title: 2618, 4 d after Fg inoculation, rep 2

description:
2618 +2DL Fg rep2
Gene expression data from Fg-inoculated 2618 spikelets

source_name: Fusarium graminearum-inoculated 2618 spikelets_4 d

value: near isogenic spring wheat line 2618

value: heads after mid-anthesis

value: Fusarium graminearum


title: genomic DNA from BrainTemporal of a 112 year old female subject (Sample30)

status: Public on Jun 03 2015

type: genomic

city: Los Angeles

first: Steve

last: Horvath

state: CA

address: 695 Charles E. Young Drive South, Box 708822

department: Human Genetics

country: USA

institute: University of California, Los Angeles

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

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

data_processing:
BeadStudio software v3.2.
Unmethylated and methylated signal intensities and detection p values included in Series supplementary file

label: Cy3 and Cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: BrainTemporal

label_protocol: Standard Illumina Protocol

growth_protocol: DNA extracted from fresh frozen tissue

extract_protocol: genomic DNA was extracted and purified from fresh frozen tissue using the AllPrep DNA/RNA mini kit according to standard instructions.

tag: tissue

value: Brain Temporal

tag: subject id

tag: Sex

value: female

tag: predicted gender

tag: age

tag: dna methylation age

tag: cor sample vs gold standard

tag: mean abs difference sample vs gold standard


title: 2890, 4 d after Fg inoculation, rep 2

type: RNA

city: Ottawa

first: Thérèse

last: Ouellet

state: ON

address: 960 Carling Ave, room 2091

department: Eastern Cereal and Oilseed Research Centre

country: Canada

institute: Agriculture and Agri-Food Canada

description:
2890 null Fg rep2
Gene expression data from Fg-inoculated 2890-spikelets

hyb_protocol: According to Affymetrix instructions for the GeneChip® HT One-Cycle Target Labeling and Controls Kit. All samples were processed in one experimental batch.

scan_protocol: According to Affymetrix instructions for the GeneChip® HT One-Cycle Target Labeling and Controls Kit, using the Affymetrix GeneChip® 3000 Scanner.

data_processing: The probe-level data for the whole profiling experiment were assembled into one dataset using the Robust Multichip Analysis (Irizarry et al, 2002) implemented in the software Acuity 4.0 (Molecular Devices, CA, USA), with quantile normalization and summarization by median polish.

label: biotin

molecule: total RNA

organism: Triticum aestivum

source_name: Fusarium graminearum-inoculated 2890 spikelets_4 d

growth_protocol: Plants were grown in growth cabinets at 20 C/16 hrs daylight; 16 C/8 hrs night until heads reach mid anthesis; then they were moved to the misting room.

extract_protocol: Total RNA from each sample was isolated using a modified form of the guanidine isothiocyanate-cesium chloride method of Chirgwin et al (Biochem. 18: 5294-5299, 1979), as outlined in Ohan and Heikkila (Dev. Genet. 17: 176-184, 1995).  The RNA samples were treated with an RNase-free DNase (Qiagen, Mississauga, Canada) and cleaned up using the RNeasy Mini Kit (Qiagen) according to manufacturer’s instructions.

treatment_protocol: Wheat heads at mid-anthesis were inoculated using the point inoculation method: 10 µl of a 100,000 spores/ml suspension of the isolate Fusarium graminearum strain DAOM 180378 was point-inoculated into each of two basal florets of each developed spikelet of the wheat heads.  Water was used as a mock-inoculation treatment.  The inoculated plants were mist-irrigated for 10 second intervals every 15 minutes for 48 hours to maintain high humidity at a temperature of 25 oC. Five treated heads were used for each biological replicate, and inoculated spikelets were sampled at 4 days after inoculation.  The sampled tissues were immediately frozen in liquid nitrogen and stored at -80 C until used.

tag: wheat line

value: near isogenic spring wheat line 2890

value: inoculated spikelets

tag: tissue age

tag: inoculated with


title: 72h_PB-8

city: Houston

first: Wencai

last: Ma

address: 7455 Fannin st

institute: MD Anderson Cancer Center

hyb_protocol: As per Illumina instructions, with detection by Streptavidin-Cy3 conjugate.

scan_protocol: As per instructions for Illumina BeadArray Reader

data_processing: The non-normalized data were generated by GenomeStudio. The normalized data were generated from bead-level data by methods previously described (PMID: 20805315). In brief, bead-level values were quantile-normalized, adjusted by a model-based background correction method (PMID: 18450815), trimmed by the 3-MAD method employed by Illumina, and then averaged to give a single probe-level value.

source_name: Human AML cell line OCI-AML3

label_protocol: 100 ng of total RNA was first reverse-transcribed and amplified with unlabeled ribonucleotides, using the MessageAmp™ II aRNA Amplification Kit (Ambion). 1000 ng of aRNA was then amplified and biotin-labeled using an Illumina TotalPrep RNA Amplification kit (Ambion).

extract_protocol: Total RNA was extracted using the RNAqueous kit (Ambion, Austin, TX).

treatment_protocol: LY2510924 treatment was 2.5 mg/kg subcutaneously, daily

tag: cell line

tag: strain

value: NOD/SCID/IL-2rγnull (NSG)

tag: treatment

value: 72 hours with daily injections of LY2510294

tag: cell source

value: peripheral blood


title: 2618, 4 d after Fg inoculation, rep 3

description:
2618 +2DL Fg rep3
Gene expression data from Fg-inoculated 2618 spikelets

label_protocol: According to Affymetrix instructions for the GeneChip® HT One-Cycle Target Labeling and Controls Kit. All samples were processed in one experimental batch.


title: 72h_SP-8

value: spleen


title: 72h_PB-9


title: genomic DNA from BrainFrontal of a 112 year old female subject (Sample19)

source_name: BrainFrontal

value: Brain Frontal


title: 2890, 4 d after Fg inoculation, rep 1

description:
2890 null Fg rep1
Gene expression data from Fg-inoculated 2890-spikelets


title: genomic DNA from Bone of a 112 year old female subject (Sample22)

source_name: Bone

value: Bone


title: genomic DNA from Lung of a 112 year old female subject (Sample20)

source_name: Lung

value: Lung


title: 2614, 4 d after water inoculation, rep 1

description:
2614 +2DL+3BS+5A H rep1
Gene expression data from water-inoculated 2614-spikelets

source_name: Water-inoculated 2614 spikelets_4 d

value: near isogenic spring wheat line 2614

value: Water


title: genomic DNA from BoneMarrow of a 112 year old female subject (Sample15)

source_name: BoneMarrow

value: Bone Marrow


title: 72h_BM-8

value: bone marrow


title: CTRL_BM-6


title: 2890, 4 d after water inoculation, rep 2

description:
2890 null H rep2
Gene expression data from water-inoculated 2890-spikelets

source_name: Water-inoculated 2890 spikelets_4 d

value: heads after mid-anthesis


title: 2890, 4 d after water inoculation, rep 1

description:
2890 null H rep1
Gene expression data from water-inoculated 2890-spikelets


title: 2614, 4 d after water inoculation, rep 2

description:
2614 +2DL+3BS+5A H rep2
Gene expression data from water-inoculated 2614-spikelets


title: genomic DNA from Cartilage of a 112 year old female subject (Sample17)

source_name: Cartilage

value: Cartilage


title: genomic DNA from Spleen of a 112 year old female subject (Sample16)

source_name: Spleen

value: Spleen


title: genomic DNA from Esophagus of a 112 year old female subject (Sample18)

source_name: Esophagus

value: Esophagus

value: female


title: CTRL_SP-5


title: CTRL_SP-6


title: 72h_SP-9


title: genomic DNA from Bone of a 112 year old female subject (Sample14)


title: TE-5R

city: Kyoto

first: Osamu

last: Kikuchi

address: 54 Shogoin-Kawaharacho Sakyoku

department: Therapeutic Oncology

country: Japan

institute: Kyoto University

hyb_protocol: Scanned on an Agilent SureScan scanner.

scan_protocol: Images were quantified using Agilent Feature Extraction Software

data_processing: Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization.

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

growth_protocol: TE-5 and TE-5R cells were cultured in RPMI1640 medium supplemented with 10% fetal bovine serum, 100 μg/ml streptomycin and 100 units/ml penicillin at 37 ºC in a 5% CO2 incubator.

extract_protocol: Genomic DNA was extracted from TE-5 and TE-5R cells and labelled according to Oligonucleotide Array-Based CGH for Genomic DNA Analysis Protocol.

treatment_protocol: TE-5 cells were treated with continuous and step-wise concentrations of 5-FU (1, 2, 5, and 10 μM), and consequently 5-FU-resistant ESCC cells were established and named as TE-5R cells.

value: TE-5R (5-FU-resistant subline)

source_name: Control

tag: reference

value: Human Reference DNA Female


title: Roblin, 4 d after Fg +DON inoculation, rep 2

description:
Rb F4-2 +DON
Gene expression data from Fg strain DAOM 233423- inoculated Roblin spikelets , 4 d after inoculation

source_name: Fg strain DAOM 233423 inoculated Roblin spikelets_4 d

growth_protocol: Plants were grown in growth cabinets at 20 C/16 hrs daylight; 16 C/8 hrs night until heads reach mid anthesis; then they were moved to another cabinet with misting.

treatment_protocol: Wheat heads at mid-anthesis were inoculated as follow: 10 µl of a 100,000 spores/ml suspension of either the isolate Fusarium graminearum strain GZ2629 (also called DAOM 233423) or Fg strain Tri5- (also called DAOM 221141) was point-inoculated into each of two basal florets of each developed spikelet of the wheat heads.  Water was used as a mock-inoculation treatment.  The inoculated plants were mist-irrigated for 20 second intervals every 15 minutes for 48 hours to maintain high humidity at a temperature of 25 oC. Five treated heads were used for each biological replicate, and inoculated spikelets were sampled at 2 and 4 days after inoculation.  The sampled tissues were immediately frozen in liquid nitrogen and stored at -80 C until used.

tag: genotype

value: spring wheat cv Roblin

value: inoculated spikelets

value: Fg strain GZ3639 (DAOM 233423)

tag: day after inoculation


title: CTRL_PB-5

value: NOD/SCID/IL-2rγnull (NSG)

value: peripheral blood


title: TE-5

value: TE-5 (parental cell line)


title: CTRL_PB-6


title: CTRL_BM-5


title: genomic DNA from BoneMarrow of a 112 year old female subject (Sample23)

tag: tissue

tag: subject id


title: Roblin, 4 d after Fg +DON inoculation, rep 1

description:
Rb F4-1 +DON
Gene expression data from Fg strain DAOM 233423- inoculated Roblin spikelets , 4 d after inoculation


title: genomic DNA from BrainMidbrain of a 112 year old female subject (Sample12)

source_name: BrainMidbrain

value: Brain MidBrain

tag: Sex

tag: predicted gender


title: genomic DNA from BrainCRBM of a 112 year old female subject (Sample9)

source_name: BrainCRBM

value: Brain CRBM

tag: age

tag: dna methylation age


title: Roblin, 2 d after Fg +DON inoculation, rep 2

description:
Rb F2-2 +DON
Gene expression data from Fg strain DAOM 233423- inoculated Roblin spikelets , 2 d after inoculation

source_name: Fg strain DAOM 233423 inoculated Roblin spikelets_2 d


title: CTRL_SP-4

value: spleen


title: genomic DNA from Thyroid of a 112 year old female subject (Sample8)

source_name: Thyroid

value: Thyroid

tag: cor sample vs gold standard

tag: mean abs difference sample vs gold standard


title: genomic DNA from BrainHippocampus of a 112 year old female subject (Sample10)

source_name: BrainHippocampus

value: Brain Hippocampus


title: genomic DNA from Liver of a 112 year old female subject (Sample11)

source_name: Liver

value: Liver


title: CTRL_BM-4

source_name: Human AML cell line OCI-AML3

value: bone marrow


title: Roblin, 2 d after Fg +DON inoculation, rep 3

description:
Rb F2-3 +DON
Gene expression data from Fg strain DAOM 233423- inoculated Roblin spikelets , 2 d after inoculation

tag: tissue age

value: heads after mid-anthesis


title: 24h_PB-3

value: 24 hours with daily injections of LY2510294


title: 24h_SP-3


title: CTRL_PB-4


title: 24h_BM-3


title: Roblin, 4 d after Fg -DON inoculation, rep 2

description:
Rb F4-2 -DON
Gene expression data from Fg strain DAOM 221141- inoculated Roblin spikelets , 4 d after inoculation

source_name: Fg strain DAOM 221141 inoculated Roblin spikelets_4 d

tag: inoculated with

value: Fg strain Tri5- (DAOM 221141)


title: Roblin, 2 d after Fg -DON inoculation, rep 3

description:
Rb F2-3 -DON
Gene expression data from Fg strain DAOM 221141- inoculated Roblin spikelets , 2 d after inoculation

source_name: Fg strain DAOM 221141 inoculated Roblin spikelets_2 d


title: genomic DNA from Adipose of a 112 year old female subject (Sample13)

