title: genetic line: Morex - rep3

description: (Organism Part); first leaf unfolded (Development Stage); 0 days after imbibition (Age); vermiculite (Growth Media).

source_name: (genetic line: Morex)

value: leaves

value: Morex


title: Western European 65

status: Public on Nov 22 2011

type: genomic

city: Evry

first: Cyril

last: Dalmasso

address: 23 bd de France

department: Mathématiques

country: France

institute: Université d'Evry Val d'Essonne

hyb_protocol: Samples were processed and hybridized to Affymetrix Genome-Wide Human SNP 6.0 arrays according to the manufacturer’s specifications in the same center.

data_processing: DNA copy-number changes, we considered the log-ratio between the signal and a reference signal estimated from a pool of hybridized samples corresponding to HapMap data, that were matched for ethnicity. Systematic sources of variation (GC content, fragment length) were removed by subtracting for each log-ratio its estimated predicted values inferred from the least squares estimates of the parameters. Data from the sex chromosomes were not considered. To reduce measurement variability while keeping a sufficient level of resolution, we averaged the intensities over fifty consecutive probes leading to a total of 17,769 genomic segments (average size of 150kb) providing tiling coverage of the human genome.

label: biotin

molecule: genomic DNA

organism: Homo sapiens

source_name: Lung adenocarcinoma, Western European

growth_protocol: Tumor samples were immediately frozen at –80°C until retrieved.

extract_protocol: DNA was extracted from frozen samples using the Nucleon DNA extraction kit (BACC2, Amersham Biosciences, Buckinghamshire, UK).

treatment_protocol: Only tissue samples with tumor cells >50% were selected.

tag: origin

value: Western European

tag: cell type

value: Lung adenocarcinoma


title: genetic line: Morex - rep2

type: RNA

city: Ames

first: PLEXdb Curator

middle: Sudhansu

state: IA

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

department: Virtual Reality Application Center

country: USA

institute: Iowa State University

hyb_protocol: Affy- Eukaryotic Target Hybridization

scan_protocol: Affy- Array Scanning

data_processing: The MAS5.0 Normalization is performed using the justMAS function in the simpleaffy package of Bioconductor (www.bioconductor.org). The target value is 500 for all cases. The code was developed using R2.4.1, Bioconductor 1.9, and simpleaffy 2.8.0. The CDF files were downloaded from the Bioconductor website at http://www.bioconductor.org/packages/release/AffymetrixChip.html. The normalization scripts are available from the PLEXdb team by request.

molecule: total RNA

organism: Hordeum vulgare

label_protocol: Affy-Eukaryotic Target Preparation

extract_protocol: Hot Phenol/Guanidine Thiocyanate and RNeasy Clean up

tag: tissue

tag: line


title: Western European 62

scan_protocol: Samples were processed and hybridized to Affymetrix Genome-Wide Human SNP 6.0 arrays according to the manufacturer’s specifications in the same center.


title: Western European 63

label_protocol: Samples were processed and hybridized to Affymetrix Genome-Wide Human SNP 6.0 arrays according to the manufacturer’s specifications in the same center.


title: genetic line: Steptoe - rep2

source_name: (genetic line: Steptoe)

value: Steptoe


title: Western European 60


title: genetic line: Steptoe - rep3


title: genetic line: Steptoe - rep1


title: genetic line: SM200 - rep1

source_name: (genetic line: SM200)


title: genetic line: Morex - rep1


title: genetic line: SM184 - rep1

source_name: (genetic line: SM184)


title: Western European 58


title: genetic line: SM173 - rep1

source_name: (genetic line: SM173)


title: Western European 59


title: genetic line: SM169 - rep1

source_name: (genetic line: SM169)


title: genetic line: SM177 - rep1

source_name: (genetic line: SM177)


title: genetic line: SM160 - rep1

source_name: (genetic line: SM160)


title: Western European 56


title: genetic line: SM167 - rep1

source_name: (genetic line: SM167)


title: Western European 57


title: genetic line: SM155 - rep1

source_name: (genetic line: SM155)


title: Western European 55


title: Western European 53


title: Western European 52


title: genetic line: SM152 - rep1

source_name: (genetic line: SM152)


title: Western European 51


title: genetic line: SM141 - rep1

source_name: (genetic line: SM141)


title: Western European 50


title: genetic line: SM146 - rep1

source_name: (genetic line: SM146)


title: Western European 54


title: Western European 44


title: Western European 48


title: Western European 49


title: Western European 61


title: genetic line: SM135 - rep1

source_name: (genetic line: SM135)


title: genetic line: SM136 - rep1

source_name: (genetic line: SM136)


title: genetic line: SM130 - rep1

source_name: (genetic line: SM130)


title: Western European 45


title: genetic line: SM140 - rep1

source_name: (genetic line: SM140)


title: genetic line: SM116 - rep1

source_name: (genetic line: SM116)


title: Western European 46

source_name: Lung adenocarcinoma, Western European


title: Western European 41


title: Western European 43


title: Western European 47


title: Western European 42


title: genetic line: SM079 - rep1

source_name: (genetic line: SM079)


title: genetic line: SM089 - rep1

source_name: (genetic line: SM089)


title: genetic line: SM085 - rep1

source_name: (genetic line: SM085)


title: Western European 38


title: Western European 40


title: Western European 35


title: genetic line: SM088 - rep1

source_name: (genetic line: SM088)


title: Western European 37


title: genetic line: SM074 - rep1

source_name: (genetic line: SM074)


title: genetic line: SM046 - rep1

source_name: (genetic line: SM046)


title: genetic line: SM061 - rep1

source_name: (genetic line: SM061)


title: Western European 33


title: genetic line: SM073 - rep1

source_name: (genetic line: SM073)


title: genetic line: SM044 - rep1

source_name: (genetic line: SM044)


title: Western European 39


title: genetic line: SM043 - rep1

source_name: (genetic line: SM043)


title: genetic line: SM063 - rep1

source_name: (genetic line: SM063)


title: genetic line: SM027 - rep1

source_name: (genetic line: SM027)


title: genetic line: SM041 - rep1

source_name: (genetic line: SM041)


title: Western European 36


title: genetic line: SM024 - rep1

source_name: (genetic line: SM024)


title: Western European 34


title: Western European 31


title: Western European 30


title: genetic line: SM022 - rep1

source_name: (genetic line: SM022)


title: genetic line: SM013 - rep1

source_name: (genetic line: SM013)


title: Western European 29

source_name: Lung adenocarcinoma, Western European


title: genetic line: SM007 - rep1

source_name: (genetic line: SM007)


title: Western European 25


title: genetic line: SM004 - rep1

source_name: (genetic line: SM004)


title: genetic line: SM012 - rep1

source_name: (genetic line: SM012)


title: Western European 28


title: genotype: Optic - rep3

description: (Organism Part); 2.2 first leaf unfolded (Development Stage); 12 days after imbibition (Age); vermiculite (Growth Media).

source_name: (genotype: Optic)

value: seedling leaves

tag: cultivar

value: Optic


title: Western European 26


title: genotype: Optic - rep1


title: genotype: Optic - rep2


title: Western European 23


title: Western European 27


title: Western European 22


title: genotype: Golden Promise - rep3

source_name: (genotype: Golden Promise)

value: Golden Promise


title: Western European 32


title: Western European 19


title: Western European 20


title: genotype: Golden Promise - rep1


title: genotype: Golden Promise - rep2


title: Western European 15


title: Western European 16


title: genotype: Haruna Nijo - rep2

source_name: (genotype: Haruna Nijo)

value: Haruna Nijo


title: genotype: Haruna Nijo - rep1


title: Western European 18


title: genotype: Barke - rep3

source_name: (genotype: Barke)

value: Barke


title: Western European 12


title: genotype: Haruna Nijo - rep3


title: genotype: Barke - rep1


title: Western European 21


title: Western European 13


title: Western European 24


title: genotype: OWB DOM - rep2

source_name: (genotype: OWB DOM)

value: OWB DOM


title: genotype: Barke - rep2


title: Western European 10


title: genotype: OWB DOM - rep3


title: Western European 7


title: genotype: OWB REC - rep3

source_name: (genotype: OWB REC)

value: OWB REC


title: genotype: OWB REC - rep2


title: Western European 17


title: genotype: OWB REC - rep1


title: Western European 14


title: Western European 4


title: Western European 2


title: genotype: Steptoe - rep2

source_name: (genotype: Steptoe)


title: Western European 11


title: Western European 8


title: genotype: Steptoe - rep3


title: Western European 6


title: genotype: Steptoe - rep1


title: Western European 9


title: genotype: Morex - rep1

source_name: (genotype: Morex)


title: genotype: Morex - rep2


title: genotype: Morex - rep3


title: Western European 1


title: genotype: 9472  - time: 32 - Treated or untreated: Non-inoculated - rep3

description: (organism part); gro: 0007060 (Development Stage); 7 days after planting (Age);

source_name: (genotype: 9472  - time: 32 - Treated or untreated: Non-inoculated)

tag: genotype

tag: time

tag: infection

value: Non-inoculated


title: East Asian 157

source_name: Lung adenocarcinoma, East Asian

value: East Asian


title: genotype: OWB DOM - rep1


title: East Asian 155


title: East Asian 156


title: genotype: 9472  - time: 32 - Treated or untreated: Non-inoculated - rep2


title: East Asian 154


title: East Asian 153


title: genotype: 9472  - time: 32 - Treated or untreated: Non-inoculated - rep1


title: genotype: 9472  - time: 32 - Treated or untreated: Inoculated  - rep3

source_name: (genotype: 9472  - time: 32 - Treated or untreated: Inoculated )

value: Blumeria graminis f. sp. hordei (Bgh) isolates 5874 (AvrMla1, AvrMla6)


title: East Asian 151


title: genotype: 9472  - time: 32 - Treated or untreated: Inoculated  - rep1


title: genotype: 9472  - time: 24 - Treated or untreated: Non-inoculated - rep3

source_name: (genotype: 9472  - time: 24 - Treated or untreated: Non-inoculated)


title: East Asian 145


title: genotype: 9472  - time: 24 - Treated or untreated: Non-inoculated - rep2


title: genotype: 9472  - time: 24 - Treated or untreated: Non-inoculated - rep1


title: East Asian 146


title: East Asian 141


title: genotype: 9472  - time: 24 - Treated or untreated: Inoculated  - rep3

source_name: (genotype: 9472  - time: 24 - Treated or untreated: Inoculated )


title: genotype: 9472  - time: 24 - Treated or untreated: Inoculated  - rep1


title: genotype: 9472  - time: 32 - Treated or untreated: Inoculated  - rep2


title: genotype: 9472  - time: 20 - Treated or untreated: Non-inoculated - rep3

source_name: (genotype: 9472  - time: 20 - Treated or untreated: Non-inoculated)


title: East Asian 134


title: genotype: 9472  - time: 24 - Treated or untreated: Inoculated  - rep2


title: East Asian 139


title: genotype: 9472  - time: 20 - Treated or untreated: Inoculated  - rep3

source_name: (genotype: 9472  - time: 20 - Treated or untreated: Inoculated )


title: East Asian 133


title: East Asian 137


title: East Asian 124


title: genotype: 9472  - time: 20 - Treated or untreated: Non-inoculated - rep1


title: genotype: 9472  - time: 20 - Treated or untreated: Non-inoculated - rep2


title: Western European 3

source_name: Lung adenocarcinoma, Western European


title: Western European 5


title: East Asian 126


title: genotype: 9472  - time: 20 - Treated or untreated: Inoculated  - rep2


title: East Asian 115


title: East Asian 132


title: East Asian 128


title: East Asian 143


title: East Asian 110


title: East Asian 122


title: East Asian 127


title: genotype: 9472  - time: 16 - Treated or untreated: Non-inoculated - rep1

source_name: (genotype: 9472  - time: 16 - Treated or untreated: Non-inoculated)


title: East Asian 138


title: genotype: 9472  - time: 20 - Treated or untreated: Inoculated  - rep1


title: East Asian 119


title: genotype: 9472  - time: 16 - Treated or untreated: Inoculated  - rep3

source_name: (genotype: 9472  - time: 16 - Treated or untreated: Inoculated )


title: genotype: 9472  - time: 16 - Treated or untreated: Inoculated  - rep2


title: East Asian 121


title: genotype: 9472  - time: 16 - Treated or untreated: Non-inoculated - rep3


title: genotype: 9472  - time: 16 - Treated or untreated: Non-inoculated - rep2


title: genotype: 9472  - time: 8 - Treated or untreated: Non-inoculated - rep2

source_name: (genotype: 9472  - time: 8 - Treated or untreated: Non-inoculated)


title: East Asian 114


title: genotype: 9472  - time: 8 - Treated or untreated: Non-inoculated - rep1


title: genotype: 9472  - time: 8 - Treated or untreated: Non-inoculated - rep3


title: genotype: 9472  - time: 16 - Treated or untreated: Inoculated  - rep1

description: po: 0009025## (Organism Part); GRO:0007060 (Development Stage); 7 days after planting (Age);

source_name: ## (genotype: 9472  - time: 16 - Treated or untreated: Inoculated )


