time=8 hai rep 3 (May still include original submitter created erros/discrepancies)


title: genotype: NIL4 (susceptible) - treatment: Fusarium graminearum strain IFA-65 - time: 72 hai - rep1

description: genotype=NIL4 (susceptible)|treatment=Fusarium graminearum strain IFA-65|time=72 hai rep 1 (May still include original submitter created erros/discrepancies)


title: genotype: NIL4 (susceptible) - treatment: water - time: 72 hai - rep3

description: genotype=NIL4 (susceptible)|treatment=water|time=72 hai rep 3 (May still include original submitter created erros/discrepancies)


title: genotype: NIL4 (susceptible) - treatment: Fusarium graminearum strain IFA-65 - time: 72 hai - rep2

description: genotype=NIL4 (susceptible)|treatment=Fusarium graminearum strain IFA-65|time=72 hai rep 2 (May still include original submitter created erros/discrepancies)


title: genotype: NIL4 (susceptible) - treatment: water - time: 72 hai - rep1

description: genotype=NIL4 (susceptible)|treatment=water|time=72 hai rep 1 (May still include original submitter created erros/discrepancies)


title: genotype: NIL4 (susceptible) - treatment: water - time: 24 hai - rep1

description: genotype=NIL4 (susceptible)|treatment=water|time=24 hai rep 1 (May still include original submitter created erros/discrepancies)


title: genotype: NIL4 (susceptible) - treatment: Fusarium graminearum strain IFA-65 - time: 24 hai - rep3

description: genotype=NIL4 (susceptible)|treatment=Fusarium graminearum strain IFA-65|time=24 hai rep 3 (May still include original submitter created erros/discrepancies)

source_name: Spike (genotype: NIL4 (susceptible) - treatment: Fusarium graminearum strain IFA-65 - time: 24 hai)


title: genotype: NIL4 (susceptible) - treatment: Fusarium graminearum strain IFA-65 - time: 8 hai - rep1

description: genotype=NIL4 (susceptible)|treatment=Fusarium graminearum strain IFA-65|time=8 hai rep 1 (May still include original submitter created erros/discrepancies)

source_name: Spike (genotype: NIL4 (susceptible) - treatment: Fusarium graminearum strain IFA-65 - time: 8 hai)


title: genotype: NIL4 (susceptible) - treatment: Fusarium graminearum strain IFA-65 - time: 24 hai - rep2

description: genotype=NIL4 (susceptible)|treatment=Fusarium graminearum strain IFA-65|time=24 hai rep 2 (May still include original submitter created erros/discrepancies)


title: genotype: NIL4 (susceptible) - treatment: Fusarium graminearum strain IFA-65 - time: 8 hai - rep3

description: genotype=NIL4 (susceptible)|treatment=Fusarium graminearum strain IFA-65|time=8 hai rep 3 (May still include original submitter created erros/discrepancies)


title: genotype: NIL4 (susceptible) - treatment: Fusarium graminearum strain IFA-65 - time: 24 hai - rep1

description: genotype=NIL4 (susceptible)|treatment=Fusarium graminearum strain IFA-65|time=24 hai rep 1 (May still include original submitter created erros/discrepancies)


title: genotype: NIL3 (moderately resistant, Qfhs.ifa-5A) - treatment: water - time: 72 hai - rep1

description: genotype=NIL3 (moderately resistant, Qfhs.ifa-5A)|treatment=water|time=72 hai rep 1 (May still include original submitter created erros/discrepancies)

source_name: Spike (genotype: NIL3 (moderately resistant, Qfhs.ifa-5A) - treatment: water - time: 72 hai)


title: genotype: NIL4 (susceptible) - treatment: Fusarium graminearum strain IFA-65 - time: 8 hai - rep2

description: genotype=NIL4 (susceptible)|treatment=Fusarium graminearum strain IFA-65|time=8 hai rep 2 (May still include original submitter created erros/discrepancies)


title: genotype: NIL3 (moderately resistant, Qfhs.ifa-5A) - treatment: water - time: 72 hai - rep3

description: genotype=NIL3 (moderately resistant, Qfhs.ifa-5A)|treatment=water|time=72 hai rep 3 (May still include original submitter created erros/discrepancies)


title: genotype: NIL3 (moderately resistant, Qfhs.ifa-5A) - treatment: water - time: 24 hai - rep2

description: genotype=NIL3 (moderately resistant, Qfhs.ifa-5A)|treatment=water|time=24 hai rep 2 (May still include original submitter created erros/discrepancies)

source_name: Spike (genotype: NIL3 (moderately resistant, Qfhs.ifa-5A) - treatment: water - time: 24 hai)


title: genotype: NIL3 (moderately resistant, Qfhs.ifa-5A) - treatment: Fusarium graminearum strain IFA-65 - time: 72 hai - rep2

description: genotype=NIL3 (moderately resistant, Qfhs.ifa-5A)|treatment=Fusarium graminearum strain IFA-65|time=72 hai rep 2 (May still include original submitter created erros/discrepancies)

source_name: Spike (genotype: NIL3 (moderately resistant, Qfhs.ifa-5A) - treatment: Fusarium graminearum strain IFA-65 - time: 72 hai)


title: genotype: NIL3 (moderately resistant, Qfhs.ifa-5A) - treatment: water - time: 8 hai - rep2

description: genotype=NIL3 (moderately resistant, Qfhs.ifa-5A)|treatment=water|time=8 hai rep 2 (May still include original submitter created erros/discrepancies)

source_name: Spike (genotype: NIL3 (moderately resistant, Qfhs.ifa-5A) - treatment: water - time: 8 hai)


title: genotype: NIL3 (moderately resistant, Qfhs.ifa-5A) - treatment: water - time: 8 hai - rep3

description: genotype=NIL3 (moderately resistant, Qfhs.ifa-5A)|treatment=water|time=8 hai rep 3 (May still include original submitter created erros/discrepancies)


title: genotype: NIL3 (moderately resistant, Qfhs.ifa-5A) - treatment: Fusarium graminearum strain IFA-65 - time: 24 hai - rep2

description: genotype=NIL3 (moderately resistant, Qfhs.ifa-5A)|treatment=Fusarium graminearum strain IFA-65|time=24 hai rep 2 (May still include original submitter created erros/discrepancies)

source_name: Spike (genotype: NIL3 (moderately resistant, Qfhs.ifa-5A) - treatment: Fusarium graminearum strain IFA-65 - time: 24 hai)


title: genotype: NIL3 (moderately resistant, Qfhs.ifa-5A) - treatment: Fusarium graminearum strain IFA-65 - time: 72 hai - rep1

description: genotype=NIL3 (moderately resistant, Qfhs.ifa-5A)|treatment=Fusarium graminearum strain IFA-65|time=72 hai rep 1 (May still include original submitter created erros/discrepancies)


title: genotype: NIL3 (moderately resistant, Qfhs.ifa-5A) - treatment: Fusarium graminearum strain IFA-65 - time: 8 hai - rep3

description: genotype=NIL3 (moderately resistant, Qfhs.ifa-5A)|treatment=Fusarium graminearum strain IFA-65|time=8 hai rep 3 (May still include original submitter created erros/discrepancies)

source_name: Spike (genotype: NIL3 (moderately resistant, Qfhs.ifa-5A) - treatment: Fusarium graminearum strain IFA-65 - time: 8 hai)


title: genotype: NIL3 (moderately resistant, Qfhs.ifa-5A) - treatment: Fusarium graminearum strain IFA-65 - time: 24 hai - rep3

description: genotype=NIL3 (moderately resistant, Qfhs.ifa-5A)|treatment=Fusarium graminearum strain IFA-65|time=24 hai rep 3 (May still include original submitter created erros/discrepancies)


title: genotype: NIL3 (moderately resistant, Qfhs.ifa-5A) - treatment: water - time: 72 hai - rep2

description: genotype=NIL3 (moderately resistant, Qfhs.ifa-5A)|treatment=water|time=72 hai rep 2 (May still include original submitter created erros/discrepancies)


title: genotype: NIL2 (moderately resistant, Fhb1) - treatment: water - time: 72 hai - rep3

description: genotype=NIL2 (moderately resistant, Fhb1)|treatment=water|time=72 hai rep 3 (May still include original submitter created erros/discrepancies)

source_name: Spike (genotype: NIL2 (moderately resistant, Fhb1) - treatment: water - time: 72 hai)

value: NIL2 (moderately resistant, Fhb1)


title: genotype: NIL3 (moderately resistant, Qfhs.ifa-5A) - treatment: Fusarium graminearum strain IFA-65 - time: 8 hai - rep2

description: genotype=NIL3 (moderately resistant, Qfhs.ifa-5A)|treatment=Fusarium graminearum strain IFA-65|time=8 hai rep 2 (May still include original submitter created erros/discrepancies)


title: genotype: NIL3 (moderately resistant, Qfhs.ifa-5A) - treatment: Fusarium graminearum strain IFA-65 - time: 24 hai - rep1

description: genotype=NIL3 (moderately resistant, Qfhs.ifa-5A)|treatment=Fusarium graminearum strain IFA-65|time=24 hai rep 1 (May still include original submitter created erros/discrepancies)


title: genotype: NIL3 (moderately resistant, Qfhs.ifa-5A) - treatment: water - time: 8 hai - rep1

description: genotype=NIL3 (moderately resistant, Qfhs.ifa-5A)|treatment=water|time=8 hai rep 1 (May still include original submitter created erros/discrepancies)


title: genotype: NIL2 (moderately resistant, Fhb1) - treatment: water - time: 72 hai - rep1

description: genotype=NIL2 (moderately resistant, Fhb1)|treatment=water|time=72 hai rep 1 (May still include original submitter created erros/discrepancies)


title: genotype: NIL2 (moderately resistant, Fhb1) - treatment: water - time: 72 hai - rep2

description: genotype=NIL2 (moderately resistant, Fhb1)|treatment=water|time=72 hai rep 2 (May still include original submitter created erros/discrepancies)


title: genotype: NIL2 (moderately resistant, Fhb1) - treatment: water - time: 24 hai - rep3

description: genotype=NIL2 (moderately resistant, Fhb1)|treatment=water|time=24 hai rep 3 (May still include original submitter created erros/discrepancies)

source_name: Spike (genotype: NIL2 (moderately resistant, Fhb1) - treatment: water - time: 24 hai)


title: genotype: CM82036 (resistant) - treatment: water - time: 8 hai - rep2

description: genotype=CM82036 (resistant)|treatment=water|time=8 hai rep 2 (May still include original submitter created erros/discrepancies)

source_name: Spike (genotype: CM82036 (resistant) - treatment: water - time: 8 hai)


title: genotype: NIL3 (moderately resistant, Qfhs.ifa-5A) - treatment: Fusarium graminearum strain IFA-65 - time: 8 hai - rep1

description: genotype=NIL3 (moderately resistant, Qfhs.ifa-5A)|treatment=Fusarium graminearum strain IFA-65|time=8 hai rep 1 (May still include original submitter created erros/discrepancies)


title: genotype: NIL3 (moderately resistant, Qfhs.ifa-5A) - treatment: Fusarium graminearum strain IFA-65 - time: 72 hai - rep3

description: genotype=NIL3 (moderately resistant, Qfhs.ifa-5A)|treatment=Fusarium graminearum strain IFA-65|time=72 hai rep 3 (May still include original submitter created erros/discrepancies)


title: Serous Ovarian Cancer 100

city: Columbus

first: Andrea

last: Vecchione

state: OH

address: 460W12th Ave

institute: The Ohio state University

data_processing: TaqMan Low-Density Array cards (TLDA) and RT-PCR data were analysed using the comparative CT (ΔΔCT) method for relative quantitation of gene expression on DataAssist ver.1.2 (Applied Biosystems, Foster City, CA). For each sample, the mean miRNA expression value was calculated as the average of Ct values smaller than 35. Samples were labeled based either on their response to first chemotherapy or other clinical parameters. One-way Anova test was applied to identify differentially expressed miRNA using R software. Global median normalization was used for the expression analysis of the TLDA cards.