source_name: Adipose

value: Adipose

value: female


title: Roblin, 4 d after Fg -DON inoculation, rep 3

description:
Rb F4-3 -DON
Gene expression data from Fg strain DAOM 221141- inoculated Roblin spikelets , 4 d after inoculation

value: spring wheat cv Roblin

value: inoculated spikelets


title: genomic DNA from Buccal of a 112 year old female subject (Sample7)

source_name: Buccal

value: Buccal


title: Roblin, 4 d after Fg -DON inoculation, rep 1

description:
Rb F4-1 -DON
Gene expression data from Fg strain DAOM 221141- inoculated Roblin spikelets , 4 d after inoculation


title: 24h_PB-2

tag: cell line

value: NOD/SCID/IL-2rγnull (NSG)

value: peripheral blood


title: Roblin, 2 d after Fg +DON inoculation, rep 1

description:
Rb F2-1 +DON
Gene expression data from Fg strain DAOM 233423- inoculated Roblin spikelets , 2 d after inoculation

value: Fg strain GZ3639 (DAOM 233423)


title: 24h_SP-2

tag: strain


title: genomic DNA from Skin of a 112 year old female subject (Sample6)

source_name: Skin

value: Skin


title: genomic DNA from BrainOccipital of a 112 year old female subject (Sample3)

source_name: BrainOccipital

value: Brain Occipital


title: Roblin, 4 d after Fg +DON inoculation, rep 3

description:
Rb F4-3 +DON
Gene expression data from Fg strain DAOM 233423- inoculated Roblin spikelets , 4 d after inoculation


title: genomic DNA from Aorta of a 112 year old female subject (Sample5)

source_name: Aorta

value: Aorta


title: genomic DNA from Pericardium of a 112 year old female subject (Sample4)

source_name: Pericardium

value: Pericardium


title: 24h_SP-1

tag: treatment

value: spleen


title: 24h_PB-1

tag: cell source


title: 24h_BM-2

value: bone marrow


title: Roblin, 2 d after Fg -DON inoculation, rep 1

description:
Rb F2-1 -DON
Gene expression data from Fg strain DAOM 221141- inoculated Roblin spikelets , 2 d after inoculation

value: heads after mid-anthesis


title: Roblin, 4 d after water inoculation (control), rep 1

description:
Rb H4-1
Gene expression data from water-inoculated Roblin spikelets , 4 d after inoculation

source_name: Water-inoculated Roblin spikelets_4 d

value: Water


title: Roblin, 2 d after water inoculation (control), rep 1

description:
Rb H2-1
Gene expression data from water-inoculated Roblin spikelets , 2 d after inoculation

source_name: Water-inoculated Roblin spikelets_2 d


title: ESC_H9_R3

city: La Jolla

first: Kristopher

middle: L.

last: Nazor

address: 10550 North Torrey Pines Road

department: Regenerative Medicine

institute: The Scripps Research Institute

hyb_protocol: 750 ng labeled RNA/sample was hybridized to HT-12v4 Expression BeadChips (Illumina, Inc.).

scan_protocol: Arrays were imaged using HiScan using standard recommended Illumina scanner settings.

data_processing: In GenomeStudio, probes were filtered for those detected at p<0.01 in at least 1 sample and exported for normalization in R using robust spline normalization (RSN).

label_protocol: 200 ng RNA per sample was amplified using the Total PrepTM RNA Amplification Kit (Illumina, Inc.) according to manufacturer’s protocol.

growth_protocol: Human ES cell lines (CyT49 and H9) were maintained using defined media (DM) conditions (Wang et al. 2007) and differentiated towards endoderm, mesoderm, ectoderm and neural crest cell types using previously described protocols (Schulz et al. 2003; 2004; 2012; Menendez et al. 2013; 2011). For pancreatic endoderm CyT49 hESC were aggregated in rotational suspension culture, then differentiated in a four-step sequential process to mesendoderm (MIXL1+), definitive endoderm (SOX17+, FOXA2+); primitive gut tube (HNF1B+, HNF4A+); posterior foregut (PDX1+); and pancreatic endoderm (NKX6-1+, PTF1A+) and endocrine cells (NGN3+, NKX2-2+, PAX4+, PAX6+). Stage 1 (days 0-1): cells were maintained in RPMI 1640 (Mediatech), 0.2% FBS (HyClone), 1x GlutaMAX-1 (Life Technologies), 1% v/v penicillin/streptomycin. 1:5000 Insulin-Transferrin-Selenium (ITS) (Life Technologies), 100 ng/mL recombinant human Activin A (R&D Systems), 50 ng/mL recombinant mouse Wnt3A (R&D Systems). Stage 2 (days 1-4): addition of 25 ng/mL recombinant human KGF (R&D Systems) and 2.5 mM TGF-β RI Kinase inhibitor IV (EMD Bioscience). Stage 3 (days 5-7) cells were maintained in DMEM HI Glucose (HyClone) supplemented with 0.5x B-27 Supplement (Life Technologies), 1x GlutaMAX-1 and 1% v/v penicillin/streptomycin, 0.25 mM KAAD-Cyclopamine (Toronto Research Chemicals), 3 nM TTNPB (Sigma-Aldrich) and 50 ng/mL recombinant human Noggin (R&D Systems). Stage 4 (days 8-12): supplemented with 50 ng/mL recombinant human KGF (R&D Systems) and 50 ng/mL recombinant human EGF (R&D Systems). Liver differentiation was carried out using modifications (medium supplemented with 100 ng/mL BMP4 (R&D Systems) and 25 ng/mL FGF2 (Sigma) to stages 2-4 resulting in an APF+, Albumin+ and TAT+ cell population (Schulz et al. 2012). For direct neural crest differentiation, hES cells were plated in defined media lacking Activin A and supplemented with 2 micromolar GSK3 inhibitor IX (BIO) and 20 micromolar SB 431542 (SB media). Neural crest identity was confirmed by immunocytochemistry and RT-PCR positive detection of p75, Hnk1, AP2 and FoxD3 NC markers, as well as negative detection of hESCs markers (Sox2, Oct4, Nanog) and neural progenitor markers (Pax6, Sox2). For mesenchymal differentiation, neural crest cells were cultured in media containing 10% FBS and passed every 4–5 d, MSCs were CD73+, CD44+ and CD13+ by day 5 (Menendez et al. 2011; 2013). Neural progenitors were derived in DM containing Noggin and SB431542 to induced neural differentiation. Cultures were split at day 7 and 14. FGF2 was added at day 14 to promote neural progenitor expansion. On day 28 the culture was split and neural progenitors expanded in DMEM/F12/B27 containing heregulin and FGF2. Q-PCR analysis demonstrated that these NP cells expressed SOX1, PAX6, and Musashi, but were negative for OCT4, Rex1, Nanog, and CD9, in comparison to undifferentiated cells. Immunofluorescence confirmed that these progenitors were negative for OCT4, but expressed Sox2 and Nestin. This population can be expanded and maintained for >3 months in defined conditions (Schulz et al. 2003; 2004).

extract_protocol: Total RNA was extracted from snap-frozen sample pellets (Ambion mirVana Kit, Life Technologies, Inc.) according to the manufacturer’s protocol. RNA quantity (QubitTM RNA BR Assay Kits, Life Technologies, Inc.) and quality (RNA6000 Nano Kit and Bioanalyzer 2100, Agilent) was determined to be optimal for each sample prior to further processing.

tag: differentiation stage

value: Embrionic stem cells


title: 24h_BM-1

value: 24 hours with daily injections of LY2510294


title: ESC_H9_R2


title: Roblin, 4 d after water inoculation (control), rep 2

description:
Rb H4-2
Gene expression data from water-inoculated Roblin spikelets , 4 d after inoculation

tag: genotype


title: Roblin, 2 d after water inoculation (control), rep 2

description:
Rb H2-2
Gene expression data from water-inoculated Roblin spikelets , 2 d after inoculation

tag: day after inoculation


title: genomic DNA from Kidney of a 112 year old female subject (Sample2)

source_name: Kidney

tag: tissue

value: Kidney

value: female


title: ESC_H9_R1


title: genomic DNA from Diaphragm of a 112 year old female subject (Sample1)

source_name: Diaphragm

value: Diaphragm

tag: subject id


title: Wuhan1, 4 d after water inoculation, rep 2

description:
WhH4 rep2
Gene expression data from water-inoculated Wuhan1 spikelets , 4 d after inoculation

source_name: Water-inoculated Wuhan1 spikelets_4 d

treatment_protocol: Wheat heads at mid-anthesis were inoculated as follow: 10 µl of a 100,000 spores/ml suspension of the isolate Fusarium graminearum strain DAOM 180378 was point-inoculated into each of two basal florets of each developed spikelet of the wheat heads.  Water was used as a mock-inoculation treatment.  The inoculated plants were mist-irrigated for 10 second intervals every 15 minutes for 48 hours to maintain high humidity at a temperature of 25 oC. Five treated heads were used for each biological replicate, and inoculated spikelets were sampled at 1, 2 and 4 days after inoculation.  The sampled tissues were immediately frozen in liquid nitrogen and stored at -80 C until used.

tag: cultivar

value: spring wheat cv Wuhan1

value: inoculated spikelets


title: genomic DNA from bone of subject 48

source_name: Bone

growth_protocol: DNA extracted from fresh frozen bone

extract_protocol: genomic DNA was extracted and purified from fresh frozen tissue using AllPrep DNA/RNA mini kit according to standard instructions. Further, we applied phenol–chloroform–isoamyl alcohol as described in  Delgado-Calle J et al (2012) Epigenetics 2012; 7: 83–91. Pubmed ID: 23124911.

value: bone

tag: Sex

tag: sexpredictedusingdnamethdata


title: genomic DNA from bone of subject 46

tag: age

tag: dna methylation age


title: Wuhan1, 4 d after water inoculation, rep 1

description:
WhH4 rep1
Gene expression data from water-inoculated Wuhan1 spikelets , 4 d after inoculation


title: genomic DNA from bone of subject 47


title: ESC_Cyt49_R9


title: Wuhan1, 2 d after water inoculation, rep 2

description:
WhH2 rep2
Gene expression data from water-inoculated Wuhan1 spikelets , 2 d after inoculation

source_name: Water-inoculated Wuhan1 spikelets_2 d


title: Wuhan1, 1 d after water inoculation, rep 2

description:
WhH1 rep2
Gene expression data from water-inoculated Wuhan1 spikelets , 1 d after inoculation

source_name: Water-inoculated Wuhan1 spikelets_1 d


title: ESC_Cyt49_R7


title: Wuhan1, 2 d after water inoculation, rep 1

description:
WhH2 rep1
Gene expression data from water-inoculated Wuhan1 spikelets , 2 d after inoculation


title: genomic DNA from bone of subject 45


title: genomic DNA from bone of subject 44


title: ESC_Cyt49_R8


title: Wuhan1, 4 d after Fg inoculation, rep 2

description:
WhF4 rep2
Gene expression data from Fusarium graminearum-inoculated Wuhan1 spikelets , 4 d after inoculation

source_name: Fusarium graminearum-inoculated Wuhan1 spikelets_4 d

value: Fusarium graminearum


title: ESC_Cyt49_R4


title: ESC_Cyt49_R5


title: ESC_Cyt49_R6


title: genomic DNA from bone of subject 42


title: genomic DNA from bone of subject 43


title: genomic DNA from bone of subject 41


title: Wuhan1, 4 d after Fg inoculation, rep 1

description:
WhF4 rep1
Gene expression data from Fusarium graminearum-inoculated Wuhan1 spikelets , 4 d after inoculation


title: genomic DNA from bone of subject 39


title: genomic DNA from bone of subject 40


title: ESC_Cyt49_R3


title: Wuhan1, 2 d after Fg inoculation, rep 1

description:
WhF2 rep1
Gene expression data from Fusarium graminearum-inoculated Wuhan1 spikelets , 2 d after inoculation

source_name: Fusarium graminearum-inoculated Wuhan1 spikelets_2 d


title: Roblin, 2 d after Fg -DON inoculation, rep 2

description:
Rb F2-2 -DON
Gene expression data from Fg strain DAOM 221141- inoculated Roblin spikelets , 2 d after inoculation

source_name: Fg strain DAOM 221141 inoculated Roblin spikelets_2 d

value: spring wheat cv Roblin

value: Fg strain Tri5- (DAOM 221141)


title: Wuhan1, 1 d after Fg inoculation, rep 2

description:
WhF1 rep2
Gene expression data from Fusarium graminearum-inoculated Wuhan1 spikelets , 1 d after inoculation

source_name: Fusarium graminearum-inoculated Wuhan1 spikelets_1 d


title: ESC_Cyt49_R1


title: ESC_Cyt49_R2


title: genomic DNA from bone of subject 37


title: Wuhan1, 2 d after Fg inoculation, rep 2

description:
WhF2 rep2
Gene expression data from Fusarium graminearum-inoculated Wuhan1 spikelets , 2 d after inoculation


title: NuyBay, 4 d after water inoculation, rep 2

description:
NB H 4d rep2
Gene expression data from water-inoculated NuyBay spikelets , 4 d after inoculation