title: genotype: 9472  - time: 8 - Treated or untreated: Inoculated  - rep3

source_name: (genotype: 9472  - time: 8 - Treated or untreated: Inoculated )


title: genotype: 9472  - time: 8 - Treated or untreated: Inoculated  - rep2


title: genotype: 9472  - time: 8 - Treated or untreated: Inoculated  - rep1


title: East Asian 118


title: genotype: 9472  - time: 0 - Treated or untreated: Non-inoculated - rep3

source_name: (genotype: 9472  - time: 0 - Treated or untreated: Non-inoculated)


title: East Asian 105


title: East Asian 108


title: East Asian 111


title: genotype: 9472  - time: 0 - Treated or untreated: Non-inoculated - rep1


title: East Asian 98


title: genotype: 9472  - time: 0 - Treated or untreated: Inoculated  - rep2

source_name: (genotype: 9472  - time: 0 - Treated or untreated: Inoculated )


title: East Asian 140


title: genotype: 9472  - time: 0 - Treated or untreated: Inoculated  - rep3


title: East Asian 97


title: East Asian 95


title: genotype: 9472  - time: 0 - Treated or untreated: Inoculated  - rep1


title: East Asian 96


title: genotype: Mla6 - time: 32 - Treated or untreated: Non-inoculated - rep3

source_name: (genotype: Mla6 - time: 32 - Treated or untreated: Non-inoculated)


title: East Asian 94


title: East Asian 89


title: East Asian 93


title: genotype: Mla6 - time: 32 - Treated or untreated: Inoculated  - rep3

source_name: (genotype: Mla6 - time: 32 - Treated or untreated: Inoculated )


title: genotype: Mla6 - time: 32 - Treated or untreated: Inoculated  - rep2


title: genotype: Mla6 - time: 32 - Treated or untreated: Non-inoculated - rep1


title: genotype: Mla6 - time: 32 - Treated or untreated: Non-inoculated - rep2


title: East Asian 91


title: genotype: 9472  - time: 0 - Treated or untreated: Non-inoculated - rep2


title: genotype: Mla6 - time: 24 - Treated or untreated: Non-inoculated - rep2

source_name: (genotype: Mla6 - time: 24 - Treated or untreated: Non-inoculated)


title: genotype: Mla6 - time: 24 - Treated or untreated: Non-inoculated - rep3


title: East Asian 85

source_name: Lung adenocarcinoma, East Asian


title: East Asian 80


title: East Asian 86


title: East Asian 83


title: genotype: Mla6 - time: 32 - Treated or untreated: Inoculated  - rep1


title: genotype: Mla6 - time: 24 - Treated or untreated: Non-inoculated - rep1


title: genotype: Mla6 - time: 24 - Treated or untreated: Inoculated  - rep3

source_name: (genotype: Mla6 - time: 24 - Treated or untreated: Inoculated )


title: M#21 M-CSF + E/P/IL-10/4/13 D6 macrophages LIDnr 6970

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

country: Germany

institute: HCI - Helmholtz Centre for Infection Research

hyb_protocol: 1.6 ug labeled cRNA was hybridized to microarrays for 16h at 68?C and scanned using the Agilent DNA Microarray Scanner.

scan_protocol: Microarrays were scanned using the Agilent Scanner System. Data extractions were performed using Feature Extraction Software 10.7.1 (Agilent) with default patrameters of the GE1_107_Sep09 extraction protocol

data_processing: log2 transformed, median normalized to all samples, signal intensity expressed as relative to median signal intensity of all samples

source_name: Monocyte

label_protocol: 500ng of total RNA were applied for Cy3-labelling reaction using the one color Quick Amp Labeling protocol (Agilent Technologies; Waldbronn, Germany).

extract_protocol: RNAeasy

tag: factors


title: genotype: Mla6 - time: 24 - Treated or untreated: Inoculated  - rep2


title: genotype: Mla6 - time: 24 - Treated or untreated: Inoculated  - rep1


title: East Asian 73


title: East Asian 68


title: East Asian 77


title: M#21 M-CSF + IL4/13 D6 macrophages LIDnr 6970

treatment_protocol: M-CSF + IL4/13 D6

value: M-CSF + IL4/13


title: genotype: Mla6 - time: 20 - Treated or untreated: Non-inoculated - rep3

source_name: (genotype: Mla6 - time: 20 - Treated or untreated: Non-inoculated)


title: M#21 M-CSF + IL-10 D6 macrophages LIDnr 6970

treatment_protocol: M-CSF + IL-10 D6

value: M-CSF + IL-10


title: genotype: Mla6 - time: 20 - Treated or untreated: Non-inoculated - rep1

value: leaves


title: East Asian 76


title: East Asian 64


title: genotype: Mla6 - time: 20 - Treated or untreated: Non-inoculated - rep2


title: genotype: Mla6 - time: 20 - Treated or untreated: Inoculated  - rep1

source_name: (genotype: Mla6 - time: 20 - Treated or untreated: Inoculated )


title: genotype: Mla6 - time: 20 - Treated or untreated: Inoculated  - rep2


title: M#21 M-CSF + E D6 macrophages LIDnr 6970

treatment_protocol: M-CSF + E D6

value: M-CSF + E


title: genotype: Mla6 - time: 20 - Treated or untreated: Inoculated  - rep3


title: East Asian 63


title: East Asian 71


title: East Asian 65


title: genotype: Mla6 - time: 16 - Treated or untreated: Non-inoculated - rep3

source_name: (genotype: Mla6 - time: 16 - Treated or untreated: Non-inoculated)


title: genotype: Mla6 - time: 16 - Treated or untreated: Non-inoculated - rep2


title: genotype: Mla6 - time: 16 - Treated or untreated: Non-inoculated - rep1


title: East Asian 61


title: M#21 M-CSF D6 macrophages LIDnr 6970

description: M#21 M-CSF D6 macrophages LIDnr 6970

treatment_protocol: M-CSF D6

value: M-CSF


title: East Asian 84

value: Lung adenocarcinoma


title: East Asian 56


title: M#21 GM-CSF/LPS/IFN D6 macrophages LIDnr 6970

treatment_protocol: GM-CSF/LPS/IFN D6

value: GM-CSF/LPS/IFN


title: genotype: Mla6 - time: 16 - Treated or untreated: Inoculated  - rep3

source_name: (genotype: Mla6 - time: 16 - Treated or untreated: Inoculated )


title: East Asian 67


title: M#21 M-CSF + P D6 macrophages LIDnr 6970

treatment_protocol: M-CSF + P D6

value: M-CSF + P


title: genotype: Mla6 - time: 16 - Treated or untreated: Inoculated  - rep2


title: genotype: Mla6 - time: 8 - Treated or untreated: Non-inoculated - rep3

source_name: (genotype: Mla6 - time: 8 - Treated or untreated: Non-inoculated)


title: genotype: Mla6 - time: 8 - Treated or untreated: Non-inoculated - rep2


title: M#20 M-CSF + E D6 macrophages LIDnr 6969


title: genotype: Mla6 - time: 8 - Treated or untreated: Non-inoculated - rep1


title: East Asian 50


title: East Asian 51


title: genotype: Mla6 - time: 8 - Treated or untreated: Inoculated  - rep3

source_name: (genotype: Mla6 - time: 8 - Treated or untreated: Inoculated )


title: East Asian 49


title: East Asian 62


title: genotype: Mla6 - time: 8 - Treated or untreated: Inoculated  - rep1


title: M#20 M-CSF + P D6 macrophages LIDnr 6969


title: M#20 GM-CSF/LPS/IFN D6 macrophages LIDnr 6969


title: genotype: Mla6 - time: 0 - Treated or untreated: Non-inoculated - rep1

source_name: (genotype: Mla6 - time: 0 - Treated or untreated: Non-inoculated)


title: genotype: Mla6 - time: 0 - Treated or untreated: Non-inoculated - rep3


title: genotype: Mla6 - time: 16 - Treated or untreated: Inoculated  - rep1


title: East Asian 57


title: East Asian 42


title: East Asian 46


title: genotype: Mla6 - time: 0 - Treated or untreated: Inoculated  - rep3

scan_protocol: Affymetrix MAS 5.0 Standard Scanning at NASC

source_name: ## (genotype: Mla6 - time: 0 - Treated or untreated: Inoculated )


title: M#20 D0 Mo LIDnr 6969

description: M#20 D0 Mo LIDnr 6969

treatment_protocol: D0 Mo

value: D0 Mo


title: genotype: Mla6 - time: 8 - Treated or untreated: Inoculated  - rep2


title: East Asian 43


title: East Asian 48


title: M#27 GM-CSF + E/P/IL-10/4/13 D6 macrophages LIDnr 6981


title: genotype: m508  - time: 32 - Treated or untreated: Non-inoculated - rep3

source_name: (genotype: m508  - time: 32 - Treated or untreated: Non-inoculated)


title: M#27 GM-CSF + IL4/13 D6 macrophages LIDnr 6981

treatment_protocol: GM-CSF + IL4/13 D6

value: GM-CSF + IL4/13


title: M#20 M-CSF D6 macrophages LIDnr 6969

description: M#20 M-CSF D6 macrophages LIDnr 6969


title: genotype: Mla6 - time: 0 - Treated or untreated: Inoculated  - rep2

source_name: (genotype: Mla6 - time: 0 - Treated or untreated: Inoculated )


title: East Asian 34


title: M#27 GM-CSF + IL-10 D6 macrophages LIDnr 6981

treatment_protocol: GM-CSF + IL-10 D6

value: GM-CSF + IL-10


title: genotype: Mla6 - time: 0 - Treated or untreated: Non-inoculated - rep2


title: genotype: Mla6 - time: 0 - Treated or untreated: Inoculated  - rep1


title: genotype: m508  - time: 32 - Treated or untreated: Non-inoculated - rep1


title: genotype: m508  - time: 32 - Treated or untreated: Inoculated  - rep3

source_name: (genotype: m508  - time: 32 - Treated or untreated: Inoculated )


title: M#27 GM-CSF + P D6 macrophages LIDnr  6981

treatment_protocol: GM-CSF + P D6

value: GM-CSF + P


title: East Asian 35


title: East Asian 33


title: genotype: m508  - time: 32 - Treated or untreated: Inoculated  - rep1


title: genotype: m508  - time: 24 - Treated or untreated: Non-inoculated - rep3

source_name: (genotype: m508  - time: 24 - Treated or untreated: Non-inoculated)


title: genotype: m508  - time: 32 - Treated or untreated: Inoculated  - rep2


title: M#27 GM-CSF D6 macrophages LIDnr 6981

description: M#27 GM-CSF D6 macrophages LIDnr 6981

treatment_protocol: GM-CSF D6

value: GM-CSF


title: M#27 GM-CSF + E D6 macrophages LIDnr 6981

treatment_protocol: GM-CSF + E D6

value: GM-CSF + E


title: genotype: m508  - time: 24 - Treated or untreated: Inoculated  - rep3

source_name: (genotype: m508  - time: 24 - Treated or untreated: Inoculated )


title: genotype: m508  - time: 24 - Treated or untreated: Non-inoculated - rep1

value: Non-inoculated


title: M#27 GM-CSF/LPS/IFN D6 macrophages LIDnr 6981


title: East Asian 40

value: East Asian


title: genotype: m508  - time: 24 - Treated or untreated: Non-inoculated - rep2


title: M#27 D0 Mo LIDnr 6981

description: M#27 D0 Mo LIDnr 6981


title: genotype: m508  - time: 32 - Treated or untreated: Non-inoculated - rep2


title: East Asian 28


title: East Asian 30


title: genotype: m508  - time: 24 - Treated or untreated: Inoculated  - rep1

value: Blumeria graminis f. sp. hordei (Bgh) isolates 5874 (AvrMla1, AvrMla6)


title: genotype: m508  - time: 24 - Treated or untreated: Inoculated  - rep2


title: East Asian 32


title: genotype: m508  - time: 20 - Treated or untreated: Non-inoculated - rep1

source_name: (genotype: m508  - time: 20 - Treated or untreated: Non-inoculated)


title: M#14 D0 Mo LIDnr 6929

description: M#14 D0 Mo LIDnr 6929


title: M#13 GM-CSF D6 macrophages LIDnr 6927

description: M#13 GM-CSF D6 macrophages LIDnr 6927


title: East Asian 23

source_name: Lung adenocarcinoma, East Asian


title: genotype: m508  - time: 20 - Treated or untreated: Inoculated  - rep1

source_name: (genotype: m508  - time: 20 - Treated or untreated: Inoculated )


title: M#13 M-CSF D6 macrophages LIDnr 6927

description: M#13 M-CSF D6 macrophages LIDnr 6927

source_name: Monocyte


title: genotype: m508  - time: 20 - Treated or untreated: Inoculated  - rep3


title: genotype: m508  - time: 20 - Treated or untreated: Inoculated  - rep2


title: M#13 GM-CSF/LPS/IFN D6 macrophages LIDnr 6927

value: GM-CSF/LPS/IFN D6


title: East Asian 26


title: genotype: m508  - time: 20 - Treated or untreated: Non-inoculated - rep3


title: genotype: m508  - time: 16 - Treated or untreated: Non-inoculated - rep3

source_name: (genotype: m508  - time: 16 - Treated or untreated: Non-inoculated)


title: genotype: m508  - time: 20 - Treated or untreated: Non-inoculated - rep2


title: genotype: m508  - time: 16 - Treated or untreated: Inoculated  - rep3

source_name: (genotype: m508  - time: 16 - Treated or untreated: Inoculated )


title: East Asian 21


title: East Asian 22


title: East Asian 25


title: Input DNA_2

city: Gothenburg

first: Claes

middle: M

last: Gustafsson

address: Medcinaregatan 9A

department: Department of Medical biochemistry and cell biology

country: Sweden

institute: Gothenburg University

description: TAP-med8 Chip repeat2

hyb_protocol: Hybridization was performed as affymetrix protocol. Samples were hybridized for 16 hr at 42C in a hybridization oven (GeneChip Hybridization Oven 640, Affymetrix)

scan_protocol: The washing and scanning protocol, provided by Affymetrix, was performed automatically on a fluidics station (GeneChip fluidics station 450, Affymetrix)

data_processing: We used affymetrix tiling array software (TAS) V1.1 to analyze our data. The raw cel data were imported into TAS as two analysis treatment group -- our IP  sample and genomic background control. We use two side test, bandwidth i 150 . Probe match chosen was PM/MM(perfect match/mismatch). Finally, we analyzed the intensity to get the Bar or CHP format signal files.