label: FAM

organism: Homo sapiens

source_name: serous epithelial ovarian carcinoma, no response

label_protocol: For miRNA cDNA synthesis, RNA was reverse transcribed using the miRNA reverse transcription kit (Applied Biosystems) in combination with the stem-loop Megaplex™ Primer Pools for the TaqMan Array Human A and B Card (Applied Biosystems).

extract_protocol: Total RNA for low-density array analysis was isolated from paraffin-embedded tissue (FFPE) using the High Pure FFPE RNA Micro Kit (Roche Applied Science, Mannheim, Germany) according to manufacturer protocol. Following extraction, total RNA was quantified using a NanoDrop Spectrophotometer (Thermo Fisher Scientific Inc., USA). All tumor samples were chosen to minimize the normal tissues (<5%) amount. Where normal tissue exceeded this limitation, we performed laser microdissection of the samples.

treatment_protocol: Patients were treated with standard protocols of Carboplatin+Taxane chemotherapy.

value: serous epithelial ovarian carcinoma

tag: age at diagnosis

tag: Stage

value: IV

tag: grading

tag: histology

value: serous

tag: surgery outcome

value: explorative laparotomy

tag: i chemotherapy

value: CBDCA+TAX

tag: response to i chemotherapy

value: no response


title: Serous Ovarian Cancer 102

source_name: serous epithelial ovarian carcinoma, complete response

value: IIIC

value: optimal resection <1cm of tumor left

value: complete response


title: Serous Ovarian Cancer 1

source_name: serous epithelial ovarian carcinoma, partial response

value: IIIB

value: suboptimal resection >1cm of tumor left

value: partial response


title: genotype: NIL2 (moderately resistant, Fhb1) - treatment: water - time: 24 hai - rep1

description: genotype=NIL2 (moderately resistant, Fhb1)|treatment=water|time=24 hai rep 1 (May still include original submitter created erros/discrepancies)

value: water

value: 24 hai

value: Remus,  CM82036

value: Spike

value: Anthesis

value: garden soil


title: genotype: NIL2 (moderately resistant, Fhb1) - treatment: water - time: 24 hai - rep2

description: genotype=NIL2 (moderately resistant, Fhb1)|treatment=water|time=24 hai rep 2 (May still include original submitter created erros/discrepancies)

value: NIL2 (moderately resistant, Fhb1)


title: c-Myc at 1 uM concentration and Max at 100 nM concentration, replicate 2

type: protein

city: Durham

first: Raluca

last: Gordan

state: NC

address: 101 Science Dr, CIEMAS 2179

department: Center for Genomic and Computational Biology

institute: Duke University

hyb_protocol: Double-stranded microarrays were first pre-moistened in PBS / 0.01% Triton X-100 for 5 min and blocked with PBS / 2% (wt/vol) nonfat dried milk (Sigma) for 1 h. Microarrays were then washed once with PBS / 0.1% (vol/vol) Tween-20 for 5 min and once with PBS / 0.01% Triton X-100 for 2 min. Proteins were diluted to 200 or 100 nM in a 175-μl protein binding reaction containing PBS / 2% (wt/vol) milk / 51.3 ng/μl salmon testes DNA (Sigma) / 0.2 μg/μl bovine serum albumin (New England Biolabs). Preincubated protein binding mixtures were applied to individual chambers of a four-chamber gasket cover slip in a steel hybridization chamber (Agilent), and the assembled microarrays were incubated for 1 h at room temperature. Microarrays were again washed once with PBS / 0.5% (vol/vol) Tween-20 for 3 min, and then once with PBS / 0.01% Triton X-100 for 2 min. Alexa-488-conjugated rabbit polyclonal antibody to GST (Invitrogen) was diluted to 50 μg/ml in PBS / 2% milk and applied to a single-chamber gasket cover slip (Agilent), and the assembled microarrays were again incubated for 1 h at 20°C. Finally, microarrays were washed twice with PBS / 0.05% (vol/vol) Tween-20 for 3 min each, and once in PBS for 2 min. After each hour-long incubation step, microarrays and cover slips were disassembled in a staining dish filled with 500 ml of the first wash solution. All washes were performed in Coplin jars on an orbital shaker at 125 r.p.m. Immediately following each series of washes, microarrays were rinsed in PBS (slowly removed over approximately 10 seconds) to ensure removal of detergent and uniform drying.

scan_protocol: Protein-bound microarrays were scanned to detect Alexa-488-conjugated antibody (488 nm ex, 522 nm em) using at least three different laser power settings to best capture a broad range of signal intensities and ensure signal intensities below saturation for all spots. Microarray TIF images were analyzed using GenePix Pro version 6.0 software (Molecular Devices), bad spots were manually flagged and removed, and data from multiple Alexa 488 scans of the same slide were combined using masliner (MicroArray LINEar Regression) software.

data_processing: To correct for any possible non-uniformities in protein binding, we adjusted the Alexa 488 signals according to their positions on the microarray. We calculated the median normalized intensity of the 15 x 15 block centered on each spot and divided the spot's signal by the ratio of the median within the block to the median over the entire chamber.

label: Alexa 488

molecule: protein

source_name: Human c-Myc and Max

label_protocol: Proteins were tagged with N-terminal GST by cloning. Protein-bound arrays were incubated with Alexa-488-conjugated rabbit polyclonal antibody to GST (Invitrogen).

growth_protocol: Plasmids were transformed into BL21 (DE3) expression strain of E. coli (New England BioLabs). Overnight bacterial culture (5 mL) was diluted into 1 L LB (10 g BACTO Tryptone (BD); 5 g BACTO Yeast Extract (BD); 10 g NaCl; pH 7.5) and grown to OD 0.6 (600 nm visible light). Protein expression was then induced with 1 mM isopropyl β-D-1-thiogalactopyranoside (IPTG) for 3 hours at 37ºC. Cells were pelleted by centrifugation @ 12,000 rpm for 10 min and stored at -20ºC. Each pellet (from 1 L culture) was thawed in 15 ml lysis buffer (150 mM Tris-HCl, pH 8.0; 150 mM NaCl; 2 mM dithiothreitol (DTT); 1 tablet complete Mini, EDTA-free protease inhibitor cocktail (Roche, #11 836 170 001); 50 uM C4H10O6Zn (zinc acetate); 1 mg/ml chicken egg white lysozyme (Sigma, # L6876)) and subjected to two freeze-thaw cycles in dry ice/ethanol. To digest DNA, to each 15 ml lysis solution was added 10 uL recombinant, RNase-free DNAse I (Roche, #04 716 728 001, 10 U/ul), 30 uL 1 M MgCl2, and 2 mL 10% Triton X-100, and digested at room temperature until solution was runny (~1 hr). Solutions were centrifuged at 12,000 rpm for 25 min at 4ºC, and supernatant was used for protein purification.

extract_protocol: Full-length open reading frames were cloned into the Gateway pDEST15 (N-terminal GST-tag) expression vector by recombinational cloning from previously created pENTR clones. All proteins were produced by over-expression in E. coli BL21 (DE3) cells (New England BioLabs), and purified by FPLC (AKTAprime plus) using GSTrapTM FF affinity columns (GE Healthcare). Anti-GST Western blots were performed to assess protein quality and concentration.

tag: transcription factor

value: c-Myc, Max

tag: protein concentration

value: 100nM Max, 1uM c-Myc


title: c-Myc at 1 uM concentration and Max at 100 nM concentration, replicate 1


title: Max at 100 nM concentration

description: Max

source_name: Human Max

value: Max

value: 100nM Max


title: Mad2 at 1 uM concentration and Max at 100 nM concentration

description: Mad

source_name: Human Mad2 and Max

value: Mad2, Max

value: 100nM Max, 1uM Mad2


title: genotype: NIL2 (moderately resistant, Fhb1) - treatment: Fusarium graminearum strain IFA-65 - time: 72 hai - rep1

description: genotype=NIL2 (moderately resistant, Fhb1)|treatment=Fusarium graminearum strain IFA-65|time=72 hai rep 1 (May still include original submitter created erros/discrepancies)

source_name: Spike (genotype: NIL2 (moderately resistant, Fhb1) - treatment: Fusarium graminearum strain IFA-65 - time: 72 hai)

tag: genotype

value: Fusarium graminearum strain IFA-65

value: 72 hai


title: Serous Ovarian Cancer 99

value: serous epithelial ovarian carcinoma

value: IIIB

value: serous

value: optimal resection <1cm of tumor left

value: CBDCA+TAX

value: no response


title: Serous Ovarian Cancer 97

value: IIIC

value: complete response


title: Serous Ovarian Cancer 98

value: suboptimal resection >1cm of tumor left


title: genotype: NIL2 (moderately resistant, Fhb1) - treatment: Fusarium graminearum strain IFA-65 - time: 72 hai - rep3

description: genotype=NIL2 (moderately resistant, Fhb1)|treatment=Fusarium graminearum strain IFA-65|time=72 hai rep 3 (May still include original submitter created erros/discrepancies)

value: NIL2 (moderately resistant, Fhb1)

value: Remus,  CM82036

value: Spike

value: Anthesis

value: garden soil


title: genotype: NIL2 (moderately resistant, Fhb1) - treatment: water - time: 8 hai - rep2

description: genotype=NIL2 (moderately resistant, Fhb1)|treatment=water|time=8 hai rep 2 (May still include original submitter created erros/discrepancies)

source_name: Spike (genotype: NIL2 (moderately resistant, Fhb1) - treatment: water - time: 8 hai)

value: water

value: 8 hai


title: genotype: NIL2 (moderately resistant, Fhb1) - treatment: Fusarium graminearum strain IFA-65 - time: 24 hai - rep1

description: genotype=NIL2 (moderately resistant, Fhb1)|treatment=Fusarium graminearum strain IFA-65|time=24 hai rep 1 (May still include original submitter created erros/discrepancies)

source_name: Spike (genotype: NIL2 (moderately resistant, Fhb1) - treatment: Fusarium graminearum strain IFA-65 - time: 24 hai)

value: Fusarium graminearum strain IFA-65

value: 24 hai


title: genotype: NIL2 (moderately resistant, Fhb1) - treatment: Fusarium graminearum strain IFA-65 - time: 24 hai - rep3

description: genotype=NIL2 (moderately resistant, Fhb1)|treatment=Fusarium graminearum strain IFA-65|time=24 hai rep 3 (May still include original submitter created erros/discrepancies)


title: genotype: NIL2 (moderately resistant, Fhb1) - treatment: Fusarium graminearum strain IFA-65 - time: 72 hai - rep2

description: genotype=NIL2 (moderately resistant, Fhb1)|treatment=Fusarium graminearum strain IFA-65|time=72 hai rep 2 (May still include original submitter created erros/discrepancies)

value: 72 hai


title: genotype: NIL2 (moderately resistant, Fhb1) - treatment: Fusarium graminearum strain IFA-65 - time: 8 hai - rep3

description: genotype=NIL2 (moderately resistant, Fhb1)|treatment=Fusarium graminearum strain IFA-65|time=8 hai rep 3 (May still include original submitter created erros/discrepancies)

