title: T19 [aCGH]

source_name: Human primary breast tumor sample T19


title: T53 [aCGH]

status: Public on Mar 01 2011

type: genomic

city: Marseille

first: Pascal

last: FINETTI

state: BdR

address: 232 Bd Ste Marguerite

department: Centre de cancérologie de Marseille

country: France

institute: Institut Paoli-Calmettes

hyb_protocol: see Agilent CGH 244k standard protocols

scan_protocol: see Agilent CGH 244k standard protocols

data_processing: Agilent Feature Extraction Software (v 10.7.1.1) was used for background subtraction and LOWESS normalization. Segmentation value obtain by CBS (DNAcopy, R package, v 1.16.0) of the normalized log2 ratio Cy5/Cy3.

molecule: genomic DNA

organism: Homo sapiens

source_name: Human primary breast tumor sample T53

label_protocol: Standard protocol with BioPrime« Array CGH Genomic Labeling System (ref:18095-011)

extract_protocol: Guanidinium isothiocyanate and centrifugation over a cesium chloride gradient.

tag: age

value: positive

source_name: A pool of 13 normal male DNA.

tag: reference

value: A pool of 13 normal male DNA


title: T11 [aCGH]

source_name: Human primary breast tumor sample T11


title: T6 [aCGH]

source_name: Human primary breast tumor sample T6


title: T5 [aCGH]

source_name: Human primary breast tumor sample T5


title: T9 [aCGH]

source_name: Human primary breast tumor sample T9


title: T12 [aCGH]

source_name: Human primary breast tumor sample T12


title: T4 [aCGH]

source_name: Human primary breast tumor sample T4


title: T1 [aCGH]

source_name: Human primary breast tumor sample T1


title: T2 [aCGH]

source_name: Human primary breast tumor sample T2


title: T-2*

city: Philadelphia

first: Minal

last: Caliskan

state: PA

address: 415 Curie Blvd., Room 540

department: Genetics

country: USA

institute: University of Pennsylvania

description:
X4968545006_K
T cell_Individual 1_rep2

hyb_protocol: Bisulphite-converted DNA was amplified, fragmented and hybridized to the Illumina Infinium Human Methylation27 Beadchip using the standard Illumina protocol.

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

data_processing:
BeadStudio software v3.2.
Beta values = methylated signal/(methylated signal + unmethylated signal).

label: Biotin

source_name: T cell_Individual 1

label_protocol: Standard Illumina labeling protocol.

extract_protocol: QIAamp DNA Blood Mini Kit.

tag: cell type

value: T cell

tag: gender

value: male

tag: individual


title: LCL10-2

description:
X4968545006_L
Lymphoblastoid cell line_Individual 5-2_rep1

source_name: Lymphoblastoid cell line_Individual 5-2

value: lymphoblastoid cell line


title: LCL14-3

description:
X4968545006_B
Lymphoblastoid cell line_Individual 6-3_rep1

source_name: Lymphoblastoid cell line_Individual 6-3


title: LCL9-6

description:
X4968545006_G
Lymphoblastoid cell line_Individual 4-4_rep1

source_name: Lymphoblastoid cell line_Individual 4-4

value: female


title: B-10

description:
X4974911018_I
B cell_Individual 5_rep1

source_name: B cell_Individual 5

value: B cell


title: LCL6-3

description:
X4974911018_L
Lymphoblastoid cell line_Individual 3-2_rep1

source_name: Lymphoblastoid cell line_Individual 3-2


title: LCL9-7*

description:
X4968545006_F
Lymphoblastoid cell line_Individual 4-5_rep2

source_name: Lymphoblastoid cell line_Individual 4-5


title: LCL6-1

description:
X4968545006_D
Lymphoblastoid cell line_Individual 3-1_rep1

source_name: Lymphoblastoid cell line_Individual 3-1


title: LCL5-5

description:
X4968545006_C
Lymphoblastoid cell line_Individual 2-5_rep1

source_name: Lymphoblastoid cell line_Individual 2-5


title: LCL6-5*

description:
X4968545006_I
Lymphoblastoid cell line_Individual 3-4_rep2

source_name: Lymphoblastoid cell line_Individual 3-4


title: LCL9-1*

description:
X4968545006_E
Lymphoblastoid cell line_Individual 4-1_rep2

source_name: Lymphoblastoid cell line_Individual 4-1


title: B-2

description:
X4968545006_A
B cell_Individual 1_rep1

source_name: B cell_Individual 1


title: LCL2-6*

description:
X4968545006_J
Lymphoblastoid cell line_Individual 1-5_rep2

source_name: Lymphoblastoid cell line_Individual 1-5


title: LCL14-6

description:
X4974911018_K
Lymphoblastoid cell line_Individual 6-6_rep1

source_name: Lymphoblastoid cell line_Individual 6-6


title: LCL14-2*

description:
X4968545006_H
Lymphoblastoid cell line_Individual 6-2_rep2

source_name: Lymphoblastoid cell line_Individual 6-2


title: LCL9-8*

description:
X4974911018_H
Lymphoblastoid cell line_Individual 4-6_rep2

source_name: Lymphoblastoid cell line_Individual 4-6


title: LCL9-3*

description:
X4974911018_B
Lymphoblastoid cell line_Individual 4-2_rep2

source_name: Lymphoblastoid cell line_Individual 4-2


title: LCL6-6*

description:
X4974911018_J
Lymphoblastoid cell line_Individual 3-5_rep2

source_name: Lymphoblastoid cell line_Individual 3-5


title: T-2

description:
X4974911018_A
T cell_Individual 1_rep1

source_name: T cell_Individual 1


title: LCL6-4*

description:
X4974911018_F
Lymphoblastoid cell line_Individual 3-3_rep2

source_name: Lymphoblastoid cell line_Individual 3-3


title: LCL2-3*

description:
X4974911018_D
Lymphoblastoid cell line_Individual 1-2_rep2

source_name: Lymphoblastoid cell line_Individual 1-2


title: B-2*

description:
X4974911018_E
B cell_Individual 1_rep2


title: LCL9-4

description:
X4974911018_G
Lymphoblastoid cell line_Individual 4-3_rep1

source_name: Lymphoblastoid cell line_Individual 4-3


title: LCL5-4

description:
X4974911018_C
Lymphoblastoid cell line_Individual 2-4_rep1

source_name: Lymphoblastoid cell line_Individual 2-4


title: LCL10-1*

description:
X4974911029_J
Lymphoblastoid cell line_Individual 5-1_rep2

source_name: Lymphoblastoid cell line_Individual 5-1


title: T-5*

description:
X4974911029_L
T cell_Individual 2_rep2

source_name: T cell_Individual 2


title: B-14

description:
X4974911029_K
B cell_Individual 6_rep1

source_name: B cell_Individual 6


title: LCL6-7

description:
X4974911029_I
Lymphoblastoid cell line_Individual 3-6_rep1

source_name: Lymphoblastoid cell line_Individual 3-6


title: B-6*

description:
X4974911029_H
B cell_Individual 3_rep2

source_name: B cell_Individual 3


title: LCL2-3

description:
X4974911029_D
Lymphoblastoid cell line_Individual 1-2_rep1


title: LCL5-6

description:
X4974911029_E
Lymphoblastoid cell line_Individual 2-6_rep1

source_name: Lymphoblastoid cell line_Individual 2-6


title: T-10

description:
X4974911029_C
T cell_Individual 5_rep1

source_name: T cell_Individual 5


title: LCL14-6*

description:
X4974911029_B
Lymphoblastoid cell line_Individual 6-6_rep2

source_name: Lymphoblastoid cell line_Individual 6-6


title: LCL5-5*

description:
X4974911029_G
Lymphoblastoid cell line_Individual 2-5_rep2

source_name: Lymphoblastoid cell line_Individual 2-5


title: LCL10-7*

description:
X5027501020_I
Lymphoblastoid cell line_Individual 5-5_rep2

source_name: Lymphoblastoid cell line_Individual 5-5


title: LCL9-1

description:
X4974911029_A
Lymphoblastoid cell line_Individual 4-1_rep1

source_name: Lymphoblastoid cell line_Individual 4-1


title: LCL10-8

description:
X5027501020_L
Lymphoblastoid cell line_Individual 5-6_rep1

source_name: Lymphoblastoid cell line_Individual 5-6


title: LCL14-4*

description:
X4974911029_F
Lymphoblastoid cell line_Individual 6-4_rep2

source_name: Lymphoblastoid cell line_Individual 6-4


title: B-5*

description:
X5027501020_K
B cell_Individual 2_rep2

source_name: B cell_Individual 2


title: LCL9-8

description:
X5027501020_E
Lymphoblastoid cell line_Individual 4-6_rep1

source_name: Lymphoblastoid cell line_Individual 4-6


title: LCL2-5*

description:
X5027501020_F
Lymphoblastoid cell line_Individual 1-4_rep2

source_name: Lymphoblastoid cell line_Individual 1-4


title: LCL2-6

description:
X5027501020_D
Lymphoblastoid cell line_Individual 1-5_rep1

source_name: Lymphoblastoid cell line_Individual 1-5


title: LCL6-7*

description:
X5027501020_C
Lymphoblastoid cell line_Individual 3-6_rep2


title: B-6

description:
X5027501020_G
B cell_Individual 3_rep1


title: T-14

description:
X5027501020_B
T cell_Individual 6_rep1

source_name: T cell_Individual 6


title: LCL14-5*

description:
X5027501020_H
Lymphoblastoid cell line_Individual 6-5_rep2

source_name: Lymphoblastoid cell line_Individual 6-5


title: LCL2-4*

description:
X5027501021_L
Lymphoblastoid cell line_Individual 1-3_rep2

source_name: Lymphoblastoid cell line_Individual 1-3


title: T35 [aCGH]

source_name: Human primary breast tumor sample T35

source_name: A pool of 13 normal male DNA.