label: Biotin

organism: Saccharomyces cerevisiae

source_name: input DNA

label_protocol: DNA was labeled with biotin-N6-dATP using terminal transferase TdT (Roche, 400U/ul)

growth_protocol: Cells in YP + 2% glucose were collected in log phase

extract_protocol: Extraction was performed as previously described (zhu et al. 2006).  For TAP-med8, we used IgG beads from GE healthcare as the normal ChIP-chip study.

tag: antibody


title: M#13 D0 Mo LIDnr 6927

description: M#13 D0 Mo LIDnr 6927


title: genotype: m508  - time: 16 - Treated or untreated: Inoculated  - rep2


title: M#26 D0 Mo LIDnr 6978

description: M#26 D0 Mo LIDnr 6978


title: Input DNA_1

description: TAP-med8 Chip repeat1


title: genotype: m508  - time: 8 - Treated or untreated: Non-inoculated - rep2

source_name: (genotype: m508  - time: 8 - Treated or untreated: Non-inoculated)


title: M#19 GM-CSF D6 macrophages LIDnr 6967

description: M#19 GM-CSF D6 macrophages LIDnr 6967


title: genotype: m508  - time: 8 - Treated or untreated: Non-inoculated - rep1


title: genotype: m508  - time: 16 - Treated or untreated: Inoculated  - rep1


title: genotype: m508  - time: 8 - Treated or untreated: Inoculated  - rep3

source_name: (genotype: m508  - time: 8 - Treated or untreated: Inoculated )


title: East Asian 18


title: TAP_med8_1

description: TAP-med8 Chip repeat1

source_name: Med8 ChIP DNA


title: M#19 D0 Mo LIDnr 6967

description: M#19 D0 Mo LIDnr 6967


title: genotype: m508  - time: 16 - Treated or untreated: Non-inoculated - rep2


title: genotype: m508  - time: 8 - Treated or untreated: Non-inoculated - rep3


title: Dec#38 Decidual macrophages (macrophages)  LIDnr 7044

source_name: Macrophages

treatment_protocol: Decidual macrophages

value: Decidual macrophages

value: Decidua


title: East Asian 20


title: TAP_med8_2

description: TAP-med8 Chip repeat2


title: M#30 M-CSF D6 macrophages LIDnr 6996

description: M#30 M-CSF D6 macrophages LIDnr 6996


title: genotype: m508  - time: 8 - Treated or untreated: Inoculated  - rep1

value: leaves


title: M#30 GM-CSF/LPS/IFN D6 macrophages LIDnr 6996


title: genotype: m508  - time: 8 - Treated or untreated: Inoculated  - rep2


title: genotype: m508  - time: 0 - Treated or untreated: Non-inoculated - rep2

source_name: (genotype: m508  - time: 0 - Treated or untreated: Non-inoculated)


title: CGH_TO_2655b_1056h_18L

city: San Francisco

first: David

last: Quigley

state: CA

address: 1450 Third St. Room 207

department: Helen Diller Comprehensive Cancer Center

institute: UCSF

hyb_protocol: The test and reference DNAs were hybridized to the BAC arrays for ~48 hrs at 37C. After post-hybridization washes, the arrays were mounted in a solution containing 90% glycerol, 10% PBS and 1 uM DAPI and sealed with a cover slip.

scan_protocol: A custom built CCD camera system was used to acquire 16 bit 1024x1024 pixel DAPI, Cy3 and Cy5 images (Pinkel et al., 1998). Image analysis was carried out using UCSF SPOT software (Jain et al., 2002).

data_processing: Images were segmented and quantified using custom software.  Data were normalized to the median log2 ratio of Cy3/Cy5.  All clones except those mapping to chromosome six, known to be frequently altered in KrasLA2 lung tumors, were used for normalization.  The mean and standard deviation (s.d.) of the normalized log2 ratios of the quadruplicate spots were calculated.  Clones were declared missing if their ratio was based only on a single spot or their s.d. exceeded 0.2.

organism: Mus musculus

source_name: Lung tumor from KrasLA2 mouse

label_protocol: We labeled 1 μg of test (tumor) DNA and reference genomic DNA (normal lung) with CY3 and CY5 (Amersham), respectively.

growth_protocol: Mice were fed standard chow and allowed water ad libitum. Mice were sacrificed at 6 months of age.

extract_protocol: Genomic DNA was extracted using the Dneasy Tissue kit (Qiagen) and further purified by phenol/choroform extraction.

tag: strain

value: FVB/N

value: Lung tumor

source_name: Normal lung from KrasLA2 mouse

value: Normal lung


title: CGH_TO_2655a_1056h_18R


title: M#29 D0 Mo LIDnr 6995

description: M#29 D0 Mo LIDnr 6995


title: genotype: m508  - time: 0 - Treated or untreated: Non-inoculated - rep3


title: CGH_TO_2655c_1056h_22R


title: East Asian 16

value: Lung adenocarcinoma


title: genotype: m508  - time: 0 - Treated or untreated: Non-inoculated - rep1


title: genotype: m508  - time: 16 - Treated or untreated: Non-inoculated - rep1


title: genotype: m508  - time: 0 - Treated or untreated: Inoculated  - rep2

source_name: (genotype: m508  - time: 0 - Treated or untreated: Inoculated )


title: genotype: m508  - time: 0 - Treated or untreated: Inoculated  - rep3


title: genotype: m508  - time: 0 - Treated or untreated: Inoculated  - rep1


title: genotype: Mla1 - time: 32 - Treated or untreated: Non-inoculated - rep3

source_name: (genotype: Mla1 - time: 32 - Treated or untreated: Non-inoculated)


title: East Asian 14


title: M#24 GM-CSF D6 macrophages LIDnr 6976

description: M#24 GM-CSF D6 macrophages LIDnr 6976


title: genotype: Mla1 - time: 32 - Treated or untreated: Non-inoculated - rep2


title: CGH_TO_2629b_1056f_72L


title: genotype: Mla1 - time: 32 - Treated or untreated: Inoculated  - rep3

source_name: (genotype: Mla1 - time: 32 - Treated or untreated: Inoculated )


title: genotype: Mla1 - time: 32 - Treated or untreated: Non-inoculated - rep1


title: genotype: Mla1 - time: 32 - Treated or untreated: Inoculated  - rep2


title: CGH_TO_2052b_1056j_6L


title: M#25 D0 Mo LIDnr 6977

description: M#25 D0 Mo LIDnr 6977

value: D0 Mo


title: Dec#39 Decidual macrophages (macrophages)  LIDnr 7045


title: East Asian 12


title: genotype: Mla1 - time: 24 - Treated or untreated: Non-inoculated - rep2

source_name: (genotype: Mla1 - time: 24 - Treated or untreated: Non-inoculated)


title: CGH_TO_2698d_1056n_44L


title: genotype: Mla1 - time: 32 - Treated or untreated: Inoculated  - rep1


title: CGH_TO_2698a_1056h_20L


title: M#23 D0 Mo LIDnr 6974

description: M#23 D0 Mo LIDnr 6974


title: East Asian 9

source_name: Lung adenocarcinoma, East Asian


title: genotype: Mla1 - time: 24 - Treated or untreated: Non-inoculated - rep3


title: East Asian 17


title: East Asian 11


title: CGH_TO_2167m1_1056b_28L


title: CGH_TO_2413e_1056h_80R


title: CGH_TO_2797c_1056n_42L


title: East Asian 13


title: Dec#39 Blood monocytes (Mo) LIDnr 7045

description: Dec#39 Blood monocytes (Mo) LIDnr 7045

treatment_protocol: Blood monocytes

value: Blood monocytes


title: CGH_TO_2319a1_1056_31Rr


title: Dec#38 Blood monocytes (Mo) LIDnr 7044

description: Dec#38 Blood monocytes (Mo) LIDnr 7044


title: CGH_TO_2464f1_1056_36Lr


title: genotype: Mla1 - time: 24 - Treated or untreated: Inoculated  - rep3

source_name: (genotype: Mla1 - time: 24 - Treated or untreated: Inoculated )


title: Dec#37 Blood monocytes (Mo) LIDnr 7032

description: Dec#37 Blood monocytes (Mo) LIDnr 7032

source_name: Monocyte


title: Dec#37 Decidual macrophages (macrophages)  LIDnr 7032


title: M#31 GM-CSF + M-CSF D6 macrophages LIDnr 6997

treatment_protocol: GM-CSF + M-CSF D6

value: GM-CSF + M-CSF


title: CGH_TO_2768a_1056J_15R


title: East Asian 8


title: CGH_TO_2647a_1056h_29R


title: genotype: Mla1 - time: 20 - Treated or untreated: Non-inoculated - rep2

source_name: (genotype: Mla1 - time: 20 - Treated or untreated: Non-inoculated)


title: M#30 GM-CSF + M-CSF +IL-10 D6 macrophages LIDnr 6996

treatment_protocol: GM-CSF + M-CSF +IL-10 D6

value: GM-CSF + M-CSF +IL-10


title: genotype: Mla1 - time: 24 - Treated or untreated: Non-inoculated - rep1


title: genotype: Mla1 - time: 20 - Treated or untreated: Non-inoculated - rep1


title: East Asian 10

treatment_protocol: Only tissue samples with tumor cells >50% were selected.


title: genotype: Mla1 - time: 16 - Treated or untreated: Non-inoculated - rep2

source_name: (genotype: Mla1 - time: 16 - Treated or untreated: Non-inoculated)


title: genotype: Mla1 - time: 16 - Treated or untreated: Inoculated  - rep2

source_name: (genotype: Mla1 - time: 16 - Treated or untreated: Inoculated )


title: genotype: Mla1 - time: 20 - Treated or untreated: Inoculated  - rep1

source_name: (genotype: Mla1 - time: 20 - Treated or untreated: Inoculated )


title: genotype: Mla1 - time: 20 - Treated or untreated: Inoculated  - rep3


title: East Asian 6


title: genotype: Mla1 - time: 24 - Treated or untreated: Inoculated  - rep2


title: genotype: Mla1 - time: 16 - Treated or untreated: Non-inoculated - rep3


title: M#30 GM-CSF + M-CSF D6 macrophages LIDnr 6996

value: M-CSF + M-CSF


title: genotype: Mla1 - time: 24 - Treated or untreated: Inoculated  - rep1


title: CGH_TO_2672b_1056J_16R


title: genotype: Mla1 - time: 16 - Treated or untreated: Inoculated  - rep1


title: genotype: Mla1 - time: 20 - Treated or untreated: Inoculated  - rep2


title: CGH_TO_2050a_1056j_5L


title: genotype: Mla1 - time: 20 - Treated or untreated: Non-inoculated - rep3


title: M#28 D0 Mo LIDnr 6985

description: M#28 D0 Mo LIDnr 6985


title: M#22 D0 Mo LIDnr 6973

description: M#22 D0 Mo LIDnr 6973


title: genotype: Mla1 - time: 16 - Treated or untreated: Non-inoculated - rep1


title: genotype: Mla1 - time: 16 - Treated or untreated: Inoculated  - rep3


title: genotype: Mla1 - time: 8 - Treated or untreated: Non-inoculated - rep3

source_name: (genotype: Mla1 - time: 8 - Treated or untreated: Non-inoculated)


title: CGH_TO_2899b_1056n_46L


title: genotype: Mla1 - time: 8 - Treated or untreated: Non-inoculated - rep2


title: East Asian 7


title: M#21 D0 Mo LIDnr 6970

description: M#21 D0 Mo LIDnr 6970


title: CGH_TO_2773a_1056J_17R


title: CGH_TO_2645a_1056h_30R


title: East Asian 3


title: CGH_TO_2335f1_1056j_12L


title: M#24 GM-CSF + IL-10 D6 macrophages LIDnr 6976

value: GM-CSF + IL-10


title: M#24 GM-CSF + IL4/13 D6 macrophages LIDnr 6976

value: GM-CSF + IL4/13


title: CGH_TO_2920a_1056n_48L


title: CGH_TO_2598a_1056h_21R


title: genotype: Mla1 - time: 0 - Treated or untreated: Non-inoculated - rep3

source_name: (genotype: Mla1 - time: 0 - Treated or untreated: Non-inoculated)

value: Non-inoculated


title: genotype: Mla1 - time: 8 - Treated or untreated: Inoculated  - rep2

source_name: (genotype: Mla1 - time: 8 - Treated or untreated: Inoculated )

value: Blumeria graminis f. sp. hordei (Bgh) isolates 5874 (AvrMla1, AvrMla6)


title: M#24 GM-CSF + P D6 macrophages LIDnr  6976

value: GM-CSF + P


title: CGH_TO_2340a1_1056h_42Lr


title: genotype: Mla1 - time: 8 - Treated or untreated: Inoculated  - rep3


title: genotype: Mla1 - time: 0 - Treated or untreated: Non-inoculated - rep2


title: genotype: Mla1 - time: 0 - Treated or untreated: Inoculated  - rep1

source_name: (genotype: Mla1 - time: 0 - Treated or untreated: Inoculated )


title: M#24 GM-CSF + E D6 macrophages LIDnr 6976

value: GM-CSF + E


title: CGH_TO_2672a_1056J_15L

source_name: Lung tumor from KrasLA2 mouse


title: genotype: Mla1 - time: 8 - Treated or untreated: Non-inoculated - rep1


title: CGH_TO_2413a_1056f_71R

source_name: Normal lung from KrasLA2 mouse


title: species: Rice - rep2

description: gro: 0005118##GRO:0005306## (Organism Part); GRO:0007060 (Development Stage); 7 days (Age);

organism: Oryza sativa

growth_protocol: Growth Description:  Seedlings were grown in the greenhouse for 7 days.