source_name: Spike (genotype: NIL2 (moderately resistant, Fhb1) - treatment: Fusarium graminearum strain IFA-65 - time: 8 hai)


title: Serous Ovarian Cancer 96

value: serous epithelial ovarian carcinoma

value: serous


title: Serous Ovarian Cancer 95

value: IIIA

value: optimal resection <1cm of tumor left

value: CBDCA+TAX


title: genotype: NIL2 (moderately resistant, Fhb1) - treatment: Fusarium graminearum strain IFA-65 - time: 8 hai - rep1

description: genotype=NIL2 (moderately resistant, Fhb1)|treatment=Fusarium graminearum strain IFA-65|time=8 hai rep 1 (May still include original submitter created erros/discrepancies)


title: genotype: NIL2 (moderately resistant, Fhb1) - treatment: Fusarium graminearum strain IFA-65 - time: 24 hai - rep2

description: genotype=NIL2 (moderately resistant, Fhb1)|treatment=Fusarium graminearum strain IFA-65|time=24 hai rep 2 (May still include original submitter created erros/discrepancies)


title: genotype: NIL1 (resistant, Fhb1, Qfhs.ifa-5A) - treatment: water - time: 72 hai - rep3

description: genotype=NIL1 (resistant, Fhb1, Qfhs.ifa-5A)|treatment=water|time=72 hai rep 3 (May still include original submitter created erros/discrepancies)

source_name: Spike (genotype: NIL1 (resistant, Fhb1, Qfhs.ifa-5A) - treatment: water - time: 72 hai)

value: NIL1 (resistant, Fhb1, Qfhs.ifa-5A)


title: Serous Ovarian Cancer 94

value: IIIB

value: suboptimal resection >1cm of tumor left

value: complete response


title: genotype: NIL2 (moderately resistant, Fhb1) - treatment: water - time: 8 hai - rep3

description: genotype=NIL2 (moderately resistant, Fhb1)|treatment=water|time=8 hai rep 3 (May still include original submitter created erros/discrepancies)

value: NIL2 (moderately resistant, Fhb1)

value: Remus,  CM82036

value: Spike


title: Serous Ovarian Cancer 93


title: genotype: NIL2 (moderately resistant, Fhb1) - treatment: Fusarium graminearum strain IFA-65 - time: 8 hai - rep2

description: genotype=NIL2 (moderately resistant, Fhb1)|treatment=Fusarium graminearum strain IFA-65|time=8 hai rep 2 (May still include original submitter created erros/discrepancies)

value: Anthesis

value: garden soil


title: genotype: NIL3 (moderately resistant, Qfhs.ifa-5A) - treatment: water - time: 24 hai - rep3

description: genotype=NIL3 (moderately resistant, Qfhs.ifa-5A)|treatment=water|time=24 hai rep 3 (May still include original submitter created erros/discrepancies)

source_name: Spike (genotype: NIL3 (moderately resistant, Qfhs.ifa-5A) - treatment: water - time: 24 hai)

value: water


title: Serous Ovarian Cancer 91

source_name: serous epithelial ovarian carcinoma, stable disease

value: IV

value: explorative laparotomy

value: stable disease


title: Serous Ovarian Cancer 90

value: serous epithelial ovarian carcinoma

value: IIIC

value: serous


title: Serous Ovarian Cancer 87

value: IA

value: optimal resection <1cm of tumor left

value: CBCDA+TAX

value: no response


title: Serous Ovarian Cancer 88

value: IC

value: CBDCA+TAX


title: Serous Ovarian Cancer 89

value: IVA

value: partial response


title: genotype: NIL1 (resistant, Fhb1, Qfhs.ifa-5A) - treatment: water - time: 72 hai - rep1

description: genotype=NIL1 (resistant, Fhb1, Qfhs.ifa-5A)|treatment=water|time=72 hai rep 1 (May still include original submitter created erros/discrepancies)

value: NIL1 (resistant, Fhb1, Qfhs.ifa-5A)

value: 72 hai

value: Remus,  CM82036

value: Spike

value: Anthesis


title: Serous Ovarian Cancer 85

value: IV

value: explorative laparotomy

value: complete response


title: Serous Ovarian Cancer 86

value: serous epithelial ovarian carcinoma

value: IIIA

value: serous


title: Serous Ovarian Cancer 84

value: IIIC

value: optimal resection <1cm of tumor left


title: Serous Ovarian Cancer 83

value: III

value: suboptimal resection >1cm of tumor left


title: genotype: NIL1 (resistant, Fhb1, Qfhs.ifa-5A) - treatment: water - time: 24 hai - rep1

description: genotype=NIL1 (resistant, Fhb1, Qfhs.ifa-5A)|treatment=water|time=24 hai rep 1 (May still include original submitter created erros/discrepancies)

source_name: Spike (genotype: NIL1 (resistant, Fhb1, Qfhs.ifa-5A) - treatment: water - time: 24 hai)

value: water

value: 24 hai

value: garden soil


title: Serous Ovarian Cancer 81

value: CBDCA+TAX


title: Serous Ovarian Cancer 82


title: Serous Ovarian Cancer 80

value: stable disease


title: genotype: NIL2 (moderately resistant, Fhb1) - treatment: water - time: 8 hai - rep1

description: genotype=NIL2 (moderately resistant, Fhb1)|treatment=water|time=8 hai rep 1 (May still include original submitter created erros/discrepancies)

value: NIL2 (moderately resistant, Fhb1)

value: 8 hai

value: Remus,  CM82036

value: Spike


title: genotype: NIL1 (resistant, Fhb1, Qfhs.ifa-5A) - treatment: water - time: 24 hai - rep3

description: genotype=NIL1 (resistant, Fhb1, Qfhs.ifa-5A)|treatment=water|time=24 hai rep 3 (May still include original submitter created erros/discrepancies)

value: NIL1 (resistant, Fhb1, Qfhs.ifa-5A)

value: Anthesis


title: genotype: NIL1 (resistant, Fhb1, Qfhs.ifa-5A) - treatment: water - time: 8 hai - rep2

description: genotype=NIL1 (resistant, Fhb1, Qfhs.ifa-5A)|treatment=water|time=8 hai rep 2 (May still include original submitter created erros/discrepancies)

source_name: Spike (genotype: NIL1 (resistant, Fhb1, Qfhs.ifa-5A) - treatment: water - time: 8 hai)


title: genotype: NIL1 (resistant, Fhb1, Qfhs.ifa-5A) - treatment: Fusarium graminearum strain IFA-65 - time: 24 hai - rep2

description: genotype=NIL1 (resistant, Fhb1, Qfhs.ifa-5A)|treatment=Fusarium graminearum strain IFA-65|time=24 hai rep 2 (May still include original submitter created erros/discrepancies)

source_name: Spike (genotype: NIL1 (resistant, Fhb1, Qfhs.ifa-5A) - treatment: Fusarium graminearum strain IFA-65 - time: 24 hai)

value: Fusarium graminearum strain IFA-65


title: genotype: NIL1 (resistant, Fhb1, Qfhs.ifa-5A) - treatment: water - time: 8 hai - rep1

description: genotype=NIL1 (resistant, Fhb1, Qfhs.ifa-5A)|treatment=water|time=8 hai rep 1 (May still include original submitter created erros/discrepancies)


title: Serous Ovarian Cancer 79

value: serous epithelial ovarian carcinoma

value: serous

value: explorative laparotomy

value: complete response


title: genotype: NIL1 (resistant, Fhb1, Qfhs.ifa-5A) - treatment: Fusarium graminearum strain IFA-65 - time: 72 hai - rep1

description: genotype=NIL1 (resistant, Fhb1, Qfhs.ifa-5A)|treatment=Fusarium graminearum strain IFA-65|time=72 hai rep 1 (May still include original submitter created erros/discrepancies)

source_name: Spike (genotype: NIL1 (resistant, Fhb1, Qfhs.ifa-5A) - treatment: Fusarium graminearum strain IFA-65 - time: 72 hai)

value: 72 hai


title: genotype: NIL1 (resistant, Fhb1, Qfhs.ifa-5A) - treatment: Fusarium graminearum strain IFA-65 - time: 72 hai - rep3

description: genotype=NIL1 (resistant, Fhb1, Qfhs.ifa-5A)|treatment=Fusarium graminearum strain IFA-65|time=72 hai rep 3 (May still include original submitter created erros/discrepancies)


title: genotype: NIL1 (resistant, Fhb1, Qfhs.ifa-5A) - treatment: Fusarium graminearum strain IFA-65 - time: 72 hai - rep2

description: genotype=NIL1 (resistant, Fhb1, Qfhs.ifa-5A)|treatment=Fusarium graminearum strain IFA-65|time=72 hai rep 2 (May still include original submitter created erros/discrepancies)


title: genotype: NIL1 (resistant, Fhb1, Qfhs.ifa-5A) - treatment: Fusarium graminearum strain IFA-65 - time: 24 hai - rep1

description: genotype=NIL1 (resistant, Fhb1, Qfhs.ifa-5A)|treatment=Fusarium graminearum strain IFA-65|time=24 hai rep 1 (May still include original submitter created erros/discrepancies)


title: Serous Ovarian Cancer 76

value: IV

value: suboptimal resection >1cm of tumor left


title: Serous Ovarian Cancer 77

value: IA

value: optimal resection <1cm of tumor left


title: Serous Ovarian Cancer 72

value: CBDCA+TAX


title: Serous Ovarian Cancer 78

value: IIIC


title: genotype: NIL1 (resistant, Fhb1, Qfhs.ifa-5A) - treatment: water - time: 8 hai - rep3

description: genotype=NIL1 (resistant, Fhb1, Qfhs.ifa-5A)|treatment=water|time=8 hai rep 3 (May still include original submitter created erros/discrepancies)

value: water

value: 8 hai

value: garden soil


title: genotype: NIL1 (resistant, Fhb1, Qfhs.ifa-5A) - treatment: Fusarium graminearum strain IFA-65 - time: 8 hai - rep3

description: genotype=NIL1 (resistant, Fhb1, Qfhs.ifa-5A)|treatment=Fusarium graminearum strain IFA-65|time=8 hai rep 3 (May still include original submitter created erros/discrepancies)

source_name: Spike (genotype: NIL1 (resistant, Fhb1, Qfhs.ifa-5A) - treatment: Fusarium graminearum strain IFA-65 - time: 8 hai)

value: NIL1 (resistant, Fhb1, Qfhs.ifa-5A)

value: Remus,  CM82036

value: Spike


title: genotype: NIL1 (resistant, Fhb1, Qfhs.ifa-5A) - treatment: Fusarium graminearum strain IFA-65 - time: 24 hai - rep3

description: genotype=NIL1 (resistant, Fhb1, Qfhs.ifa-5A)|treatment=Fusarium graminearum strain IFA-65|time=24 hai rep 3 (May still include original submitter created erros/discrepancies)

value: Fusarium graminearum strain IFA-65

value: 24 hai

value: Anthesis


title: genotype: NIL1 (resistant, Fhb1, Qfhs.ifa-5A) - treatment: Fusarium graminearum strain IFA-65 - time: 8 hai - rep2

description: genotype=NIL1 (resistant, Fhb1, Qfhs.ifa-5A)|treatment=Fusarium graminearum strain IFA-65|time=8 hai rep 2 (May still include original submitter created erros/discrepancies)


title: genotype: NIL1 (resistant, Fhb1, Qfhs.ifa-5A) - treatment: water - time: 24 hai - rep2

description: genotype=NIL1 (resistant, Fhb1, Qfhs.ifa-5A)|treatment=water|time=24 hai rep 2 (May still include original submitter created erros/discrepancies)