title: LCL5-1*

description:
X5027501020_J
Lymphoblastoid cell line_Individual 2-1_rep2

source_name: Lymphoblastoid cell line_Individual 2-1


title: B-10*

description:
X5027501021_J
B cell_Individual 5_rep2

source_name: B cell_Individual 5


title: LCL5-3

description:
X5027501021_I
Lymphoblastoid cell line_Individual 2-3_rep1

source_name: Lymphoblastoid cell line_Individual 2-3


title: LCL14-1

description:
X5027501021_F
Lymphoblastoid cell line_Individual 6-1_rep1

source_name: Lymphoblastoid cell line_Individual 6-1


title: LCL6-6

description:
X5027501021_E
Lymphoblastoid cell line_Individual 3-5_rep1

source_name: Lymphoblastoid cell line_Individual 3-5


title: LCL2-8*

description:
X5027501012_J
Lymphoblastoid cell line_Individual 1-6_rep2

source_name: Lymphoblastoid cell line_Individual 1-6


title: LCL10-4*

description:
X5027501021_B
Lymphoblastoid cell line_Individual 5-3_rep2

source_name: Lymphoblastoid cell line_Individual 5-3


title: B-9

description:
X5027501021_A
B cell_Individual 4_rep1

source_name: B cell_Individual 4


title: T-6*

description:
X5027501021_D
T cell_Individual 3_rep2

source_name: T cell_Individual 3


title: LCL10-5

description:
X5027501021_H
Lymphoblastoid cell line_Individual 5-4_rep1

source_name: Lymphoblastoid cell line_Individual 5-4


title: LCL5-2*

description:
X5027501012_L
Lymphoblastoid cell line_Individual 2-2_rep2

source_name: Lymphoblastoid cell line_Individual 2-2


title: LCL10-7

description:
X5027501012_I
Lymphoblastoid cell line_Individual 5-5_rep1

source_name: Lymphoblastoid cell line_Individual 5-5


title: T-14*

description:
X5027501012_K
T cell_Individual 6_rep2

source_name: T cell_Individual 6


title: LCL6-3*

description:
X5027501021_C
Lymphoblastoid cell line_Individual 3-2_rep2

source_name: Lymphoblastoid cell line_Individual 3-2


title: LCL2-2*

description:
X5027501012_G
Lymphoblastoid cell line_Individual 1-1_rep2

source_name: Lymphoblastoid cell line_Individual 1-1


title: LCL9-6*

description:
X5027501012_E
Lymphoblastoid cell line_Individual 4-4_rep2

source_name: Lymphoblastoid cell line_Individual 4-4


title: T-9

description:
X5027501012_C
T cell_Individual 4_rep1

source_name: T cell_Individual 4


title: LCL5-1

description:
X5027501012_F
Lymphoblastoid cell line_Individual 2-1_rep1

source_name: Lymphoblastoid cell line_Individual 2-1


title: B-9*

description:
X5027501012_H
B cell_Individual 4_rep2


title: LCL9-7

description:
X5027501002_L
Lymphoblastoid cell line_Individual 4-5_rep1

source_name: Lymphoblastoid cell line_Individual 4-5


title: LCL14-2

description:
X5027501012_D
Lymphoblastoid cell line_Individual 6-2_rep1

source_name: Lymphoblastoid cell line_Individual 6-2


title: LCL9-4*

description:
X5027501002_I
Lymphoblastoid cell line_Individual 4-3_rep2

source_name: Lymphoblastoid cell line_Individual 4-3


title: LCL14-5

description:
X5027501002_J
Lymphoblastoid cell line_Individual 6-5_rep1

source_name: Lymphoblastoid cell line_Individual 6-5


title: B-14*

description:
X5027501002_H
B cell_Individual 6_rep2

source_name: B cell_Individual 6


title: T-5

description:
X5027501002_G
T cell_Individual 2_rep1

source_name: T cell_Individual 2


title: LCL6-5

description:
X5027501012_A
Lymphoblastoid cell line_Individual 3-4_rep1

source_name: Lymphoblastoid cell line_Individual 3-4


title: LCL14-1*

description:
X5027501002_F
Lymphoblastoid cell line_Individual 6-1_rep2

source_name: Lymphoblastoid cell line_Individual 6-1


title: LCL10-8*

description:
X4974911023_L
Lymphoblastoid cell line_Individual 5-6_rep2

source_name: Lymphoblastoid cell line_Individual 5-6


title: LCL5-6*

description:
X5027501002_E
Lymphoblastoid cell line_Individual 2-6_rep2

source_name: Lymphoblastoid cell line_Individual 2-6


title: LCL10-5*

description:
X4974911023_J
Lymphoblastoid cell line_Individual 5-4_rep2

source_name: Lymphoblastoid cell line_Individual 5-4


title: LCL2-5

description:
X5027501012_B
Lymphoblastoid cell line_Individual 1-4_rep1

source_name: Lymphoblastoid cell line_Individual 1-4


title: LCL10-4

description:
X4974911023_G
Lymphoblastoid cell line_Individual 5-3_rep1

source_name: Lymphoblastoid cell line_Individual 5-3


title: B-5

description:
X4974911023_I
B cell_Individual 2_rep1

source_name: B cell_Individual 2


title: LCL5-3*

description:
X4974911023_F
Lymphoblastoid cell line_Individual 2-3_rep2

source_name: Lymphoblastoid cell line_Individual 2-3


title: T-10*

description:
X5027501002_D
T cell_Individual 5_rep2

source_name: T cell_Individual 5


title: LCL10-1

description:
X5027501002_C
Lymphoblastoid cell line_Individual 5-1_rep1

source_name: Lymphoblastoid cell line_Individual 5-1


title: LCL2-4

description:
X5027501002_B
Lymphoblastoid cell line_Individual 1-3_rep1

source_name: Lymphoblastoid cell line_Individual 1-3


title: LCL6-1*

description:
X4974911023_K
Lymphoblastoid cell line_Individual 3-1_rep2

source_name: Lymphoblastoid cell line_Individual 3-1


title: LCL2-2

description:
X4974911023_E
Lymphoblastoid cell line_Individual 1-1_rep1

source_name: Lymphoblastoid cell line_Individual 1-1


title: T-9*

description:
X4974911023_D
T cell_Individual 4_rep2

source_name: T cell_Individual 4


title: LCL14-4

description:
X4974911023_C
Lymphoblastoid cell line_Individual 6-4_rep1

source_name: Lymphoblastoid cell line_Individual 6-4


title: spleen vs. pool

type: RNA

city: Seattle

first: Xinwei

last: She

state: WA

address: 401 Terry Ave. N

department: Molecular Informatics

institute: Rosetta Inpharmatics, Merck

description: 42 diverse human tissues were hybridized. Samples were purchased as pools from multiple donors, typically over 10 (Clontech, Mountainview, CA). Pooled RNA from 20 diverse disease-free adult tissue pools comprised the reference pool.

hyb_protocol: Microarrays are incubated at 40°C for 48 hours in a rotating carousel. Hybridizations to custom Agilent microarrays are completed as previously described (Hughes et al.Nat Biotech (2001), 19(4):342-7). Microarrays are washed to remove non-specific hybridized sample. Afterwards, microarrays are dried in an ozone-free nitrogen chamber.

scan_protocol: Microarrays are scanned using the Agilent LP2 laser scanner. The scanner output is a Tiff file, which contains the quantitative hybridization data from each individual microarray. The Tiff files are then processed using Rosetta custom feature extraction software.

data_processing: Data were processed using the Rosetta Resolver® system.

molecule: polyA RNA

source_name: spleen

label_protocol: custom automated version of the aminoallyl MessageAmp II kit from Ambion.

extract_protocol: Total RNA isolated using Qiagen RNeasy spin columns with DNAse treatment; polyA+ RNA isolated from total RNA via magnetic bead-based mRNA extraction (Ambion, Poly(A) Purist)

tag: tissue

value: spleen

source_name: Pool

value: Pool of 20 adult tissues


title: prostate vs. pool

source_name: prostate

value: prostate


title: ovary vs. pool

source_name: Ovary

value: Ovary


title: salivary gland vs. pool

source_name: salivary gland

value: salivary gland


title: testis vs. pool

source_name: testis

value: testis


title: skin vs. pool

source_name: skin

value: skin


title: pituitary gland vs. pool

source_name: pituitary gland

value: pituitary gland


title: LCL5-4*

description:
X4974911023_B
Lymphoblastoid cell line_Individual 2-4_rep2

source_name: Lymphoblastoid cell line_Individual 2-4


title: jejunum vs. pool

source_name: jejunum

value: jejunum


title: placenta vs. pool

source_name: placenta

value: placenta


title: thymus vs. pool

source_name: thymus

value: thymus


title: trachea vs. pool

source_name: trachea

value: trachea


title: stomach vs. pool

source_name: stomach

value: stomach


title: spinal cord vs. pool

source_name: spinal cord

value: spinal cord


title: duodenum vs. pool

source_name: duodenum

value: duodenum


title: ileum vs. pool

source_name: ileum

value: ileum


title: LCL9-3

description:
X4974911023_A
Lymphoblastoid cell line_Individual 4-2_rep1

source_name: Lymphoblastoid cell line_Individual 4-2

value: lymphoblastoid cell line

value: female


title: thyroid vs. pool

source_name: thyroid

value: thyroid

source_name: Pool

value: Pool of 20 adult tissues


title: mammary gland vs. pool

source_name: Mammary gland

value: Mammary gland


title: skeletal muscle vs. pool

source_name: skeletal muscle

value: skeletal muscle


title: retinal vs. pool

source_name: retinal

value: retinal


title: lymph node vs. pool

source_name: lymph node

value: lymph node


title: fetal lung vs. pool

source_name: fetal lung

value: fetal lung


title: lung vs. pool

source_name: lung

value: lung


title: fetal liver vs. pool

source_name: featl liver

value: featl liver


title: LCL14-3*

description:
X5027501021_G
Lymphoblastoid cell line_Individual 6-3_rep2

source_name: Lymphoblastoid cell line_Individual 6-3

value: male


title: fetal brain vs. pool

source_name: Fedal brain

value: Fedal brain


title: epididymis  vs. pool

source_name: epididymis

value: epididymis


title: CD4+ T cell vs. pool

source_name: CD4+ T cell

value: CD4+ T cell


title: cerebral cortex vs. pool

source_name: cerebral cortex

value: cerebral cortex


title: cervix vs. pool

source_name: cervix

value: cervix


title: fetal kidney vs. pool

source_name: fetal kidney

value: fetal kidney


title: cerebellum vs. pool

description: 42 diverse human tissues were hybridized. Samples were purchased as pools from multiple donors, typically over 10 (Clontech, Mountainview, CA) Pooled RNA from 20 diverse disease-free adult tissue pools comprised the reference pool.

source_name: cerebellum

value: cerebellum


title: CD8+ T cell vs. pool

source_name: CD8+ T cell

value: CD8+ T cell


title: heart vs. pool

source_name: heart

value: heart

source_name: Pool

value: Pool of 20 adult tissues


title: adipose vs. pool

source_name: Adipose

value: Adipose


title: colon vs. pool

source_name: Colon

value: Colon


title: kidney vs. pool

source_name: kidney

value: kidney


title: thalamus vs. pool

source_name: Thalamus

value: Thalamus


title: hippocampus vs. pool

source_name: hippocampus

value: hippocampus


title: LCL10-2*

description:
X5027501002_K
Lymphoblastoid cell line_Individual 5-2_rep2

source_name: Lymphoblastoid cell line_Individual 5-2

value: lymphoblastoid cell line


title: brain vs. pool

source_name: Brain

value: Brain


title: bone marrow vs. pool

source_name: Bone marrow

value: Bone marrow


title: adrenal gland vs. pool

source_name: adrenal gland

value: adrenal gland


title: bladder vs. pool

source_name: Bladder

value: Bladder


title: liver vs. pool

source_name: liver

value: liver


title: 4351_Udder_Right_front_quarter_E.coli_T=192h

city: Tjele

first: A.J. (Bart)

last: Buitenhuis

address: Blichers allé 20

department: Faculty of Agricultural Sciences, Dept. of Genetics and Biotechnology

country: Denmark

institute: Aarhus University

description:
4351_HF_E.coli_192
A377-94.CEL

hyb_protocol: Fifteen micrograms of cRNA was fragmented at 94 C for 35 min in a final volume of 40 ul in a buffer containing 40mM Tris-acetate pH 8.1, 100mM KOAc, and 30 mM MgOAc. Next, 260 ul of 6x SSPE-T hybridization buffer (1 M NaCl, 10 mM Tris pH 7.6, 0.005% Triton) was added and the cRNA was denatured by heating to 95 C for 5 min. The hybridization mixture was loaded onto the Affymetrix probe array cartridge (Affymetrix Bovine Genome Array) and incubated for 16 hr at 45 C at constant rotation (60 rpm). The washing and staining procedure was performed in the Affymetrix Fluidics Station. The probe array was exposed to 10 washes in 6x SSPE-T at 25 C followed by 4 washes in 0.5x SSPE-T at 50 C. The biotinylated cRNA was stained with a streptavidin-phycoerythrin conjugate, final concentration 2 ug/ul (Molecular Probes, Eugene, OR) in 6x SSPE-T for 30 min at 25 C followed by 10 washes in 6x SSPE-T at 25 C. An antibody amplification step followed, using normal goat IgG as blocking reagent, final concentration 0.1 mg/ml (Sigma, St. Louis), and biotinylated anti-streptavidin antibody (goat), final concentration 3 ug/ml (Vector Laboratories, Burlingame, CA). This was followed by a staining step with a streptavidinphycoerythrin conjugate, final concentration 2 ug/ul (Molecular Probes, Eugene, OR) in 6x SSPE-T for 30 min at 25 C and10 washes in 6x SSPE-T at 25 C (Kristensen et al. 2005: Genetics 171: 157–167).

scan_protocol: The arrays were scanned at 560 nm using a confocal microscope (Hewlett Packard GeneArray Scanner G2500A)

data_processing: The data was analyzed using R (version 2.10.0) (http://www.r-project.org/). The Bovine genome array annotation is available from the NetAffx Analysis Center (Bovine.na29.annot.csv). Additional and updated annotation was obtained from the Ensemble database, using the biomaRt package (version 2.0.0) in R. Normalization of the expression values for the udder samples were performed using the Robust Multi-array Average (RMA) algorithm as implemented in the Affy package (version 1.24.2).Differential expression of each gene was assessed using linear modeling and empirical Bayes methods, which were implemented using the R package Limma (version 3.2.1). The linear models allowed for changes for time points. The contrasts tested were 24 h p.i. vs. 24 h control (T24 – C24) and 192 h p.i. vs. 192 h control (T192 – C192), respectively. Each transcript targeted by a probe was tested for its expression change using a modified t-test. In the modified t-test, the residual standard deviations are moderated across the probe sets to ensure that there is a more stable inference for each transcript. The moderated standard deviations are a compromise between the individual transcript-wise standard deviations and the pooled standard deviation. Multiple testing was accounted for using the bonferroni correction. Probes were considered differentially expressed (DE) if the corrected P-value was below 0.05 and had a minimum log2-fold change of 1 for both T=24h and T=192h. A hyper geometric gene-set enrichment test (GOstats package version 2.12.0) was performed based on the clusters identified in at T=24h and T=192h, separately. Overrepresentation of gene sets defined by the group of biological processes (BP) in the Gene Ontology database (GO) (http://www.geneontology.org/) or the Kyoto Encyclopedia of Genes and Genomes database (KEGG) (http://www.genome.jp/kegg/) was tested using the Fisher’s exact test. For this test only the significant genes which were annotated with an Entrez gene id were included. When a gene had a duplicate on the array only one gene id was used. A gene-set was considered significant if P < 0.05.