tag: age

value: seedling


title: genotype: Mla1 - time: 8 - Treated or untreated: Inoculated  - rep1

value: leaves


title: M#24 GM-CSF/LPS/IFN D6 macrophages LIDnr 6976

value: GM-CSF/LPS/IFN


title: M#30 GM-CSF D6 macrophages LIDnr 6996

description: M#30 GM-CSF D6 macrophages LIDnr 6996

value: GM-CSF


title: species: Rice - rep1

growth_protocol: Growth Description:  We grew seedlings in the greenhouse for 7 days.


title: genotype: Mla1 - time: 0 - Treated or untreated: Non-inoculated - rep1


title: species: Corn - rep2

organism: Zea mays


title: CGH_TO_2340e1_1056_92R

value: FVB/N

value: Lung tumor

value: Normal lung


title: genotype: Mla1 - time: 0 - Treated or untreated: Inoculated  - rep3


title: M#23 GM-CSF + E/P/IL-10/4/13 D6 macrophages LIDnr 6974


title: genotype: Mla1 - time: 0 - Treated or untreated: Inoculated  - rep2


title: M#24 D0 Mo LIDnr 6976

description: M#24 D0 Mo LIDnr 6976

value: D0 Mo


title: M#23 GM-CSF + IL4/13 D6 macrophages LIDnr 6974


title: CGH_TO_2413d_1056f_72Rb


title: species: Corn - rep1


title: CGH_TO_2593a_1056f_73L


title: M#30 D0 Mo LIDnr 6996

description: M#30 D0 Mo LIDnr 6996


title: M#29 GM-CSF + M-CSF +IL-10 D6 macrophages LIDnr 6995

value: GM-CSF + M-CSF


title: species: Oat - rep2

organism: Avena sativa


title: species: Wheat - rep2

organism: Triticum aestivum


title: M#29 GM-CSF + M-CSF D6 macrophages LIDnr 6995


title: CGH_TO_2643b_1056h_27L


title: species: Oat - rep1


title: CGH_TO_2672c_1056J_16L


title: species: Sorghum - rep2

organism: Sorghum bicolor

source_name: 8##GRO:0005306## (species: Sorghum)


title: species: Sorghum - rep1


title: species: Barley - rep2

source_name: 8##GRO:0005306## (species: Barley)


title: species: Barley - rep1

growth_protocol: Growth Description:   Seedlings were grown in the greenhouse for 7 days.


title: species: Wheat - rep1


title: E2A CLP LY6D-, biological rep4

city: La Jolla

first: Eva

last: Welinder

address: 9500 Gilman Drive

institute: UCSD

description: Gene expression data from FACS sorted LY6D- CLP cells (LIN-FLT3+CD127+)

hyb_protocol: Following fragmentation, 10 microg of cRNA was hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Chips were scanned using an Affymetrix GeneChip Scanner 3000. Chip target intensity was arbitrarily scaled to 100 before rendering CHP file

data_processing: Expression values were calculated by RMA express (http://rmaexpress.bmbolstad.com/) using background adjustment and quantile normalization.

source_name: Murine bone marrow from C57bl/6 mice

label_protocol: Biotinylated cRNA was prepared according to the standard AffymetrixTM; Small Sample Labelling Protocol v.2, with the exception that the second round of in vitro transcription (IVT) was performed using AffymetrixTM GeneChipTM Expression 3íamplification kit.

extract_protocol: Cells (LIN-FLT3+CD127+LY6D- bone marrow) were directly sorted into buffer RLT and RNA prepared using RNeasy Micro (Qiagen) according to manufacturer's instructions.

value: bone marrow

value: 10-13 weeks old


title: M#29 GM-CSF D6 macrophages LIDnr 6995

description: M#29 GM-CSF D6 macrophages LIDnr 6995


title: M#23 GM-CSF + IL-10 D6 macrophages LIDnr 6974

value: GM-CSF + IL-10


title: CGH_TO_2902b_1056n_45R


title: CGH_TO_2593b_1056f_74R


title: CGH_TO_2655d_1056h_22L


title: M#29 GM-CSF/LPS/IFN D6 macrophages LIDnr 6995


title: CGH_TO_2043Lc1_1056b_27R


title: CGH_TO_2899a_1056n_46R


title: M#23 GM-CSF + P D6 macrophages LIDnr  6974


title: CGH_TO_2599a_1056h_45L


title: M#23 GM-CSF + E D6 macrophages LIDnr 6974


title: E2A CLP LY6D-, biological rep2

value: FACS sorted LY6D- CLP cells (LIN-FLT3+CD127+)


title: CGH_TO_2043m1_1056b_26R


title: CGH_TO_2321e1_1056_91L


title: M#23 GM-CSF/LPS/IFN D6 macrophages LIDnr 6974


title: M#29 M-CSF D6 macrophages LIDnr 6995

description: M#29 M-CSF D6 macrophages LIDnr 6995

value: M-CSF


title: CGH_TO_2413b_1056j_13L


title: M#25 M-CSF + E/P/IL-10/4/13 D6 macrophages LIDnr 6977


title: M#25 M-CSF + IL4/13 D6 macrophages LIDnr 6977

treatment_protocol: M-CSF + IL4/13 D6

value: M-CSF + IL4/13


title: HEB CLP LY6D-, biological rep2

value: HEB-KO


title: E2A CLP LY6D-, biological rep3


title: E2A CLP LY6D-, biological rep1


title: WT CLP LY6D-, biological rep1

value: Wild type


title: M#25 M-CSF + IL-10 D6 macrophages LIDnr 6977

treatment_protocol: M-CSF + IL-10 D6

value: M-CSF + IL-10


title: HEB CLP LY6D-, biological rep1


title: M#25 M-CSF + P D6 macrophages LIDnr 6977

value: M-CSF + P


title: WT CLP LY6D-, biological rep2


title: M#25 M-CSF + E D6 macrophages LIDnr 6977

treatment_protocol: M-CSF + E D6

value: M-CSF + E


title: CGH_TO_2257a_1056_89R


title: CGH_TO_2768b_1056n_41R


title: CGH_TO_2899d_1056n_47R


title: FJ001_ko3_2

city: Utrecht

first: Marian

last: Groot Koerkamp

state: Utrecht

address: Heidelberglaan 25

department: Research

country: Netherlands

institute: Princess Maxima Center for Pediatric Oncology

hyb_protocol: Tecan HS4800 hybridization

scan_protocol: scanning of slides using Agilent G256BA Imagene feature extraction

data_processing: genes, no bg corr

label_protocol: robot amplification and labeling v1.0

extract_protocol: RNA extraction cellLine


title: FJ001_ko3_1


title: M#25 M-CSF D6 macrophages LIDnr 6977

description: M#25 M-CSF D6 macrophages LIDnr 6977

treatment_protocol: M-CSF D6


title: CGH_TO_2647b_1056h_29L


title: FJ001_ko1_2


title: CGH_TO_2321b_1056_90L


title: FJ001_ko2_2


title: 0-19

city: Lund

first: Rolf

last: Søkilde

address: Scheelevägen 2

department: Department of Oncology

institute: Lund University, Sweden

hyb_protocol: The Hy3-labelled samples were hybridized to miRCURY LNA arrays (v11.0) (Exiqon, Denmark), containing capture probes targeting all human miRNAs registered in the miRBASE version 15.0 at the Sanger Institute. The hybridization was performed overnight at 56°C according to manufacturer specifications using a Tecan HS4800 hybridization station (Tecan, Austria). Since it was not possible to hybridize all arrays in one go, samples were randomly split into 5 batches as to minimize day to day variation in the hybridization process.

scan_protocol: After hybridization the microarray slides were scanned using an Agilent G2565BA Microarray Scanner System (Agilent Technologies, Inc., USA) at 5µm resolution, and the resulting TIFF images were analyzed using the ImaGene 8.0 software on standard settings (BioDiscovery, Inc., USA).

data_processing: Probe signals were background corrected by fitting a convolution of normal and exponential distributions to the foreground intensities using the background intensities as a covariate 4. Four technical replicate spots for each probe were combined to produce one signal by taking the logarithmic base-2 mean of reliable spots. If all four replicates for a given probe were judged unreliable that probe was removed from further analysis. A reference data vector R was calculated as the median signal of each probe across all samples. For all probe signals in a given sample, represented by the sample data vector S, a curve F was determined by locally weighted polynomial regression so as to provide the best fit between S and R. A normalized sample vector M was calculated from this by transforming it with the function F, so that M = F(S). In this manner, all samples were normalized to the reference R. This normalization procedure largely follows that outlined in Rosenfeld et al., 2008. Remote data points (probes in sparsely sampled intensity regions with less than 15 probes per signal unit) were considered unreliably adjusted by this method and removed before further analysis.

source_name: human skin

label_protocol: From each sample 100 ng of total RNA was labeled with Hy3 fluorescent dye using the miRCURY LNA Array power labeling kit (Exiqon, Denmark). All samples were labeled the same day with the same master mix, in order to minimize technical variation.

extract_protocol: Total RNA was isolated from six 10 µm tissue sections using the RecoverAll Total Nucleic Acid Isolation Kit (Applied Biosystems/Ambion, USA) according to manufacturer guidelines. Total RNA quantity and quality were checked by spectrophotometer (Nanodrop ND-1000).

tag: malign

value: skin

tag: diagnosis

value: AD


title: 0-20


title: FJ001_ko2_1


title: M#20 M-CSF + E/P/IL-10/4/13 D6 macrophages LIDnr 6969


title: Megakaryopoietic M_3

city: Bethesda

first: Jennifer

last: Barb

state: MD

address: 12 South Drive Bldg 12A Room 2001

department: DCB

institute: NIH

description:
differentiated CD34+ cells
lineage-specific differentiation, was induced using growth factors for erythropoietic differentiation, SCF (50 ng/ml), Flt3-ligand (50 ng/ml), IL-3 (10 ng/ml), EPO (10 U/ml); for granulopoietic differentiation, SCF (50 ng/ml), Flt3-ligand (50 ng/ml), IL-3 (10 ng/ml), G-CSF, and GM-CSF (each, 10 ng/ml); for megakaryopoietic differentiation, SCF (50 ng/ml), Flt3-ligand (50 ng/ml), TPO (20 ng/ml).

hyb_protocol: Labeled and Fragmented ST cDNA was hybridized to Human Exon 1.0St arrays for 16 hours at 45C in an hybridization oven. Hybridized probes were detected by Streptavidin-Phycoerythrin stain

scan_protocol: Stained chips were scanned in Affymetrix GCS 3000G scanner

data_processing: RMA

source_name: Megakaryopoietic M_3

label_protocol: Target labeling of RNA for Human exon arrays was done using the Affymetrix/Ambion WT cDNA synthsis and labeling protocol

growth_protocol: CD34+ PBCs were cultured in X-VIVO10  supplemented with 1% human serum albumin (HSA).  At least 1 x 106 CD34+ cells were assayed in 6-well plates and incubated at 37°C and 5% CO2 in a fully humidified atmosphere in air.