title: Serous Ovarian Cancer 66

source_name: serous epithelial ovarian carcinoma, no response

value: serous epithelial ovarian carcinoma

value: serous

value: explorative laparotomy

value: no response


title: Serous Ovarian Cancer 71

source_name: serous epithelial ovarian carcinoma, complete response

value: suboptimal resection >1cm of tumor left

value: complete response


title: Serous Ovarian Cancer 67

value: IVB

value: CBDCA+TAX


title: Serous Ovarian Cancer 70

source_name: serous epithelial ovarian carcinoma, partial response

value: IVA

value: partial response


title: Serous Ovarian Cancer 60

value: IIIC


title: Serous Ovarian Cancer 63

value: IIC

value: optimal resection <1cm of tumor left


title: Serous Ovarian Cancer 65


title: genotype: NIL1 (resistant, Fhb1, Qfhs.ifa-5A) - treatment: Fusarium graminearum strain IFA-65 - time: 8 hai - rep1

description:
Inoculum production, inoculation and tissue sampling
The intermediate aggressive Fusarium graminearum isolate ’IFA 65‘ was used for the production of macroconidia in liquid mungbean medium as described by (Buerstmayr et al. 2002; Buerstmayr et al. 2000). Spores were harvested from the medium by multiple centrifugation and washing steps with double-distilled water. Aliquotes of 20,000 spores/ml were shock-frozen at - 80°C and used as 100 x stocks for subsequent wheat inoculations. Aggressiveness of the inoculum was checked by inoculation of several wheat-heads of cv. Remus weeks prior the main experiment.
As plants gradually reached anthesis the lines were challenged by inoculating with 10 μl of the Fusarium spore suspension (20 conidia per μl) or water, pipetted between palea and lemma of the two basal florets of six central spikelets per spike. After inoculation heads were sprayed with water and covered with clear plastic bags for 24 hours to maintain high humidity. Five heads per genotype, treatment and replication were harvested 8, 24 and 72 hours after inoculation. Treated spikelets were separated into lemma, palea and the subtending section of the rachis and the reproductive tissues, immediately shock frozen in liquid nitrogen and stored at − 80°C.
For phenotype scoring one central spikelet (two florets) of 50 wheat heads per genotype was inoculated on the field with 100 conidia per floret and diseased spikelets were counted after 12, 18 and 24 days. Statistical significant differences were calculated by t-test. The experiment was replicated twice.
RNA preparation and microarray hybridization
Of the 15 biological replicates each five samples derived from lemma, palea and rachis were pooled and ground to fine powder using a mixer mill (type MM 301, Retsch, Düsseldorf, Germany), resulting in a total of 90 samples (5 genotypes × 2 inoculation treatments × 3 sampling times x 3 replications,). RNA was extracted from 100 mg ground tissue (peqGOLD RNAPure, peqLab, Erlangen, Germany), treated with DnaseI (Invitrogen, Carlsbad, CA, USA) and purified using the RNeasy Mini Kit (Qiagen, Hilden, Germany). In total about 1 g of ground tissue was used for extraction of genomic DNA and metabolites described in the following sections.
We employed the Affymetrix wheat Genome Array (Affymetrix, Santa Clara, CA) for identification of differential transcript accumulation in our samples. The microarray design consists of 61,127 probe sets, representing 55,052 transcripts generated from public Genbank and EST content (Unigene build #38, April 24, 2004). Generation of labeled cRNA, hybridization and data acquisition were performed at the Microarray Facility of the University of Minnesota following the manufacturers protocol. (May still include original submitter created erros/discrepancies)

value: NIL1 (resistant, Fhb1, Qfhs.ifa-5A)

value: 8 hai

value: Remus,  CM82036

value: Spike

value: garden soil


title: Serous Ovarian Cancer 57

value: serous epithelial ovarian carcinoma

value: serous


title: Serous Ovarian Cancer 56


title: Serous Ovarian Cancer 59

value: stable disease


title: Serous Ovarian Cancer 64

value: suboptimal resection >1cm of tumor left

value: no response


title: Serous Ovarian Cancer 55

value: explorative laparotomy


title: Serous Ovarian Cancer 54

value: IIIB

value: CBDCA+TAX

value: complete response


title: Serous Ovarian Cancer 51


title: Serous Ovarian Cancer 52

value: IIIC


title: Serous Ovarian Cancer 49


title: Serous Ovarian Cancer 53

value: IIC


title: Serous Ovarian Cancer 50

value: IV


title: Serous Ovarian Cancer 48


title: genotype: NIL1 (resistant, Fhb1, Qfhs.ifa-5A) - treatment: water - time: 72 hai - rep2

description: genotype=NIL1 (resistant, Fhb1, Qfhs.ifa-5A)|treatment=water|time=72 hai rep 2 (May still include original submitter created erros/discrepancies)

value: NIL1 (resistant, Fhb1, Qfhs.ifa-5A)

value: water

value: 72 hai

value: Anthesis


title: genotype: NIL3 (moderately resistant, Qfhs.ifa-5A) - treatment: water - time: 24 hai - rep1

description: genotype=NIL3 (moderately resistant, Qfhs.ifa-5A)|treatment=water|time=24 hai rep 1 (May still include original submitter created erros/discrepancies)

value: 24 hai

value: Remus,  CM82036

value: Spike

value: garden soil


title: Serous Ovarian Cancer 46

value: serous epithelial ovarian carcinoma

value: serous

value: partial response


title: Serous Ovarian Cancer 47

value: explorative laparotomy


title: P28 (W028)

city: Stanford

first: Bo

last: Wu

state: Ca

address: 300 Pasteur Dr. Grant/S259

department: Urology

institute: Stanford University

description: Image: http://smd.stanford.edu/MicroArray/gifs/2009-04/83271.gif

hyb_protocol: not provided

scan_protocol: Scanner Model: G2505C

data_processing: VALUE log RED/GREEN

source_name: Mouse universal reference RNA

label_protocol: not provided

extract_protocol: not provided

tag: reference

value: Mouse universal reference RNA

source_name: Normal mice kidney RNA day 28

label_protocol: 5 ug of total RNA were primed with T7 Promoter Primer at 65 oC for 10 min, then reversed transcribed at 40 oC for 2 h in the presence of MMLV-RT, and 10 mM dNTP, Cy3- or Cy5-label

growth_protocol: operation_protocol: Mice were anesthetized and subjected to unilateral obstruction for 1 day, 2 days, 5 days or 9 days. The left ureter was ligated to generate an obstructed kidney. For each time point additional mice underwent dissection of the left ureter without ligation to serve as sham controls

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

tag: strain

value: kidney

tag: age


title: Serous Ovarian Cancer 44

value: CBDCA+TAX

value: no response


title: P03 (W016)

description: Image: http://smd.stanford.edu/MicroArray/gifs/2009-04/83267.gif

source_name: Normal mice kidney RNA day 3

value: 3 d


title: P07 (W004)

description: Image: http://smd.stanford.edu/MicroArray/gifs/2009-03/83059.gif

source_name: Normal mice kidney RNA day 7

value: 7 d


title: Serous Ovarian Cancer 42

value: IIA

value: complete response


title: P14 (W006)

description: Image: http://smd.stanford.edu/MicroArray/gifs/2009-03/83060.gif

source_name: Normal mice kidney RNA day 14


title: P05 (W003)

description: Image: http://smd.stanford.edu/MicroArray/gifs/2009-03/83224.gif

source_name: Normal mice kidney RNA day 5

value: 5 d


title: P35 (W058)

description: Image: http://smd.stanford.edu/MicroArray/gifs/2009-04/83278.gif

source_name: Normal mice kidney RNA day 35


title: Serous Ovarian Cancer 41

value: IIIC

value: optimal resection <1cm of tumor left


title: P21 (W051)

description: Image: http://smd.stanford.edu/MicroArray/gifs/2009-03/83062.gif

source_name: Normal mice kidney RNA day 21


title: Serous Ovarian Cancer 39

value: IIIB

value: suboptimal resection >1cm of tumor left


title: Serous Ovarian Cancer 38

value: serous epithelial ovarian carcinoma


title: P03 (W001)

description: Image: http://smd.stanford.edu/MicroArray/gifs/2009-03/83056.gif


title: P05 (W002)

description: Image: http://smd.stanford.edu/MicroArray/gifs/2009-03/83058.gif


title: Serous Ovarian Cancer 40

source_name: serous epithelial ovarian carcinoma, stable disease

value: serous

value: stable disease


title: P28 (W027)

description: Image: http://smd.stanford.edu/MicroArray/gifs/2009-04/83270.gif


title: Serous Ovarian Cancer 36


title: E19 (W061)

description: Image: http://smd.stanford.edu/MicroArray/gifs/2009-04/83279.gif

source_name: Normal mice kidney RNA embryo 19

value: Embryo stage 19 d


title: P10 (W012)

description: Image: http://smd.stanford.edu/MicroArray/gifs/2009-03/83057.gif

value: Mouse universal reference RNA

source_name: Normal mice kidney RNA day 10


title: P10 (W013)

description: Image: http://smd.stanford.edu/MicroArray/gifs/2009-03/83227.gif

value: kidney


title: Serous Ovarian Cancer 45

value: IV

value: CBDCA+TAX


title: P35 (W030)

description: Image: http://smd.stanford.edu/MicroArray/gifs/2009-04/83273.gif


title: P07 (W005)

description: Image: http://smd.stanford.edu/MicroArray/gifs/2009-03/83225.gif


title: P10 (W037)

description: Image: http://smd.stanford.edu/MicroArray/gifs/2009-04/83274.gif


title: P05 (W010)

description: Image: http://smd.stanford.edu/MicroArray/gifs/2009-04/83265.gif


title: P14 (W039)

description: Image: http://smd.stanford.edu/MicroArray/gifs/2009-04/83275.gif


title: E19 (W060)

description: Image: http://smd.stanford.edu/MicroArray/gifs/2009-03/83063.gif


title: E19 (W062)

description: Image: http://smd.stanford.edu/MicroArray/gifs/2009-03/83232.gif


title: P01 (W019)

description: Image: http://smd.stanford.edu/MicroArray/gifs/2009-04/83269.gif

source_name: Normal mice kidney RNA day 1

value: 1 d


title: P14 (W007)

description: Image: http://smd.stanford.edu/MicroArray/gifs/2009-03/83226.gif


title: P01 (W014)

description: Image: http://smd.stanford.edu/MicroArray/gifs/2009-03/83061.gif


title: Serous Ovarian Cancer 35

value: IB

value: explorative laparotomy

value: partial response


title: Serous Ovarian Cancer 30

value: no response


title: Serous Ovarian Cancer 31


title: antral (aspirated) granulosa - after LH - Biological Rep 2 - Cow B

city: Kansas City

first: Sumedha

last: Gunewardena

state: Kansas

address: 3901 Rainbow Boulevard

institute: University of Kansas Medical Center

description: gene expresssion data from bovine ovarian cells

hyb_protocol: 200ul hybridization solution per GeneChip using GeneChip Hybridization, Wash and Stain Kit.

scan_protocol: Single Scan; Affymetrix GeneChip Scanner 3000 7G with Autoloader; Affymetrix GeneChip Command Console (AGCC) ver. 1.1

data_processing: The data were analyzed with Partek Genomics Suite version 6.5 (RMA) using RMA default analysis settings: RMA Background Correction; Quantile Normalization; Median Polish probeset summarization.