label: biotin

molecule: total RNA

organism: Bos taurus

source_name: lobuloalveolar gland region

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Udder biopsies were collected from the infected quarter and a healthy control quarter of each cow at 24 h and 192 h after the E.coli challenge. The udder biopsies were frozen immediately in liquid nitrogen and transported to the laboratory where the tissues were stored at −80 C until RNA extraction. Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Sixteen, healthy primiparous Danish Holstein-Friesian cows were challenged intra mammarily with E.coli (k2bh2) (20-40 CFU/ml) 4 to 6 weeks after parturition in one quarter. Quarters for E.coli inoculation and biopsy were selected based on CMT scores (≤ 2) and SCC in fore milk using the portable DeLaval Cell Counter (DCC; DeLaval, Tumba, Sweden) (range 1-6000 x 103 cells/ml). The front quarter with the lowest SCC (< 27,000 cells /ml) was chosen for E.coli inoculations. Control quarters where determined on the bacteriological examinations conducted prior to E.coli inoculation and on the quarter fore milk SCC at 24 h (< 181.000 cells /ml). The cows were housed in a traditional straw-bedded tiestall barn, where they were fed individually, and with free access to water. A total mixed ration (TMR) diet including vitamins and minerals was fed ad libitum twice a day in equal portions at 8.00 a.m. and 15.30 p.m. The cows were milked at 6.00 a.m. and again at 17.00 p.m. All procedures involving animals were approved by the Danish Animal Experiments Inspectorate and complied with the Danish Ministry of Justice Laws concerning animal experimentation and care of experimental animals (Buitenhuis et al. 2010: In: Proceedings of the 9th World Congress on Genetics Applied to Livestock Production, Leipzig, Germany. 1-6 August. CD-ROM communication no. 0250_PP4-167).

tag: breed

value: Danish Holstein Friesian cow

value: lobuloalveolar gland region

tag: animal number

tag: e. coli inoculation site

value: Right front quarter

tag: treatment group

value: E.coli T=192h


title: LCL6-4

description:
X5027501002_A
Lymphoblastoid cell line_Individual 3-3_rep1

source_name: Lymphoblastoid cell line_Individual 3-3

value: female


title: LCL5-2

description:
X5027501020_A
Lymphoblastoid cell line_Individual 2-2_rep1

source_name: Lymphoblastoid cell line_Individual 2-2


title: LCL2-8

description:
X5027501021_K
Lymphoblastoid cell line_Individual 1-6_rep1

source_name: Lymphoblastoid cell line_Individual 1-6

value: male


title: 3341_Udder_Left_front_quarter_E.coli_T=192h

description:
3341_VF_E.coli_192
A377-110.CEL

value: Left front quarter


title: 3141_Udder_Left_front_quarter_E.coli_T=192h

description:
3141_VF_E.coli_192
A377-80.CEL


title: 2428_Udder_Right_hind_quarter_control_T=192h

description:
2428_HB_kontrol_192
A377-95.CEL

value: Right hind quarter

value: control T=192h


title: 2428_Udder_Left_front_quarter_E.coli_T=192h

description:
2428_VF_E.coli_192
A377-96.CEL


title: 3341_Udder_Right_front_quarter_control_T=24h

description:
3341_HF_kontrol_24
A377-101.CEL

value: control T=24h


title: 3341_Udder_Right_front_quarter_control_T=192h

description:
3341_HF_kontrol_192
A377-109.CEL


title: 1981_Udder_Right_front_quarter_control_T=192h

description:
1981_HF_kontrol_192
A377-125.CEL


title: 1981_Udder_Left_front_quarter_E.coli_T=192h

description:
1981_VF_E.coli_192
A377-126.CEL


title: 1922_Udder_Left_front_quarter_E.coli_T=192h

description:
1922_VF_E.coli_192
A377-108.CEL


title: 3141_Udder_Right_front_quarter_control_T=24h

description:
3141_HF_kontrol_24
A377-65.CEL


title: 1920_Udder_Left_front_quarter_E.coli_T=192h

description:
1920_VF_E.coli_192
A377-106.CEL


title: 1922_Udder_Left_front_quarter_E.coli_T=24h

description:
1922_VF_E.coli_24
A377-100.CEL

value: E.coli T=24h


title: 2428_Udder_Left_front_quarter_E.coli_T=24h

description:
2428_VF_E.coli_24
A377-88.CEL


title: 1922_Udder_Right_front_quarter_control_T=24h

description:
1922_HF_kontrol_24
A377-99.CEL


title: 1920_Udder_Right_front_quarter_control_T=192h

description:
1920_HF_kontrol_192
A377-105.CEL


title: 3141_Udder_Left_front_quarter_E.coli_T=24h

description:
3141_VF_E.coli_24
A377-66.CEL


title: 1920_Udder_Right_front_quarter_control_T=24h

description:
1920_HF_kontrol_24
A377-97.CEL


title: 3141_Udder_Right_front_quarter_control_T=192h

description:
3141_HF_kontrol_192
A377-79.CEL


title: 1922_Udder_Right_front_quarter_control_T=192h

description:
1922_HF_kontrol_192
A377-107.CEL


title: T-6

description:
X4974911023_H
T cell_Individual 3_rep1

source_name: T cell_Individual 3

value: T cell


title: 1586_Udder_Left_front_quarter_E.coli_T=192h

description:
1586_VF_E.coli_192
A377-112.CEL


title: 1920_Udder_Left_front_quarter_E.coli_T=24h

description:
1920_VF_E.coli_24
A377-98.CEL


title: 1867_Udder_Right_front_quarter_E.coli_T=24h

description:
1867_HF_E.coli_24
A377-84.CEL


title: 1867_Udder_Left_front_quarter_control_T=24h

description:
1867_VF_kontrol_24
A377-83.CEL


title: 1586_Udder_Right_front_quarter_control_T=192h

description:
1586_HF_kontrol_192
A377-111.CEL


title: 1867_Udder_Left_front_quarter_control_T=192h

description:
1867_VF_kontrol_192
A377-91.CEL


title: 1415_Udder_Left_front_quarter_E.coli_T=192h

description:
1415_VF_E.coli_192
A377-122.CEL


title: 1415_Udder_Left_hind_quarter_control_T=24h

description:
1415_VB_kontrol_24
A377-113.CEL

value: Left hind quarter


title: 1415_Udder_Left_front_quarter_E.coli_T=24h

description:
1415_VF_E.coli_24
A377-114.CEL


title: 1586_Udder_Right_front_quarter_control_T=24h

description:
1586_HF_kontrol_24
A377-103.CEL


title: 1385_Udder_Right_front_quarter_control_T=24h

description:
1385_HF_kontrol_24
A377-71.CEL


title: 1586_Udder_Left_front_quarter_E.coli_T=24h

description:
1586_VF_E.coli_24
A377-104.CEL


title: 1385_Udder_Left_front_quarter_E.coli_T=24h

description:
1385_VF_E.coli_24
A377-72.CEL


title: 1289_Udder_Right_front_quarter_control_T=24h

description:
1289_HF_kontrol_24
A377-115.CEL


title: 1112_Udder_Left_front_quarter_E.coli_T=24h

description:
1112_VF_E.coli_24
A377-70.CEL


title: 1867_Udder_Right_front_quarter_E.coli_T=192h

description:
1867_HF_E.coli_192
A377-92.CEL


title: 1112_Udder_Right_front_quarter_control_T=192h

description:
1112_HF_kontrol_192
A377-77.CEL


title: 1289_Udder_Left_front_quarter_E.coli_T=24h

description:
1289_VF_E.coli_24
A377-116.CEL


title: 993_Udder_Left_front_quarter_E.coli_T=192h

description:
993_VF_E.coli_192
A377-128.CEL


title: 3341_Udder_Left_front_quarter_E.coli_T=24h

description:
3341_VF_E.coli_24
A377-102.CEL


title: 1385_Udder_Right_front_quarter_control_T=192h

description:
1385_HF_kontrol_192
A377-73.CEL


title: 993_Udder_Left_front_quarter_E.coli_T=24h

description:
993_VF_E.coli_24
A377-120.CEL


title: 1289_Udder_Right_front_quarter_control_T=192h

description:
1289_HF_kontrol_192
A377-123.CEL


title: 993_Udder_Right_hind_quarter_control_T=192h

description:
993_HB_kontrol_192
A377-127.CEL


title: 1289_Udder_Left_front_quarter_E.coli_T=192h

description:
1289_VF_E.coli_192
A377-124.CEL


title: 1415_Udder_Left_hind_quarter_control_T=192h

description:
1415_VB_kontrol_192
A377-121.CEL


title: 1112_Udder_Left_front_quarter_E.coli_T=192h

description:
1112_VF_E.coli_192
A377-78.CEL


title: 1385_Udder_Left_front_quarter_E.coli_T=192h

description:
1385_VF_E.coli_192
A377-74.CEL


title: Analysis of Gene Expression in the Chicken Otocyst

type: SAGE

anchor: NlaIII

city: Palo Alto

first: Samuel

last: Myllykangas

state: CA

address: 269 Campus Drive, CCSR 3240

department: Oncology

institute: Stanford University

data_processing: 39,326 individual 17-bp tags were extracted from the 10,000 sequencing data files using SAGE2000 analysis software (Version 4.5, Invitrogen).

organism: Gallus gallus

source_name: Chicken otocyst, Embryonic day 3

extract_protocol: RNeasy Mini Kit (Qiagen, Hilden, Germany)

value: Chicken otocyst


title: 4351_Udder_Left_hind_quarter_control_T=192h

description:
4351_VB_kontrol_192
A377-93.CEL


title: SKOV3 cells tranfected to express  LHR, without LH trearment, replicate 1

city: Athens

first: Juan

last: Cui

address: 120 Green Street

department: Biochemistry and Molecular Biology

institute: University of Georgia

hyb_protocol: The resultant fragmented and labeled cDNA was added to the hybridization cocktail in accordance with the NuGEN guidelines for hybridization onto Affymetrix human genome U133 Plus2 Arrays.Following hybridization for 18 h at 45°C, the array was washed and stained on the GeneChip® Fluidics Station 450 using the appropriate fluidics script

scan_protocol: GeneChip® Scanner 3000

data_processing: The raw probe intensities was normalized using the quartile normalization approach, and the PLIER method. was utilized to summarize the probe signal to both the exon- and gene-level expressions

source_name: transfected SKOV3 cell with LHR expression

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

growth_protocol: cultured human ovarian cancer cell SKOV3

extract_protocol: Total RNA was extracted from the 18 SKOV-3 samples [14] and was amplified using the NuGEN™ Ovation™ RNA Amplification System V2.

treatment_protocol: transfected with LHR and then treated with LH

tag: cell line

tag: transfection

value: LHR


title: SKOV3 cells tranfected to express  LHR, with LH treatment (50ng/ml, 20h) , replicate 1

source_name: LH treated (20h) LHR+ SKOV3 cell

tag: treatment

value: LH treatment (50ng/ml)

tag: time


title: SKOV3 cells tranfected to express  LHR, with LH treatment (50ng/ml, 20h) , replicate 2


title: SKOV3 cells tranfected to express  LHR, with LH treatment (50ng/ml, 8h) , replicate 3

source_name: LH treated (8h) LHR+ SKOV3 cell


title: SKOV3 cells tranfected to express  LHR, with LH treatment (50ng/ml, 8h) , replicate 2


title: SKOV3 cells tranfected to express  LHR, without LH trearment , replicate 2


title: SKOV3 cells tranfected to express  LHR, with LH treatment (50ng/ml, 1h), replicate 1

source_name: LH treated (1h) LHR+ SKOV3 cell


title: SKOV3 cells tranfected to express  LHR, with LH treatment (50ng/ml, 1h) , replicate 3


title: SKOV3 cells without expressing LHR, replicate 2

source_name: control human ovarian cancer SKOV3 cell


title: SKOV3 cells tranfected to express  LHR, with LH treatment (50ng/ml, 4h) , replicate 1

source_name: LH treated (4h) LHR+ SKOV3 cell


title: SKOV3 cells without expressing LHR, replicate 3


title: SKOV3 cells without expressing LHR, replicate 1


title: SKOV3 cells tranfected to express  LHR, with LH treatment (50ng/ml, 8h), replicate 1


title: SKOV3 cells tranfected to express  LHR, with LH treatment (50ng/ml, 4h) , replicate 3


title: SKOV3 cells tranfected to express  LHR, with LH treatment (50ng/ml, 4h) , replicate 2


title: SKOV3 cells tranfected to express  LHR, without LH trearment, replicate 3


title: SKOV3 cells tranfected to express  LHR, with LH treatment (50ng/ml, 1h) , replicate 2


title: SKOV3 cells tranfected to express  LHR, with LH treatment (50ng/ml, 20h) , replicate 3


title: B-CLL PB P249

city: Prague 2

first: Vojtěch

last: Kulvait

address: U Nemocnice 5

department: Institute of Pathological Physiology

country: Czech Republic

institute: Charles University in Prague - 1st Faculty of Medicine

description: Additional information and characteristics in the referred paper supplement xls table.