extract_protocol: RNA extraction was performed using the RNEasy plus kit following qigen's protocol

treatment_protocol: To induce lineage-specific differentiation, growth factors (R&D Systems, Wiesbaden-Nor-denstadt, Germany, were added as follows: for erythropoietic differentiation, SCF (50 ng/ml), Flt3-ligand (50 ng/ml), IL-3 (10 ng/ml), EPO (10 U/ml); for granulopoietic differentiation, SCF (50 ng/ml), Flt3-ligand (50 ng/ml), IL-3 (10 ng/ml), G-CSF, and GM-CSF (each, 10 ng/ml); for megakaryopoietic differentiation, SCF (50 ng/ml), Flt3-ligand (50 ng/ml), TPO (20 ng/ml)

value: Megakaryopoietic


title: M#25 GM-CSF/LPS/IFN D6 macrophages LIDnr 6977

treatment_protocol: GM-CSF/LPS/IFN D6

value: GM-CSF/LPS/IFN


title: Megakaryopoietic M_2

source_name: Megakaryopoietic M_2


title: M#20 M-CSF + IL4/13 D6 macrophages LIDnr 6969

source_name: Monocyte


title: Megakaryopoietic M_1

source_name: Megakaryopoietic M_1


title: 0-18


title: CGH_TO_2043m2_1056e_26L

value: FVB/N

value: Lung tumor

value: Normal lung


title: CGH_TO_2599b_1056j_14L


title: CGH_TO_2335e_1056j_14R


title: M#20 M-CSF + IL-10 D6 macrophages LIDnr 6969


title: 1-52

value: CTCL


title: Granulopoietic G_2

source_name: Granulopoietic G_2

value: Granulopoietic


title: Granulopoietic G_3

source_name: Granulopoietic G_3


title: 0-17


title: CGH_TO_2260b_1056_88R


title: Granulopoietic G_1

source_name: Granulopoietic G_1


title: 0-130

value: PP


title: 0-129


title: Erythropoietic E_3

source_name: Erythropoietic E_3

value: Erythropoietic


title: CGH_TO_2645d_1056h_31Lb


title: 0-128


title: CGH_TO_2643c_1056h_28R


title: CGH_TO_2629a_1056h_79L


title: CGH_TO_2899f_1056n_48R


title: Erythropoietic E_2

source_name: Erythropoietic E_2


title: FJ001_ko1_1


title: 0-127


title: 0-126


title: 0-77

value: PN


title: CGH_TO_2645b_1056h_30L


title: 0-76


title: CD34 3

description:
CD34+ cells
CD34+ PBCs were cultured in X-VIVO10 (BioWhittaker, Walkersville, MD) supplemented with 1% human serum albumin (HSA).


title: Erythropoietic E_1

source_name: Erythropoietic E_1


title: CGH_TO_2698b_1056h_20R


title: CGH_TO_2797b_1056n_42R


title: CGH_TO_2599f_1056n_43L


title: 0-73


title: 0-75


title: 0-74


title: CGH_TO_2190m3_1056e_27L


title: CGH_TO_2643d_1056h_28L


title: Conspecific song vs control replicate 4

city: Uppsala

first: Göran

last: Arnqvist

address: Norbyvägen 18D

department: Ecology and Genetics

institute: Uppsala University

description:
Biological replicate 4 out of 4
Raw data file: mel_songVSno_song4.txt

hyb_protocol: Hybridisation to amino-modified long oligonucleotide microarrays using a Genomic Solutions hybridisation station with the Biosolutions

scan_protocol: Operating instructions for the Genepix 4000B dual laser scanner (http://www.flychip.org.uk/protocols/imaging/) Spot finding and quantitation via the Dapple package

data_processing: Subsetting raw data to include only transcripts enriched in head tissue (data from FLYATLAS:www.flyatlas.org). Normalization with loess (within array) and quantile (between arrays). Replicate probes averaged. Preprocessing steps performed with limma package (Bioconductor)

organism: Drosophila melanogaster

source_name: Control

label_protocol: Klenow Labelling: Between 3 to 5µg total RNA are reverse transcribed to cDNA [anchored oligo (dT)23 (Sigma), Superscript III

extract_protocol: Medium scale RNA extraction using TRIzol (http://www.flychip.org.uk/protocols/gene_expression/)

treatment_protocol: Females exposed to white-noise from load-speaker switched on for 15min

tag: gender

value: Female

value: Oregon-K

value: Head

tag: developmental stage

value: adult

value: 5d old

tag: mating status

value: virgin

source_name: D. melanogaster song stimulation

treatment_protocol: Females stimulated with synthetic D. melanogaster male song for 15min


title: CD34 2


title: CD34 1


title: 0-72

value: skin


title: 0-94


title: Conspecific vs heterospecific song replicate 3

description:
Biological replicate 3 out of 3
Raw data file: mel_songVSsim_song3.txt

source_name: D. simulans song stimulation

treatment_protocol: Females stimulated with synthetic D. simulans male song for 15min


title: CGH_TO_2768c_1056n_41L

source_name: Lung tumor from KrasLA2 mouse

source_name: Normal lung from KrasLA2 mouse


title: CGH_TO_2629d_1056f_81R


title: Conspecific song vs control replicate 3

description:
Biological replicate 3 out of 4
Raw data file: mel_songVSno_song3.txt


title: 0-93


title: Conspecific song vs control replicate 2

description:
Biological replicate 2 out of 4
Raw data file: mel_songVSno_song2.txt


title: Conspecific vs heterospecific song replicate 2

description:
Biological replicate 2 out of 3
Raw data file: mel_songVSsim_song2.txt


title: Conspecific vs heterospecific song replicate 1

description:
Biological replicate 1 out of 3
Raw data file: mel_songVSsim_song1.txt


title: 0-282

value: AD


title: Conspecific song vs control replicate 1

description:
Biological replicate 1 out of 4
Raw data file: mel_songVSno_song1.txt


title: CGH_TO_2598c_1056n_43R


title: HNPCC 8

city: Barcelona

first: Juanjo

last: Lozano

address: C/ Rosselló 153

department: Plataforma de Bioinformatica

country: Spain

institute: CIBEREHD

description:
Colorectal cancer  sample: HNPCC 8
HNPCC8

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with Bioconductor (v.2.4) Lumi R-package

source_name: human colon tissue

label_protocol: Biotinylated cDNA were prepared with the Illumina® TotalPrep™ RNA Amplification Kit (Ambion)

extract_protocol: Total RNA from formalin-fixed paraffin-embedded tissue blocks was isolated using the RecoverAll Total Nucleic Acid Isolation Kit (Ambion) according to manufacturer instructions.

tag: tissue type

value: colon

tag: disease state

value: Colorectal cancer

tag: group

value: Hereditary non-polyposis colon cancer

tag: mlh1/msh2/msh6 germline mutational analysis

value: no mutation

tag: microsatellite instability testing

value: MSI-H

value: Loss of MSH2/MSH6

tag: Sex

value: male

tag: tumor location

value: cecum

tag: race

value: Caucasian

tag: tumor stage

value: I


title: HNPCC 9

description:
Colorectal cancer  sample: HNPCC 9
HNPCC9

value: Loss of MLH1/PMS2

value: Philippine

value: II


title: HNPCC 6

description:
Colorectal cancer  sample: HNPCC 6
HNPCC6

value: ascending

value: III


title: 1-281

source_name: human skin

tag: tissue

value: skin

value: CTCL


title: CGH_TO_2645c_1056h_31R

tag: strain

value: FVB/N

value: Lung tumor

value: Normal lung


title: HNPCC 7

description:
Colorectal cancer  sample: HNPCC 7
HNPCC7

value: colon

value: Colorectal cancer

value: Hereditary non-polyposis colon cancer

value: no mutation

tag: age

value: female


title: 1-280

tag: malign


title: HNPCC 3

description:
Colorectal cancer  sample: HNPCC 3
HNPCC3

value: MSI-H

value: male

value: cecum

value: Caucasian


title: HNPCC 5

description:
Colorectal cancer  sample: HNPCC 5
HNPCC5

value: not done

value: Loss of MLH1

value: descending


title: 1-106

value: skin

tag: diagnosis


title: CGH_TO_2413c_1056h_79R


title: HNPCC 4

description:
Colorectal cancer  sample: HNPCC 4
HNPCC4

value: Loss of MLH1/PMS2

value: recto-sigmoid

value: I


title: CGH_TO_2900b_1056o_12L

value: FVB/N

value: Lung tumor

value: Normal lung


title: CGH_TO_2900a_1056o_6L


title: HNPCC 2

description:
Colorectal cancer  sample: HNPCC 2
HNPCC2

value: colon

value: Colorectal cancer

value: Hereditary non-polyposis colon cancer

value: Loss of MSH2/MSH6

value: tranverse

value: III


title: CGH_TO_2647d_1056_47L


title: 1-58

value: CTCL


title: CGH_TO_2647e_1056h_48R


title: 1-59


title: HNPCC 1

description:
Colorectal cancer  sample: HNPCC 1
HNPCC1

value: no mutation

value: MSI-H

value: male

value: cecum

value: Caucasian

value: II


title: 1-48

value: skin


title: CGH_TO_2899g_1056L_37L

value: FVB/N


title: 1-97


title: MSS 29

description:
Colorectal cancer  sample: MSS 29
MSS29

value: MSS tumor

value: not done

value: MSS

value: Normal expression

value: female

value: sigmoid


title: 1-40


title: 1-30


title: CGH_TO_2629e_1056f_81L

value: Lung tumor

value: Normal lung


title: MSS 27

description:
Colorectal cancer  sample: MSS 27
MSS27

value: colon

value: Colorectal cancer

value: ascending


title: CGH_TO_2599d_1056h_49L


title: 1-29

value: CTCL


title: 1-22


title: MSS 25

description:
Colorectal cancer  sample: MSS 25
MSS25

value: male

value: Afroamerican


title: MSS 20

description:
Colorectal cancer  sample: MSS 20
MSS20

value: recto-sigmoid

value: Caucasian

value: II


title: MSS 23

description:
Colorectal cancer  sample: MSS 23
MSS23

value: MSS tumor

value: rectum

value: III


title: CGH_TO_2645f_1056h_48L

value: FVB/N


title: MSS 21

description:
Colorectal cancer  sample: MSS 21
MSS21

value: not done

value: MSS

value: Normal expression


title: 0-16

value: skin

value: AD


title: MSS 18

description:
Colorectal cancer  sample: MSS 18
MSS18

value: colon

value: Colorectal cancer

value: female

value: sigmoid

value: unknown


title: liver-mets-rep1

city: Miami

last: Clarke

state: FL

address: 1120 NW 14th Street

department: Epidemiology and Public Health

institute: University of Miami

description: Metastatic liver xenografts of MDA-MB-231 cells were harvested by gross surgical dissection ~50 days following implantation into the abdominal mammary fat pads of eight week old female NOD scid gamma mice (The Jackson Laboratory). Mice were injected unilaterally with 2.5 x 106 cells in 200 μL of 50:50 Matrigel/Collagen I into the fourth abdominal fat pad by subcutaneous injection at the base of the nipple. Tumor growth was monitored externally using vernier calipers for 50 days and animals sacrificed when tumors reached 10% of body weight. Necropsies were performed to identify liver macro-metastases.

hyb_protocol: Samples were prepared according to the manufacturer’s instructions and analyzed using HumanHT-12 v4 Expression BeadChips (Illumina, Inc.)

data_processing: Raw expression data from BeadStudio software was background corrected, normalized, and VST transformed using the lumi package v. 2.2.0 in Bioconductor. Probes with detection p-values < 0.05 in all three independent replicates were considered 'present' and included in further analyses.

source_name: MDA-MB-231 liver metatasis

extract_protocol: RNA was extracted from cultured MDA-MB-231 cells, MDA-MB-231 liver metastases and mouse liver using Trizol Reagent (Invitrogen) according to the manufacturer’s instructions. Concentration and yield of RNA samples were determined using a NanoDrop ND-1000 Spectrophotometer (NanoDrop Technologies). RNA integrity was determined by analysis on an Agilent 2100 Bioanalyzer (Agilent Technologies) following the manufacturer’s recommendations. Only samples with a RIN score >7.0 were used for microarray analysis.

value: MDA-MB-231 xenograft liver metastasis

value: 50 days


title: cultured-MDA-MB-231-rep2

description: MDA-MB-231 human breast carcinoma cell line was obtained from the American Type Culture Collection (ATCC) and maintained according to the supplier’s instructions. RNA was isolated from three independent cultures of sub-confluent MDA-MB-231 cells in the exponential phase of growth

scan_protocol: Samples were prepared according to the manufacturer’s instructions and analyzed using HumanHT-12 v4 Expression BeadChips (Illumina, Inc.)

value: MDA-MB-231 cell line grown in vitro


title: 0-15


title: liver-mets-rep3

label_protocol: Samples were prepared according to the manufacturer’s instructions and analyzed using HumanHT-12 v4 Expression BeadChips (Illumina, Inc.)