organism: Bos taurus

source_name: bovine preovulatory follicle - post GnRH

label_protocol: Biotinylated In-vitro Transcription using the GeneChip 3` IVT Express Kit

growth_protocol: Samples were collected before the LH surge and after 22 hours after the LH surge

extract_protocol: Trizol / Phase lock gel protocol

treatment_protocol: Ovarian granulosa (aspirated/antral and membrane-associated) and theca cells were isolated from ovaries of cows before and after the LH surge. GC = membrane associated, Antral = aspirated granulosa cells, Th = thecal cells.

tag: cell type

value: antral (aspirated) granulosa


title: P01 (W015)

description: Image: http://smd.stanford.edu/MicroArray/gifs/2009-04/83266.gif

tag: tissue


title: Serous Ovarian Cancer 28

value: IIIC


title: P35 (W029)

description: Image: http://smd.stanford.edu/MicroArray/gifs/2009-04/83272.gif


title: Serous Ovarian Cancer 34

value: IIC


title: P03 (W017)

description: Image: http://smd.stanford.edu/MicroArray/gifs/2009-04/83268.gif

value: 3 d


title: antral (aspirated) granulosa - after LH - Biological Rep 3 - Cow C


title: antral (aspirated) granulosa - before LH - Biological Rep 1 - Cow D

source_name: bovine preovulatory follicle - pre GnRH


title: P35 (W055)

description: Image: http://smd.stanford.edu/MicroArray/gifs/2009-03/83231.gif


title: Serous Ovarian Cancer 27

value: serous epithelial ovarian carcinoma

value: suboptimal resection >1cm of tumor left


title: Serous Ovarian Cancer 32

source_name: serous epithelial ovarian carcinoma, no response

value: IA

value: serous


title: Serous Ovarian Cancer 24

source_name: serous epithelial ovarian carcinoma, complete response

value: IIA

value: complete response


title: Serous Ovarian Cancer 26


title: Serous Ovarian Cancer 22


title: theca - after LH - Biological Rep 3 - Cow C

value: theca


title: Serous Ovarian Cancer 29

source_name: serous epithelial ovarian carcinoma, partial response

value: CBDCA+TAX


title: P07 (W021)

description: Image: http://smd.stanford.edu/MicroArray/gifs/2009-03/83228.gif

source_name: Mouse universal reference RNA

value: Mouse universal reference RNA

value: kidney

value: 7 d


title: P21 (W042)

description: Image: http://smd.stanford.edu/MicroArray/gifs/2009-04/83277.gif


title: Serous Ovarian Cancer 23


title: Serous Ovarian Cancer 21

value: optimal resection <1cm of tumor left


title: antral (aspirated) granulosa - after LH - Biological Rep 1 - Cow A


title: Serous Ovarian Cancer 19

value: IB


title: Serous Ovarian Cancer 20

value: IV

value: explorative laparotomy

value: no response


title: Serous Ovarian Cancer 18


title: theca - before LH - Biological Rep 2 - Cow F


title: theca - after LH - Biological Rep 2 - Cow B


title: theca - before LH - Biological Rep 3 - Cow G


title: membrane-associated Granulosa - before LH - Biological Rep 3 - Cow G

value: membrane-associated Granulosa


title: P03 (W008)

description: Image: http://smd.stanford.edu/MicroArray/gifs/2009-04/83264.gif

value: 3 d


title: Serous Ovarian Cancer 16

value: serous epithelial ovarian carcinoma

value: IIIC

value: suboptimal resection >1cm of tumor left


title: P28 (W024)

description: Image: http://smd.stanford.edu/MicroArray/gifs/2009-03/83229.gif

source_name: Normal mice kidney RNA day 28


title: membrane-associated Granulosa - after LH - Biological Rep 1 - Cow A


title: theca - before LH - Biological Rep 1 - Cow D


title: membrane-associated Granulosa - after LH - Biological Rep 3 - Cow C


title: Serous Ovarian Cancer 11

value: IIIB

value: serous


title: Serous Ovarian Cancer 15

value: stable disease


title: Serous Ovarian Cancer 12

value: IIA

value: CBDCA+TAX


title: Serous Ovarian Cancer 14

value: complete response


title: Serous Ovarian Cancer 13


title: Biological replicate 2 of 2; the pH shift experiment sample

city: Groningen

first: Ana

last: Solopova

address: Nijenborgh 7

department: MolGen

country: Netherlands

institute: RUG

hyb_protocol: cDNA of concentration 200ng/µL with label incorporation of at least 1pmol/µL was used for hybridisation. Samples were incubated at 94°C for 2 min. Preheated (68°C) Hybridisation buffer was added and the whole sample incubated for 5 min at 68°C. Then 40µL of the sample was loaded on the microarray slide and hybridised at 45°C in the hybridisation oven overnight.

scan_protocol: Slides were scanned using GenePix 4200 slide scanner using 10µm resolution

data_processing: Slide images were analyzed using ArrayPro 4.5 (Media Cybernetics Inc., Silver Spring, MD). Processing and normalization (LOWESS spot pin based) of slides were done with MicroPrep software

label: Cy3 (A)

organism: Lactococcus cremoris subsp. cremoris MG1363

source_name: Shift pH 6.5 to 5.1

label_protocol: Amino allyl labelled cNA was purified using NucleoSpin extract II columns and Cy3 or Cy5 dyes were incorporated at pH 9.0

growth_protocol: L. lactis was grown in a 2-liter fermenter in chemically defined medium containing 1% (wt/vol) glucose at 30°C with pH controlled at 6.5 or 5.1.

extract_protocol: Total RNA was extracted using Roche RNA isolation kit. 10-20 µg of total RNA was mixed with random nonamers and amino allyl-dUTP/nucleotide mix, Superscript III reverse transcriptase and the buffer was added to the reaction mix. Reaction was performed in 42°C for 16 hours.

treatment_protocol: Cells were harvested during mid-exponential phase, washed with 5mM potassium phosphate (KPi) and suspended in 50mM KPi buffer of either pH 6.5 or 5.1.

label: Cy5 (B)

source_name: Control pH 5.1 to 5.1


title: Biological replicate 1 of 2; dye swap; control experiment, pre-adapted cells


title: Serous Ovarian Cancer 10

value: partial response


title: antral (aspirated) granulosa - before LH - Biological Rep 2 - Cow F

value: antral (aspirated) granulosa


title: theca - after LH - Biological Rep 1 - Cow A

value: theca


title: Biological replicate 2 of 2; dye swap; control experiment, pre-adapted cells


title: Biological replicate 2 of 2, dye swap; the pH shift experiment sample


title: Biological replicate 2 of 2; control experiment, pre-adapted cells


title: Serous Ovarian Cancer 9

value: optimal resection <1cm of tumor left


title: Biological replicate 1 of 2; control experiment, pre-adapted cells


title: membrane-associated Granulosa - after LH - Biological Rep 2 - Cow B


title: Biological replicate 1 of 2; dye swap; the pH shift experiment


title: Serous Ovarian Cancer 7

value: IV


title: Serous Ovarian Cancer 5

value: explorative laparotomy


title: antral (aspirated) granulosa - before LH - Biological Rep 3 - Cow G


title: membrane-associated Granulosa - before LH - Biological Rep 2 - Cow F

value: membrane-associated Granulosa


title: Serous Ovarian Cancer 8

value: IIIA


title: Biological replicate 1 of 2; the pH shift experiment


title: membrane-associated Granulosa - before LH - Biological Rep 1 - Cow D


title: Serous Ovarian Cancer 3

value: serous epithelial ovarian carcinoma


title: Serous Ovarian Cancer 2

value: no response


title: Serous Ovarian Cancer 6

value: IIIC


title: optic nerve head, control, biological rep4

city: Boston

first: Tatjana

last: Jakobs

state: MA

address: 20 Staniford Street

department: Howe Laboratory of Ophthalmology

institute: Massachusetts Eye and Ear Infirmary

description: gene expression data from normal contralateral control optic nerve heads

hyb_protocol: Fragmented cDNA was hybridized to the GeneChip Mouse Genome 430A 2.0 arrays in an Affymetrix hybridization oven 645. Affymetrix GeneChip Fluidics Station 450 was used for array washing and staining.

scan_protocol: Affymetrix GeneChip Scanner 3000 was used for array scanning and generating scan data.

data_processing: The data were analyzed using DChip software.  The overall intensity of each array was normalized to the median intensity of all the arrays using the “Invariant Set Normalization” method.

source_name: optic nerve head, contralateral control, normal

label_protocol: 30 ng of total RNA from each sample was reversed transcribed and amplified using the Ovation RNA Amplification System V2 (NuGEN).  The amplified cDNA was biotin labeled using Encore Biotin Module (NuGen).

growth_protocol: Mice were housed under standard conditions.

extract_protocol: Total RNA was extracted using RNeasy Plus Micro Kit (Qiagen).  The integrity and concentration of the isolated total RNA was confirmed by analysis on a Bioanalyzer 2100 using PicoChips (Agilent Technologies).  The RNA integrity number (RIN) for all samples was greater than 9.1.

treatment_protocol: The intraocular pressure of the right eye was elevated to 30 mmHg for 1 hour by cannulating the anterior chamber with a glass micropipette attached to a sterile saline bag. The left eye was not operated on. The optic nerve head was collected 3 days after the surgery.

tag: gender

value: male

value: 6-8 weeks


title: optic nerve head, high IOP, biological rep3

description: gene expression data from optic nerve heads that experienced elevated intraocular pressure

source_name: optic nerve head, IOP at 30 mmHg for 1 hour, recover for 3 days


title: optic nerve head, high IOP, biological rep5


title: optic nerve head, high IOP, biological rep2


title: optic nerve head, control, biological rep3


title: optic nerve head, control, biological rep2


title: Liver from 12 weeks old rat, biological rep 2

city: Delhi

first: aparna

last: dixit

address: New Meharuli Road,

country: India

institute: JNU

description: gene expression data from liver of 12 weeks old rat

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: The data was RMA summarized in Expression Console software and subsequently analyzed for differential expression. The  statistical analysis was performed using R-programming language and the biological analysis was carried out using GenowizTM software.

organism: Rattus norvegicus

source_name: liver of 12 weeks old animal

label_protocol: Standard Affymetrix protocol

growth_protocol: Healthy female Wistar rats of different age groups (2 weeks, 4 weeks and 12 weeks) were procured from the Animal House facility of Jawaharlal Nehru University, New Delhi. . Partially hepatectomized rats and all other different age group rats were maintained in a properly ventalized air conditioned rooms in animal house having controlled temperature (25ºC to 28ºC) with a photoperiod of 12 h and were cared for according to the guidelines laid down by the Institutional Animal Ethics Committee of the University.

extract_protocol: Total RNA was isolated from each frozen liver samples using Tri reagent (Trizol) as per the manufacturer’s protocol. Each sample was collected in duplicate and  checked for quality of total RNA.

treatment_protocol: For collecting regenerating rat liver, animals were subjected to partial hepatectomy by removal of 2/3 mass of liver (removal of lateral liver lobes), ligation of the remaing liver lobes, followed by closure of the abdominal cavity using standard surgical procedure. The animals were given post-operative care.The partially hepatectomized animals were sacrificed at 8 h post-surgery to obtain samples of regenerting rat livers.   Liver tissue samples were collected from different age group animals and partially hepatectomized animals  in RNA later and stored in -80 ºC.