source_name: Water-inoculated NuyBay spikelets_4 d

value: spring wheat cv NuyBay

value: water (control)


title: Splanc_H9_R2

value: Splanchnic mesoderm


title: Splanc_H9_R1


title: NuyBay, 2 d after water inoculation, rep 2

description:
NB H 2d rep2
Gene expression data from water-inoculated NuyBay spikelets , 2 d after inoculation

source_name: Water-inoculated NuyBay spikelets_2 d


title: genomic DNA from bone of subject 35


title: genomic DNA from bone of subject 36


title: NuyBay, 4 d after water inoculation, rep 1

description:
NB H 4d rep1
Gene expression data from water-inoculated NuyBay spikelets , 4 d after inoculation


title: genomic DNA from bone of subject 34


title: Splanc_Cyt49_R1


title: genomic DNA from bone of subject 33


title: NuyBay, 2 d after water inoculation, rep 1

description:
NB H 2d rep1
Gene expression data from water-inoculated NuyBay spikelets , 2 d after inoculation


title: Splanc_Cyt49_R2


title: NuyBay, 1 d after water inoculation, rep 2

description:
NB H 1d rep2
Gene expression data from water-inoculated NuyBay spikelets , 1 d after inoculation

source_name: Water-inoculated NuyBay spikelets_1 d


title: NuyBay, 1 d after water inoculation, rep 1

description:
NB H 1d rep1
Gene expression data from water-inoculated NuyBay spikelets , 1 d after inoculation


title: NuyBay, 4 d after Fg inoculation, rep 2

description:
NB FG 4d rep2
Gene expression data from Fusarium graminearum-inoculated NuyBay spikelets , 4 d after inoculation

source_name: Fusarium graminearum-inoculated NuyBay spikelets_4 d


title: Splanc_Cyt49_R3


title: SM_H9_R2

value: Smooth Muscle


title: SM_H9_R1


title: NuyBay, 4 d after Fg inoculation, rep 1

description:
NB FG 4d rep1
Gene expression data from Fusarium graminearum-inoculated NuyBay spikelets , 4 d after inoculation

value: heads after mid-anthesis


title: genomic DNA from bone of subject 32


title: Panc_d8_Cyt49_R1

value: Pancreatic (pre-pancreatic endoderm)


title: Panc_d5_Cyt49_R3

value: Pancreatic (foregut endoderm)


title: NuyBay, 2 d after Fg inoculation, rep 2

description:
NB FG 2d rep2.
Gene expression data from Fusarium graminearum-inoculated NuyBay spikelets , 2 d after inoculation

source_name: Fusarium graminearum-inoculated NuyBay spikelets_2 d


title: genomic DNA from bone of subject 28


title: genomic DNA from bone of subject 38


title: NuyBay, 2 d after Fg inoculation, rep 1

description:
NB FG 2d rep1
Gene expression data from Fusarium graminearum-inoculated NuyBay spikelets , 2 d after inoculation


title: Panc_d8_Cyt49_R3


title: genomic DNA from bone of subject 31


title: NuyBay, 1 d after Fg inoculation, rep 1

description:
NB FG 1d rep1
Gene expression data from Fusarium graminearum-inoculated NuyBay spikelets , 1 d after inoculation

source_name: Fusarium graminearum-inoculated NuyBay spikelets_1 d


title: genomic DNA from bone of subject 26


title: genomic DNA from bone of subject 30


title: Panc_d5_Cyt49_R2


title: genomic DNA from bone of subject 29


title: genomic DNA from bone of subject 27


title: genomic DNA from bone of subject 25


title: Panc_d5_Cyt49_R1


title: genomic DNA from bone of subject 21


title: Dream, 4 d after water inoculation, rep 2

description: Dream H 4d rep2

source_name: Water-inoculated Dream spikelets_4 d

treatment_protocol: Wheat heads at mid-anthesis were inoculated as follow: 10 µl of a 100,000 spores/ml suspension of the isolate Fusarium graminearum strain DAOM 180378 was point-inoculated into each of two basal florets of each developed spikelet of the wheat heads.  Water was used as a mock-inoculation treatment.  The inoculated plants were mist-irrigated for 10 second intervals every 15 minutes for 48 hours to maintain high humidity at a temperature of 25 oC. Five treated heads were used for each biological replicate, and inoculated spikelets were sampled at 0 hour and 4 days after inoculation.  The sampled tissues were immediately frozen in liquid nitrogen and stored at -80 C until used.

value: winter wheat cv Dream


title: Panc_d12_Cyt49_R2

value: Pancreatic (pancreatic endoderm)


title: genomic DNA from bone of subject 19

value: female


title: Panc_d12_Cyt49_R3


title: Dream, 4 d after water inoculation, rep 1

description: Dream H 4d rep1


title: Panc_d12_Cyt49_R1


title: Dream, 4 d after water inoculation, rep 3

description: Dream H 4d rep3


title: genomic DNA from bone of subject 24


title: genomic DNA from bone of subject 23


title: genomic DNA from bone of subject 20


title: Dream, 0 d after water inoculation, rep 3

description: Dream H 0d rep3

source_name: Water-inoculated Dream spikelets_0 d


title: Dream, 0 d after water inoculation, rep 2

description: Dream H 0d rep2


title: Dream, 0 d after water inoculation, rep 1

description: Dream H 0d rep1


title: NPC_H9_R2

value: Neural progenitors


title: genomic DNA from bone of subject 22


title: NPC_H9_R3


title: NPC_H9_R1


title: Dream, 4 d after Fg inoculation, rep 2

description: Dream Fg 4d rep2

source_name: Fusarium graminearum-inoculated Dream spikelets_4 d


title: genomic DNA from bone of subject 18


title: Dream, 4 d after Fg inoculation, rep 3

description: Dream Fg 4d rep3


title: MSC_H9_R3

value: Mesenchimal stem cells


title: MSC_H9_R2


title: genomic DNA from bone of subject 14


title: MSC_H9_R1


title: Dream, 4 d after Fg inoculation, rep 1

description: Dream Fg 4d rep1

value: inoculated spikelets


title: genomic DNA from bone of subject 13

value: bone


title: genomic DNA from bone of subject 17


title: genomic DNA from bone of subject 12


title: NC_H9_R2

value: Neural Crest


title: genomic DNA from bone of subject 15

value: male


title: Dream, 0 d after Fg inoculation, rep 3

description: Dream Fg 0d rep3

source_name: Fusarium graminearum-inoculated Dream spikelets_0 d

value: Fusarium graminearum


title: Dream, 0 d after Fg inoculation, rep 2

description: Dream Fg 0d rep2


title: NC_H9_R3


title: NC_H9_R1


title: 2-2674, 4 d after Fg inoculation by spray, rep 1

description:
2-2674 null-S2 Fg-S-1
Gene expression data from Fg-inoculated 2-2674 spikelets (spray inoculation)

source_name: Fusarium graminearum-inoculated 2-2674 spikelets_4 d

treatment_protocol: Wheat heads at mid-anthesis were inoculated using one of the two following methods: Point - 10 µl of a 100,000 spores/ml suspension of the isolate Fusarium graminearum strain DAOM 180378 was point-inoculated into each of two basal florets of each developed spikelet of the wheat heads; or Spray - a suspension of 1000,000 spores/ml was sprayed onto heads until run off occured.  Water was used as a mock-inoculation treatment for either point ans spray inoculations.  The inoculated plants were mist-irrigated for 10 second intervals every 15 minutes for 48 hours to maintain high humidity at a temperature of 25 oC. Five treated heads were used for each biological replicate, and inoculated spikelets were sampled at 4 days after inoculation.  The sampled tissues were immediately frozen in liquid nitrogen and stored at -80 C until used.

tag: wheat line

value: near isogenic spring wheat line 2-2674

tag: inoculation method

value: spray


title: 2-2674, 4 d after Fg inoculation by spray, rep 3

description:
2-2674 null-S2 Fg-S-3
Gene expression data from Fg-inoculated 2-2674 spikelets (spray inoculation)

tag: tissue age

tag: inoculated with


title: genomic DNA from bone of subject 16

source_name: Bone


title: genomic DNA from bone of subject 11


title: NC_Cyt49_R3


title: 2-2674, 4 d after Fg inoculation by spray, rep 2

description:
2-2674 null-S2 Fg-S-2
Gene expression data from Fg-inoculated 2-2674 spikelets (spray inoculation)


title: Dream, 0 d after Fg inoculation, rep 1

description: Dream Fg 0d rep1


title: NC_Cyt49_R2


title: LPM_H9_R3

value: Lateral Plate Mesoderm


title: genomic DNA from bone of subject 10


title: NuyBay, 1 d after Fg inoculation, rep 2

description:
NB FG 1d rep2
Gene expression data from Fusarium graminearum-inoculated NuyBay spikelets , 1 d after inoculation

value: spring wheat cv NuyBay


title: 2-2674, 4 d after water inoculation by spray, rep 2

description:
2-2674 null-S2 H-S-2
Gene expression data from water-inoculated 2-2674 spikelets (spray inoculation)

source_name: Water-inoculated 2-2674 spikelets_4 d

value: heads after mid-anthesis

value: water (control)


title: LPM_H9_R2


title: 2-2674, 4 d after water inoculation by spray, rep 1

description:
2-2674 null-S2 H-S-1
Gene expression data from water-inoculated 2-2674 spikelets (spray inoculation)


title: NC_Cyt49_R1


title: 2-2674, 4 d after water inoculation by spray, rep 3

description:
2-2674 null-S2 H-S-3
Gene expression data from water-inoculated 2-2674 spikelets (spray inoculation)


title: 2-2890, 4 d after Fg inoculation by spray, rep 2

description:
2-2890 null-S1 Fg-S-2
Gene expression data from Fg-inoculated 2-2890-spikelets (spray inoculation)

source_name: Fusarium graminearum-inoculated 2-2890 spikelets_4 d

value: near isogenic spring wheat line 2-2890


title: 2-2890, 4 d after Fg inoculation by spray, rep 3

description:
2-2890 null-S1 Fg-S-3
Gene expression data from Fg-inoculated 2-2890-spikelets (spray inoculation)


title: genomic DNA from bone of subject 8


title: Liver_d8_Cyt49_R3

value: Liver day 8


title: Liver_d8_Cyt49_R1


title: Panc_d8_Cyt49_R2

value: Pancreatic (pre-pancreatic endoderm)


title: 2-2890, 4 d after water inoculation by spray, rep 4

description:
2-2890 null-S1 H-S-4
Gene expression data from water-inoculated 2-2890-spikelets (spray inoculation)

source_name: Water-inoculated 2-2890 spikelets_4 d


title: genomic DNA from bone of subject 6

value: female


title: genomic DNA from bone of subject 4


title: Liver_d8_Cyt49_R2


title: genomic DNA from bone of subject 7


title: genomic DNA from bone of subject 5


title: 2-2890, 4 d after Fg inoculation by spray, rep 1

description:
2-2890 null-S1 Fg-S-1
Gene expression data from Fg-inoculated 2-2890-spikelets (spray inoculation)


title: Liver_d5_Cyt49_R3

value: Liver day 5


title: genomic DNA from bone of subject 2


title: genomic DNA from bone of subject 3


title: Liver_d16_Cyt49_R3

value: Liver day 16


title: 2-2618, 4 d after Fg inoculation by spray, rep 3

description:
2-2618 +2DL-S1 Fg-S-3
Gene expression data from Fg-inoculated 2-2618 spikelets (spray inoculation)

source_name: Fusarium graminearum-inoculated 2-2618 spikelets_4 d

value: near isogenic spring wheat line 2-2618

value: inoculated spikelets


title: Liver_d5_Cyt49_R2


title: genomic DNA from bone of subject 1

value: bone


title: genomic DNA from bone of subject 9


title: DNA from control K19

city: Ulm

first: Ole

last: Ammerpohl

address: Albert-Einstein-Allee 11

country: Germany

institute: UK Ulm

scan_protocol: Arrays were scanned using the Illumina iScan

data_processing: GenomeStudio software (version 2011.1, Methylation module version 1.9.0)

label: Cy5 and Cy3

source_name: PB

extract_protocol: various DNA extraction methods

tag: diagnosis

value: normal (control)

value: peripheral blood

tag: rhgh treatment

value: no treatment


title: Liver_d5_Cyt49_R1


title: Liver_d16_Cyt49_R1


title: Liver_d16_Cyt49_R2


title: 2-2618, 4 d after water inoculation by spray, rep 2

description:
2-2618 +2DL-S1 H-S-2
Gene expression data from water-inoculated 2-2618 spikelets (spray inoculation)

source_name: Water-inoculated 2-2618 spikelets_4 d

value: spray


title: 2-2618, 4 d after Fg inoculation by spray, rep 2

description:
2-2618 +2DL-S1 Fg-S-2
Gene expression data from Fg-inoculated 2-2618 spikelets (spray inoculation)

value: Fusarium graminearum


title: 2-2890, 4 d after water inoculation by spray, rep 2

description:
2-2890 null-S1 H-S-2
Gene expression data from water-inoculated 2-2890-spikelets (spray inoculation)