title: cultured-MDA-MB-231-rep3


title: CGH_TO_2655e_1056h_47R

value: Lung tumor

value: Normal lung


title: CGH_TO_2645e_1056j_12R


title: 0-14


title: MSS 19

description:
Colorectal cancer  sample: MSS 19
MSS19

value: MSS tumor

value: male

value: Philippine

value: I


title: cultured-MDA-MB-231-rep1


title: CGH_TO_2900c_1056o_10L

value: FVB/N


title: CGH_TO_2599c_1056h_50R


title: 0-13

value: skin


title: 1-110

value: CTCL


title: 0-125

value: PP


title: mouseliver-normal-rep1

source_name: mouse liver

value: mouse liver

value: eight weeks

tag: gender

value: NOD scid gamma (The Jackson Laboratory)


title: liver-mets-rep2


title: mouseliver-normal-rep2

value: female


title: mouseliver-normal-rep3


title: MSS 13

description:
Colorectal cancer  sample: MSS 13
MSS13

value: colon

value: Colorectal cancer

value: not done

value: MSS

value: Normal expression

value: unknown

value: Caucasian

value: III


title: 0-122


title: CGH_TO_2599g_1056h_50L

value: Lung tumor

value: Normal lung


title: MSS 16

description:
Colorectal cancer  sample: MSS 16
MSS16

value: MSS tumor

value: II


title: MSS 15

description:
Colorectal cancer  sample: MSS 15
MSS15

value: male

value: ascending

value: Hispanic


title: CGH_TO_2916b_1056o_3R

value: FVB/N


title: CGH_TO_2598b_1056h_21L


title: CGH_TO_2655f_1056h_19L


title: MSS 14

description:
Colorectal cancer  sample: MSS 14
MSS14

value: female


title: MSS 11

description:
Colorectal cancer  sample: MSS 11
MSS11

value: colon

value: I


title: Estrogen (6 h) + Velcade J2

city: Goettingen

first: Frank

last: Kramer

address: Humboldtallee 32

department: Department of Medical Statistics

institute: University Medical Center Göttingen

hyb_protocol: Illumina Whole-Genome Gene Expression Direct Hybridization Assay Guide (11286331)

scan_protocol: Illumina iScan Scanner

data_processing: log2 transformation of signal intensity, quantile normalization, R/Bioconductor, BeadStudio

label_protocol: Illumina TotalPrep RNA Amplification Kit (Ambion, Inc., Cat # IL1791); 200ng total RNA input

growth_protocol: Cells were grown in phenol-red free DMEM containing 5% charcoal-dextran treated FBS for 48 hours prior to treatment with Bortezomib or estrogen.

extract_protocol: Total RNA was extracted using Qiazol (Qiagen) according to the manufacturer's instructions.

treatment_protocol: Where indicated, cells were pretreated with 50 nM Bortezomib for 15 minutes followed by 10 nM 17-  -estradiol for 6 hours.

tag: cell line

tag: treatment

value: estrogen (6h) + velcade stimulated


title: CGH_TO_2918a_1056n_49L


title: CGH_TO_2167m5_1056b_29L


title: 0-121

value: skin

value: PP


title: MSS 10

description:
Colorectal cancer  sample: MSS 10
MSS10

tag: tissue type

value: Colorectal cancer

value: not done

value: MSS

value: Normal expression

value: sigmoid


title: Velcade I3

value: velcade stimulated


title: Estrogen (6 h) + Velcade J1


title: 0-123


title: Velcade I1


title: Estrogen (6 h) + Velcade J3


title: 0-120


title: CGH_TO_2167m3_1056b_29R

value: Lung tumor

value: Normal lung


title: MSS 9

description:
Colorectal cancer  sample: MSS 9
MSS9

tag: disease state

value: MSS tumor

value: male

value: ascending

value: IV


title: Velcade I2


title: MSS 7

description:
Colorectal cancer  sample: MSS 7
MSS7

value: colon

tag: group

value: female

value: Caucasian

value: III


title: 0-71

value: skin

value: PN


title: MSS 5

description:
Colorectal cancer  sample: MSS 5
MSS5

value: Colorectal cancer

tag: mlh1/msh2/msh6 germline mutational analysis

value: not done

value: II


title: MSS 6

description:
Colorectal cancer  sample: MSS 6
MSS6

tag: microsatellite instability testing

value: MSS

value: Normal expression


title: CGH_TO_2645g_1056h_49R

value: FVB/N

value: Lung tumor


title: 0-70

value: PP


title: 0-68


title: 0-69


title: Lung tissue from human TGFβ1-BAC TG mouse treated with vehicle

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

country: Japan

institute: Toray Industries,Inc.

description:
Lung sample was taken on week 4 of the experimental protocol
hTGFβ1-BAC TG/vehicle

hyb_protocol: Hybridized for 16h at 37C with rotary shake (250rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: ScanArray Express (PerkinElmer Japan Co., Ltd.) was used for scanning. Images were quantified using GenePix Pro version 6.0(Axon Instruments).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals. Measurements of both duplicate spots with the signal intensities greater than 2 standard deviations (SD) of the background signal intensity were considered to be valid. A relative expression level of a given miRNA was calculated by comparing the signal intensities of the averaged valid spots with their mean value throughout the microarray experiments.

source_name: Human TGFβ1-BAC transgenic mouse treated intratracheally with human vehicle

label_protocol: Extracted total RNA was labeled with Hy5 using the miRCURY LNA Array miR labeling kit (Exiqon, Vedbaek, Denmark)

growth_protocol: Female 9-12 weeks old C57BL/6 wild type (WT) mice weighing 20-22g were used for evaluating the effect of siRNAs on lung fibrosis.  They were maintained in the animal house of Mie University. After 21 days all animals were sacrificed by intraperitoneal overdose of pentobarbital for sample collection.

extract_protocol: RNA samples were extracted from cells using miRNesy mini kit (Quiagen).

treatment_protocol: To determine which phase was optimal for inhibition of lung fibrosis, mice were treated with 5 mg/kg  TGFβ1 siRNA in the acute phase (days 3 and 7), in the chronic phase (days 12 and 16) or in both phases (days 3, 7, and 14) of the disease. The effect of a single dose of  TGFβ1 siRNA was also evaluated by treating the mice only on day 14 after initiating administration of BLM.

tag: strain background

tag: genotype/variation

value: human TGFβ1-BAC transgenic

value: 12 weeks

value: lung


title: Lung tissue from human TGFβ1-BAC TG mouse treated with TGFβ1 siRNA

description:
Lung sample was taken on week 4 of the experimental protocol
hTGFβ1-BAC TG/TGFβ1 siRNA

source_name: Human TGFβ1-BAC transgenic mouse treated intratracheally with human TGFβ1 siRNA


title: Estrogen H2

value: estrogen stimulated


title: Lung tissue from untreated wild type mouse

description:
Lung sample was taken on day 21 of the experimental protocol
Wild type mouse

source_name: Untreated wild type mouse (C57BL/6)

value: wild type

value: female


title: 0-67


title: MSS 3

description:
Colorectal cancer  sample: MSS 3
MSS3

value: colon

value: MSS tumor

tag: Sex

tag: tumor location

value: sigmoid

tag: race

value: Caucasian


title: 0-66

tag: tissue

value: skin


title: Lung tissue from mouse with lung fibrosis treated with TGFβ1 siRNA, days 3, 7, and 14

description:
Lung sample was taken on day 21 of the experimental protocol
BLM/TGFβ1 siRNA days 3+7+14

source_name: Mouse receiving bleomycin by subcutaneous infusion and TGFβ1 siRNA intratracheally on days 3, 7, and 14

tag: age

value: 9 weeks


title: MSI 27

description:
Colorectal cancer  sample: MSI 27
MSI27

value: Colorectal cancer

value: MSI tumor

value: not done

value: MSI-H

value: Loss of MLH1

value: ascending

tag: tumor stage

value: II


title: MSI 25

description:
Colorectal cancer  sample: MSI 25
MSI25

value: descending

value: III


title: MSI 24

description:
Colorectal cancer  sample: MSI 24
MSI24

value: cecum


title: Lung tissue from mouse receiving only subcutaneous saline

description:
Lung sample was taken on day 21 of the experimental protocol
SAL/vehicle

source_name: Mouse receiving only saline by subcutaneous infusion

value: wild type

value: female

value: lung


title: Estrogen H3

value: estrogen stimulated


title: 0-92

tag: malign

tag: diagnosis

value: PN


title: MSI 23

description:
Colorectal cancer  sample: MSI 23
MSI23

value: colon

value: tranverse

value: Caucasian

value: IV


title: Estrogen H1

tag: cell line


title: Cont G3

tag: treatment


title: Lung tissue from mouse with lung fibrosis treated with TGFβ1 siRNA, days 12 and 16

description:
Lung sample was taken on day 21 of the experimental protocol
BLM/TGFβ1 siRNA days 12+16

source_name: Mouse receiving bleomycin by subcutaneous infusion and TGFβ1 siRNA intratracheally on days 12 and 16

tag: gender

value: 9 weeks


title: Cont G2


title: 0-91

value: skin

value: PP


title: Cont G1


title: Lung tissue from mouse with lung fibrosis treated with TGFβ1 siRNA, day 14

description:
Lung sample was taken on day 21 of the experimental protocol
BLM/TGFβ1 siRNA days 14

source_name: Mouse receiving bleomycin by subcutaneous infusion and TGFβ1 siRNA intratracheally on day 14


title: Lung tissue from mouse with lung fibrosis treated with TGFβ1 siRNA, days 3 and 7

description:
Lung sample was taken on day 21 of the experimental protocol
BLM/TGFβ1 siRNA days 3+7

source_name: Mouse receiving bleomycin by subcutaneous infusion and TGFβ1 siRNA intratracheally on days 3 and 7


title: 1-290

value: CTCL


title: genotype: IRBB7 - time: 24 hai - rep1

description: cultivar irbb7 (germplasm name); po: 0009006 shoot, (Organism Part); PO:0007106 LP.03 three leaves visible (Development Stage); LC-1 Soil Mix (Growth Media).

source_name: shoot (genotype: IRBB7 - time: 24 hai)

growth_protocol: Growth Description:  Rice plants were grown for a total of 15 days in growth chambers under a 12-h light and a 12-h dark cycle. Fertilizer and iron chelate micronutrient were applied with watering every two days at rates of 0.25 and 4.5 g/l, respectively.  Environmental Conditions:  Growth chamber 28ºC day/light, 25ºC night/dark cycle; relative humidity: 80-90%

value: whole organism

tag: genotype

tag: time

value: 24 hai

tag: infection

value: Xanthomonas oryzae pv. oryzae


title: genotype: IRBB7 - time: 24 hai - rep3


title: genotype: IRBB7 - time: 24 hai - rep2


title: MSI 21

description:
Colorectal cancer  sample: MSI 21
MSI21

tag: tissue type

tag: disease state

value: Colorectal cancer

tag: group

value: MSI tumor

tag: mlh1/msh2/msh6 germline mutational analysis

value: not done

tag: microsatellite instability testing

value: MSI-H

value: Loss of MLH1

value: ascending

value: II


title: 1-289


title: genotype: IRBB7 - time: 12 hai - rep3

source_name: shoot (genotype: IRBB7 - time: 12 hai)

value: 12 hai


title: MSI 15

description:
Colorectal cancer  sample: MSI 15
MSI15

value: colon

tag: Sex

value: male

tag: tumor location

value: tranverse

tag: race

value: Caucasian

value: III


title: 1-105

tag: tissue

value: skin

value: CTCL


title: 1-104

tag: malign


title: genotype: IRBB7 - time: 12 hai - rep2

value: whole organism


title: Lung tissue from untreated mouse with lung fibrosis

description:
Lung sample was taken on day 21 of the experimental protocol
BLM/vehicle

source_name: Mouse receiving bleomycin by subcutaneous infusion and vehicle intratracheally

tag: strain background

tag: genotype/variation

value: wild type

value: female

tag: age

value: 9 weeks

value: lung


title: 1-96

tag: diagnosis


title: MSI 13

description:
Colorectal cancer  sample: MSI 13
MSI13

value: Colorectal cancer

value: MSI tumor

value: not done

value: MSI-H

value: sigmoid

tag: tumor stage


title: MSI 16

description:
Colorectal cancer  sample: MSI 16
MSI16

value: colon

value: Loss of MLH1

value: II


title: genotype: IRBB7 - time: 12 hai - rep1

tag: genotype

tag: time

value: 12 hai

value: Xanthomonas oryzae pv. oryzae


title: MSI 9

description:
Colorectal cancer  sample: MSI 9
MSI9

tag: tissue type

value: ascending

value: Caucasian


title: 1-57

value: skin

value: CTCL


title: genotype: IRBB7 - time: 6 hai - rep3

source_name: shoot (genotype: IRBB7 - time: 6 hai)

value: whole organism

value: 6 hai

tag: infection


title: genotype: IRBB7 - time: 6 hai - rep2


title: MSI 8

description:
Colorectal cancer  sample: MSI 8
MSI8

tag: disease state

tag: group

value: female

value: I


title: 1-56


title: MSI 5

description:
Colorectal cancer  sample: MSI 5
MSI5

value: Colorectal cancer

value: MSI tumor

tag: mlh1/msh2/msh6 germline mutational analysis

tag: microsatellite instability testing

value: III


title: MSI 2

description:
Colorectal cancer  sample: MSI 2
MSI2

value: not done

value: MSI-H

tag: Sex

tag: tumor location

value: sigmoid


title: genotype: Embrapa48 - time: 168 - Treated or untreated: Mock - rep2

description: at inoculation (Age); field soil (Growth Media).