hyb_protocol: RNA was proceeded according to Affymetrix 3‘ – IVT Express Kit protocol. cDNA was hybridized for 16 hr to the Affymetrix array as described in the Expression Analysis Technical Manual. GeneChips were washed and stained in the Affymetrix Fluidics Station.

scan_protocol: GeneChips were processed using the Agilent GeneArray Scanner 3000 7G system in the Genomics Facility of the New York University Cancer Institute.

data_processing: Data were summarized using GeneSpring implementation of RMA algorithm and expression data were normalized on median of control samples.

source_name: B-CLL PB P249

label_protocol: RNA was proceeded according to Affymetrix 3‘ – IVT Express Kit protocol. cDNA were prepared using the recommended Affymetrix reagents and kits.

growth_protocol: Peripheral blood from B-CLL patients as well as from healthy donors were firstly separated by Ficoll gradient (GE Healthcare), obtained peripheral mononuclear cells (PBMC). PBMC were shortly incubated in IMDM (Isove’s Modified Dulbecco’s) medium supplemented with 10% fetal calf serum, 1% non essential amino acids, 1% antibiotics. PBMCs from healthy donors were separated by autoMACS Pro Separator and anti FITC microbeads, CD19 human FITC antibody were used.

extract_protocol: Total RNA was extracted by TRIzol Reagent following the manufacturer protocol.   Precipitation by isopropyl alcohol (0.5mL per 1mL TRIzol) was done over night. As carrier of the aqueous phase the Acrylamide was used. The RNA pellets were washed with 75% ethanol (1mL per 1mL TRIzol) and dry pellets were resuspend in 20 uL of RNAse free water.

tag: disease state

value: B-CLL

value: peripheral blood


title: B-CLL PB P271

source_name: B-CLL PB P271


title: B-CLL PB P255

source_name: B-CLL PB P255


title: B-CLL PB P137

source_name: B-CLL PB P137


title: B-CLL PB P136

source_name: B-CLL PB P136


title: B-CLL PB P155

source_name: B-CLL PB P155


title: B-CLL PB P250

source_name: B-CLL PB P250


title: B-CLL PB P86

source_name: B-CLL PB P86


title: B-CLL PB P143

source_name: B-CLL PB P143


title: B-CLL PB P254

source_name: B-CLL PB P254


title: B-CLL PB P33

source_name: B-CLL PB P33


title: B-CLL PB P138

source_name: B-CLL PB P138


title: Muscle-Diabetes-6

city: Boston

first: Mary Elizabeth

last: Patti

state: MA

address: 1 Joslin Place

department: Research Division

institute: Joslin Diabetes Center

description:
Jos3748
Gene expression of skeletal muscle from subject with type 2 diabetes

hyb_protocol: 15ug of biotinylated cRNA were hybridized for 16hr at 45C to the Affymetrix GeneChip Human Genome U133 Plus 2.0 array. Following hybridization, arrays were washed and stained on the Affymetrix Fluidics Station 400.

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

data_processing: Data were analyzed using Affymetrix GCOS v.1.3, MAS5.0 algorithm, and globally scaled with the trimmed mean target intensity set to 1500.

source_name: skeletal muscle

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

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

value: skeletal muscle

tag: age (years)

tag: family history

value: DM

tag: body mass index (kg/m2)

tag: fasting glucose (ogtt)

tag: 2 hour glucose (ogtt)

tag: hemoglobin a1c

tag: fasting glucose (iv0gavg)

tag: fasting insulin (iv0inavg)

tag: si

tag: waist hip ratio


title: Muscle-FamilyHistoryPositive-22

description:
Jos3736
Gene expression of skeletal muscle from subject without diabetes

tag: tissue

tag: gender

value: Family history positive - 2 parents


title: Muscle-Diabetes-10

description:
Jos3752
Gene expression of skeletal muscle from subject with type 2 diabetes

value: female


title: Muscle-FamilyHistoryPositive-20

description:
Jos3732
Gene expression of skeletal muscle from subject without diabetes


title: Muscle-Diabetes-2

description:
Jos3744
Gene expression of skeletal muscle from subject with type 2 diabetes


title: Muscle-FamilyHistoryPositive-25

description:
Jos3793
Gene expression of skeletal muscle from subject without diabetes

value: Family history positive - 1 parent


title: Muscle-FamilyHistoryNegative-14

description:
Jos3782
Gene expression of skeletal muscle from subject without diabetes

value: male

value: Family history negative


title: Muscle-Diabetes-3

description:
Jos3745
Gene expression of skeletal muscle from subject with type 2 diabetes


title: Muscle-Diabetes-7

description:
Jos3749
Gene expression of skeletal muscle from subject with type 2 diabetes


title: Muscle-FamilyHistoryPositive-18

description:
Jos3728
Gene expression of skeletal muscle from subject without diabetes


title: Muscle-FamilyHistoryPositive-23

description:
Jos3738
Gene expression of skeletal muscle from subject without diabetes


title: Muscle-Diabetes-4

description:
Jos3746
Gene expression of skeletal muscle from subject with type 2 diabetes


title: Muscle-FamilyHistoryPositive-19

description:
Jos3730
Gene expression of skeletal muscle from subject without diabetes


title: Muscle-FamilyHistoryPositive-16

description:
Jos3724
Gene expression of skeletal muscle from subject without diabetes


title: Muscle-FamilyHistoryPositive-15

description:
Jos3722
Gene expression of skeletal muscle from subject without diabetes


title: Muscle-Diabetes-1

description:
Jos3742
Gene expression of skeletal muscle from subject with type 2 diabetes


title: Muscle-FamilyHistoryPositive-21

description:
Jos3734
Gene expression of skeletal muscle from subject without diabetes


title: Muscle-FamilyHistoryPositive-17

description:
Jos3726
Gene expression of skeletal muscle from subject without diabetes


title: Muscle-FamilyHistoryNegative-15

description:
Jos3792
Gene expression of skeletal muscle from subject without diabetes


title: Muscle-Diabetes-5

description:
Jos3747
Gene expression of skeletal muscle from subject with type 2 diabetes


title: Muscle-Diabetes-9

description:
Jos3751
Gene expression of skeletal muscle from subject with type 2 diabetes


title: Muscle-FamilyHistoryPositive-14

description:
Jos3720
Gene expression of skeletal muscle from subject without diabetes


title: Muscle-FamilyHistoryPositive-24

description:
Jos3790
Gene expression of skeletal muscle from subject without diabetes


title: Muscle-FamilyHistoryPositive-12

description:
Jos3716
Gene expression of skeletal muscle from subject without diabetes


title: Muscle-FamilyHistoryPositive-6

description:
Jos3702
Gene expression of skeletal muscle from subject without diabetes


title: Muscle-FamilyHistoryPositive-13

description:
Jos3718
Gene expression of skeletal muscle from subject without diabetes


title: Muscle-FamilyHistoryPositive-9

description:
Jos3710
Gene expression of skeletal muscle from subject without diabetes


title: Muscle-FamilyHistoryPositive-11

description:
Jos3714
Gene expression of skeletal muscle from subject without diabetes


title: Muscle-FamilyHistoryPositive-5

description:
Jos3700
Gene expression of skeletal muscle from subject without diabetes


title: Muscle-FamilyHistoryPositive-2

description:
Jos3692
Gene expression of skeletal muscle from subject without diabetes


title: Muscle-FamilyHistoryPositive-3

description:
Jos3694
Gene expression of skeletal muscle from subject without diabetes


title: Muscle-FamilyHistoryNegative-12

description:
Jos3686
Gene expression of skeletal muscle from subject without diabetes


title: Muscle-Diabetes-8

description:
Jos3750
Gene expression of skeletal muscle from subject with type 2 diabetes


title: Muscle-FamilyHistoryNegative-13

description:
Jos3688
Gene expression of skeletal muscle from subject without diabetes


title: Muscle-FamilyHistoryNegative-10

description:
Jos3678
Gene expression of skeletal muscle from subject without diabetes


title: Muscle-FamilyHistoryPositive-1

description:
Jos3690
Gene expression of skeletal muscle from subject without diabetes


title: Muscle-FamilyHistoryPositive-10

description:
Jos3712
Gene expression of skeletal muscle from subject without diabetes


title: Muscle-FamilyHistoryPositive-4

description:
Jos3696
Gene expression of skeletal muscle from subject without diabetes


title: Muscle-FamilyHistoryNegative-11

description:
Jos3684
Gene expression of skeletal muscle from subject without diabetes


title: Muscle-FamilyHistoryNegative-8

description:
Jos3674
Gene expression of skeletal muscle from subject without diabetes


title: Muscle-FamilyHistoryPositive-7

description:
Jos3706
Gene expression of skeletal muscle from subject without diabetes


title: Muscle-FamilyHistoryNegative-9

description:
Jos3676
Gene expression of skeletal muscle from subject without diabetes


title: Muscle-FamilyHistoryPositive-8

description:
Jos3708
Gene expression of skeletal muscle from subject without diabetes


title: Muscle-FamilyHistoryNegative-6

description:
Jos3670
Gene expression of skeletal muscle from subject without diabetes


title: Muscle-FamilyHistoryNegative-1

description:
Jos3660
Gene expression of skeletal muscle from subject without diabetes


title: Muscle-FamilyHistoryNegative-3

description:
Jos3664
Gene expression of skeletal muscle from subject without diabetes


title: Muscle-FamilyHistoryNegative-2

description:
Jos3662
Gene expression of skeletal muscle from subject without diabetes


title: T192

description: Primary breast tumor

hyb_protocol: see Affymetrix standard protocols (www.affymetrix.com)

data_processing: RMA using a quantile normalization (R package affy, v 1.20.0)

source_name: human breast cancer tumors

value: negative


title: Muscle-FamilyHistoryNegative-4

description:
Jos3666
Gene expression of skeletal muscle from subject without diabetes


title: Muscle-FamilyHistoryNegative-7

description:
Jos3672
Gene expression of skeletal muscle from subject without diabetes


title: T195

description: Primary breast tumor

scan_protocol: see Affymetrix standard protocols (www.affymetrix.com)

value: positive


title: T197

description: Primary breast tumor

label_protocol: see Affymetrix standard protocols (www.affymetrix.com)


title: T191

description: Primary breast tumor


title: TUP1-IP_BY4741:TUP1-tap:sut1D_2

city: Buffalo

first: Michael

last: Buck

state: NY

address: 701 Ellicott St

department: Biochemistry

institute: SUNY at Buffalo

description: TUP1 ChIP-chip using TAP affinity tag in sut1 knockout. Antibody affinity purified by IgG sepharose.

hyb_protocol: Direct hybridization 4X SSC, 0.2% SDS

scan_protocol: Images were acquired using a GenePix 4000B scanner and GenePix software

data_processing: The DNA microarrays were normalized by block-by-block lowess with the limma R package as part of Bioconductor.

organism: Saccharomyces cerevisiae

source_name: Input DNA

label_protocol: samples and references were amplified using a random primed PCR-based method (see Bohlander et al., 1992)

growth_protocol: Expontential Growth (OD 0.6-1.0)

extract_protocol: genomic DNA extraction as in Buck and Lieb 2006

treatment_protocol: Rich Media (YPD 2% glucose)

tag: strain

source_name: TUP1-tap IP


title: TUP1-IP_BY4741:TUP1-tap:sko1D_1

description: TUP1 ChIP-chip using TAP affinity tag in sko1 knockout. Antibody affinity purified by IgG sepharose.


title: TUP1-IP_BY4741:TUP1-tap:sut1D_1


title: TUP1-IP_BY4741:TUP1-tap:sko1D_2


title: TUP1-IP_BY4741:TUP1-tap:sut1D_3


title: T187

description: Primary breast tumor


title: TUP1-IP_BY4741:TUP1-tap:sko1D_3


title: T180

description: Primary breast tumor


title: TUP1-IP_BY4741:TUP1-tap:rox1D_1

description: TUP1 ChIP-chip using TAP affinity tag in rox1 knockout. Antibody affinity purified by IgG sepharose.


title: TUP1-IP_BY4741:TUP1-tap:rox1D_3


title: T175

description: Primary breast tumor


title: TUP1-IP_BY4741:TUP1-tap:nrg1D_1

description: TUP1 ChIP-chip using TAP affinity tag in nrg1 knockout. Antibody affinity purified by IgG sepharose.


title: T181

description: Primary breast tumor


title: T179

description: Primary breast tumor


title: T182

description: Primary breast tumor


title: TUP1-IP_BY4741:TUP1-tap:rox1D_2


title: T174

description: Primary breast tumor


title: T188

description: Primary breast tumor


title: TUP1-IP_BY4741:TUP1-tap:nrg1D_2


title: TUP1-IP_BY4741:TUP1-tap:mig1D_1

description: TUP1 ChIP-chip using TAP affinity tag in mig1 knockout. Antibody affinity purified by IgG sepharose.