title: 2-2618, 4 d after Fg inoculation by spray, rep 1

description:
2-2618 +2DL-S1 Fg-S-1
Gene expression data from Fg-inoculated 2-2618 spikelets (spray inoculation)


title: Mesothelium_H9_R3

value: Mesothelium


title: 2-2618, 4 d after water inoculation by spray, rep 3

description:
2-2618 +2DL-S1 H-S-3
Gene expression data from water-inoculated 2-2618 spikelets (spray inoculation)

value: heads after mid-anthesis


title: LPM_H9_R1

value: Lateral Plate Mesoderm


title: DNA from control K18


title: 2-2890, 4 d after water inoculation by spray, rep 3

description:
2-2890 null-S1 H-S-3
Gene expression data from water-inoculated 2-2890-spikelets (spray inoculation)

value: near isogenic spring wheat line 2-2890

value: water (control)


title: 2-2618, 4 d after water inoculation by spray, rep 1

description:
2-2618 +2DL-S1 H-S-1
Gene expression data from water-inoculated 2-2618 spikelets (spray inoculation)


title: DNA from control K15


title: 2-2674, 4 d after Fg inoculation by point, rep 3

description:
2-2674 null-S2 Fg-P-3
Gene expression data from Fg-inoculated 2-2674 spikelets (point inoculation)

value: near isogenic spring wheat line 2-2674

value: point


title: 2-2674, 4 d after Fg inoculation by point, rep 2

description:
2-2674 null-S2 Fg-P-2
Gene expression data from Fg-inoculated 2-2674 spikelets (point inoculation)


title: DNA from control K17


title: Mesothelium_H9_R2


title: DNA from control K16


title: DE_Cyt49_R6

value: Definitive Endoderm


title: DNA from control K13


title: DE_Cyt49_R5


title: 2-2890, 4 d after Fg inoculation by point, rep 3

description:
2-2890 null-S1 Fg-P-3
Gene expression data from Fg-inoculated 2-2890-spikelets (point inoculation)


title: DNA from control K10


title: Mesothelium_Cyt49_R1


title: 2-2890, 4 d after water inoculation by point, rep 2

description:
2-2890 null-S1 H-P-2
Gene expression data from water-inoculated 2-2890-spikelets (point inoculation)


title: 2-2890, 4 d after Fg inoculation by point, rep 2

description:
2-2890 null-S1 Fg-P-2
Gene expression data from Fg-inoculated 2-2890-spikelets (point inoculation)


title: 2-2674, 4 d after water inoculation by point, rep 1

description:
2-2674 null-S2 H-P-1
Gene expression data from water-inoculated 2-2674 spikelets (point inoculation)


title: DNA from control K14


title: Mesothelium_Cyt49_R2


title: DE_Cyt49_R4


title: 2-2890, 4 d after water inoculation by point, rep 1

description:
2-2890 null-S1 H-P-1
Gene expression data from water-inoculated 2-2890-spikelets (point inoculation)


title: 2-2674, 4 d after water inoculation by point, rep 2

description:
2-2674 null-S2 H-P-2
Gene expression data from water-inoculated 2-2674 spikelets (point inoculation)


title: DE_Cyt49_R3


title: DNA from control K11


title: 2-2618, 4 d after Fg inoculation by point, rep 3

description:
2-2618 +2DL-S1 Fg-P-3
Gene expression data from Fg-inoculated 2-2618 spikelets (point inoculation)


title: DNA from control K8


title: 2-2618, 4 d after Fg inoculation by point, rep 2

description:
2-2618 +2DL-S1 Fg-P-2
Gene expression data from Fg-inoculated 2-2618 spikelets (point inoculation)


title: DE_Cyt49_R2


title: DNA from control K9


title: HCT116_shPLD1 rep1

city: Busan

first: Do Sik

last: Min

address: 30 Jangjeon-dong, Geumjeong-gu

department: Molecular Biology

country: South Korea

institute: Pusan National University

description: replicate 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

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

source_name: Colon cancer cells_HCT116_shPLD1 rep1

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

growth_protocol: DLD1 and HCT116 cells were cultured with DMEM medium supplemented with 1% heat-inactivated fetal bovine serum. The cultures were incubated for 36 hr at 37 ºC in a humidified incubator with 5% CO2.

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

treatment_protocol: DLD1 and HCT116 cells were treated with PLD1-Inh (10 μM) or transduced with shCTRL, shPLD1, or shPLD1/shE2F1.

tag: serum concentration

value: 1% FBS condition

value: colon cancer

tag: cell line


title: DE_Cyt49_R1

tag: differentiation stage


title: HCT116_shPLD1_shE2F1 rep1

description: replicate 1

source_name: Colon cancer cells_HCT116_shPLD1_shE2F1 rep1


title: 2-2618, 4 d after water inoculation by point, rep 1

description:
2-2618 +2DL-S1 H-P-1
Gene expression data from water-inoculated 2-2618 spikelets (point inoculation)

value: near isogenic spring wheat line 2-2618

value: inoculated spikelets


title: DNA from control K2

value: normal (control)


title: 2-2618, 4 d after water inoculation by point, rep 2

description:
2-2618 +2DL-S1 H-P-2
Gene expression data from water-inoculated 2-2618 spikelets (point inoculation)


title: DNA from control K12

value: peripheral blood


title: HCT116_shCTRL_PLD1_Inh rep1

description: replicate 1

source_name: Colon cancer cells_HCT116_shCTRL_PLD1_Inh rep1


title: DNA from control K6

value: no treatment


title: Mesothelium_Cyt49_R3


title: Mesothelium_H9_R1


title: DNA from control K5


title: DNA from control K4


title: DNA from control K3


title: Roblin, 4 d after water inoculation, rep 2

description: Gene expression data from water-inoculated Roblin spikelets , 4 d after inoculation

source_name: Water-inoculated Roblin spikelets, 4 d

tag: genotype

value: spring wheat cv Roblin

tag: inoculation treatment

value: Water

tag: day after inoculation


title: DNA from control K7

tag: tissue


title: Roblin, 2 d after water inoculation, rep 2

description: Gene expression data from water-inoculated Roblin spikelets , 2 d after inoculation

source_name: Water-inoculated Roblin spikelets, 2 d


title: Roblin, 4 d after water inoculation, rep 1


title: DLD1_shPLD1_shE2F1 rep1

description: replicate 1

source_name: Colon cancer cells_DLD1_shPLD1_shE2F1 rep1

growth_protocol: DLD1 and HCT116 cells were cultured with DMEM medium supplemented with 1% heat-inactivated fetal bovine serum. The cultures were incubated for 36 hr at 37 å¼C in a humidified incubator with 5% CO2.

treatment_protocol: DLD1 and HCT116 cells were treated with PLD1-Inh (10 µM) or transduced with shCTRL, shPLD1, or shPLD1/shE2F1.


title: Roblin, 1 d after water inoculation, rep 2

description: Gene expression data from water-inoculated Roblin spikelets , 1 d after inoculation

source_name: Water-inoculated Roblin spikelets, 1 d


title: DNA from control K1


title: HCT116_shCTRL rep1

description: replicate 1

source_name: Colon cancer cells_HCT116_shCTRL rep1


title: DLD1_shCTRL_PLD1_Inh rep1

description: replicate 1

source_name: Colon cancer cells_DLD1_shCTRL_PLD1_Inh rep1


title: DNA from ID individual 80

value: intellectual disability (ID)


title: Roblin, 1 d after water inoculation, rep 1

value: heads after mid-anthesis


title: Roblin, 2 d after water inoculation, rep 1


title: DLD1_shCTRL rep1

description: replicate 1

source_name: Colon cancer cells_DLD1_shCTRL rep1


title: Roblin, 4 d after Fg inoculation, rep 2

description: Gene expression data from Fusarium graminearum-inoculated Roblin spikelets , 4 d after inoculation

source_name: Fusarium graminearum-inoculated Roblin spikelets, 4 d

value: Fusarium graminearum


title: Roblin, 4 d after Fg inoculation, rep 1


title: DNA from ID individual 78


title: DNA from ID individual 77


title: DNA from ID individual 81


title: Roblin, 2 d after Fg inoculation, rep 2

description: Gene expression data from Fusarium graminearum-inoculated Roblin spikelets , 2 d after inoculation

source_name: Fusarium graminearum-inoculated Roblin spikelets, 2 d


title: DNA from ID individual 82


title: DNA from ID individual 76


title: DLD1_shPLD1 rep1

description: replicate 1

source_name: Colon cancer cells_DLD1_shPLD1 rep1


title: male ASP+MSG+TFA diet adipose, biological replicate 3

city: Riyadh

first: Kate

middle: S

last: Collison

address: Department Biological & Medical Research

country: Saudi Arabia

institute: King Faisal Specialist Hospital & Research Centre

description:
Gene expression data from 20-week male TFA+ASP+MSG diet adipose tissue
FAT # 12_(MoGene-1_0-st-v1).CEL.pimg

hyb_protocol: Following fragmentation, 5.5 ug of ssDNA was hybridized for 17 hr at 45°C on GeneChip Mouse Gene 1.0ST arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix 3000 7G Scanner and GeneChip Operating Software version 1.4 to produce .CEL files

data_processing: Microarray analysis was performed using the Partek genomic suite software version 6.3 (Partek, MO, USA).  Probe set data were summarized, background adjusted, and quantile normalized using the GC-Robust Multi-Array (GCRMA) algorithm.

organism: Mus musculus

source_name: male ASP+MSG+TFA diet adipose

label_protocol: Biotinylated ssDNA were prepared according to the standard Affymetrix protocol from 250ng total RNA (Affymetrix GeneChip WT Terminal Labeling and Hybridization user manual, 2010, in conjunction with the Ambion WT Expression Kit protocol, 2009).

growth_protocol: Our study animals were bred from female C57Bl/6J mice fed a standard chow diet until 6 weeks of age whereupon they were placed on one of 4 different dietary regimens for a period of 3 weeks prior to mating.

extract_protocol: Total RNA was prepared from snap-frozen adipose tissue using QIAGEN RNeasy® Lipid Tissue Kit according to manufacturers' instructions. The integrity of the RNA was measured using a 2100 Bioanalyzer instrument and an RNA 6000 Nano LabChip assay (Agilent Technologies).

treatment_protocol: The four dietary regimens used in this study were:[1] TFA diet: consisting of 20% (w/w) Partially Hydrogenated Vegetable Shortening (Test Diet #5C4M containing 8.68% w/w Trans fatty acids; Test Diet Purina, USA), with ad lib drinking water. [2] TFA+MSG diet: TFA diet with ad lib drinking water containing 0.75 g/L of L -Glutamic acid monosodium salt hydrate (MSG catalog G1626 Sigma Aldrich). [3] TFA+ ASP diet: (TFA diet with ad lib drinking water containing 0.25 g/L Asp-Phe methyl ester (aspartame, ASP, catalog A5139 Sigma Aldrich). [4] TFA+ASP+MSG diet: TFA diet with ad lib drinking water containing 0.25 g/L aspartame and 0.75 g/L monosodium glutamate.  After the 3-week period of adjustment to the respective diets, 15 male offspring were bred, weaned and maintained on these diets for the duration of the study. Offspring were weaned at 4 weeks of age

tag: strain background

tag: gender

value: male

value: adipose tissue

value: 20 wks

tag: diet group

value: ASP+MSG+TFA (aspartame + monosodium glutamate + Trans Fatty Acids)


title: Roblin, 2 d after Fg inoculation, rep 1


title: DNA from ID individual 79


title: male ASP+MSG+TFA diet adipose, biological replicate 2

description:
Gene expression data from 20-week male TFA+ASP+MSG diet adipose tissue
FAT # 11_(MoGene-1_0-st-v1).CEL.pimg

tag: age


title: Roblin, 1 d after Fg inoculation, rep 2

description: Gene expression data from Fusarium graminearum-inoculated Roblin spikelets , 1 d after inoculation

source_name: Fusarium graminearum-inoculated Roblin spikelets, 1 d


title: male ASP+MSG+TFA diet adipose, biological replicate 1

description:
Gene expression data from 20-week male TFA+ASP+MSG diet adipose tissue
FAT # 10_(MoGene-1_0-st-v1).CEL.pimg


title: DNA from ID individual 73

source_name: PB


title: Roblin, 1 d after Fg inoculation, rep 1


title: DNA from ID individual 75


title: male ASP+TFA  diet adipose, biological replicate 2

description:
Gene expression data from 20-week male TFA+ASP diet adipose tissue
FAT # 8_(MoGene-1_0-st-v1).CEL.pimg

source_name: male ASP+TFA diet adipose

value: ASP+TFA (aspartame + Trans Fatty Acids)


title: DNA from ID individual 74


title: DNA from ID individual 72


title: male MSG+TFA  diet adipose, biological replicate 3

description:
Gene expression data from 20-week male TFA+MSG diet adipose tissue
FAT # 6_(MoGene-1_0-st-v1).CEL.pimg

source_name: male MSG+TFA diet adipose

value: MSG+TFA (monosodium glutamate + Trans Fatty Acids)