organism: Glycine max

source_name: (genotype: Embrapa48 - time: 168 - Treated or untreated: Mock)

growth_protocol: Growth Description:  mix of natural soil from the field, cattle manure and sand (3:2:1)

extract_protocol: RNA Isolation Using Trizol And Qiagen RNAeasy Columns

tag: tissue

value: Mock


title: 1-47

tag: malign


title: genotype: Embrapa48 - time: 168 - Treated or untreated: Mock - rep3


title: MSI 1

description:
Colorectal cancer  sample: MSI 1
MSI1

source_name: human colon tissue

value: colon

value: Loss of MLH1

value: male

tag: race

value: II


title: genotype: Embrapa48 - time: 168 - Treated or untreated: Mock - rep1


title: 1-39

source_name: human skin

value: skin


title: genotype: IRBB7 - time: 6 hai - rep1

value: Xanthomonas oryzae pv. oryzae


title: 1-38

value: CTCL


title: 1-28


title: Lynch 21

description:
Colorectal cancer  sample: Lynch 21
Lynch21

value: Lynch syndrome tumor

value: Loss of MSH2/MSH6

value: ascending

value: Caucasian


title: genotype: IRBB7 - time: 0 hai - rep3

source_name: shoot (genotype: IRBB7 - time: 0 hai)

value: whole organism

value: 0 hai


title: genotype: Embrapa48 - time: 168 - Treated or untreated: SBR - rep2

source_name: (genotype: Embrapa48 - time: 168 - Treated or untreated: SBR)

value: SBR


title: Lynch 22

description:
Colorectal cancer  sample: Lynch 22
Lynch22

value: Colorectal cancer

value: not done

value: female

value: I


title: genotype: IRBB7 - time: 3 hai - rep2

source_name: shoot (genotype: IRBB7 - time: 3 hai)

value: 3 hai


title: genotype: IRBB7 - time: 3 hai - rep1


title: Lynch 20

description:
Colorectal cancer  sample: Lynch 20
Lynch20

value: colon

value: MSI-H

value: Loss of MSH2

value: male

value: rectum


title: genotype: Embrapa48 - time: 168 - Treated or untreated: SBR - rep3


title: genotype: Embrapa48 - time: 120 - Treated or untreated: Mock - rep3

source_name: (genotype: Embrapa48 - time: 120 - Treated or untreated: Mock)

value: Mock


title: 1-27

value: skin

value: CTCL


title: genotype: Embrapa48 - time: 168 - Treated or untreated: SBR - rep1


title: genotype: IRBB7 - time: 3 hai - rep3

value: Xanthomonas oryzae pv. oryzae


title: Lynch 19

description:
Colorectal cancer  sample: Lynch 19
Lynch19

value: Lynch syndrome tumor

value: ascending

value: Caucasian

value: II


title: genotype: IRBB7 - time: 0 hai - rep2

value: whole organism

value: 0 hai


title: 1-109


title: genotype: IRBB5 - time: 24 hai - rep3

description: cultivar irbb5 (germplasm name); po: 0009006 shoot, (Organism Part); PO:0007106 LP.03 three leaves visible (Development Stage); LC-1 Soil Mix (Growth Media).

source_name: shoot (genotype: IRBB5 - time: 24 hai)

value: 24 hai


title: genotype: Embrapa48 - time: 120 - Treated or untreated: Mock - rep2


title: genotype: Embrapa48 - time: 120 - Treated or untreated: Mock - rep1


title: 1-108


title: 0-12

value: AD


title: Lynch 17

description:
Colorectal cancer  sample: Lynch 17
Lynch17

value: colon

value: Colorectal cancer

value: Loss of MLH1

value: female

value: cecum

value: III


title: 0-11

value: skin


title: genotype: IRBB7 - time: 0 hai - rep1


title: Lynch 18

description:
Colorectal cancer  sample: Lynch 18
Lynch18

value: not done


title: genotype: Embrapa48 - time: 120 - Treated or untreated: SBR - rep3

source_name: (genotype: Embrapa48 - time: 120 - Treated or untreated: SBR)

value: SBR


title: Lynch 16

description:
Colorectal cancer  sample: Lynch 16
Lynch16

value: Lynch syndrome tumor

value: recto-sigmoid


title: Lynch 14

description:
Colorectal cancer  sample: Lynch 14
Lynch14

value: MSI-H

value: ascending

value: Caucasian

value: unknown


title: genotype: IRBB5 - time: 24 hai - rep2

value: whole organism

value: 24 hai

value: Xanthomonas oryzae pv. oryzae


title: 0-10

value: AD


title: genotype: IRBB5 - time: 24 hai - rep1


title: genotype: Embrapa48 - time: 096 - Treated or untreated: Mock - rep3

source_name: (genotype: Embrapa48 - time: 096 - Treated or untreated: Mock)

value: Mock


title: 0-9


title: genotype: IRBB5 - time: 12 hai - rep3

source_name: shoot (genotype: IRBB5 - time: 12 hai)

value: 12 hai


title: genotype: Embrapa48 - time: 120 - Treated or untreated: SBR - rep1


title: 0-119

value: PP


title: genotype: IRBB5 - time: 12 hai - rep1


title: genotype: IRBB5 - time: 12 hai - rep2


title: Lynch 13

description:
Colorectal cancer  sample: Lynch 13
Lynch13

value: colon

value: Colorectal cancer

value: Loss of MSH6

value: female

value: II


title: Lynch 12

description:
Colorectal cancer  sample: Lynch 12
Lynch12

value: Lynch syndrome tumor

value: not done

value: male

value: recto-sigmoid

value: IV


title: 0-117

value: skin


title: 0-116


title: Lynch 11

description:
Colorectal cancer  sample: Lynch 11
Lynch11

value: MSI-H

value: Loss of MLH1/PMS2

value: cecum

value: Caucasian


title: genotype: IRBB5 - time: 6 hai - rep2

source_name: shoot (genotype: IRBB5 - time: 6 hai)

value: whole organism

value: 6 hai

value: Xanthomonas oryzae pv. oryzae


title: genotype: Embrapa48 - time: 096 - Treated or untreated: SBR - rep2

source_name: (genotype: Embrapa48 - time: 096 - Treated or untreated: SBR)

value: SBR


title: genotype: Embrapa48 - time: 096 - Treated or untreated: SBR - rep3


title: 0-118

value: PP


title: Lynch 1

description:
Colorectal cancer  sample: Lynch 1
Lynch1

value: colon

value: Colorectal cancer

value: Loss of MSH2/MSH6

value: female

value: descending

value: III


title: 21N

description:
Non-neoplastic colon  sample: 21N
X21N

value: Non-neoplastic colon

value: normal colonic mucosa

value: not done


title: genotype: IRBB5 - time: 6 hai - rep1


title: 0-115

value: skin


title: genotype: IRBB5 - time: 6 hai - rep3


title: genotype: IRBB5 - time: 3 hai - rep3

source_name: shoot (genotype: IRBB5 - time: 3 hai)

value: 3 hai


title: genotype: Embrapa48 - time: 096 - Treated or untreated: Mock - rep1

value: Mock


title: genotype: Embrapa48 - time: 096 - Treated or untreated: SBR - rep1

value: whole organism


title: genotype: Embrapa48 - time: 072 - Treated or untreated: Mock - rep2

source_name: (genotype: Embrapa48 - time: 072 - Treated or untreated: Mock)


title: genotype: IRBB5 - time: 3 hai - rep1


title: genotype: IRBB5 - time: 3 hai - rep2


title: genotype: Embrapa48 - time: 072 - Treated or untreated: Mock - rep1


title: genotype: Embrapa48 - time: 072 - Treated or untreated: Mock - rep3


title: 0-64


title: genotype: IRBB5 - time: 0 hai - rep3

source_name: shoot (genotype: IRBB5 - time: 0 hai)

value: 0 hai


title: 0-62

value: PN


title: 0-63


title: genotype: IRBB5 - time: 0 hai - rep2

value: Xanthomonas oryzae pv. oryzae


title: 19N

description:
Non-neoplastic colon  sample: 19N
X19N

value: Caucasian


title: 20N

description:
Non-neoplastic colon  sample: 20N
X20N

value: colon


title: genotype: Embrapa48 - time: 072 - Treated or untreated: SBR - rep2

source_name: (genotype: Embrapa48 - time: 072 - Treated or untreated: SBR)

value: SBR


title: genotype: Embrapa48 - time: 072 - Treated or untreated: SBR - rep3


title: 0-61


title: 14N

description:
Non-neoplastic colon  sample: 14N
X14N

value: male


title: 17N

description:
Non-neoplastic colon  sample: 17N
X17N

value: female


title: 15N

description:
Non-neoplastic colon  sample: 15N
X15N


title: 0-60

value: PP


title: genotype: IRBB5 - time: 0 hai - rep1


title: 16N

description:
Non-neoplastic colon  sample: 16N
X16N


title: genotype: Embrapa48 - time: 048 - Treated or untreated: Mock - rep3

source_name: (genotype: Embrapa48 - time: 048 - Treated or untreated: Mock)


title: genotype: Embrapa48 - time: 072 - Treated or untreated: SBR - rep1


title: genotype: Embrapa48 - time: 048 - Treated or untreated: Mock - rep1


title: genotype: IR24 - time: 24 hai - rep2

description: cultivar ir24 (germplasm name); po: 0009006 shoot, (Organism Part); PO:0007106 LP.03 three leaves visible (Development Stage); LC-1 Soil Mix (Growth Media).

source_name: shoot (genotype: IR24 - time: 24 hai)

value: 24 hai


title: genotype: IR24 - time: 12 hai - rep3

source_name: shoot (genotype: IR24 - time: 12 hai)

value: 12 hai


title: genotype: IR24 - time: 24 hai - rep1


title: genotype: Embrapa48 - time: 048 - Treated or untreated: Mock - rep2


title: genotype: Embrapa48 - time: 120 - Treated or untreated: SBR - rep2


title: genotype: IR24 - time: 12 hai - rep2


title: 12N

description:
Non-neoplastic colon  sample: 12N
X12N

source_name: human colon tissue

value: Non-neoplastic colon

value: normal colonic mucosa


title: 1-103

source_name: human skin

value: skin

value: CTCL


title: 11N

description:
Non-neoplastic colon  sample: 11N
X11N

value: not done


title: genotype: IR24 - time: 24 hai - rep3

value: whole organism


title: 13N

description:
Non-neoplastic colon  sample: 13N
X13N


title: genotype: Embrapa48 - time: 048 - Treated or untreated: SBR - rep3

source_name: (genotype: Embrapa48 - time: 048 - Treated or untreated: SBR)


title: 1-102


title: 10N

description:
Non-neoplastic colon  sample: 10N
X10N


title: 1-46


title: 1-55


title: 1-53


title: genotype: IR24 - time: 12 hai - rep1


title: genotype: Embrapa48 - time: 048 - Treated or untreated: SBR - rep1


title: 1-95


title: 8N

description:
Non-neoplastic colon  sample: 8N
X8N


title: 7N

description:
Non-neoplastic colon  sample: 7N
X7N


title: genotype: Embrapa48 - time: 036 - Treated or untreated: Mock - rep2

source_name: (genotype: Embrapa48 - time: 036 - Treated or untreated: Mock)

value: Mock


title: genotype: Embrapa48 - time: 048 - Treated or untreated: SBR - rep2


title: 5N

description:
Non-neoplastic colon  sample: 5N
X5N


title: genotype: Embrapa48 - time: 036 - Treated or untreated: Mock - rep3


title: genotype: IR24 - time: 6 hai - rep2

source_name: shoot (genotype: IR24 - time: 6 hai)

value: 6 hai


title: genotype: Embrapa48 - time: 036 - Treated or untreated: Mock - rep1


title: genotype: Embrapa48 - time: 036 - Treated or untreated: SBR - rep3

source_name: (genotype: Embrapa48 - time: 036 - Treated or untreated: SBR)


title: genotype: IR24 - time: 6 hai - rep1

value: Xanthomonas oryzae pv. oryzae


title: 1-37


title: 9N

description:
Non-neoplastic colon  sample: 9N
X9N

value: Caucasian


title: 6N

description:
Non-neoplastic colon  sample: 6N
X6N

value: colon


title: genotype: IR24 - time: 3 hai - rep3

source_name: shoot (genotype: IR24 - time: 3 hai)

value: 3 hai


title: Lynch 2

description:
Colorectal cancer  sample: Lynch 2
Lynch2

value: Colorectal cancer

value: Lynch syndrome tumor

value: MSI-H

value: Loss of MSH2

value: cecum

value: II


title: 1-36


title: genotype: Embrapa48 - time: 036 - Treated or untreated: SBR - rep2

value: SBR


title: 0-65

value: skin

value: PN


title: 1-26

value: CTCL


title: 1-25


title: 4N

description:
Non-neoplastic colon  sample: 4N
X4N

value: Non-neoplastic colon

value: normal colonic mucosa

value: not done

value: female


title: 3N

description:
Non-neoplastic colon  sample: 3N
X3N

value: Caucasian


title: 1-99


title: 1N

description:
Non-neoplastic colon  sample: 1N
X1N

value: colon


title: genotype: Embrapa48 - time: 096 - Treated or untreated: Mock - rep2

source_name: (genotype: Embrapa48 - time: 096 - Treated or untreated: Mock)