value: Wistar

value: adult liver

value: female


title: WT_root_0.25_uM_Cd_4_days_biological_rep3

city: Warsaw

first: Danuta

middle: Maria

last: Antosiewicz

address: Miecznikowa 1

department: Plant Anatomy and Cytology

country: Poland

institute: University of Warsaw

description: gene expression of Wild typ tobacco exposed for Cd

hyb_protocol: RNA hybridization to tobacco cDNA microarray Affymetrix ATCTOBa520488 (Edwards et al., 2010) was conducted in the Nottingham Arabidopsis Stock Centre (NASC, http://arabidopsis.info/) (Craigon et al., 2004) according to manufacturer’s recommendations (Affymetrix)

scan_protocol: Agilent 2500A GeneArray Scanner

data_processing: The data were analyzed with dCHIP using default analysis settings and invariant set and running median smoothing (Li and Wong 2001) as normalization method acording to dCHIP analysis protocol.  Baseline array used was: Antosiewicz_3_WT_Roots_Rep3_ATCTOBa (Median probe intesity 109).

organism: Nicotiana tabacum

source_name: 4 weeks old tobacco plants exposed for 0.25 uM of Cd for 4 days

label_protocol: Labelling of RNA samples was performed by use of the Affymetrix 3’ IVT-Express kit (Affymetrix UK Ltd., High Wycombe, UK) following standard Affymetrix protocols (Affymetrix UK Ltd., High Wycombe, UK).

growth_protocol: Seeds were surface sterilized in 8% sodium hypochloride and germinated on ¼ Knop’s medium supplemented with 2% (v:v) sucrose and solidified with 1% agar on Petri dishes positioned vertically. Two-week old seedlings were transferred to 2-L pots containing ¼ Knop’s liquid medium for two weeks. The nutrient solution was renewed every 4 days. General conditions of plant cultivation: growth chamber, 23/16 C day/night temperatures, 40-50% humidity, with a 16-h photoperiod at a quantum flux density (PAR) of 250 µmol m-2 s-1 using fluorescent Flora tubes

extract_protocol: RNeasy Plant Mini Kit (Qiagen, Hilden, Germany) according to manufacturer’s recommendations, followed by DNase I digestion (Invitrogen)

treatment_protocol: The plants of the same size were transferred to basic nutrient solution (1/4 Knop's medium) supplemented with 0.25 µM Cd (added as CdCl2) for four days.

tag: organ

value: roots

value: var. Xanthi wild type

value: 5 weeks


title: optic nerve head, control, biological rep5


title: Liver from 12 weeks old rat, biological rep 1


title: 35S:AtHMA4_root_0.25_uM_Cd_4_days_biological_rep1

description: gene expression of 35S::AtHMA4 expressing tobacco exposed for Cd

value: var. Xanthi, 35S:AtHMA4 expressing


title: optic nerve head, control, biological rep1


title: optic nerve head, high IOP, biological rep1


title: optic nerve head, high IOP, biological rep4


title: 35S:AtHMA4_root_0.25_uM_Cd_4_days_biological_rep2


title: Liver from 4 weeks old rat, biological rep 2

description: gene expression data from liver of 4 weeks old rat

source_name: liver of 4 weeks old animal

value: developing liver


title: 35S:AtHMA4_root_0.25_uM_Cd_4_days_biological_rep3


title: BD-5

city: Osaka

first: Tsukasa

last: Kawaguchi

address: 2-2 Yamada-oka, Suita

department: Gastroenterology and Hepatology

country: Japan

institute: Osaka University Graduate School of Medicine

description: Gene expression after 2hr in CBZ-treated mouse liver

hyb_protocol: Cy3 labeled cRNAs were hybridized overnight (17 hours, 65°C) to Agilent Whole Mouse Genome Oligo Microarrays 8x60K using Agilent’s recommended hybridization chamber and oven.Finally, microarrays were washed once with wash buffer 1 for 1 min at RT followed by a second wash with wash buffer 2 for 1 min at 37°C.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent’s Microarray Scanner System (G2505C, Agilent Technologies, Palo Alto, USA).

data_processing: The Agilent Feature Extraction Software (FES 10.7.3.1 ) was used to read out and process the microarray image files.

source_name: Whole liver, 2hr, CBZ, 2

label_protocol: 100 ng of each RNA was used as template to produce Cy3- labeled cRNA. The RNA samples were amplified and labeled using the Low Input Quick Amp Labeling Kit (Agilent Technologies) following the manufacturer’s protocol.

extract_protocol: Total RNA was isolated from liver tissue using  RNeasy Mini kit (QIAGEN) following manufacturer's instructions

treatment_protocol: C57BL6/J mice were orally administered 250 mg/kg of CBZ or DMSO and sacrificed 2 hours later.

value: whole liver


title: BD-2

description: Gene expression after 2hr in DMSO-treated mouse liver

source_name: Whole liver, 2hr, DMSO, 2


title: BD-4

source_name: Whole liver, 2hr, CBZ, 1


title: BD-1

source_name: Whole liver, 2hr, DMSO, 1


title: WT_root_0.25_uM_Cd_4_days_biological_rep2


title: BD-6

source_name: Whole liver, 2hr, CBZ, 3


title: Liver from 4 weeks old rat, biological rep 1


title: BD-3

source_name: Whole liver, 2hr, DMSO, 3


title: WT_root_0.25_uM_Cd_4_days_biological_rep1


title: MYC2 VIGS_1h_Os_induction_rep3

city: Jena

first: Klaus

last: Gase

address: Hans-Knoell-Strasse 8

department: Molecular Ecology

institute: Max-Planck-Institute for Chemical Ecology

description: Gene expression after 1hr of induction with oral secretions from Manduca sexta larvae

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent platform GPL13527 for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed at room temperature with GE Wash Buffer 1 (Agilent) and at 37°C with GE Wash buffer 2 (Agilent) as outlined in the One-Color Microarray-Based Gene Expression Analysis manual (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565BA) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: Data was acquired with the Agilent Scan Control software (version A.7.0.1 for the B scanner) and extracted using the Agilent Feature Extraction software (version 9.5). Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. 75 percentile normalization was performed for each array of raw data (keeping the controls in the list). Log transformation was done. Controls were removed from the list. All replicated probes were averaged.

organism: Nicotiana attenuata

source_name: MYC2 VIGS leaves, 1hr, oral secretion elicitation, replicate 3

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the Quick Amp labeling kit (Agilent, Santa Clara, CA) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Hilden, Germany).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Seeds from N. attenuata WT plants were grown in the growth chamber under high-pressure sodium lamps (200-300 µmol s-1 m-2 light) with a day/night cycle of 16 h /8 h, 22°C and 45 to 55% humidity. Transcripts of NaMYC2 were knocked down using Virus Induced Gene Silencing.

extract_protocol: Total RNA was extracted from leaves using the Plant RNeasy kit (Qiagen, Hilden, Germany) and its quality checked by spectrophotometry (NanoDrop, Wilmington, DE). Genomic DNA was removed by DNAse treatment following commercial instructions (Turbo DNase; Ambion, Europe), RNA was cleaned up with RNeasy MinElute columns (Qiagen) and the RNA quality was checked with the RNA 6000 Nano kit (Agilent, Santa Clara, CA) using an Agilent 2100 Bioanalyzer (Agilent).

treatment_protocol: For elicitation treatment, leaves were wounded by rolling a fabric-pattern wheel three times on each side of the midvein and the wounds were supplemented with 20 microliters of Manduca sexta oral secretions diluted 1/5 (v/v) in water.

value: leaves

tag: knockdown

tag: treatment

value: oral secretions of Manduca sexta larvae


title: main population-DPCs

city: Okayama-shi

first: Emilio

middle: Satoshi

last: Hara

state: Okayama-ken

address: Shikata-cho 2-5-1

institute: Okayama University

description: enriched in differentiated cells

hyb_protocol: Denature the solution at 95 ℃ for 5 min.  Centrifuge at 12,000 g at 4 ℃ for 2 min.  Add 30 μL of 20 x salt Buffer to ditch of “Hybridization Chamber”.  Slide is capped by “MASTUNAMI Gap Cover Glass (CG00044 or 24*60 25PCS)”.  Fill the gap with 45 μL of the solution.  Incubate in 56 ℃ water bath for 16-20 hr.  <Day2>  Wash  Separate gap cover glass from the slide in “Wash buffer A” (pre-heated at 56 ℃).  Wash with “Wash buffer A” (pre-heated at 56 ℃) for 2 min.  Wash briefly (one plunge) with “Wash buffer B”.  Wash with “Wash buffer B” for 2 min.  Wash with “Wash buffer C” for 2 min.  Centrifuge at 1000 rpm for 5 min.

scan_protocol: Scanner; G2505C (Agilent)  Software; Agilent Scan Control (Agilent)  Green and Red PMT: 100 %, Scan resolution: 10 um,

data_processing: Software; Feature Extraction 10.7.3.1 (Agilent) ・Probe Name, ・Gene Name, ・gProcessed Signal (Hy3), Calculate the average of replicated spots (Hy3 data). Average of signal intensity in 4 repeated spots in the array was considered as the final data for each probe.

source_name: main population of human dental pulp cells

label_protocol: （miRCURY LNA microRNA Array Hi-Power Labeling kit）  (Mixture: 1 rxn.)  -------------------------------  Labeling Buffer: 3 μL  DMSO: 2 μL  Labeling enzyme: 1 μL  -------------------------------  Total: 6 μL  Add  CIP reaction: 5 μL  Hy3 Fluorescent label: 1.5 μL  Incubate at 16 ℃ for 2 hr, at 65 ℃ 15 min.

extract_protocol: total RNA was collected with RNAzol RT (Molecular Research Center, OH, USA). A total of 250 ng of total RNA from MP cells was used for microRNA array. In the case of SP cells, since there was not satisfactory amount of RNA due to the extremely low number of sorted cells (0.1%), a total of 3 μL was applied for the array.


title: side population-DPCs

description: enriched in stell cells

source_name: side population of human dental pulp cells


title: side population-PDLCs

description: enriched in stell cells

source_name: side population of human periodontal ligament cells


title: MYC2 VIGS_1h_Os_induction_rep1

source_name: MYC2 VIGS leaves, 1hr, oral secretion elicitation, replicate 1


title: main population-PDLCs

description: enriched in differentiated cells

source_name: main population of human periodontal ligament cells


title: P21 (W041)

description: Image: http://smd.stanford.edu/MicroArray/gifs/2009-04/83276.gif

source_name: Mouse universal reference RNA

value: Mouse universal reference RNA

source_name: Normal mice kidney RNA day 21

value: kidney


title: EV_1h_Os_induction_rep3

source_name: Empty vector leaves, 1hr, oral secretion elicitation, replicate 3

value: control


title: Regenerating rat liver, biological rep 2

description: gene expression data of 8h regenerating rat liver

source_name: liver from partially hepatectomized (2/3 hepatectomy) rat at 8h post-surgery

value: regenerating  liver


title: B6, CD4+ T cells, rep2

city: Burlington

first: Laure

last: Case

address: 89 Beaumont Ave

institute: University of Vermont

hyb_protocol: After purification and fragmentation, biotinylated-cDNA targets were hybridized to the Mouse Gene 1.0 ST Arrays oligonucleotide arrays for 16 hours at 45oC. Hybridized arrays were washed and stained with streptavidin-phycoerythrin followed by sequential incubations with biotin-coupled polyclonal anti-streptavidin antibody and streptavidin phycoerythrin as a fluorescent amplification step.

scan_protocol: After staining, arrays were scanned (3000-7G Scanner, Affymetrix Inc., Santa Clara, CA) and data collected for statistical analysis.