title: male MSG+TFA  diet adipose, biological replicate 2

description:
Gene expression data from 20-week male TFA+MSG diet adipose tissue
FAT # 5_(MoGene-1_0-st-v1).CEL.pimg


title: male ASP+TFA  diet adipose, biological replicate 3

description:
Gene expression data from 20-week male TFA+ASP diet adipose tissue
FAT # 9_(MoGene-1_0-st-v1).CEL.pimg


title: male ASP+TFA  diet adipose, biological replicate 1

description:
Gene expression data from 20-week male TFA+ASP diet adipose tissue
FAT # 7_(MoGene-1_0-st-v1).CEL.pimg


title: DNA from ID individual 68


title: DNA from ID individual 71


title: male TFA diet adipose, biological replicate 3

description:
Gene expression data from 20-week male TFA diet adipose tissue
FAT # 3_(MoGene-1_0-st-v1).CEL.pimg

source_name: male TFA diet adipose

value: TFA (Trans Fatty Acids)


title: male TFA diet adipose, biological replicate 2

description:
Gene expression data from 20-week male TFA diet adipose tissue
FAT # 2_(MoGene-1_0-st-v1).CEL.pimg


title: male MSG+TFA diet adipose, biological replicate 1

description:
Gene expression data from 20-week male TFA+MSG diet adipose tissue
FAT # 4_(MoGene-1_0-st-v1).CEL.pimg


title: DNA from ID individual 70


title: male TFA diet adipose, biological replicate 1

description:
Gene expression data from 20-week male TFA diet adipose tissue
FAT # 1_(MoGene-1_0-st-v1).CEL.pimg


title: male ASP+MSG+TFA diet liver, biological replicate 3

description:
Gene expression data from 20-week male TFA+ASP+MSG diet liver tissue
Liver 12_(MoGene-1_0-st-v1).CEL.pimg

source_name: male ASP+MSG+TFA diet liver

extract_protocol: Total RNA was prepared from snap-frozen liver tissue using QIAGEN RNeasy® Kit according to manufacturers' instructions. The integrity of the RNA was measured using a 2100 Bioanalyzer instrument and an RNA 6000 Nano LabChip assay (Agilent Technologies).

treatment_protocol: The four dietary regimens used in this study were:[1] TFA diet: consisting of 20% (w/w) Partially Hydrogenated Vegetable Shortening (Test Diet #5C4M containing 8.68% w/w Trans fatty acids; Test Diet Purina, USA), with ad lib drinking water. [2] MSG+TFA diet: TFA diet with ad lib drinking water containing 0.75 g/L of L -Glutamic acid monosodium salt hydrate (MSG catalog G1626 Sigma Aldrich). [3] ASP+TFA diet: (TFA diet with ad lib drinking water containing 0.25 g/L Asp-Phe methyl ester (aspartame, ASP, catalog A5139 Sigma Aldrich). [4] ASP+MSG+TFA diet: TFA diet with ad lib drinking water containing 0.25 g/L aspartame and 0.75 g/L monosodium glutamate. After the 3-week period of adjustment to the respective diets, 15 male offspring were bred, weaned and maintained on these diets for the duration of the study. Offspring were weaned at 4 weeks of age.

value: liver


title: DNA from ID individual 67


title: male ASP+TFA  diet liver, biological replicate 3

description:
Gene expression data from 20-week male TFA+ASP diet liver tissue
Liver 9_(MoGene-1_0-st-v1).CEL.pimg

source_name: male ASP+TFA diet liver


title: male ASP+TFA  diet liver, biological replicate 1

description:
Gene expression data from 20-week male TFA+ASP diet liver tissue
Liver 7_(MoGene-1_0-st-v1).CEL.pimg


title: male ASP+MSG+TFA diet liver, biological replicate 1

description:
Gene expression data from 20-week male TFA+ASP+MSG diet liver tissue
Liver 10_(MoGene-1_0-st-v1).CEL.pimg


title: DNA from ID individual 62


title: DNA from ID individual 69


title: DNA from ID individual 66


title: male ASP+MSG+TFA diet liver, biological replicate 2

description:
Gene expression data from 20-week male TFA+ASP+MSG diet liver tissue
Liver 11_(MoGene-1_0-st-v1).CEL.pimg


title: male ASP+TFA  diet liver, biological replicate 2

description:
Gene expression data from 20-week male TFA+ASP diet liver tissue
Liver 8_(MoGene-1_0-st-v1).CEL.pimg


title: DNA from ID individual 61


title: male MSG+TFA  diet liver, biological replicate 2

description:
Gene expression data from 20-week male TFA+MSG diet liver tissue
Liver 5_(MoGene-1_0-st-v1).CEL.pimg

source_name: male MSG+TFA diet liver


title: male MSG+TFA  diet liver, biological replicate 3

description:
Gene expression data from 20-week male TFA+MSG diet liver tissue
Liver 6_(MoGene-1_0-st-v1).CEL.pimg


title: male MSG+TFA diet liver, biological replicate 1

description:
Gene expression data from 20-week male TFA+MSG diet liver tissue
Liver 4_(MoGene-1_0-st-v1).CEL.pimg


title: male TFA diet liver, biological replicate 3

description:
Gene expression data from 20-week male TFA diet liver tissue
Liver 3_(MoGene-1_0-st-v1).CEL.pimg

source_name: male TFA diet liver


title: DNA from ID individual 60


title: DNA from ID individual 65


title: DNA from ID individual 58


title: DNA from ID individual 52


title: DNA from ID individual 57


title: male TFA diet liver, biological replicate 2

description:
Gene expression data from 20-week male TFA diet liver tissue
Liver 2_(MoGene-1_0-st-v1).CEL.pimg


title: DNA from ID individual 63


title: DNA from ID individual 59


title: male TFA diet liver, biological replicate 1

description:
Gene expression data from 20-week male TFA diet liver tissue
Liver 1_(MoGene-1_0-st-v1).CEL.pimg


title: DNA from ID individual 51


title: DNA from ID individual 53


title: DNA from ID individual 55


title: DNA from ID individual 54


title: DNA from ID individual 50


title: DNA from ID individual 49


title: DNA from ID individual 47


title: DNA from ID individual 48


title: DNA from ID individual 46


title: DNA from ID individual 42


title: DNA from ID individual 43


title: DNA from ID individual 64


title: DNA from ID individual 41


title: DNA from ID individual 36


title: DNA from ID individual 37


title: DNA from ID individual 39


title: DNA from ID individual 33


title: DNA from ID individual 38


title: DNA from ID individual 44


title: DNA from ID individual 31


title: DNA from ID individual 28


title: DNA from ID individual 40


title: DNA from ID individual 35


title: DNA from ID individual 19


title: DNA from ID individual 26


title: DNA from ID individual 32


title: DNA from ID individual 23


title: DNA from ID individual 27


title: DNA from ID individual 34


title: DNA from ID individual 25


title: DNA from ID individual 24


title: DNA from ID individual 29


title: DNA from ID individual 30


title: DNA from ID individual 17


title: DNA from ID individual 20


title: DNA from ID individual 14


title: DNA from ID individual 16


title: DNA from ID individual 15


title: DNA from ID individual 22


title: DNA from ID individual 21


title: DNA from ID individual 13


title: DNA from ID individual 12


title: DNA from ID individual 18


title: DNA from ID individual 11


title: DNA from ID individual 10


title: DNA from ID individual 45


title: DNA from ID individual 9


title: DNA from ID individual 7


title: MCF7 Treatment_SAHA_1

city: Jacksonville

first: Catherine

last: Dumur

state: FL

address: 5008 Mustang Rd

department: Anatomic Pathology

institute: Sonic Healthcare USA

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on HG-U133A 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GC3000 scanner.

data_processing: After scanning, the raw intensities for every probe were stored in electronic files (in .DAT and .CEL formats) by the Affymetrix GeneChip Operating Software (GCOSv1.4). Background correction, normalization, and estimation of probe set expression summaries was performed using the log-scale Robust Multiarray Analysis (RMA) method.

source_name: Human MCF7 cells_treated with SAHA_replicate 1

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 500 ng total RNA (GeneChip® Expression Analysis Technical Manual, Affymetrix).

growth_protocol: MCF-7 cells were cultured in phenol red-free IMEM supplemented with 0.25% glucose and 10% FBS.

extract_protocol: Trizol lysates were used for the extraction of total RNA on the MagMAX™ Express Magnetic Particle Processor using the MagMAX™-96 for Microarrays Total RNA Isolation Kit (Ambion/InvitrogenTM Life Technologies, Carlsbad, CA)

treatment_protocol: MCF7 cells treated with vehicle, S1P (100 nM), FTY720 (1 μM) or SAHA (1 μM) for 24 hrs.


title: DNA from ID individual 5


title: DNA from ID individual 6


title: MCF7 Treatment_SAHA_3

source_name: Human MCF7 cells_treated with SAHA_replicate 3


title: MCF7 Treatment_SAHA_2

source_name: Human MCF7 cells_treated with SAHA_replicate 2


title: DNA from ID individual 4


title: DNA from ID individual 3


title: DNA from ID individual 8


title: NB31

city: Esplugues de Llobregat

first: Cinzia

last: Lavarino

state: Barcelona

address: Santa Rosa 39-57

department: Oncology

country: Spain

institute: Hospital Sant Joan de Déu

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium HumanMethylation450K BeadChip using standard Illumina protocol.

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

data_processing: GenomeStudio (Illumina) and R Package (Du P et al. Bioinformatics 2008) version 3.0.1; available through Bioconductor (www.bioconductor.org). The non_normalized_*.txt contains unmethylated and methylated signal intensities

source_name: Neuroblastoma

label_protocol: Standard Illumina Protocol.

extract_protocol: Genomic DNA was isolated from snap-frozen samples using Wizard DNA Purification Kit from Promega following manufacturers’ protocols.

tag: tissue type

value: Neuroblastoma

tag: tissue group

value: tumoral tissue

tag: tumor stage (inss classification)

value: Stage 3

tag: mycn status

value: non-amplified

tag: age at diagnosis (months)


title: MCF7 Treatment_FTY720_1

source_name: Human MCF7 cells_treated with FTY720_replicate 1


title: NB32

value: Stage 4s


title: MCF7 Treatment_S1P_2

source_name: Human MCF7 cells_treated with S1P_replicate 2


title: MCF7 Treatment_S1P_1

source_name: Human MCF7 cells_treated with S1P_replicate 1


title: MCF7 Treatment_S1P_3

source_name: Human MCF7 cells_treated with S1P_replicate 3


title: MCF7 Treatment_FTY720_2

source_name: Human MCF7 cells_treated with FTY720_replicate 2


title: MCF7 Treatment_FTY720_3

source_name: Human MCF7 cells_treated with FTY720_replicate 3


title: NB35

value: Stage 4


title: MCF7 Control_vehicle_3

source_name: Human MCF7 cells_treated with vehicle_replicate 3


title: MCF7 Control_vehicle_2

source_name: Human MCF7 cells_treated with vehicle_replicate 2


title: MCF7 Control_vehicle_1

source_name: Human MCF7 cells_treated with vehicle_replicate 1


title: NB34


title: NB30


title: NB24


title: MCF7 Control_parental_3

source_name: Human MCF7 cells_replicate 3


title: MCF7 Control_parental_2

source_name: Human MCF7 cells_replicate 2


title: NB23


title: NB29


title: MCF7 Control_parental_1

source_name: Human MCF7 cells_replicate 1


title: NB33

value: amplified


title: Tem CD8+ - repeat 3

city: Doha

first: Francesco

middle: Maria

last: Marincola

address: Al Nasr Tower, AL Corniche Street, PO Box 26999

country: Qatar

institute: Sidra Medical and Research Center

description: No additional information.

hyb_protocol: Affymetrix Hybridization Protocol Other: cDNAs were fragmented and hybridized to Mouse Gene 1.0 ST arrays (Affymetrix) according to manufacturer's instructions .

scan_protocol: Affymetrix Scanning Protocol Other: Probe-level intensities were called from images using the GeneChip Operating Software (GCOS) v1.1.1 software.

data_processing:
Data Processing Protocol
Calculation Method: The probe intensities stored in CEL files were then background adjusted, quantile-normalized, and summarized into probeset-level and gene transcript-level expression levels using the RMA algorithm as implemented in the Affymetrix Power Tools' apt137 probeset-summarize tool (used with "-a rma" option and Affymetrix's MoGene-1_0-st-v1.r4 pgf/clf/qcc/mps files). Two outlier samples revealed by principal component (see supplemental dataset 2) were removed from further analysis. We also excluded gene transcripts flagged with potential cross-hybridization in the transcript annotations file provided by Affymetrix, and those not detected in all four cell types (where a transcript is defined as detected in a cell type if at least half of its exons are detected above background at P < 0.05 in at least half the samples of this cell type (or all samples if only two samples in this cell type), with the detection P computed using apt-probeset-summarize tool with the "-a dabg" option). Since the samples were done in three cell preparation batches, we accounted for batch effects 19 by applying a standard adjustment procedure (viz., fitting a linear model of each gene's expression levels across samples to the batch covariate and taking the intercept-added residuals from this fit as the adjusted expression data for further analyses).