title: T176

description: Primary breast tumor


title: TUP1-IP_BY4741:TUP1-tap:mig1D_2


title: TUP1-IP_BY4741:TUP1-tap:aft1D_1

description: TUP1 ChIP-chip using TAP affinity tag in aft1 knockout. Antibody affinity purified by IgG sepharose.


title: SSN6-IP_BY4741:SSN6-tap_2

description: SSN6 ChIP-chip using TAP affinity tag in wildtype background. Antibody affinity purified by IgG sepharose.

source_name: SSN6-tap IP


title: TUP1-IP_BY4741:TUP1-tap:aft1D_2


title: TUP1-IP_BY4741:TUP1-tap:crt1D_2

description: TUP1 ChIP-chip using TAP affinity tag in crt1 knockout. Antibody affinity purified by IgG sepharose.


title: TUP1-IP_BY4741:TUP1-tap:aft1D_3


title: TUP1-IP_BY4741:TUP1-tap:crt1D_1


title: T171

description: Primary breast tumor


title: TUP1-IP_BY4741:TUP1-tap_21

description: TUP1 ChIP-chip using TAP affinity tag in wildtype background. Antibody affinity purified by IgG sepharose.


title: MOCK-IP_BY4742_3

description: MOCK ChIP-chip using TAP affinity tag in wildtype background. Antibody affinity purified by IgG sepharose.

source_name: MOCK-tap IP


title: TUP1-IP_BY4741:TUP1-tap_18


title: SSN6-IP_BY4741:SSN6-tap_1


title: T169

description: Primary breast tumor


title: T170

description: Primary breast tumor


title: T168

description: Primary breast tumor


title: MOCK-IP_BY4742_2


title: TUP1-IP_BY4741:TUP1-tap_15


title: TUP1-IP_BY4741:TUP1-tap_20


title: TUP1-IP_BY4741:TUP1-tap_19


title: TUP1-IP_BY4741:TUP1-tap_14


title: T166

description: Primary breast tumor


title: MOCK-IP_BY4741_1


title: T167

description: Primary breast tumor


title: TUP1-IP_BY4741:TUP1-tap_16


title: TUP1-IP_BY4741:TUP1-tap_6


title: T164

description: Primary breast tumor


title: TUP1-IP_BY4741:TUP1-tap_11


title: TUP1-IP_BY4741:TUP1-tap_7


title: TUP1-IP_BY4741:TUP1-tap_17


title: TUP1-IP_BY4741:TUP1-tap_5


title: MOCK-IP_BY4742_4


title: TUP1-IP_BY4741:TUP1-tap_13


title: T165

description: Primary breast tumor


title: T163

description: Primary breast tumor


title: TUP1-IP_BY4741:TUP1-tap_8


title: TUP1-IP_BY4741:TUP1-tap_4


title: TUP1-IP_BY4741:TUP1-tap_9


title: TUP1-IP_BY4741:TUP1-tap_12


title: TUP1-IP_BY4741:TUP1-tap_10


title: TUP1-IP_BY4742:TUP1-tap_3


title: TUP1-IP_BY4742:TUP1-tap_1


title: TUP1-IP_BY4742:TUP1-tap_2


title: Gata6 Mut3 vs WT3

first: Ying

last: Tian

address: 421 Curie Blvd

department: Medicine

institute: Univeristy of Pennsylvania

description: Analysis used total RNA from Sftpc-rtTA:tetO-cre lungs at E14.5 as control samples (WT) for comparison to the experimental samples of total RNA from Gata6flox/flox: Sftpc-rtTA: tetO-Cre mutant lungs at E14.5.

hyb_protocol: Hybridization using Exiqon Hybridization Program. Samples were applied to microarrays enclosed in hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Array scanned using Axon GenePix 4000B

data_processing: Data analysis was carried out using GeneSpring v.7.3.1. Median intensity was determined for present features (2xBG). All intensities were normalized to median. Ratio was calculated for normalized and averaged Mut over normalized and averaged WT. The mean values from each channel were log2 transformed and normalized using the LOWESS algorithm to remove intensity dependent effects within the calculated values. Normalised values were used to calculate the Cy3/Cy5 fluorescence ratios from experimental and biological repeats with all replicates combined. Data was compiled from three control (WT) and three Gata6 mutants.

organism: Mus musculus

source_name: Embryonic lung at E14.5 from Sftpc-rtTA:tetO-cre

label_protocol: 1 µg of total RNA were labelled with miRCURY Power Labeling Kit (Exiqon) for usewith Exiqon miRNA arrays

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

value: mixed C57BL/6:129SVJ background

tag: genotype/variation

value: wildtype

source_name: Embryonic lung at E14.5 from Gata6flox/flox: Sftpc-rtTA: tetO-Cre mutant

value: Gata6 Mut


title: T158

description: Primary breast tumor


title: T157

description: Primary breast tumor


title: T159

description: Primary breast tumor


title: T156

description: Primary breast tumor


title: Gata6 Mut2 vs WT2


title: Gata6 Mut1 vs WT1


title: T148

description: Primary breast tumor


title: T154

description: Primary breast tumor


title: Female rats vs male rats rep3

city: Stockholm

first: Carolina

last: Gustavsson

address: CMM L8:01

department: Molecular medicine and surgery

country: Sweden

institute: Karolinska institutet

description: Biological replicate 3 of 4.

hyb_protocol: Cy3- and Cy5 labelled samples were purifyed and mixed before addition of a hybridization buffer and added to respectively array for 18h of hybridization. After hybridization, the slides were washed multiple times, all according to the Pronto! Plus systems and the manufacturer´s instructions (Corning and Promega).

scan_protocol: Scanning was performed using a Genepix 4200A scanner (Axon). Images were quantified using Genepix 6.0 software (Axon).

data_processing: Background was subtracted using the in-house Easy Filter software. The data was normalized by the LOWESS method using the R language. The normalized data was finally statistically analyzed using SAM.

organism: Rattus norvegicus

source_name: Liver from female Sprague-Dawley rat

label_protocol: 5µg of total RNA was used for a first strand cDNA synthesis of each sample, labelled with either Cy3- or Cy5-dCTP. The microarray experiment was performed using the Pronto! Plus systems according to the manufacturer´s instructions (Corning and Promega).

extract_protocol: Total RNA was extracted from frozen livers using Trizol following manufacturer's instructions

tag: sex

value: Female

tag: age

value: 7-weeks old

value: Liver

value: Sprague-Dawley

source_name: Liver from male Sprague-Dawley rat

value: Male


title: T141

description: Primary breast tumor


title: T143

description: Primary breast tumor


title: T151

description: Primary breast tumor


title: T144

description: Primary breast tumor


title: T153

description: Primary breast tumor


title: T147

description: Primary breast tumor


title: T142

description: Primary breast tumor


title: T145

description: Primary breast tumor


title: Male rats vs Female rats rep4

description: Biological replicate 4 of 4.


title: T138

description: Primary breast tumor


title: T139

description: Primary breast tumor


title: Male rats vs Female rats rep1

description: Biological replicate 1 of 4.


title: T137

description: Primary breast tumor


title: T140

description: Primary breast tumor


title: T136

description: Primary breast tumor


title: whole-blood_2_Rep81

city: CA

first: James

middle: A.

last: Wingrove

address: 2500 Faber Place

institute: CardioDx, Inc.

hyb_protocol: Labeled RNAs were hybridized using the Agilent protocol (Agilent, version 4.0.1)

scan_protocol: Agilent Feature Extraction Software (version 9.5.3.1) was used for background subtraction and LOWESS normalization.

data_processing: Agilent processed signal values were used;  values were scaled to a trimmed mean of 100 using an R script developed in-house at CardioDx.

label_protocol: 200 ng of each patient whole blood RNA was labeled with Cy3 using Agilent's Low RNA Input Linear Amplification Kit following the recommended protocol.

growth_protocol: Whole blood (2.5 ml) was collected via syringe during catheterization.

extract_protocol: RNA was extracted per manufacturers protocol (PreAnalytix, Franklin Lakes, NJ)

treatment_protocol: Collected blood was aliquoted into PaxGene tubes, inverted 10X and then frozen at -20 C until further processing

tag: disease state

value: Case (2)


title: T132

description: Primary breast tumor


title: whole-blood_2_Rep85


title: T127

description: Primary breast tumor


title: whole-blood_2_Rep86


title: T133

description: Primary breast tumor


title: whole-blood_2_Rep82


title: T126

description: Primary breast tumor


title: whole-blood_2_Rep79


title: whole-blood_2_Rep83


title: T125

description: Primary breast tumor


title: whole-blood_2_Rep77


title: whole-blood_2_Rep71


title: whole-blood_2_Rep74


title: whole-blood_2_Rep78


title: whole-blood_2_Rep80


title: T119

description: Primary breast tumor


title: whole-blood_2_Rep84


title: whole-blood_2_Rep70


title: Female rats vs male rats rep2

description: Biological replicate 2 of 4.


title: whole-blood_2_Rep87


title: whole-blood_2_Rep75


title: whole-blood_2_Rep73


title: whole-blood_2_Rep67


title: whole-blood_2_Rep69


title: whole-blood_2_Rep68


title: whole-blood_2_Rep72


title: whole-blood_2_Rep76


title: T121

description: Primary breast tumor


title: whole-blood_2_Rep65


title: whole-blood_2_Rep64


title: whole-blood_2_Rep66


title: T116

description: Primary breast tumor


title: T122

description: Primary breast tumor


title: T124

description: Primary breast tumor


title: whole-blood_2_Rep63


title: T118

description: Primary breast tumor


title: T114

description: Primary breast tumor


title: whole-blood_2_Rep62


title: T115

description: Primary breast tumor


title: T112

description: Primary breast tumor


title: whole-blood_2_Rep60


title: T111

description: Primary breast tumor


title: whole-blood_2_Rep57


title: T110

description: Primary breast tumor


title: whole-blood_2_Rep59


title: whole-blood_2_Rep61


title: whole-blood_2_Rep58


title: whole-blood_2_Rep55


title: whole-blood_2_Rep53


title: T102

description: Primary breast tumor


title: whole-blood_2_Rep49


title: whole-blood_2_Rep50


title: T103

description: Primary breast tumor


title: T99

description: Primary breast tumor


title: whole-blood_2_Rep52


title: whole-blood_2_Rep48


title: whole-blood_2_Rep51


title: whole-blood_2_Rep42


title: whole-blood_2_Rep46


title: whole-blood_2_Rep44


title: T101

description: Primary breast tumor


title: T97

description: Primary breast tumor


title: whole-blood_2_Rep41


title: whole-blood_2_Rep45


title: whole-blood_2_Rep43


title: whole-blood_2_Rep47


title: T93

description: Primary breast tumor


title: whole-blood_2_Rep40


title: T96

description: Primary breast tumor


title: T92

description: Primary breast tumor


title: whole-blood_2_Rep39


title: whole-blood_2_Rep38


title: T91

description: Primary breast tumor


title: T90

description: Primary breast tumor


title: whole-blood_2_Rep37


title: T88

description: Primary breast tumor


title: T89

description: Primary breast tumor


title: whole-blood_2_Rep32


title: whole-blood_2_Rep33


title: whole-blood_2_Rep36


title: T86

description: Primary breast tumor


title: whole-blood_2_Rep34


title: whole-blood_2_Rep35


title: T87

description: Primary breast tumor


title: whole-blood_2_Rep30


title: T84

description: Primary breast tumor


title: whole-blood_2_Rep28


title: whole-blood_2_Rep31


title: whole-blood_2_Rep54


title: T85

description: Primary breast tumor


title: whole-blood_2_Rep29


title: whole-blood_2_Rep27


title: whole-blood_2_Rep26


title: T83

description: Primary breast tumor


title: whole-blood_2_Rep24


title: T82

description: Primary breast tumor


title: whole-blood_2_Rep25


title: whole-blood_2_Rep23


title: T80

description: Primary breast tumor


title: whole-blood_2_Rep22


title: T75

description: Primary breast tumor


title: whole-blood_2_Rep56


title: whole-blood_2_Rep19


title: whole-blood_2_Rep14


title: whole-blood_2_Rep16


title: whole-blood_2_Rep20


title: whole-blood_2_Rep13


title: whole-blood_2_Rep18


title: T78

description: Primary breast tumor


title: whole-blood_2_Rep17


title: T81

description: Primary breast tumor


title: whole-blood_2_Rep21


title: whole-blood_2_Rep12


title: T66

description: Primary breast tumor


title: T74

description: Primary breast tumor


title: T67

description: Primary breast tumor


title: whole-blood_2_Rep11


title: whole-blood_2_Rep10


title: whole-blood_2_Rep15


title: whole-blood_2_Rep7


title: Keratinocytes untreated control, 48h

city: New York

first: Miroslav

last: Blumenberg

address: 455 First Ave #874

department: Dermatology

institute: NYU School of Medicine

description: Rebecca 10 082206.CEL

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: MAS5 GCOS, RMAExpress summarized using PLM and log2 transformed

source_name: Epidermal keratinocytes untreated control, 48h

label_protocol: Standard Affymetrix protocol

growth_protocol: Standard e.g. as in Banno et al., J Biol Chem 279(31): 32633-32642.