data_processing:
Raw GeneChip data (one DAT file for each chip) includes a collection of images, one for each probe and chip. Each image was summarized by Affymetrix GCOS software using one probe intensity (in CEL files, one per chip).sample.
Information from multiple probes was combined to obtain a single measure of expression for each probe set and sample. Probe-level intensities were calculated using the Robust Multichip Average (RMA) algorithm, including background-correction, normalization (quantile), and summarization (median polish), for each probe set and sample, as is implemented in Partek Genomic Suites®, version 6.6 (Copyright © 2009, Partek Inc., St. Louis, MO, USA).
probe group file: MoGene-1_0-st-v1.r4.pgf
meta-probeset file: MoGene-1_0-st-v1.na32.mm9.transcript.csv

label: Biotin

source_name: C57BL/6J, CD4+TCRB+ cells, naive

label_protocol: Oligonucleotide microarray analysis of RNA expression levels was performed in the Vermont Genetics Network Microarray Facility using the Affymetrix GeneChip Platform (Affymetrix Inc., Santa Clara, CA) according to manufacturer's protocols. In brief, the Nugen Ovation system v.2 with SPIA® RNA amplification was employed to convert 50ng of total RNA to cDNA. This isothermal RNA amplification system produces 5-12 ug of anti-sense cDNA targets that is followed by several steps to produce sense strand cDNA to be fragmented, biotinylated and hybridized to the GeneChip.

extract_protocol: Three biological replicates were pooled from the axillary, brachial, and inguinal lymph nodes from 5 mice for each replicate. Cells were washed with PBS/1%FCS, pelleted at 300g for 5 min at 4oC. A working stock of Live/Dead-775 dye (Invitrogen L10119) was made by adding 1ul of reconstituted dye to 1ml PBS and cells were resuspended in 100ul of working stock per 1x10^6 cells. Cells were incubated for 30 minutes on ice in the dark. Cells were washed with cold PBS/1%FCS, pelleted, and resuspended in 100ul of an antibody mixture containing 1ug/ml PerCp-Cy5.5 anti-mouse TCRβ chain and 1ug/ml Alexa Flour® 488 anti-mouse CD4 antibodies in PBS/1%FCS. Cells were incubated on ice in the dark for 30 minutes then washed with cold PBS/1%FCS, pelleted, and resuspended at a concentration of 10x10^6 cells per 1ml of PBS/10%FCS. Cells were filtered through 50um nylon mesh and sorted using BD FACSAria to collect ~3x106 CD4+ T cells per sample. RNA was isolated using the Qiagen RNeasy® Plus Mini Kit following the manufacturer's instructions (Qiagen, Valencia, CA).

tag: strain/background

value: male

value: 8 weeks

value: lymph nodes

value: CD4+TCRB+ T cells


title: Liver from 2 weeks old rat, biological rep 1

description: gene expression data from liver of 2 weeks old rat

source_name: liver of 2 weeks old animal

value: Wistar

value: female


title: B6-ChrY^SJL, CD4+ T cells, rep1

source_name: C57BL/6J-ChrY^SJL, CD4+TCRB+ cells, naive


title: EV_1h_Os_induction_rep2

source_name: Empty vector leaves, 1hr, oral secretion elicitation, replicate 2


title: Liver from 2 weeks old rat, biological rep 2


title: Regenerating rat liver, biological rep 1

value: regenerating liver


title: B6-ChrY^SJL, CD4+ T cells, rep2


title: tumor_A2B5-_18

status: Public on May 16 2013

city: Rochester

first: Steven

last: Goldman

state: NY

address: 601 Elmwood Ave

department: Center for Translational Neuromedicine

institute: University of Rochester

description:
FJS301_Goldman_U133Plus_2
high grade tumor

hyb_protocol: Standard Affymetrix protocol for U133 Plus 2.0 Arrays

data_processing: Affymetrix .cel raw data files were normalized using RMA. All data processing was performed using R and the Bioconductor package.

source_name: tumor, anaplastic oligodendroglioma high grade, A2B5- sort

label_protocol: Nugen Ovation biotin labeling system using the standard protocol

growth_protocol: Adult human white matter and cortex tissues from epileptic patients and glioma tissue were dissociated using papain. Glial progenitor cells derived from adult human brain and glioma were cultured in DMEM/F12/N2 media supplemented with bFGF, EGF, and PDGF-AA (20ng/ml) in cell suspension plates.

extract_protocol: Total RNA was extracted using RNeasy (Qiagen) and amplified using 3 -biased ribo-SPIA (NuGen Ovation), according to the manufacturer's instructions.

treatment_protocol: Glioma and non-neoplastic A2B5+ GPCs were isolated using magnetic-beads (MACS) or fluorescent-activated (FACS) cell sorting followed by confirmation of the purity of the separated cell populations. CD11b+ microglia were isolated from adult human non-neoplastic tissue using a similar procedure. . The purity of sorted CD11b+ microglia was verified using RCA-lectin staining (Vector Labs). Acutely isolated cells were frozen for RNA extraction

value: tumor

tag: pathology

value: anaplastic oligodendroglioma

tag: sort population

tag: tumor grade (who)

value: III


title: EV_1h_Os_induction_rep1

source_name: Empty vector leaves, 1hr, oral secretion elicitation, replicate 1


title: tumor_unsorted_19

description:
FJS363_Goldman_U133Plus_2
low grade tumor

scan_protocol: Standard Affymetrix protocol for U133 Plus 2.0 Arrays

source_name: tumor, oligodendroglioma low grade, unsorted

value: oligodendroglioma

value: unsorted

value: II


title: tumor_unsorted_14

description:
FJS204_Goldman_U133Plus_2
low grade tumor

source_name: tumor, oligoastrocytoma low grade, unsorted

value: oligoastrocytoma


title: tumor_A2B5-_19

description:
FJS365_Goldman_U133Plus_2
low grade tumor

source_name: tumor, oligodendroglioma low grade, A2B5- sort


title: tumor_unsorted_20

description:
FJS366_Goldman_U133Plus_2
low grade tumor


title: tumor_A2B5-_20

description:
FJS368_Goldman_U133Plus_2
low grade tumor


title: B6, CD4+ T cells, rep3


title: tumor_A2B5-_17

description:
FJS275_Goldman_U133Plus_2
low grade tumor

source_name: tumor, ganglioglioma low grade, A2B5- sort

value: ganglioglioma


title: tumor_unsorted_16

description:
FJS219_Goldman_U133Plus_2
high grade tumor

source_name: tumor, anaplastic oligoastrocytoma high grade, unsorted

value: anaplastic oligoastrocytoma


title: MYC2 VIGS_1h_Os_induction_rep2

source_name: MYC2 VIGS leaves, 1hr, oral secretion elicitation, replicate 2

value: leaves

value: oral secretions of Manduca sexta larvae


title: tumor_unsorted_15

description:
FJS215_Goldman_U133Plus_2
low grade tumor


title: B6-ChrY^SJL, CD4+ T cells, rep3

value: male

value: 8 weeks


title: B6, CD4+ T cells, rep1

value: lymph nodes

value: CD4+TCRB+ T cells


title: tumor_unsorted_17

description:
FJS276_Goldman_U133Plus_2
low grade tumor

source_name: tumor, ganglioglioma low grade, unsorted


title: tumor_A2B5-_14

description:
FJS203_Goldman_U133Plus_2
low grade tumor

source_name: tumor, oligoastrocytoma low grade, A2B5- sort


title: tumor_A2B5-_10

description:
CGCLG_120808_HG-U133_Plus_2_AF28980_1
high grade tumor

source_name: tumor, anaplastic astrocytoma high grade, A2B5- sort

value: anaplastic astrocytoma


title: tumor_unsorted_13

description:
CGCLG_120908_HG-U133_Plus_2_AF28973_1
high grade tumor

source_name: tumor, glioblastoma small cell high grade, unsorted

value: glioblastoma, small cell

value: IV


title: tumor_unsorted_11

description:
CGCLG_120808_HG-U133_Plus_2_AF28981_1
low grade tumor

source_name: tumor, astrocytoma low grade, unsorted

value: tumor

value: astrocytoma


title: tumor_A2B5-_11

description:
CGCLG_120808_HG-U133_Plus_2_AF28983_1
low grade tumor

source_name: tumor, astrocytoma low grade, A2B5- sort


title: tumor_A2B5-_13

description:
CGCLG_120808_HG-U133_Plus_2_AF28975_1_2
high grade tumor

source_name: tumor, glioblastoma small cell high grade, A2B5- sort


title: tumor_unsorted_10

description:
CGCLG_120808_HG-U133_Plus_2_AF28978_1
high grade tumor

source_name: tumor, anaplastic astrocytoma high grade, unsorted

value: III


title: tumor_A2B5-_12

description:
CGCLG_120908_HG-U133_Plus_2_AF28972_1_2
high grade tumor

source_name: tumor, gliosarcoma high grade, A2B5- sort

value: gliosarcoma


title: tumor_A2B5-_08

description:
CGCLG_120808_HG-U133_Plus_2_AF28969_1
high grade tumor

source_name: tumor, glioblastoma high grade, A2B5- sort

value: glioblastoma


title: tumor_unsorted_07

description:
CGCLG_062108_HG-U133_Plus_2_AF28496_1
high grade tumor

source_name: tumor, glioblastoma high grade, unsorted

value: unsorted


title: tumor_A2B5-_03

description:
CGCLG_062108_HG-U133_Plus_2_AF28488_1
high grade tumor


title: tumor_A2B5-_07

description:
CGCLG_062108_HG-U133_Plus_2_AF28498_1
high grade tumor


title: tumor_unsorted_12

description:
CGCLG_120908_HG-U133_Plus_2_AF28970_1_2
high grade tumor

source_name: tumor, gliosarcoma high grade, unsorted


title: tumor_A2B5-_06

description:
CGCLG_062108_HG-U133_Plus_2_AF28495_1
high grade tumor


title: tumor_A2B5-_02

description:
CGCLG_062108_HG-U133_Plus_2_AF28485_1
low grade tumor

value: II


title: tumor_A2B5-_01

description:
CGCLG_062108_HG-U133_Plus_2_AF28483_1
low grade tumor

value: oligodendroglioma


title: tumor_unsorted_01

description:
CGCLG_062108_HG-U133_Plus_2_AF28481_1
low grade tumor

source_name: tumor, oligodendroglioma low grade, unsorted


title: tumor_unsorted_06

description:
CGCLG_062108_HG-U133_Plus_2_AF28493_1
high grade tumor


title: tumor_A2B5-_09

description:
CGCLG_120808_HG-U133_Plus_2_AF28977_1
high grade tumor


title: tumor_A2B5-_04

description:
CGCLG_062108_HG-U133_Plus_2_AF28490_1
low grade tumor

value: oligoastrocytoma


title: tumor_unsorted_03

description:
CGCLG_062108_HG-U133_Plus_2_AF28486_1
high grade tumor


title: temperature: 20/15 C - light: 200 μmol·m−2·s−1 - rep3

description: temperature=20/15 C|light=200 μmol·m−2·s−1 rep 3 (May still include original submitter created erros/discrepancies)

hyb_protocol: CNB Grapegen Affymetrix hybridization

scan_protocol: CNB Grapegen Affymetrix scanning

data_processing: RMA normalization was performed for Affymetrix Platforms: Using APT (apt-1.12.0: apt-probeset-summarize.cpp,v 1.178).

organism: Vitis vinifera

source_name: pericarp (temperature: 20/15 C - light: 200 μmol·m−2·s−1)

label_protocol: CNB Grapegen Affymetrix labeling

extract_protocol: Optimized grapevine RNA isolation

value: temperature 20/15 C - light 200 µmol·m-2·s-1)

tag: cultivar

value: Muscat Hamburg cv.