source_name: Tem CD8+

label_protocol:
Affymetrix Labeling Protocol
Other: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug of mRNA.

extract_protocol:
Trizol Extraction Protocol
Other: Total cellular RNA was extracted with TRIzol reagent (Invitrogen) according to manufacturer's protocol.

treatment_protocol: In-vitro treatment: CD8+ T cells were isolated from C57BL/6J mice. Effector memory (TEM) T cells were generated in vitro with functional anti-CD3 (1 ug/ml) and anti-CD28 (1 ug/ml) antibody with IL-2-containing (100 IU/ml) complete media. T cells were cultured for 5 days and subsequently FACS-sorted based on CD62L and CD44 expression.

tag: strain

value: spleen

tag: cell type

value: CD8+ T-cell


title: Tem CD8+ - repeat 2

description: No additional information.


title: Tem CD8+ - repeat 1

description: No additional information.


title: NB28


title: NB25


title: NB21


title: NB22


title: NB20

value: Stage 1


title: Tcm CD8+ - repeat 1

description: No additional information.

source_name: Tcm CD8+

treatment_protocol: In-vitro treatment: CD8+ T cells were isolated from C57BL/6J mice. Central memory (TCM) T cells were generated in vitro with functional anti-CD3 (1 ug/ml) and anti-CD28 (1 ug/ml) antibody with IL-2-containing (100 IU/ml) complete media. T cells were cultured for 5 days and subsequently FACS-sorted based on CD62L and CD44 expression.


title: NB17


title: NB26


title: Tcm CD8+ - repeat 3

description: No additional information.


title: Tcm CD8+ - repeat 2

description: No additional information.


title: NB19


title: NB18


title: Tscm CD8+ - repeat 3

description: No additional information.

source_name: Tscm CD8+

treatment_protocol: In-vitro treatment: CD8+ T cells were isolated from C57BL/6J mice. Stem-cell memory (TSCM) T cells were cultured in the same conditions as TCM and TEM with the addition of an inhibitor of GSK-3beta (5 uM TWS119 Tocris Bioscience). TSCM were FACS-sorted based on expression of CD62L, CD44 and SCA-1.


title: NB16


title: NB15


title: NB14


title: NB9


title: Tscm CD8+ - repeat 1

description: No additional information.


title: DNA from ID individual 1

source_name: PB

tag: diagnosis

value: intellectual disability (ID)

value: peripheral blood

tag: rhgh treatment

value: no treatment


title: Tn CD8+ - repeat 3

description: No additional information.

source_name: Tn CD8+

treatment_protocol: In-vitro treatment: Naive splenic (TN) CD8+ T cells from C57BL/6J mice were isolated by MACS purification using the CD8+ T cell isolation kit (Milenyi Biotec) and biotinylated CD44 antibody (clone IM7).


title: Tn CD8+ - repeat 2

description: No additional information.


title: Tn CD8+ - repeat 1

description: No additional information.


title: 3784 - Untreated TIL - repeat 3 - mAdbID:125993

description: mAdb experiment ID: 125993

hyb_protocol: Hybridization Protocol Other: Biotinylated cDNA was hybridized to Human Gene 1.0 ST arrays (Affymetrix) overnight at 45°C according to manufacturer's instructions.

scan_protocol: Affymetrix Scanning Protocol Other: Arrays were scanned on a GeneChip Scanner 3000 7G (Affymetrix).

data_processing:
Affymetrix RMA Data Processing
Calculation Method: Expression summary values were calculated using the Bioconductor implemented version of RMA (Robust Multichip Average).

source_name: 3784 - Untreated TIL

label_protocol:
Encore Biotin Module
Other: Samples were fragmentated and biotinylated using the Encore Biotin Module (NuGEN) according to the manufacturer's instructions.

extract_protocol:
Ovation Pico WTA System V2
Other: RNA (100 ng) was extracted from CD8+ TILs using Ovation Pico WTA System V2 (NuGEN) according to the manufacturer's instructions.

treatment_protocol:
Agent: DMSO
Treatment time: 30 days
In-vitro treatment: Human tumor-infiltrating cytotoxic T lymphocytes (TIL) were were cultured in 6000 IU/mL IL-2 for 2 weeks, and subsequently expanded with a rapid expansion protocol using 30 ng/mL OKT3 (anti-CD3) antibody (Miltenyi Biotech) and 6000 IU/mL IL-2 in the presence of irradiated (50 Gy) allogeneic feeder cells at a 200:1 ratio of feeder cells to TIL. TIL were harvested 30 days after initiation of culture in the presence of DMSO.

value: tumor

value: Tumor-infiltrating lymphocytes (TIL)

tag: disease state

value: melanoma

tag: individual


title: NB8

source_name: Neuroblastoma


title: NB7


title: NB10


title: 3784 - Untreated TIL - repeat 2 - mAdbID:125992

description: mAdb experiment ID: 125992


title: 3784 - Untreated TIL - repeat 4 - mAdbID:125994

description: mAdb experiment ID: 125994


title: NB32

hyb_protocol: Standard Affyemtrix protocol.

scan_protocol: Arrays were imaged using standard recommended Affyemtrix scanner setting.

data_processing: R Package (Du P et al. Bioinformatics 2008) version 3.0.1; available through Bioconductor (www.bioconductor.org).

label_protocol: Standard Affymetrix Protocol.

extract_protocol: RNA was isolated from snap-frozen samples using TriReagent from Sigma following manufacturers’ protocols.

tag: stumor stage (inss classification)


title: NB12


title: 3784 - Untreated TIL - repeat 1 - mAdbID:125991

description: mAdb experiment ID: 125991

tag: tissue


title: NB33


title: NB13


title: Reference6_GN2

source_name: Ganglioneuroma

value: Ganglioneuroma


title: NB30

value: Neuroblastoma


title: NB2

value: tumoral tissue


title: 3784 - Akt treated TIL - repeat 4 - mAdbID:125990

description: mAdb experiment ID: 125990

source_name: 3784 - Akt treated TIL

treatment_protocol:
Agent: Akt inhibitor
Treatment dose: 1 uM
Treatment time: 30 days
In-vitro treatment: Human tumor-infiltrating cytotoxic T lymphocytes (TIL) were were cultured in 6000 IU/mL IL-2 for 2 weeks, and subsequently expanded with a rapid expansion protocol using 30 ng/mL OKT3 (anti-CD3) antibody (Miltenyi Biotech) and 6000 IU/mL IL-2 in the presence of irradiated (50 Gy) allogeneic feeder cells at a 200:1 ratio of feeder cells to TIL. TIL were harvested 30 days after initiation of culture in the presence of Akt inhibitor (1uM).


title: NB6

value: Stage 3


title: NB28


title: NB5

value: non-amplified


title: 3784 - Akt treated TIL - repeat 3 - mAdbID:125989

description: mAdb experiment ID: 125989


title: 3784 - Akt treated TIL - repeat 2 - mAdbID:125988

description: mAdb experiment ID: 125988


title: NB24

value: Stage 4s


title: Reference5_GN1


title: 3289 - Untreated TIL - repeat 4 - mAdbID:125986

description: mAdb experiment ID: 125986

source_name: 3289 - Untreated TIL


title: NB25


title: NB27

value: Stage 4


title: 3289 - Untreated TIL - repeat 3 - mAdbID:125985

description: mAdb experiment ID: 125985


title: Tscm CD8+ - repeat 2

description: No additional information.


title: NB23


title: NB20


title: Reference4_FB2

source_name: Fetal Brain

value: Fetal Brain

value: normal tissue


title: 3784 - Akt treated TIL - repeat 1 - mAdbID:125987

description: mAdb experiment ID: 125987


title: NB26


title: 3289 - Akt treated TIL - repeat 4 - mAdbID:125982

description: mAdb experiment ID: 125982

source_name: 3289 - Akt treated TIL


title: NB19

value: amplified


title: 3289 - Untreated TIL - repeat 1 - mAdbID:125983

description: mAdb experiment ID: 125983


title: NB18

value: Stage 1


title: KAI3_cell_A404P

city: shanghai

first: Mingjie

last: Wang

address: 197 Ruijin Er Road

country: China

institute: Ruijin Hospital,Shanghai Jiaotong University,School of Medicine

description: Gene expression

hyb_protocol: Agilent standard One-Color Microarray-Based Exon analysis protocol

scan_protocol: Scanned on an Agilent G2505C scanner. Images were quatified using Agilent Feature Extraction Software (version 11.0.1.1)

data_processing: The data were quantile normalized using software R

source_name: NK cell line KAI3, A404P

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

tag: cell line


title: Reference2_AG2

source_name: Adrenal gland

value: Adrenal gland


title: KAI3_cell_E348K

description: Gene expression

source_name: NK cell line KAI3, E348K

label_protocol: Agilent standard One-Color Microarray-Based Exon analysis protocol


title: Reference3_FB1


title: NB14


title: 3289 - Akt treated TIL - repeat 3 - mAdbID:125981

description: mAdb experiment ID: 125981


title: KAI3_cell_wild_type

description: Gene expression

source_name: NK cell line KAI3, wild_type


title: Reference1_AG1


title: 3289 - Akt treated TIL - repeat 2 - mAdbID:125980

description: mAdb experiment ID: 125980


title: NB1


title: NB10


title: NB11


title: tumor_tissue_DDX3X_wildtype_4

description: Gene expression

source_name: tumor_tissue, DDX3X_wildtype, 4

value: tumor tissue


title: NB8


title: NB4


title: 2818 - Untreated TIL - repeat 3 - mAdbID:125977

description: mAdb experiment ID: 125977

source_name: 2818 - Untreated TIL


title: NB2


title: 2818 - Untreated TIL - repeat 2 - mAdbID:125976

description: mAdb experiment ID: 125976


title: 2818 - Untreated TIL - repeat 4 - mAdbID:125978

description: mAdb experiment ID: 125978


title: tumor_tissue_DDX3X_wildtype_3

description: Gene expression

source_name: tumor_tissue, DDX3X_wildtype, 3


title: tumor_tissue_DDX3X_wildtype_5

description: Gene expression

source_name: tumor_tissue, DDX3X_wildtype, 5


title: DNA from ID individual 2

source_name: PB

value: intellectual disability (ID)

value: peripheral blood

value: no treatment


title: 2818 - Untreated TIL - repeat 1 - mAdbID:125975

description: mAdb experiment ID: 125975

value: tumor

value: Tumor-infiltrating lymphocytes (TIL)

value: melanoma


title: tumor_tissue_DDX3X_wildtype_2

description: Gene expression

source_name: tumor_tissue, DDX3X_wildtype, 2


title: tumor_tissue_DDX3X_wildtype_1

description: Gene expression

source_name: tumor_tissue, DDX3X_wildtype, 1


title: NB1

source_name: Neuroblastoma

value: Neuroblastoma

value: tumoral tissue


title: 3289 - Akt treated TIL - repeat 1 - mAdbID:125979

description: mAdb experiment ID: 125979


title: tumor_tissue_DDX3X_mutation_5

description: Gene expression

source_name: tumor tissue, DDX3X_mutation, 5


title: NB27


title: NB4

value: non-amplified


title: 2818 - Akt treated TIL - repeat 4 - mAdbID:125974

description: mAdb experiment ID: 125974

source_name: 2818 - Akt treated TIL


title: Reference8_FB2

value: NA (non-tumoral)


title: tumor_tissue_DDX3X_mutation_4

description: Gene expression

source_name: tumor tissue, DDX3X_mutation, 4


title: decitabine treatment, biological rep 2

city: Boston

first: Michael

middle: Solomon

last: Goldberg

state: MA

address: 450 Brookline Avenue

department: Cancer Immunology and AIDS

institute: Dana-Farber Cancer Institute

description: gene expression data from cultured BR5FVB1-Akt cells with dectabine treatment

hyb_protocol: Affymetrix GeneChip WT Terminal Lebeling and Hybridization (cat# 702808).  the Affymetrix GeneChip WT Terminal Labeling.