treatment_protocol: ~70% confluent keratinocytes treated with 25 ng.ml of EphB2 or EFNA4-Fc conjugates (Sigma)

tag: agent

value: control (untreated)

tag: time


title: whole-blood_2_Rep9


title: whole-blood_2_Rep8


title: T65

description: Primary breast tumor


title: T69

description: Primary breast tumor


title: T64

description: Primary breast tumor


title: T62

description: Primary breast tumor


title: Keratinocytes treated with EFNA4 for 48h

description: Rebecca 12 082206.CEL

source_name: Epidermal keratinocytes treated with EFNA4 for 48h

extract_protocol: Standard e.g. as in Banno et al., J Biol Chem 279(31): 32633-32642.

value: EFNA4-Fc conjugate


title: whole-blood_2_Rep6


title: Keratinocytes treated with EphB2 for 4h

description: Rebecca 5 082206.CEL

source_name: Epidermal keratinocytes treated with EphB2 for 4h

value: EphB2-Fc conjugate


title: T60

description: Primary breast tumor


title: T61

description: Primary breast tumor


title: Keratinocytes treated with EFNA4 for 24h

description: Rebecca 9 080706.CEL

source_name: Epidermal keratinocytes treated with EFNA4 for 24h


title: Keratinocytes treated with EphB2 for 48h

description: Rebecca 11 082206.CEL

source_name: Epidermal keratinocytes treated with EphB2 for 48h


title: Keratinocytes treated with EphB2 for 24h

description: Rebecca 8 080706.CEL

source_name: Epidermal keratinocytes treated with EphB2 for 24h


title: whole-blood_2_Rep4


title: Keratinocytes untreated control, 4h

description: Rebecca 4 082206.CEL

source_name: Epidermal keratinocytes untreated control, 4h


title: Keratinocytes untreated control, 24h

description: Rebecca 7(2) 080706.CEL

source_name: Epidermal keratinocytes untreated control, 24h


title: T58

description: Primary breast tumor

source_name: human breast cancer tumors


title: Keratinocytes treated with EFNA4 for 4h

description: Rebecca 6 082206.CEL

source_name: Epidermal keratinocytes treated with EFNA4 for 4h


title: whole-blood_2_Rep3


title: whole-blood_2_Rep5


title: whole-blood_2_Rep2


title: Keratinocytes untreated control, 1h

description: Rebecca 1 082206.CEL

source_name: Epidermal keratinocytes untreated control, 1h


title: whole-blood_1_Rep56

value: Intermediate (1)


title: T56

description: Primary breast tumor


title: T55

description: Primary breast tumor


title: Keratinocytes treated with EFNA4 for 1h

description: Rebecca 3 082206.CEL

source_name: Epidermal keratinocytes treated with EFNA4 for 1h


title: whole-blood_2_Rep1


title: whole-blood_1_Rep55


title: whole-blood_1_Rep54


title: whole-blood_1_Rep53


title: Patient I-840-N, normal colonic mucosa

city: Helsinki

first: Pia

last: Vahteristo

address: Haartmaninkatu 8

country: Finland

institute: University of Helsinki

description:
I-840-N
Gene expression data from human normal colonic mucosa sample.

hyb_protocol: Fragmented cRNA was hybridized to the Affymetrix HG-U133A chip according to the manufacturer's instructions.

scan_protocol: The chips were scanned at 570 nm with 3um resolution in an Affymetrix GeneChip scanner (Hewlett Packard).

data_processing: The readings from the quantitative scanning were analyzed by the Affymetrix MAS5.0 and normalized using the quantile normalization procedure implemented in robust multiarray analysis (RMA) with GeneSpring software (Silicon Genetics, CA, USA).

source_name: normal colonic mucosa

label_protocol: Biotinylated cRNA was prepared from 10ug of total RNA according to the standard Affymetrix protocol.

growth_protocol: Fresh-frozen tissue samples.

extract_protocol: RNA was extracted with Trizol reagent (Invitrogen) according to the manufacturer's instructions.

value: normal colonic mucosa


title: Patient 97N, normal colonic mucosa

description:
97N
Gene expression data from human normal colonic mucosa sample.


title: T53

description: Primary breast tumor


title: T52

description: Primary breast tumor


title: Patient 150N, normal colonic mucosa

description:
150N
Gene expression data from human normal colonic mucosa sample.


title: whole-blood_1_Rep52


title: T51

description: Primary breast tumor


title: Patient S-414-N, normal colonic mucosa

description:
S-414-N
Gene expression data from human normal colonic mucosa sample.


title: Patient 90N, normal colonic mucosa

description:
90N
Gene expression data from human normal colonic mucosa sample.


title: Patient 65N, normal colonic mucosa

description:
65N
Gene expression data from human normal colonic mucosa sample.


title: whole-blood_1_Rep51


title: Patient S-337-N, normal colonic mucosa

description:
S-337-N
Gene expression data from human normal colonic mucosa sample.


title: Patient I-1031-N, normal colonic mucosa

description:
I-1031-N
Gene expression data from human normal colonic mucosa sample.


title: Patient S-316-N, normal colonic mucosa

description:
S-316-N
Gene expression data from human normal colonic mucosa sample.


title: Patient S-855-N, normal colonic mucosa

description:
S-855-N
Gene expression data from human normal colonic mucosa sample.


title: whole-blood_1_Rep50


title: Keratinocytes treated with EphB2 for 1h

description: Rebecca 2 082206.CEL

source_name: Epidermal keratinocytes treated with EphB2 for 1h


title: Patient M030-827N, normal colonic mucosa

description:
M030-827N
Gene expression data from human normal colonic mucosa sample.


title: Patient H-615-N, normal colonic mucosa

description:
H-615-N
Gene expression data from human normal colonic mucosa sample.


title: Patient H-137-N, normal colonic mucosa

description:
H-137-N
Gene expression data from human normal colonic mucosa sample.


title: T50

description: Primary breast tumor


title: Patient H-661-N, normal colonic mucosa

description:
H-661-N
Gene expression data from human normal colonic mucosa sample.


title: Patient M030-258N, normal colonic mucosa

description:
M030-258N
Gene expression data from human normal colonic mucosa sample.


title: Patient S238, MSI colorectal tumor

description:
S238
Gene expression data from human colorectal cancer sample.

source_name: MSI colorectal tumor

value: microsatellite instability (MSI) colorectal tumor


title: Patient S196, MSI colorectal tumor

description:
S196
Gene expression data from human colorectal cancer sample.


title: whole-blood_1_Rep49


title: Patient S242, MSI colorectal tumor

description:
S242
Gene expression data from human colorectal cancer sample.


title: whole-blood_1_Rep47


title: Patient S120, MSI colorectal tumor

description:
S120
Gene expression data from human colorectal cancer sample.


title: whole-blood_1_Rep48


title: Patient I-u58T, MSI colorectal tumor

description:
I-u58T
Gene expression data from human colorectal cancer sample.


title: Patient I-c840T, MSI colorectal tumor

description:
I-c840T
Gene expression data from human colorectal cancer sample.


title: Patient I-c451T, MSI colorectal tumor

description:
I-c451T
Gene expression data from human colorectal cancer sample.


title: Patient I-c800T, MSI colorectal tumor

description:
I-c800T
Gene expression data from human colorectal cancer sample.


title: T46

description: Primary breast tumor

value: negative


title: T43

description: Primary breast tumor

value: positive


title: Patient I-c406T, MSI colorectal tumor

description:
I-c406T
Gene expression data from human colorectal cancer sample.


title: T47

description: Primary breast tumor


title: Patient I-c532T, MSI colorectal tumor

description:
I-c532T
Gene expression data from human colorectal cancer sample.


title: whole-blood_1_Rep46


title: whole-blood_1_Rep44


title: whole-blood_1_Rep45


title: Patient I-c1034T, MSI colorectal tumor

description:
I-c1034T
Gene expression data from human colorectal cancer sample.


title: Patient I-c671T, MSI colorectal tumor

description:
I-c671T
Gene expression data from human colorectal cancer sample.


title: T42

description: Primary breast tumor


title: whole-blood_1_Rep42


title: Patient I-c226T, MSI colorectal tumor

description:
I-c226T
Gene expression data from human colorectal cancer sample.


title: Patient C-c691T, MSI colorectal tumor

description:
C-c691T
Gene expression data from human colorectal cancer sample.


title: Patient I-c396T, MSI colorectal tumor

description:
I-c396T
Gene expression data from human colorectal cancer sample.


title: whole-blood_1_Rep43


title: T39

description: Primary breast tumor


title: whole-blood_1_Rep41


title: Patient M030-230, MSI colorectal tumor

description:
M030-230
Gene expression data from human colorectal cancer sample.


title: Random priming, cancer tissue, patient #15

city: Fujisawa

first: Rintaro

last: Saito

state: Kanagawa

address: 5322 Endo

country: Japan

institute: Keio University

description: Custom oligo (60mer) microarray was manufactured by Agilent Technologies.

hyb_protocol: The protocols supplied by Agilent Technologies were used.

data_processing: The quantitations based on the images were performed using Feature Extraction software (Agilent Technologies). The RNA samples were labeled with single color Cy3, hybridized to the oligo DNA on the chip, and dye-normalized; the processed signals were obtained by using Feature Extraction software (Agilent Technologies). The data on all genes on the chip were used to enable the Feature Extraction software to produce the processed signals. For further analysis, the Cy3-labeled processed signal was used as the processed signal from the expression of a particular gene. The total mean signal on the human chip in each hybridization experiment was adjusted to 1491.6, so that the relative differences in gene expression could be compared among cell lines and tissues.

source_name: Cancer tissue, patient #15

label_protocol: RNA was labeled using Fluorescent Direct Label Kits (oligo dT-primed labeling) (Agilent Technologies), according to the manufacturer’s protocols.

extract_protocol: For microarray analysis, we prepared colon cancer tissue and normal tissue samples from the normal tissues surrounding the cancer tissue, from six patients. The colon cancer and normal tissue samples were obtained during surgical resection of solitary cancerous lesions in the colon. Each tissue sample was homogenized in liquid nitrogen and total RNA was extracted using TRIzol Reagent (Gibco BRL, Carlsbad, California). Transcripts were labeled with fluorescent dyes by using either oligo dT or random priming.

tag: priming method

value: Random priming

tag: tissue type

value: colon cancer tissue

tag: patient number


title: Patient C-c215T, MSI colorectal tumor

description:
C-c215T
Gene expression data from human colorectal cancer sample.


title: Patient H-s115T, MSI colorectal tumor

description:
H-s115T
Gene expression data from human colorectal cancer sample.


title: Patient I-c852T, MSI colorectal tumor

description:
I-c852T
Gene expression data from human colorectal cancer sample.


title: Patient H-s124T, MSI colorectal tumor

description:
H-s124T
Gene expression data from human colorectal cancer sample.


title: Patient M030-55B, MSI colorectal tumor

description:
M030-55B
Gene expression data from human colorectal cancer sample.


title: whole-blood_1_Rep40


title: T38

description: Primary breast tumor


title: whole-blood_1_Rep39


title: T37

description: Primary breast tumor


title: Patient M030-161C, MSI colorectal tumor

description:
M030-161C
Gene expression data from human colorectal cancer sample.


title: T36

description: Primary breast tumor


title: whole-blood_1_Rep38


title: Patient M030-827T, MSI colorectal tumor

description:
M030-827T
Gene expression data from human colorectal cancer sample.


title: whole-blood_1_Rep37


title: Patient H-c661T, MSI colorectal tumor

description:
H-c661T
Gene expression data from human colorectal cancer sample.


title: Random priming, cancer tissue, patient #13

scan_protocol: The protocols supplied by Agilent Technologies were used.

source_name: Cancer tissue, patient #13


title: Random priming, Cancer tissue, patient #12

source_name: Cancer tissue, patient #12


title: Random priming, cancer tissue, patient #1

source_name: Cancer tissue, patient #1


title: Random priming, normal tissue, patient #13

source_name: Normal tissue, patient #13

value: normal colon tissue


title: Random priming, normal tissue, patient #15

source_name: Normal tissue, patient #15


title: Random priming, cancer tissue, patient #2

source_name: Cancer tissue, patient #2


title: Random priming, normal tissue, patient #12

source_name: Normal tissue, patient #12


title: Random priming, cancer tissue, patient #7

source_name: Cancer tissue, patient #7


title: Random priming, normal tissue, patient #7

source_name: Normal tissue, patient #7


title: T34

description: Primary breast tumor

source_name: human breast cancer tumors


title: T33

description: Primary breast tumor


title: whole-blood_1_Rep32


title: whole-blood_1_Rep31


title: T35

description: Primary breast tumor


title: Random priming, normal tissue, patient #2

source_name: Normal tissue, patient #2


title: whole-blood_1_Rep35


title: T30

description: Primary breast tumor


title: whole-blood_1_Rep34


title: whole-blood_1_Rep30


title: Patient H-c870T, MSI colorectal tumor

description:
H-c870T
Gene expression data from human colorectal cancer sample.