tag: development stage

tag: growth media

value: perlite/vermiculite/sand


title: control-siRNA-ST1

city: Osaka-Sayama

first: Tomonori

last: Higuchi

state: Osaka

address: 377-2 Ohno-Higashi

department: Department of Microbiology

institute: Kinki University Faculty of Medicine

hyb_protocol: Hybridization was performed on the Affymetrix GeneChip HG-U133 Plus2.0 array for 16 hours at 45C.

scan_protocol: GeneChips were scanned using the GeneChip®Scanner3000 (Affymetrix) ) and converted to numerical data with GeneChip Operating Software, Ver.1 (Affymetrix).

data_processing: The analysis was performed using the BRB Array Tools software version 3.3.0 (http://linus.nci.nih.gov/BRB-ArrayTools.html) developed by Richard Simon and Amy Peng. A log base 2 transformation was applied to the microarray raw data, and global normalization was used to median over entire array. Genes were excluded if percent of data missing or filtered out exceeds 20%.

label_protocol: cRNA was synthesized with the GeneChip® 3’-Amplification Reagents One-Cycle cDNA Synthesis Kit (Affymetrix). The labeled cRNAs were then purified and used for probes.

extract_protocol: ISOGEN® (NIPPON GENE, Tokyo, Japan) extraction of total RNA was performed according to the manufacturer's instructions. The total RNA was analyzed with the Agilent 2100 Bioanalyzer (Agilent Technologies, Waldbronn, Germany).

tag: cell line

tag: cell line source

value: adult T cell leukemia/lymphoma patient (ATLL)

tag: genotype/variation

value: CD4+, CCR4+, Tax-

tag: transfected with

value: control siRNA


title: temperature: 20/15 C - light: 200 μmol·m−2·s−1 - rep2

description: temperature=20/15 C|light=200 μmol·m−2·s−1 rep 2 (May still include original submitter created erros/discrepancies)


title: WM_unsorted_02

description:
FJS264_Goldman_U133Plus_2
normal

source_name: white matter, unsorted

value: white matter

value: epilepsy

tag: cell type

value: non-tumor


title: WM_unsorted_04

description:
FJS321_Goldman_U133Plus_2
normal

tag: tissue


title: SOX4-siRNA-ST1


title: temperature: 20/15 C - light: 200 μmol·m−2·s−1 - rep1

description: temperature=20/15 C|light=200 μmol·m−2·s−1 rep 1 (May still include original submitter created erros/discrepancies)


title: WM_CD11b+_03

description:
SID6_36F WM CD11b Pos_Goldman_U133Plus_2
normal

source_name: white matter, microglia, CD11b+ sort

value: microglia


title: temperature: 20/15 C - light: 400 μmol·m−2·s−1 - rep3

description: temperature=20/15 C|light=400 μmol·m−2·s−1 rep 3 (May still include original submitter created erros/discrepancies)

source_name: pericarp (temperature: 20/15 C - light: 400 μmol·m−2·s−1)

value: temperature 20/15 C - light 400 µmol·m-2·s-1)


title: WM_unsorted_03

description:
FJS315_Goldman_U133Plus_2
normal


title: temperature: 20/15 C - light: 400 μmol·m−2·s−1 - rep2

description: temperature=20/15 C|light=400 μmol·m−2·s−1 rep 2 (May still include original submitter created erros/discrepancies)


title: WM_CD11b+_04

description:
SID7_53M WM CD11b Pos_Goldman_U133Plus_2
normal


title: temperature: 20/15 C - light: 400 μmol·m−2·s−1 - rep1

description: temperature=20/15 C|light=400 μmol·m−2·s−1 rep 1 (May still include original submitter created erros/discrepancies)


title: WM_CD11b+_02

description:
9M_CD11b+_Goldman_U133Plus_2
normal


title: WM_CD11b+_01

description:
25M_CD11b+_Goldman_U133Plus_2
normal


title: WM_unsorted_01

description:
FJS195_Goldman_U133Plus_2
normal


title: WM_A2B5+_01

description:
FJS193_R_Goldman_U133Plus_2
normal

source_name: white matter, glial progenitor cell, A2B5+ sort

value: glial progenitor cell


title: temperature: 30/25 C - light: 400 μmol·m−2·s−1 - rep2

description: temperature=30/25 C|light=400 μmol·m−2·s−1 rep 2 (May still include original submitter created erros/discrepancies)

source_name: pericarp (temperature: 30/25 C - light: 400 μmol·m−2·s−1)

value: temperature 30/25 C - light 400 µmol·m-2·s-1)


title: temperature: 30/25 C - light: 200 μmol·m−2·s−1 - rep3

description: temperature=30/25 C|light=200 μmol·m−2·s−1 rep 3 (May still include original submitter created erros/discrepancies)

source_name: pericarp (temperature: 30/25 C - light: 200 μmol·m−2·s−1)

value: temperature 30/25 C - light 200 µmol·m-2·s-1)


title: WM_A2B5+_02

description:
FJS262_Goldman_U133Plus_2
normal


title: temperature: 30/25 C - light: 200 μmol·m−2·s−1 - rep1

description: temperature=30/25 C|light=200 μmol·m−2·s−1 rep 1 (May still include original submitter created erros/discrepancies)


title: temperature: 30/25 C - light: 200 μmol·m−2·s−1 - rep2

description: temperature=30/25 C|light=200 μmol·m−2·s−1 rep 2 (May still include original submitter created erros/discrepancies)


title: tumor_A2B5+_20

description:
FJS367_Goldman_U133Plus_2
low grade tumor

source_name: tumor, oligodendroglioma low grade, A2B5+ sort

value: tumor

value: II


title: WM_A2B5+_04

description:
FJS322_Goldman_U133Plus_2
normal


title: Newly formed developing xylem, CB2009304-A, biological rep1

city: Canberra

first: xiaohui

last: yang

address: Ross

country: Australia

institute: CSIRO

description: Expression data from two-year-old cambium zone of Populus tomentosa.

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

scan_protocol: Slides were scanned by GeneChip® Scanner 3000 (Cat#00-00212, Affymetrix, Santa Clara, CA, US) and Command Console Software 3.1 (Affymetrix, Santa Clara, CA, US) with default settings.

data_processing: Raw data were normalized by MAS 5.0 algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

organism: Populus tomentosa

source_name: Populus tomentosa newly formed developing xylem from natural condition

label_protocol: Total RNA were amplified, labeled and purified by using GeneChip 3’IVT Express Kit (Cat#901229, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions to obtain biotin labeled cRNA.

growth_protocol: The seedlings were planted in the field of Xiaotangshan, Beijing, China. After growth for about two years, all the plantation for sampling with approximately the same crown size and equal height were chosen.

extract_protocol: Total RNAs were extracted using the RNeasy Plant Mini Kits (Qiagen, Inc. Valencia, CA, USA).

treatment_protocol: Five trees grew under natural condition.

tag: age

value: two-year-old

value: newly formed developing xylem


title: Newly formed developing xylem, CB2009304-B, biological rep2


title: tumor_A2B5+_19

description:
FJS364_Goldman_U133Plus_2
low grade tumor

value: oligodendroglioma


title: Blood_AMS_MVL457-1

city: Quebec

first: Frederic

last: Guenard

address: 2440, Hochelage blvd

country: Canada

institute: Laval University

hyb_protocol: See Illumina protocols

scan_protocol: See Illumina protocols

data_processing: Lumi algorithm was used for expression data correction and normalization (RMA background adjustment; log base 2 variance stabilization; quantile normalization). A probe had to show a detection p-value ≤ 0.05 in at least 25% of samples of a group to be considered as detected.

source_name: whole blood from offspring born after maternal bariatric surgery

label_protocol: See Illumina protocols

growth_protocol: Blood samples were collected after an over-night fast from an antecubital vein

extract_protocol: PAXgene™ Blood RNA Kit (Qiagen)

treatment_protocol: Born before (BMS) or after (AMS) maternal bariatric surgery

tag: status

value: AMS

tag: Sex

value: Male

value: Whole blood


title: WM_A2B5+_03

description:
FJS316_Goldman_U133Plus_2
normal


title: temperature: 30/25 C - light: 400 μmol·m−2·s−1 - rep3

city: Ames

first: PLEXdb Curator

address: 1023  Crop Genomes Informatics Lab (Iowa State University)

institute: Iowa State University

description: temperature=30/25 C|light=400 μmol·m−2·s−1 rep 3 (May still include original submitter created erros/discrepancies)

tag: treatment

value: Muscat Hamburg cv.

value: perlite/vermiculite/sand


title: Blood_BMS_MVL454-1

source_name: whole blood from offspring born before maternal bariatric surgery

value: BMS

value: Female


title: Blood_AMS_MVL455-1


title: Blood_AMS_MVL452-1


title: temperature: 30/25 C - light: 400 μmol·m−2·s−1 - rep1

description: 30/25ºC and 400 umol·m-2·s-2 in a 14h photoperiod (May still include original submitter created erros/discrepancies)


title: tumor_A2B5+_18

description:
FJS300_Goldman_U133Plus_2
high grade tumor

source_name: tumor, anaplastic oligodendroglioma high grade, A2B5+ sort

value: anaplastic oligodendroglioma

value: III


title: tumor_A2B5+_17

description:
FJS274_Goldman_U133Plus_2
low grade tumor

source_name: tumor, ganglioglioma low grade, A2B5+ sort

value: ganglioglioma


title: tumor_A2B5+_16

description:
FJS218_Goldman_U133Plus_2
high grade tumor

source_name: tumor, anaplastic oligoastrocytoma high grade, A2B5+ sort

value: anaplastic oligoastrocytoma


title: tumor_A2B5+_15

description:
FJS213_Goldman_U133Plus_2
low grade tumor

source_name: tumor, oligoastrocytoma low grade, A2B5+ sort

value: oligoastrocytoma


title: Blood_BMS_MVL443-1


title: Blood_AMS_MVL437-1


title: Blood_AMS_MVL430-1


title: tumor_A2B5+_13

description:
CGCLG_120908_HG-U133_Plus_2_AF28974_1
high grade tumor

source_name: tumor, glioblastoma small cell high grade, A2B5+ sort

value: tumor

value: glioblastoma, small cell

value: IV


title: tumor_A2B5+_14

description:
FJS202_Goldman_U133Plus_2
low grade tumor

value: II


title: Blood_BMS_MVL429-1


title: tumor_A2B5+_11

description:
CGCLG_120808_HG-U133_Plus_2_AF28982_1_2
low grade tumor

source_name: tumor, astrocytoma low grade, A2B5+ sort

value: astrocytoma


title: Blood_AMS_5958091030_R05C02

type: genomic

hyb_protocol: standard illumina protocol

scan_protocol: standard illumina protocol

data_processing:
The GenomeStudio® software version 2011.1 (Illumina Inc.) and the Methylation Module were used. Beta values were estimated and data correction (background subtraction and normalization) was applied using internal control probe pairs. CpG sites with a detection p-value > 0.05 were removed from analysis.
SIGNAL A IS UNMETHYLATED AND SIGNAL B IS METHYLATED

label: Cy5 and Cy3

molecule: genomic DNA

source_name: Whole blood

label_protocol: standard illumina protocol

extract_protocol: Genomic DNA was isolated from buffy coat using the GenElute™ Blood Genomic DNA kit (Sigma, St Louis, MO, USA)

value: AMS


title: tumor_A2B5+_12

description:
CGCLG_120908_HG-U133_Plus_2_AF28971_1_2
high grade tumor

source_name: tumor, gliosarcoma high grade, A2B5+ sort

value: gliosarcoma