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

data_processing: The data were analyzed using Affymetrix Transcroptome Analysis Console software.

source_name: decitabine-treated BR5FVB1-Akt cells

label_protocol: The samples were processed following the Affymetrix GeneChip WT Plus Reagent Kit (cat # 703174), followed by the Affymetrix GeneChip WT Terminal Lebeling and Hybridization (cat# 702808) onto Affymetrix Mouse Gene 2.0ST arrays.  the Affymetrix GeneChip WT Terminal Labeling.

growth_protocol: BR5FVB1-Akt cells were cultured in DMEM with 10% FBS and 1% Penicillin/ Streptomycin at 37C.

extract_protocol: Total RNA was extracted using Qiagen RNeasy Mini Kit.

treatment_protocol: BR5FVB1-Akt cells were treated with 10 uM of decitabine for 72 hours.

value: ovarian cancer


title: Reference3_FB1

source_name: Fetal Brain

value: Fetal Brain


title: 2818 - Akt treated TIL - repeat 1 - mAdbID:125971

description: mAdb experiment ID: 125971


title: 2818 - Akt treated TIL - repeat 2 - mAdbID:125972

description: mAdb experiment ID: 125972


title: Reference7_AG1

value: normal tissue


title: NB3

value: Stage 4s


title: Reference2_AG2


title: tumor_tissue_DDX3X_mutation_2

description: Gene expression

source_name: tumor tissue, DDX3X_mutation, 2


title: control, biological rep 2

description: gene expression data from cultured BR5FVB1-Akt cells

source_name: BR5FVB1-Akt cells


title: 2818 - Akt treated TIL - repeat 3 - mAdbID:125973

description: mAdb experiment ID: 125973


title: control, biological rep 1


title: tumor_tissue_DDX3X_mutation_1

description: Gene expression

source_name: tumor tissue, DDX3X_mutation, 1


title: 076B

status: Public on Jun 02 2015

city: Krakow

first: Szymon

last: Skoczen

address: Wielicka 265

department: Clinical Immunology

country: Poland

institute: Chair of Clinical Immunology and Transplantation, Jagiellonian University Medical College

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: GeneSpring 12.6-GX-PA software; RMA16 – summarization algorithm; no baseline transformation; Analysis type: Exon; Experiment type: Affymetrix Exon Expression

source_name: POST HSCT_blood mononuclears

label_protocol: Gene Chip Whole Transcript Sense Target Labeling Assay

extract_protocol: Ambion RiboPure

tag: sample/subject id

tag: subject status

value: haematopoietic stem cell transplantation (HSCT) children

tag: sample group

value: POST HSCT

value: blood mononuclear cells


title: 072B


title: 073B


title: 057B


title: 053B


title: 051B


title: 074B


title: 041B


title: 042B


title: 029B


title: 038B


title: 027B


title: 033B


title: 018B


title: 011B


title: tumor_tissue_DDX3X_mutation_3

description: Gene expression

source_name: tumor tissue, DDX3X_mutation, 3

value: tumor tissue

tag: age


title: 010B


title: 009B


title: 002B


title: 001C


title: 082A

source_name: PRE HSCT_blood mononuclears

value: PRE HSCT


title: 085A


title: 078A


title: 086A

description: 86A _(HuGene-1_0-st-v1).CEL


title: 075A


title: 079A


title: 080A


title: 074A


title: 072A


title: 067A


title: 076A


title: 057A


title: 073A


title: 059A


title: 053A

description: 53A _(HuGene-1_0-st-v1).CEL


title: 056A


title: 042A

description: 42A _(HuGene-1_0-st-v1).CEL


title: 051A

description: 51A _(HuGene-1_0-st-v1).CEL


title: 066A


title: 041A


title: 3289 - Untreated TIL - repeat 2 - mAdbID:125984

description: mAdb experiment ID: 125984

source_name: 3289 - Untreated TIL


title: 038A

description: 38A _(HuGene-1_0-st-v1).CEL


title: 029A


title: 033A


title: 020A


title: 024A


title: 018A


title: 011A


title: 010A


title: 009A


title: 019A


title: 001A


title: 027A


title: Cord_blood_derived_Oct4_induced_neural_progenitors_without_inhibitors_rep1

city: Hamilton

first: Mickie

last: Bhatia

state: Ontario

address: 1200 Main Street West

department: Stem Cell and Cancer Research Institute (SCC-RI)

institute: McMaster University

hyb_protocol: In accordance with manufacturer's protocols

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

data_processing: Data was normalized using Robust Multichip Averaging (RMA) algorithm using Partek Genomics Suite 6.6 software.

source_name: Cord blood derived Oct4 induced neural progenitors

growth_protocol: Fibroblasts were cultured in DMEM 10% FCS. hCB_34pos were cultured in stemspan supplemented with SCF, Flt-3L, IL3, and TPO.  Fib_iNPC and BD_iNPC were cultured in DMEMF12 1xN2 1xB27 20ng/mL EGF 20ng/mL FGF.  Samples noted with Inhibitors are described in treatment protocol

extract_protocol: Extraction of total RNA using total RNA purification kit (Norgen Biotek, Canada) was performed according to the manufacturer's instructions.

treatment_protocol: Inhibitors noted samples were cultured in DMEMF12 1xN2 1xB27 and treated with 10μM SB431542, 100nM LDN-193189 , 100ng/mL Noggin and 3μM CHIR99021 for two  weeks


title: Cord_blood_derived_Oct4_induced_neural_progenitors_with_inhibitors_rep2

label_protocol: In accordance with manufacturer's protocols

value: Cord blood derived Oct4 induced neural progenitors


title: Fibroblast_derived_Oct4_induced_neural_progenitors_without_inhibitors_rep2

source_name: Fibroblast derived Oct4 induced neural progenitors


title: Cord_blood_derived_Oct4_induced_neural_progenitors_with_inhibitors_rep1


title: Fibroblast_derived_Oct4_induced_neural_progenitors_with_inhibitors_rep1

value: Fibroblast derived Oct4 induced neural progenitors


title: Human_dermal_fibroblasts_rep1

source_name: Human dermal fibroblasts

value: Human dermal fibroblasts


title: Fibroblast_derived_Oct4_induced_neural_progenitors_without_inhibitors_rep1


title: Human_cord_blood_CD34positive_rep1

source_name: Human cord blood CD34 positive cells

value: Human cord blood CD34 positive cells


title: Human_cord_blood_CD34positive_rep2


title: Human_dermal_fibroblasts_rep2


title: LSC3

city: Atlanta

first: Viren

last: Patel

state: GA

address: 101 Woodruff Circle

department: EICC

institute: Emory University School of Medicine

data_processing: The data were normalised using quantile normalization in Illumina Genome Studio 2011.1

source_name: Myogenic cells from limb muscle

label_protocol: NuGEN WT-Ovation Pico amplification kit and Encore biotin IL.

extract_protocol: RNA was isolated using Qiagen miRNEAsy kit with on-column DNAse treatment followed by one round of amplification using NuGEN’s WT-Ovation Pico amplification kit.

value: 8-10 weeks

tag: gender

value: male

value: Limb Muscle

value: sorted satellite cells


title: LSC2


title: LSC1


title: 002A


title: Cord_blood_derived_Oct4_induced_neural_progenitors_without_inhibitors_rep2


title: Fibroblast_derived_Oct4_induced_neural_progenitors_with_inhibitors_rep2


title: PSC1

source_name: Myogenic cells from pharyngeal muscle

value: Pharyngeal Muscle


title: decitabine treatment, biological rep 1

tag: tissue type

value: ovarian cancer


title: PSC3


title: aorta_DKO_rep3

city: Morgantown

first: Mary

middle: E

last: Davis

state: WV

address: 1 Medical Center Drive

institute: West Virginia University Health Sciences Center

hyb_protocol: Samples (with added hybridization controls) were hybridized to the mouse GeneChip 1.0 ST Gene Arrays (Affymetrix) at 45°C for 17 hours in GeneChip Hybridization Oven 640 (Affymetrix). Mouse GeneChip 1.0 ST Gene Arrays were stained using the FS 450_0007 protocol in Affymetrix GeneChip Fluidics Station 450. Briefly: Biotin-labeled cDNA was reacted using two rounds of washes with a solution containing a streptavidin-phycoerythrin complex, with an intermediate treatment of biotin-labeled anti-streptavidin antibody to amplify the signal.

scan_protocol: Phycoerythrin labeling was detected within the Affymetrix GeneChip Scanner 3000 7G Plus using 532 nm light and detected by a photomultiplier tube. Expression Consol software (Affymetrix) was used to check quality controls of hybridized chips.

data_processing:
Data were log2 transformed, and then RMA background correction, quantile normalization and median polish probeset summarization were applied using Partek software. Two-way ANOVA (genotype and chip processing batch effects), assuming non-equal variance, and Least Significant Difference test were performed and used, with fold-change, to filter the genes for pathways and gene-gene interaction network analysis using Ingenuity Pathways Analysis (IPA, Redwood City, CA). Significance Analysis of Microarrays (SAM) was used to determine genes with significant changes (also controlling for batch effects) and using a FDR of 10%.
Expression values with gene assignment "---" were filtered out prior to analysis.
Probe group file: MoGene-1_0-st-v1.r4.pgf
Meta-probeset file: MoGene-1_0-st-v1.na32.mm9.transcript.csv

source_name: aorta, apoe-/- adora1-/-

label_protocol: cDNA was fragmented and biotin labeled using the Gene Chip WT Terminal Labeling Kit (Affymetrix).

growth_protocol: Mice were housed under normal conditions and used when 20 weeks old.

extract_protocol: RNA was isolated from tissues using the RNase Micro Kit (Qiagen), and processed using the Ambion WT Expression Kit.

treatment_protocol: Not applicable.

tag: genotype

value: apoe-/- adora1-/-

value: aorta

value: 20 weeks


title: aorta_APOE-KO_rep1

source_name: aorta, apoe-/-

value: apoe-/-


title: PSC2


title: aorta_DKO_rep2


title: aorta_APOE-KO_rep2


title: aorta_APOE-KO_rep3


title: aorta_DKO_rep1


title: Vehicle Ctrl + Glucagon_3

city: South San Francisco

first: Matthew

last: Brauer

state: California

address: 1 DNA Way

department: Bioinformatics

institute: Genentech, Inc.

hyb_protocol: Agilent In Situ Hybridization Kit Plus was used where Cy-dye labeled control and test samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, the arrays were washed twice, dried and then scanned.

scan_protocol: Scanned on an Agilent G2505C scanner. Images were quantified using Agilent Feature Extraction Software version 10.7.

data_processing: Agilent Feature Extraction Software version 10.7 was used for background subtraction and LOWESS normalization.

source_name: Vehicle Ctrl + Glucagon

label_protocol: Total RNA was converted to double-stranded cDNA and then into Cy-dye labeled cRNA using Agilent’s Quick Amp Labeling Kit. For all samples, 750 ng of the labeled cRNA was fragmented and hybridized against Cy3-labeled Universal human reference.

extract_protocol: After glucagon stimulation cells will be harvested in Qiazol & RNA will be isolated, DNAse treated, concentrated by ethanol precipitation and resuspended in nuclease free water.

tag: treatment

value: +GCG

value: Liver

source_name: Universal human reference (UHR)

tag: sample type

value: Universal human reference (UHR)


title: Vehicle Ctrl + Glucagon_2


title: NB13

source_name: Neuroblastoma

value: Neuroblastoma

tag: tissue group

value: tumoral tissue

value: Stage 4

tag: mycn status

value: non-amplified

tag: age at diagnosis (months)


title: Vehicle Ctrl - Glucagon_1

source_name: Vehicle Ctrl - Glucagon

value: -GCG


title: Vehicle Ctrl + Glucagon_1


title: N12

city: Taipei

first: Ming Che

last: Shih

address: No.128, Sec. 2, Academia Rd., Nangang Dist

department: Agricultural Biotechnology Research Center

country: Taiwan

institute: Academia Sinica, Taiwan

description: Gene expression profiling of root

hyb_protocol: All microarray hybridizations were followed Agilent Hybridization procedure at 65℃ for 17 hours.

scan_protocol: All chips were scanned by Agilent Microarray Scanner and scan settings were followed the manufacture suggestion.

data_processing: All Microarray data were processed using 75% percentile normalization in GeneSpring GX 11 (Agilent, CA, USA)

organism: Phalaenopsis aphrodite

source_name: root

label_protocol: First strand cDNA was synthesized from 20 µg total RNA via Oligo dT-V primer and Superscript III Reverse Transcriptase (Invitrogen, USA), and cDNA indirect labeling was done by incorporating aminoallyl modified UTPs during reverse transcription and following coupling reaction with Alex Fluor 555 dye (Cy 3).

extract_protocol: Orchid total RNA was isolated as described previously with minor modification (Yu and Goh 2000). Plant tissues were frozen and ground in liquid nitrogen. RNA was extracted by vortexing with 5 to10 volumes (w/v) of extraction buffer (2% hexadecyltrimethylammonium bromide, 1% polyvinylpyrrolidone 40, 100 mM Tris-HCl pH 7.5, 20 mM EDTA, 2 M NaCl, 2% 2-mercaptoethanol) pre-warmed at 65°C. The homogenate was incubated at 65°C for 15 minutes with frequent mixing. The homogenate was centrifuged at 3,000xg for 10 minutes at room temperature. The supernatant was extracted twice with an equal volume of chloroform:isoamyl alcohol (24:1, v/v) and centrifuged at 8,000xg for 15 minutes. One-third volume of 8M lithium chloride was added to the aqueous phase to precipitate total RNA at -20°C overnight. The RNA pellet was harvested by centrifugation at 12,000xg for 30 minutes at 4°C, washed with ice-cold 75% ethanol, and resuspended in RNase-free water. RNA purity and concentration were determined by Nanodrop 2000 (Thermo Scientific, MA, USA) or Qubit (Invitrogen, CA, USA) measurement. The quality of RNA was evaluated on an Agilent 2100 Bioanalyzer (Agilent, CA, USA).