title: Patient H-c615T, MSI colorectal tumor

description:
H-c615T
Gene expression data from human colorectal cancer sample.


title: Patient H-c558T, MSI colorectal tumor

description:
H-c558T
Gene expression data from human colorectal cancer sample.


title: Patient H-c1027T, MSI colorectal tumor

description:
H-c1027T
Gene expression data from human colorectal cancer sample.


title: whole-blood_1_Rep33


title: Patient H-c883T, MSI colorectal tumor

description:
H-c883T
Gene expression data from human colorectal cancer sample.


title: T32

description: Primary breast tumor


title: Random priming, normal tissue, patient #1

source_name: Normal tissue, patient #1


title: T29

description: Primary breast tumor


title: whole-blood_1_Rep28


title: Oligo dT priming, cancer tissue, patient #15

value: Oligo dT priming


title: Patient H-c1095T, MSI colorectal tumor

description:
H-c1095T
Gene expression data from human colorectal cancer sample.


title: Oligo dT priming, cancer tissue, patient #13


title: T31

description: Primary breast tumor


title: Patient H-c614T-W, MSI colorectal tumor

description:
H-c614T-W
Gene expression data from human colorectal cancer sample.


title: whole-blood_1_Rep27


title: T28

description: Primary breast tumor


title: Patient H-c340T, MSI colorectal tumor

description:
H-c340T
Gene expression data from human colorectal cancer sample.


title: T26

description: Primary breast tumor


title: E1 (3)

city: Singapore

first: Puei Nam

last: Tay

address: Yong Loo Lin School of Medicine, Blk MD9, 2 Medical Drive

department: Physiology

country: Singapore

institute: National University of Singapore

description: In-vivo derived Metastatic colon cancer cell line E1

hyb_protocol: According to protocol outlined in Affymetrix technical manual

data_processing: Three independent biological replicates were profiled for each of the cell lines. MicroArray Suite 5.0 (MAS) (Affymetrix Inc) was used for the initial analysis of the scanned images. For absolute analysis, each chip (n=3) was scaled to a target intensity of 500 and probe sets were assigned a signal intensity and detection call of Present, Marginal or Absent.

source_name: Metastatic colon cancer cell line E1, 3rd of triplicates

extract_protocol: Trizol extraction

tag: cell line

tag: cell type

value: colon cancer cell line


title: T27

description: Primary breast tumor


title: whole-blood_1_Rep26


title: T25

description: Primary breast tumor


title: whole-blood_1_Rep29


title: Patient H-c587T, MSI colorectal tumor

description:
H-c587T
Gene expression data from human colorectal cancer sample.


title: Patient C-c145T, MSI colorectal tumor

description:
C-c145T
Gene expression data from human colorectal cancer sample.


title: Oligo dT priming, cancer tissue, patient #2

description: Custom oligo (60mer) microarray was manufactured by Agilent Technologies.


title: T24

description: Primary breast tumor


title: whole-blood_1_Rep24


title: whole-blood_1_Rep25


title: HCT116 (3)

description: Poorly metastatic colon cancer cell line

scan_protocol: According to protocol outlined in Affymetrix technical manual

data_processing: Three independent biological replicates were profiled for each of the cell lines. MicroArray Suite 5.0 (MAS) (Affymetrix Inc) was used for the initial analysis of the scanned images. For absolute analysis, each chip (n=3) was scaled to a target intensity of 500 and probe sets were assigned a signal intensity and detection call ofPresent, Marginal or Absent.

source_name: HCT116 colon cancer cell line, 3rd of triplicates


title: whole-blood_1_Rep36


title: E1 (1)

source_name: Metastatic colon cancer cell line E1, 1st of triplicates

label_protocol: According to protocol outlined in Affymetrix technical manual


title: HCT116 (2)

source_name: HCT116 colon cancer cell line, 2nd of triplicates


title: T23

description: Primary breast tumor


title: E1 (2)

source_name: Metastatic colon cancer cell line E1, 2nd of triplicates


title: Oligo dT priming, cancer tissue, patient #12


title: T19

description: Primary breast tumor


title: Oligo dT priming, normal tissue, patient #13


title: whole-blood_1_Rep23


title: Oligo dT priming, normal tissue, patient #15


title: Oligo dT priming, normal tissue, patient #7


title: T20

description: Primary breast tumor


title: whole-blood_1_Rep18


title: T21

description: Primary breast tumor


title: Oligo dT priming, cancer tissue, patient #7


title: Oligo dT priming, cancer tissue, patient #1


title: T17

description: Primary breast tumor


title: whole-blood_1_Rep22


title: T18

description: Primary breast tumor


title: Oligo dT priming, normal tissue, patient #2


title: detached-A.thaliana-leaf_24hpi_rep3

city: Cape Town

first: Joseph

middle: Mary Kusasira

last: Mulema

state: Western Cape

address: Private Bag, Rondebosch

department: Molecular and Cell Biology

country: South Africa

institute: University of Cape Town

hyb_protocol: Microarray slides were prepared based on Manufacturers instructions (Galbraith Laboratory, Arizona, USA) Labeled probes were concetrated, quantified and mixed in equal concentrations of labeled cDNA. Hybridization solution ( 20 μL of 20X SSC, 12 μL of 10% (v/v) BSA, 8 μL of SDS) was added and the volume made to 200 μL with Milli-Q water. The labeled probe was denatured by placing in boiling water for 2 min and transferred immediately to ice. The microarray slide was placed on a 65 oC heating block (label-side-up); the labeled probe was applied and covered with a coverslip avoiding trapping any air bubbles. The slide was incubated in a sealed chamber in a 55 oC water bath for 8-12 hrs. Slides were washed in 2X SSC, 0.5% (v/v) SDS for 5 min at 55 oC followed by 0.5X SSC for 5 min and 0.05X SSC for 5 min at room temperature.

scan_protocol: Slided were scanned on a GenePix scanner 4200A (Axon Instruments, Union City, CA). Images were analyzed with Genepix (Version 5.1) (Axon Instruments, Union City, CA) to generate fluorescent and background intensity values for each spot in both the Cy3 (green) and Cy5 (red) channels.

data_processing:
Print-tip LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal.
Following normalization, spot replication within each slide were merged based on average

organism: Arabidopsis thaliana

source_name: Control A. thaliana leaves harvested after 24 hr

label_protocol:
25 µg of total RNA were reversed transcribed at 46°C overnight for in the presence of 200 U SuperScript II RTase (Invitrogen), 10 mM aminoallyl-dUTP, 15 mM dTTP and 25 mM each of dATP, dCTP, dGTP.
Synthesized cDNA was prurified using the RNeasy mini columns (Qiagen, Valencia, CA) based on manufacturer’s instructions and its concentration determined with a NanoDrop.
Purified cDNA was dried under vacuum and resuspended in 0.1 M NaHCO3 and labeled with 5 µL of cyanine 3 (Cy3) and cyanine 5 (Cy5) (Amersham Pharmacia, UK) for 1 hr in the dark mixing every 15 min.
cDNA from mock-treated and infected leaves was labelled with Cy5 and Cy3 in the first replicate (dye-swap) respectively. In the last four replicates (rep 2-5), cDNA from mock treated and infected leaves was labelled with Cy3 and Cy5 respectively.

growth_protocol: Arabidopsis thalaina plants (Col-0 ecotype) were grown in a mixture of soil composed of peat plugs and vermiculite (1:1 ratio) in a controlled environment room at 22°C under fluorescent light (80-100 μmol photon/sec/m2) with a 16 hr light and 8 hr dark cycle.

extract_protocol: Total RNA extracted using Phenol-Lithium chloride method

treatment_protocol:
Control leaves were inoculated with half-stregnth commercial grape juice with no spores.
Leaves were harvested 12 aand 24 hpurs after inoculation

tag: ecotype

value: leaves

source_name: B. cinerea-treated A. thaliana leaves harvested after 24 hr

treatment_protocol:
Four-week Arabidopsis thaliana plants were inoculated with Botrytis cinerea (Pepper isolate) at a concentration of 500,000 spores ml-1 prepared in half strength commercial grape juice. The detarched leaf method was used in which 8-10 drops of 10 μl spore suspension depending on the size of the leaf were placed on top of each leaf.
Leaves were harvested 12 aand 24 hpurs after inoculation


title: whole-blood_1_Rep14


title: HCT116 (1)

source_name: HCT116 colon cancer cell line, 1st of triplicates


title: T22

first: Pascal

last: FINETTI

address: 232 Bd Ste Marguerite

institute: Institut Paoli-Calmettes

description: Primary breast tumor

extract_protocol: Guanidinium isothiocyanate and centrifugation over a cesium chloride gradient.


title: whole-blood_1_Rep19


title: Oligo dT priming, normal tissue, patient #12


title: Oligo dT priming, normal tissue, patient #1


title: Random priming, cancer tissue, patient #15

source_name: Cancer tissue, patient #15


title: Random priming, cancer tissue, patient #13

source_name: Cancer tissue, patient #13


title: whole-blood_1_Rep16


title: T16

description: Primary breast tumor


title: whole-blood_1_Rep20


title: T15

description: Primary breast tumor


title: T14

description: Primary breast tumor


title: detached-A.thaliana-leaf_12hpi_rep3

source_name: Control A. thaliana leaves harvested after 12 hr

source_name: B. cinerea-treated A. thaliana leaves harvested after 12 hr


title: T12

description: Primary breast tumor


title: whole-blood_1_Rep17


title: whole-blood_1_Rep13


title: T13

description: Primary breast tumor


title: T11

description: Primary breast tumor


title: whole-blood_1_Rep15


title: whole-blood_1_Rep21


title: Random priming, cancer tissue, patient #12

source_name: Cancer tissue, patient #12


title: whole-blood_1_Rep11


title: whole-blood_1_Rep10


title: T7

description: Primary breast tumor


title: Random priming, cancer tissue, patient #7

source_name: Cancer tissue, patient #7


title: whole-blood_1_Rep12


title: Random priming, normal tissue, patient #15

source_name: Normal tissue, patient #15


title: T6

description: Primary breast tumor

source_name: human breast cancer tumors


title: T9

description: Primary breast tumor


title: whole-blood_1_Rep8


title: T10

description: Primary breast tumor


title: whole-blood_1_Rep7


title: T8

description: Primary breast tumor


title: Random priming, normal tissue, patient #13

source_name: Normal tissue, patient #13


title: whole-blood_1_Rep9


title: Random priming, cancer tissue, patient #2

source_name: Cancer tissue, patient #2


title: Random priming, cancer tissue, patient #1

source_name: Cancer tissue, patient #1


title: Random priming, normal tissue, patient #12

source_name: Normal tissue, patient #12


title: Random priming, normal tissue, patient #7

source_name: Normal tissue, patient #7


title: whole-blood_1_Rep5


title: Oligo dT priming, Cancer tissue, patient #15


title: Oligo dT priming, cancer tissue, patient #13


title: T3

description: Primary breast tumor


title: T5

description: Primary breast tumor


title: T2

description: Primary breast tumor


title: whole-blood_1_Rep3


title: T1

description: Primary breast tumor


title: Oligo dT priming, cancer tissue, patient #2


title: Oligo dT priming, cancer tissue, patient #7


title: T4

description: Primary breast tumor


title: whole-blood_1_Rep6


title: whole-blood_1_Rep2


title: whole-blood_0_Rep51

value: Control (0)


title: Oligo dT priming, cancer tissue, patient #1


title: whole-blood_0_Rep52


title: whole-blood_1_Rep1


title: Oligo dT priming, normal tissue, patient #15


title: Oligo dT priming, cancer tissue, patient #12


title: whole-blood_0_Rep49


title: whole-blood_0_Rep50


title: Random priming, normal tissue, patient #2

source_name: Normal tissue, patient #2


title: Oligo dT priming, normal tissue, patient #13


title: whole-blood_0_Rep45


title: MALT CD4 cells - after stimulation - proband43

city: Freiburg

first: Petros

last: Christopoulos

address: Hugstetter Str. 55

department: Medizin I.