value: Phalaenopsis aphrodite, diploid

value: root


title: N08

description: Gene expression profiling of flower

source_name: flower

value: flower


title: Vehicle Ctrl - Glucagon_3


title: N06

description: Gene expression profiling of leaf

source_name: leaf

value: leaf


title: N05

description: Gene expression profiling of flower


title: N10

description: Gene expression profiling of root

value: Phalaenopsis V3 hybrid, tetraploid


title: N04

description: Gene expression profiling of leaf


title: Vehicle Ctrl - Glucagon_2


title: N01

description: Gene expression profiling of flower


title: N11

description: Gene expression profiling of root


title: N09

description: Gene expression profiling of leaf


title: N07

description: Gene expression profiling of flower


title: N03

description: Gene expression profiling of leaf


title: N02

description: Gene expression profiling of leaf


title: N13

description: Gene expression profiling of root


title: 067B

source_name: POST HSCT_blood mononuclears

value: haematopoietic stem cell transplantation (HSCT) children

value: POST HSCT

tag: cell type

value: blood mononuclear cells


title: PA036

description: gene expression profile of inflorescence

source_name: F (inflorescence)

label_protocol: RNA amplification was performed with MessageAmp™ II aRNA Amplification Kit (Ambion Inc., Austin, TX, USA) starting with 1 µg total RNA and following the manufacture procedures including first strand cDNA synthesis, second strand cDNA synthesis and in vitro transcription for cRNA synthesis. Finally, 1.65 µg of amplified aminallyl labeled cRNA was coupled with Alex Fluor 555 dye (Cy 3) and then the dye-coupled aRNA was fragmented before hybridization.

value: F (inflorescence)


title: PA037

description: gene expression profile of young inflorescence

source_name: YF (young inflorescence)

value: YF (young inflorescence)


title: PA035

description: gene expression profile of flower stalk

source_name: Stalk

value: Stalk


title: PA038

description: gene expression profile of bud

source_name: Bud

value: Bud


title: PA039

description: gene expression profile of bud


title: PA041


title: PA028

description: gene expression profile of leaf

source_name: Pa-Leaf

value: Pa-Leaf


title: PA031

description: gene expression profile of flower

source_name: Pa-Flower

value: Pa-Flower


title: PA034

description: gene expression profile of flower stalk


title: PA026

description: gene expression profile of large bud (>1cm in diameter)

source_name: Bud-L, > 1 cm bud

value: Bud-L, > 1 cm bud


title: PA027

description: gene expression profile of leaf


title: PA040


title: PA033

description: gene expression profile of root

source_name: Pa-Root

value: Pa-Root


title: PA032

description: gene expression profile of root


title: PA029

description: gene expression profile of leaf


title: PA025


title: PA030

description: gene expression profile of flower


title: PA017

description: gene expression profile of flower 3 day post pollination

source_name: SF-3d, 3 DAP (Day after pollination)

value: SF-3d, 3 DAP (Day after pollination)


title: PA019

description: gene expression profile of flower 1 day post pollination

source_name: SF-1d, 1 DAP (Day after pollination)

value: SF-1d, 1 DAP (Day after pollination)


title: PA016

description: gene expression profile of flower 15 day post pollination

source_name: SF-15d, 15 DAP (Day after pollination)

value: SF-15d, 15 DAP (Day after pollination)


title: PA021

description: gene expression profile of commercial hybrid, V3, mature flower, whole


title: PA024

description: gene expression profile of small bud (<1cm in diameter)

source_name: Bud-s, < 1cm bud

value: Bud-s, < 1cm bud


title: PA015

description: gene expression profile of flower 8 day post pollination

source_name: SF-8d, 8 DAP (Day after pollination)

value: SF-8d, 8 DAP (Day after pollination)


title: PA023

value: Phalaenopsis V3 hybrid, tetraploid


title: PA014


title: PA020


title: PA018


title: PA013


title: MP570 tumor, LBH589 12 hrs

first: Kun-Wei

last: Liu

address: 10901 N Torrey Pines Rd

institute: Sanford-Burnham Medical Research Institute

description: Gene expression data from cells MP tumor cells treated with LBH589 for 12 hrs

hyb_protocol: The labeled sscDNA was then hybridized onto GeneChip Mouse Gene 2.0 ST Array (Affymetrix), which analyzes ~30,000 coding and non-coding transcripts using ~ 760,000 probe sets (on average 22 probes per transcripts). The staining and washing of the arrays were conducted using a Fluidics 450 station

scan_protocol: GeneChips were scanned using Affymetrix GeneChip Command Console Software (AGCC) and GeneChip® Scanner 3000 7G.

data_processing: The intensities of the scanned fluorescence images were extracted with Agilent Feature Extraction software Ver 10.7.3.1.  The mean signals were background corrected and transformed to the log2 scale.  Then the data were normalized between arrays by quantile approach.

source_name: Murine MP tumor cells treated with LBH589 for 12 hrs

label_protocol: The single-stranded cDNA was generated using the 400 ng of total RNA according to Whole Transcript (WT) Sense Target Labeling Assay protocol using Ambion’s WT Expression kit (p/n 4411974). The 5.5 mg of sscDNA was then fragmented and labeled using GeneChip WT Terminal Labeling kit (PN 900671).

growth_protocol: Tumor cells were isolated from cerebella of NSG mice and dissociated into single cells for plating in neurocult media plus proliferation supplement in vitro.

extract_protocol: Extraction of total RNA was performed using Qiagen RNeasy Kit according to the manufacturer's instructions.

treatment_protocol: After plating, 0.00025% DMSO or 25nM LBH589 were added into the culture. Cells were then lysed after 6 or 12 hours of incubation.

tag: tumor

value: LBH589 for 12 hrs


title: PA012

description: gene expression profile of mature flower pollinia

source_name: Pollinia

value: Pollinia


title: MP570 tumor, DMSO 12 hrs

description: Gene expression data from cells MP tumor cells treated with DMSO for 12 hrs

source_name: Murine MP tumor cells treated with DMSO for 12 hrs

value: DMSO for 12 hrs


title: PA022


title: MP570 tumor, LBH589 6 hrs

description: Gene expression data from cells MP tumor cells treated with LBH589 for 6 hrs

source_name: Murine MP tumor cells treated with LBH589 for 6 hrs

value: LBH589 for 6 hrs


title: MP567 tumor, LBH589 12 hrs


title: MP570 tumor, DMSO 6 hrs

description: Gene expression data from cells MP tumor cells treated with DMSO for 6 hrs

source_name: Murine MP tumor cells treated with DMSO for 6 hrs

value: DMSO for 6 hrs


title: PA009


title: MP567 tumor, LBH589 6 hrs


title: PA007

description: gene expression profile of mature flower pedicel

source_name: Pedicel

value: Pedicel


title: PA010

description: gene expression profile of mature flower column

source_name: Column

value: Column


title: PA005


title: MP525 tumor, DMSO 12 hrs


title: PA008

description: gene expression profile of mature flower sepal

source_name: Sepal

value: Sepal


title: MP567 tumor, DMSO 12 hrs


title: MP525 tumor, LBH589 12 hrs


title: PA011


title: MP525 tumor, DMSO 6 hrs


title: MP525 tumor, LBH589 6 hrs


title: PA004

description: gene expression profile of mature flower petal

source_name: Petal

value: Petal


title: PA002

description: gene expression profile of mature flower lip

source_name: Lip

value: Lip


title: P. syringae pv tomato DC3000 wildtype 13 hours biorep D

city: Norwich

first: Jonathan

middle: David

last: Moore

address: Norwich Research Park

department: Platforms and Pipelines

country: United Kingdom

institute: The Genome Analysis Centre

description: Randomised loop design providing dye-swaps between treatments, time points and bioreps

hyb_protocol: The order in which the 288 slides were hybridized and scanned was randomised to minimise the impact on differences between samples of any potential variation in the processing conditions. According to this randomised experimental design combinations of labelled samples were hybridized to slides overnight at 42oC.

scan_protocol: Following hybridization, slides were washed and scanned using an Affymetrix 428 array scanner at 532nm (Cy3) and 635nm (Cy5). Scanned data were quantified using Imagene 7.5.0 software (BioDiscovery, Inc.).

data_processing: Quantified microarray data were Lowess normalized within pintip groups and within arrays, then variation due to arrays and dyes was removed by a random effects model, and averaged, in log space, using R/MAANOVA (MicroArray ANalysis Of VAriance) (Wu et al. 2003). Oligo sequences of CATMA array probes were mapped to individual mRNA sequences of transcripts from the TAIR9 genome assembly using BLASTn with e-value cutoff of 0.01.  Additionally, alignments were filtered to exclude alignments shorter than 30bp or with less than 80% sequence identity.

label: Cy3 or Cy5

organism: Arabidopsis thaliana

label_protocol: Cy3 and Cy5 labelled cDNA probes were prepared by reverse transcribing 5µg of aRNA with Cy3- or Cy5- dCTP (GE Healthcare) and a modified dNTP mix (10mM each dATP, dGTP and dTTP; 2mM dCTP) using random primers (Invitrogen) and SuperScript II reverse transcriptase (Invitrogen), with the inclusion of RNase inhibitor (RNaseOUT, Invitrogen) and DTT. Labelled probes were purified using QiaQuick PCR Purification columns (Qiagen), freeze-dried, and resuspended in 50µl hybridization buffer (25% formamide, 5xSSC, 0.1% SDS, 0.5µg/µl yeast tRNA [Invitrogen]).

growth_protocol: Arabidopsis plants Col-0 were grown under a 16:8 hr light:dark cycle (lights on 04:00 to 20:00) at 20°C, 60% humidity and light intensity of 100 μmol photons.m-2.s-1. Arabidopsis seed was stratified for three days in 0.1% agar at 4°C before sowing onto Arabidopsis soil mix (Scotts Levingtons F2s compost:sand:fine grade vermiculite in a ratio of 6:1:1).

extract_protocol: Total RNA was isolated from four individual leaves from each sampled time point (arbitrarily labelled as biological replicates A, B, C and D) using TRIzol reagent (Invitrogen), purified with RNeasy columns (Qiagen) and amplified using the MessageAmp II aRNA Amplification kit (Ambion) in accordance with the kit protocol with a single round of amplification.

tag: strain

value: Infected P. syringae pv tomato DC3000 wildtype

value: leaf


title: Liver_3c7.v44 mAb_6

scan_protocol: Scanned on an Agilent scanner, images were processed using Agilent Feature Extraction software version 11.

data_processing: Agilent Feature Extraction Software version 11 was used for background subtraction and LOWESS normalization.

source_name: Liver_3c7.v44 mAb

label_protocol: Total RNA was converted to double-stranded cDNA and then into Cy-dye labeled cRNA using Agilent’s Quick Amp Labeling Kit. For all samples, 750 ng of the labeled cRNA was fragmented and hybridized against Cy3-labeled Universal mouse reference (Stratagene).

extract_protocol: Total RNA was prepared by Qiagen RNeasy kit with on column DNase digestion.

tag: tissue

value: Liver

value: mAb treated

value: db/db

source_name: Universal mouse reference (UMR) from Stratagene

value: pooled mouse reference RNA


title: MP567 tumor, DMSO 6 hrs


title: P. syringae pv tomato DC3000 wildtype 12 hours biorep D


title: Liver_3c7.v44 mAb_4


title: Liver_3c7.v44 mAb_2


title: Liver_3c7.v44 mAb_3


title: Liver_3c7.v44 mAb_1


title: Liver_PBS_4

value: PBS


title: P. syringae pv tomato DC3000 wildtype 10 hours biorep D


title: Liver_PBS_5


title: Liver_PBS_1


title: Liver_3c7.v44 mAb_5


title: PA006

value: Phalaenopsis V3 hybrid, tetraploid


title: P. syringae pv tomato DC3000 wildtype 7 hours biorep D


title: Liver_PBS_6


title: P. syringae pv tomato DC3000 wildtype 8 hours biorep D


title: P. syringae pv tomato DC3000 wildtype 11 hours biorep D


title: P. syringae pv tomato DC3000 wildtype 5 hours biorep D


title: P. syringae pv tomato DC3000 wildtype 6 hours biorep D


title: P7.5 KO_3

source_name: P7.5 KO

value: GCGR knockout


title: P. syringae pv tomato DC3000 wildtype 3 hours biorep D


title: P. syringae pv tomato DC3000 wildtype 2 hours biorep D


title: P. syringae pv tomato DC3000 wildtype 4 hours biorep D


title: P. syringae pv tomato DC3000 wildtype 9 hours biorep D


title: P7.5 KO_4


title: P7.5 KO_2


title: Liver_PBS_3


title: P. syringae pv tomato DC3000 wildtype 13 hours biorep C


title: P. syringae pv tomato DC3000 wildtype 12 hours biorep C


title: P2.5 KO_4

source_name: P2.5 KO


title: E18.5 KO_4


title: P2.5 KO_1


title: P. syringae pv tomato DC3000 wildtype 11 hours biorep C


title: P2.5 KO_3


title: P. syringae pv tomato DC3000 wildtype 10 hours biorep C


title: P. syringae pv tomato DC3000 wildtype 3 hours biorep C


title: P7.5 wt_4

source_name: P7.5 wt

value: wildtype