country: Germany

institute: Uniklinik Freiburg

description:
peripheral blood CD4 cells, purified (>95% purity), after 40h of in vitro stimulation (10e5 cells/well, 100μl/well) on CD3-coated plates (BD Biosciences Biocoat) with 3 µg/ml anti-CD28 (BD Biosciences) in AIM-V medium (Invitrogen) under serum-free conditions
Gene expression data from peripheral blood CD4 cells after in vitro stimulation with anti-CD3 and anti-CD28 for 40 h

hyb_protocol: Following fragmentation, 15 μg of cRNA were hybridized for 16 hr at 45C on U133 Plus 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 (Affymetrix)

data_processing: Microarray data were analyzed with Expressionist v5.3.3 software (Genedata). Gene expression values for subsequent analyses were calculated from raw data (.CEL files) with GC-RMA condensation after quantile normalization. Groups of differentially regulated genes cells were determined with an unpaired t-test including estimation of false-positive results by Benjamini-Hochberg Q values. The samples used in each group of patients and control donors are denoted above in the columns H-I (column title: characteristics: used in xx vs healthy comparison). The gene expression profiles corresponding to external, non-expression data, like the production of IFNγ or IL-4 in FL/eMZL CD4 cells, were determined through a “profile distance search” as correlations of ranks. The statistical significance of overrepresentation of members of specific pathways among various groups of deregulated genes was tested with Fisher’s exact test after import of the KEGG pathway annotations included in the current Bioconductor package v2.5 (annotation package hgu133plus2.db v2.3.5) based on KEGG release 52 (September 2009), which includes 358 human pathways (www.bioconductor.org).

source_name: CD4 cells - after stimulation - proband43 - rep1

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 5 μg total RNA with the Affymetrix “One-Cycle kit” (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: CD4+ T cells were obtained from heparinized blood by Ficoll-Hypaque density gradient centrifugation and enriched to >95% purity (CD4+ T-cell isolation kit; Miltenyi Biotech) as verified by flow cytometry. In the case of CLL samples, B cells were depleted with microbead-conjugated CD19 antibodies (Miltenyi) prior to T cell purification.

extract_protocol: Total RNA was extracted from cryopreserved cell lysates (RNeasy Mini kit, QIAGEN), precipitated with ethanol, and reconstituted at 0.5 µg/µl. RNA quality was confirmed by a median RNA integrity number of 10 (range: 9.3-10) (Agilent 2100 Bioanalyzer; Agilent).

treatment_protocol: For gene expression profiling and activation phenotyping, 10e5 purified CD4+ T cells were stimulated (10e6 cells/ml) on CD3-coated plates (BD Biosciences) with 3 µg/ml anti-CD28 (BD Biosciences) in AIM-V medium (Invitrogen) under serum-free conditions. After 40 h, cells were harvested and preserved in RNAlater (Ambion).

value: peripheral blood CD4 cells

value: MALT

tag: age in years

tag: used in fl/emzl vs healthy comparison (1-yes)

tag: used in cll vs healthy comparison (1-yes)

tag: used in mgus vs healthy comparison (1-yes)


title: whole-blood_0_Rep47


title: Random priming, normal tissue, patient #1

source_name: Normal tissue, patient #1


title: whole-blood_0_Rep46


title: whole-blood_1_Rep4


title: FL CD4 cells - after stimulation - proband45

source_name: CD4 cells - after stimulation - proband45 - rep1

value: FL


title: Oligo dT priming, normal tissue, patient #12


title: whole-blood_0_Rep48


title: Oligo dT priming, normal tissue, patient #1

data_processing: The quantitations based on the images were performed using Feature Extraction software (Agilent Technologies). The RNA samples were labeled with single color Cy3, hybridized to the oligo DNA on the chip, and dye-normalized; the processed signals were obtained by using Feature Extraction software (Agilent Technologies).  The data on all genes on the chip were used to enable the Feature Extraction software to produce the processed signals. For further analysis, the Cy3-labeled processed signal was used as the processed signal from the expression of a particular gene. The total mean signal on the human chip in each hybridization experiment was adjusted to 1491.6, so that the relative differences in gene expression could be compared among cell lines and tissues.


title: Oligo dT priming, normal tissue, patient #2


title: Oligo dT priming, normal tissue, patient #7


title: MGUS CD4 cells - after stimulation - proband41

source_name: CD4 cells - after stimulation - proband41 - rep1

value: MGUS


title: FL CD4 cells - after stimulation - proband42

source_name: CD4 cells - after stimulation - proband42 - rep1


title: whole-blood_0_Rep41


title: healthy CD4 cells - after stimulation - proband37

source_name: CD4 cells - after stimulation - proband37 - rep1

value: healthy


title: whole-blood_0_Rep44


title: whole-blood_0_Rep39


title: whole-blood_0_Rep38


title: whole-blood_0_Rep43


title: whole-blood_0_Rep40


title: IFNARKO BMDMs LPS 3hr

city: La Jolla

first: Alexander

last: Hoffmann

address: UCSD m/c 0375, NSB 3318 9500, Gilman Dr

department: Chemistry and Biochemistry

institute: UCSD

description: BMDM expression in response to LPS, CpG or IFNb

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Quantile normalized using Illumina Inc. BeadStudio

source_name: Bone marrow derived macrophages

label_protocol: Biotinylated cRNA was prepared with the Ambion Message Amp kit for Illumina arrays

growth_protocol: BMDMs were cultured in L929 cell conditioned medium for 5 to 8 days

extract_protocol: Total RNA was extracted from BMDMs with Rneasy columns (Qiagen)

treatment_protocol: BMDMs were stimulated with LPS, CpG or IFNb

tag: strain

value: BMDM

value: IFNARKO

value: LPS


title: WT BMDMs IFNb 3hr

tag: genotype/variation

value: wild type

value: IFNb


title: whole-blood_0_Rep37


title: p50KO BMDMs IFNb 1hr


title: MALT CD4 cells - after stimulation - proband30

source_name: CD4 cells - after stimulation - proband30 - rep1


title: p50KO BMDMs LPS 8hr


title: WT BMDMs IFNb 1hr


title: IFNARKO BMDMs LPS 0hr


title: p50KO BMDMs IFNb 8hr


title: whole-blood_0_Rep34


title: p50KO BMDMs IFNb 3hr


title: whole-blood_0_Rep33


title: CLL CD4 cells - after stimulation - proband24

source_name: CD4 cells - after stimulation - proband24 - rep1

value: CLL


title: p50KO BMDMs LPS 1hr


title: WT BMDMs IFNb 8hr


title: CLL CD4 cells - after stimulation - proband25

source_name: CD4 cells - after stimulation - proband25 - rep1


title: p50KO BMDMs LPS 3hr


title: MGUS CD4 cells - after stimulation - proband23

source_name: CD4 cells - after stimulation - proband23 - rep1


title: whole-blood_0_Rep32


title: whole-blood_0_Rep30


title: whole-blood_0_Rep36


title: whole-blood_0_Rep35


title: MGUS CD4 cells - after stimulation - proband26

source_name: CD4 cells - after stimulation - proband26 - rep1


title: MALT CD4 cells - after stimulation - proband21

source_name: CD4 cells - after stimulation - proband21 - rep1


title: whole-blood_0_Rep31


title: whole-blood_0_Rep28


title: WT BMDMs LPS 0hr


title: WT BMDMs LPS 1hr


title: WT BMDMs LPS 8hr


title: WT BMDMs LPS 3hr


title: FL CD4 cells - after stimulation - proband22

source_name: CD4 cells - after stimulation - proband22 - rep1


title: MGUS CD4 cells - after stimulation - proband20

source_name: CD4 cells - after stimulation - proband20 - rep1


title: CLL CD4 cells - after stimulation - proband18

source_name: CD4 cells - after stimulation - proband18 - rep1


title: CLL CD4 cells - after stimulation - proband16

source_name: CD4 cells - after stimulation - proband16 - rep1


title: whole-blood_0_Rep25


title: whole-blood_0_Rep29


title: whole-blood_0_Rep24


title: whole-blood_0_Rep21


title: whole-blood_0_Rep27


title: MGUS CD4 cells - after stimulation - proband19

source_name: CD4 cells - after stimulation - proband19 - rep1


title: CLL CD4 cells - after stimulation - proband17

source_name: CD4 cells - after stimulation - proband17 - rep1


title: FL CD4 cells - after stimulation - proband15

source_name: CD4 cells - after stimulation - proband15 - rep1


title: MALT CD4 cells - after stimulation - proband12

source_name: CD4 cells - after stimulation - proband12 - rep1


title: WT BMDMs CpG 1hr

value: CpG


title: whole-blood_0_Rep22


title: FL CD4 cells - after stimulation - proband14

source_name: CD4 cells - after stimulation - proband14 - rep1


title: whole-blood_0_Rep26


title: p50KO BMDMs CpG 8hr


title: p50KO BMDMs CpG 3hr


title: whole-blood_0_Rep23


title: p50KO BMDMs CpG 0hr


title: WT BMDMs CpG 3hr


title: WT BMDMs CpG 8hr


title: whole-blood_0_Rep17


title: whole-blood_0_Rep19


title: whole-blood_0_Rep20


title: p50KO BMDMs CpG 1hr


title: whole-blood_0_Rep13


title: whole-blood_0_Rep18


title: MALT CD4 cells - after stimulation - proband8

source_name: CD4 cells - after stimulation - proband8 - rep1


title: whole-blood_0_Rep42


title: FL CD4 cells - after stimulation - proband10

source_name: CD4 cells - after stimulation - proband10 - rep1


title: whole-blood_0_Rep14


title: whole-blood_0_Rep12


title: CLL CD4 cells - after stimulation - proband11

source_name: CD4 cells - after stimulation - proband11 - rep1


title: FL CD4 cells - after stimulation - proband9

source_name: CD4 cells - after stimulation - proband9 - rep1


title: whole-blood_0_Rep11


title: whole-blood_0_Rep15


title: whole-blood_0_Rep16


title: whole-blood_0_Rep10


title: WT_fedL1_rep1

city: Berkeley

first: Barbara

middle: J.

last: Meyer

address: 16 Barker Hall #3204

department: MCB

institute: HHMI/UCB

description: Synchronous L1s fed for 3 hours

hyb_protocol: Following fragmentation, 15 microg of cRNA were hybridized for 16 hr at 45C on GeneChip C. ElegansGenome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix Scanner 30007G.

data_processing: Arrays were normalized by RMA (Robust Multichip Average) using Affymetrix Expression Consol software (Irizarry et al. 2003). Data were analyzed by ArrayStar. Statistical analysis was performed using a moderated t-test with FDR multiple testing correction (Benjamini-Hochberg method). Irizarry, R.A., Hobbs, B., Collin, F., Beazer-Barclay, Y.D., Antonellis, K.J., Scherf, U., and Speed, T.P. 2003. Exploration, Normalization, and Summaries of High Density Oligonucleotide Array Probe Level Data. Biostatistics 4: 249-264.

organism: Caenorhabditis elegans

source_name: embryos from worms grown on NG plates

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 8 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix)

growth_protocol: Fed L1s used for microarray analysis were obtained by feeding synchronous L1 larvae with HB101 for 3 hours

extract_protocol: Gravid adults were bleached and hatched off for 24 hours in 1XM9 at 20 degrees celcius. Synchronous L1s were placed in S medium at a density of 10 worms/uL and fed with 10 mg/mL HB101 E.coli for 3 hours at 20 degrees celcius in liquid culture. Fed L1s were harvested as described (Portman, D.S, Wombook, Profiling C. elegans gene expression with DNA microarrays) and 100 µl aliquots snap frozen in liquid nitrogen and stored at -80∞C. An aliquot was thawed at 65∞C for 10 minutes, resuspended in 1ml Trizol (Invitrogen, Carlsbad, CA), vortexed vigorously to resuspend, and incubated for 20 minutes at room temperature. The sample was then centrifuged for 15 minutes at 12,000xg at 4∞C. The aqueous phase was transferred to a new tube and 100 µl of BCP (1-bromo-3-chloropropane) (MRC, Cincinnati, OH) was added, the sample was mixed by vortexing, incubated for 15 minutes at room temperature, and centrifuged for 10 minutes at 12,000xg at 4∞C. The aqueous phase was transferred to a new tube and nucleic acid was precipitated by addition of 500 µl of isopropanol. The sample was incubated for 10 minutes at room temperature, centrifuged at 12,000xg for 8 minutes, washed in 70% ethanol and air dried for 5 minutes. Nucleic acid was resuspended in 100 µl nuclease-free water and RNA quantified with a UV spectrophotometer. One hundred micrograms of RNA was then treated with 3 µl RQ1-DNAse (Promega, Madison, WI) and RNA isolated with the RNAeasy kit as per the manufacturer's protocol (Qiagen, Valencia, CA). RNA was again quantified with a UV spectrophotometer and cDNA was prepared from 5 µg RNA using the Protoscript Kit (NEB, Ipswich, MA) and diluted 1:15 in water.

value: wild type (N2)

tag: developmental stage

value: larval stage L1

tag: protocol

value: Synchronous L1s fed for 3 hours