value: whole organism

value: Mock


title: 2N

description:
Non-neoplastic colon  sample: 2N
X2N


title: 1-107


title: genotype: IR24 - time: 3 hai - rep1

value: 3 hai

value: Xanthomonas oryzae pv. oryzae


title: genotype: IR24 - time: 0 hai - rep1

source_name: shoot (genotype: IR24 - time: 0 hai)

value: 0 hai


title: genotype: Embrapa48 - time: 036 - Treated or untreated: SBR - rep1


title: genotype: IR24 - time: 0 hai - rep2


title: genotype: IR24 - time: 3 hai - rep2


title: 0-8

value: AD


title: 0-6


title: 0-7


title: genotype: Embrapa48 - time: 024 - Treated or untreated: SBR - rep3

source_name: (genotype: Embrapa48 - time: 024 - Treated or untreated: SBR)


title: genotype: Embrapa48 - time: 024 - Treated or untreated: Mock - rep3

source_name: (genotype: Embrapa48 - time: 024 - Treated or untreated: Mock)


title: genotype: Embrapa48 - time: 024 - Treated or untreated: Mock - rep1


title: 0-287


title: BAG6_16_06_AP

city: Bergen

first: António

last: Pagarete

address: Thormøhlensgate 53 A & B

department: Department of Biology

country: Norway

institute: University of Bergen

description: Phosphate Limited

hyb_protocol: Total cRNA present in each sample was quantified using a NanoDrop ND 1000 (NanoDrop Technologies, Wilmington, DE). For each sample 7.5 µl 20 × SSC (Sigma), 1.0 µl 10% SDS and 100 ng of labelled cRNA were combined in a total volume of 45 µl. 33.3 µl of this dye-labelled target were added to 16.7 µl of pre-heated (50 °C ) 3 × Hybridisation buffer (consisting of 9 × SSC, 0.6% SDS), and incubated at 100 °C for 2 mins. of denaturation in the dark. Tubes were kept for a few minutes at 50 °C while waiting to be loaded onto microarray slide. 46 µl of target were loaded into an AO Maui mixer (BioMicro Systems, Inc.) and transferred to the preheated Maui hybridisation system (BioMicro Systems, Inc.).  Mixing was started and arrays incubated overnight for 16 h at 50°C. Microarray slides were then given three post-hybridisation washes. The first wash was in 50 ml of 1 × SSC, 2% SDS for 5 mins with constant agitation; followed by a second wash for a further 5 mins (with constant agitation) in  50 ml of 0.5 × SSC, 2% SDS; then a third wash for 10 secs in 50 ml of 0.5 × SSC. Residual liquid was removed by centrifugation at 1000 rpm for 5 mins at room temperature, and the slides stored in the dark prior to scanning.

scan_protocol: Hybridised arrays were scanned in an Agilent DNA Microarray Scanner with Surescan High-Resolution Technology with 5 µm resolution. Each array was scan at 20%, 50%, and 100% gain settings in order to determine and select the optimal scan setting producing a high dynamic signal range without saturation (Forster et al., 2003). Images from all scans were quantified and background corrected using BlueFuse for Microarrays v3.6 (7145).

data_processing: Overall fluorescence values between different microarray chips were normalized using the quantile method using R (Team RDC, 2009) and the limma package (Smyth, 2005). This method assumed that the distribution of gene abundances was nearly the same across arrays. Intensity values were first sorted and then each ranked among arrays, leading to the normalization to the same single mean value for all the arrays. For posterior analysis the 5 within-array technical replicate values were replaced by the respective median.

organism: marine metagenome

source_name: Mesosom Enclosure 6; Experimental day 16; Time 6h

label_protocol: Random amplification of the entire mRNA population was achieved using the Microarray Target Amplification Kit (Roche). This required the use of a special primer, containing a random sequence with no significant homology to any known sequences in public databases (Target Amplification Sequence, [TAS]) in addition to T7 promoter and oligo (dT) sequences, for first-strand cDNA synthesis. The TAS-region generates a 3´ anchor on the cDNA for subsequent PCR amplification with a TAS-PCR primer. First and second strand cDNA synthesis was performed from 250 ng of total RNA and purified using the Target Purification Kit (Roche).  For expression profiling, purified cDNA was randomly amplified in a 100 µl volume by 21 cycles of PCR using TAS primers according to the manufactures instructions. PCR products (produced after the appropriate number of PCR cycles) were purified using the Microarray Target Purification kit (Roche). The resulting PCR-amplified cDNA was then transcribed into Cy5 (for each sample) fluorescently labelled cRNA using the T7 Microarray RNA Target Synthesis Kit (Roche). The appropriate labelled cRNAs were combined and then purified using the Microarray Target Purification kit.

growth_protocol: Six transparent polyethylene enclosures (11 m3; 90% penetration of photosynthetically active radiation) purchased from ANI-TEX (Notodden, Norway) were mounted on floating frames moored along the south side of a raft and filled with unfiltered fjord water pumped from 10 m depth adjacent to the raft. Homogeneous water masses within the enclosures were ensured by pumping water from the bottom of the bag to the surface. The 6 enclosures (encs.) were divided in 2 treatment groups allowing triplication of each treatment: phosphate replete (encs. #1, #3 and #5) and phosphate deplete (encs. #2, #4 and #6). Nutrients were added approx 15:00 h daily at an N:P ratio of 15:1 (1.5 µM  NaNO3 and 0.1 µM KH2PO4) to the phosphate replete enclosures and at a ratio of 75:1 (1.5 µM  NaNO3 and 0.02 µM KH2PO4) to the phosphate deplete enclosures.

extract_protocol: Total RNA extracted from biological material present in 2L of water and collected in 0.2um filters. The cells were resuspended from the filter using 2 ml PBS buffer, and transferred into an Eppendorff tube. Tubes were centrifuged for 1 min at 15500 × g, and the supernatant discarded. Total RNA was extracted with RNeasy Midi Kits (Qiagen) according to the manufacturer’s instructions. Briefly, the samples were resuspended in 2 ml RLT lysis buffer, vortexed for 1 min. (5 sec. bursts), and spun for 5 min at 15500 × g. The supernatant was transferred to a new tube, and the nucleic acids were precipitated using 2 ml of 70% ethanol. The samples were loaded onto an RNA-binding midiprep column (Qiagen). The column was washed with RW1 and RPE solutions, and RNA was eluted in 200 μl of RNase free water. To remove contaminating DNA, the samples were DNase treated twice for 25 min. at 37º C with 2 U of Turbo DNA-free kit (Ambion) according to the manufacturer’s instructions. The quality of the RNA samples was determined with a Bioanalyzer 2100 (Agilent, Waldbronn, Germany). All samples tested negative for genomic DNA contamination. Samples were stored at -80º C until further use.

treatment_protocol: Four daily samples (06 h, 12 h, 18 h, and 24 h) were taken from the surface of each mesocosm with 20 l carboys. Samples were immediately brought to the lab where 2l of each sample was filtered onto 0.45-µm-pore-size 47-mm-diameter Supor-450 filters (PALL Corp.).

tag: sample

value: natural planktonic community exiting on Raunefjorden, Western Norway coast

tag: enrichment treatment

value: N:P ratio of 75:1 (1.5 µM  NaNO3 and 0.02 µM KH2PO4)


title: 0-114

value: skin

tag: diagnosis

value: PP


title: BAG6_15_06_NA

description: Phosphate Limited

source_name: Mesosom Enclosure 6; Experimental day 15; Time 6h


title: 0-112

value: NN


title: 0-5


title: genotype: Embrapa48 - time: 024 - Treated or untreated: Mock - rep2


title: BAG6_12_06_NA

description: Phosphate Limited

source_name: Mesosom Enclosure 6; Experimental day 12; Time 6h


title: BAG6_13_06_NA

description: Phosphate Limited

source_name: Mesosom Enclosure 6; Experimental day 13; Time 6h


title: 0-137


title: E. coli O157:H7 EDL933 in LB at 37oC at 7 hrs incubation with phloretin

city: Gyeongsan-Si

first: Jintae

last: Lee

state: Gyeongsangbuk-Do

address: 214-1 Daedong

department: Chemical engineering

country: South Korea

institute: Yeungnam University

description: RNA extracted from E. coli EDL933 cells grown for 7 hrs in LB at 37ºC plus phloretin

hyb_protocol: Following affymetrix protocol. Prepared hybridization cocktail for Single Probe Array (49 Format) with total 200 ul volume including 1X hybrization buffer, 50 pM B2 Control Oligo, 0.1 mg/mL Herring Sperm DNA, 0.5 mg/mL BSA, and at least 1 ug fragmented and labelled cDNA. After loading of hybridization cocktail in Affymetrix E. coli Antisense Genome Array, the hybridization was performed at 45ºC, with 60 rpm for 16 hours. After hybridization, the probe array was washed and stained using Affymetrix Genechip Fluidics Station 450 and the software GenomeChipOperating Software (GCOS).

scan_protocol: Following affymetrix protocol. After washing and staining, the probe array was scanned using Affymetrix Genechip scanner GCS3000 7G system and the software GenomeChipOperating Software (GCOS).

data_processing: MAS 5.0 Expression Analysis Default Setting

organism: Escherichia coli

source_name: rna extracted from e. coli o157: H7 EDL933 cells grown (7 hrs incubation) in LB at 37ºC with 0.05 mg/ml Phloretin

label_protocol:
Following affymetrix protocol.
cDNA was synthesized first using Promega M-MLV Reverse transcriptase (cat# M1705). After removing RNA, DNA fragmentation was performed to obtain and 50-200 base cDNA fragments. The fragmented cDNA was labelled with Biotin-ddUTP using Enzo BioArray Terminal Labeling Kit (Affymetrix, P/N 900181).

extract_protocol: E. coli O157:H7 EDL933 was inoculated in 25 ml of LB in 250 ml shake flasks with overnight cultures that were diluted 1:100. Cells were shaken at 100 rpm and 37°C for 7 hrs.  Cells were immediately chilled with dry ice and 95% ethanol (to prevent RNA degradation) for 30 sec before centrifugation in 50 ml centrifuge tubes at 13,000 g for 2 min; cell pellets were frozen immediately with dry ice and stored -80°C.  RNA was isolated using Qiagen RNeasy mini Kit (Cat# 74104) with Qiagen RNase-free DNase I (Cat# 79254).

tag: agent

value: 0.05 mg/ml Phloretin


title: BAG6_14_06_NA

description: Phosphate Limited

source_name: Mesosom Enclosure 6; Experimental day 14; Time 6h


title: 0-136


title: Irradiated testes with FSH supplementation (GnRH antagonist, androgen receptor antagonist, and Estradiol), bio rep 6

city: Houston

first: Wei

last: Zhou

state: TX

address: 1515 Holcombe Blvd

department: Department of Experimental Radiation Oncology

institute: M.D.Anderson Cancer Center

description: gene expression data from irradiated rat testes

hyb_protocol: cRNA were hybridized on GeneChip Rat Genome 230 2.0 Array using Hybridization Oven 640. The GeneChip® Fluidics Station automates the delivery, timing and temperature control of reagents for staining and washing of the probe arrays.

scan_protocol: GeneChips were scanned using GeneArray™ Scanner and quantified with Affymetrix GCOS 1.2.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. After normalization, the expression levels within each chip were divided by the median value for all the probes whose expression was regarded as present on the array, and then log base 2 transformed.

organism: Rattus norvegicus

source_name: Irradiated rat testes, with FSH supplementation (GnRH antagonist, androgen receptor antagonist, and estradiol)

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

extract_protocol: Total RNA extraction by RNeasy Midi Kit (Qiagen, Valencia, CA)

treatment_protocol: 6 Gy irradiation to the lower abdomen of the rats

tag: treatment

value: testes

tag: genotype

value: LBNF1 rat

tag: age

value: 25~27 weeks old


title: genotype: Embrapa48 - time: 024 - Treated or untreated: SBR - rep1

description: at inoculation (Age); field soil (Growth Media).

scan_protocol: Affy- Array Scanning

label_protocol: Affy-Eukaryotic Target Preparation

tag: time

tag: infection

value: SBR


title: genotype: Embrapa48 - time: 018 - Treated or untreated: Mock - rep2

source_name: (genotype: Embrapa48 - time: 018 - Treated or untreated: Mock)


title: BAG6_10_06_NA

description: Phosphate Limited

source_name: Mesosom Enclosure 6; Experimental day 10; Time 6h


title: genotype: IR24 - time: 6 hai - rep3

extract_protocol: Hot Phenol/Guanidine Thiocyanate and RNeasy Clean up

value: 6 hai


title: genotype: Embrapa48 - time: 018 - Treated or untreated: SBR - rep3

source_name: (genotype: Embrapa48 - time: 018 - Treated or untreated: SBR)

value: whole organism


title: BAG5_16_06_NA

description: High phosphate enrichment

source_name: Mesosom Enclosure 5; Experimental day 16; Time 6h

value: N:P ratio of 15:1 (1.5 µM  NaNO3 and 0.1 µM KH2PO4)


title: Irradiated testes with FSH supplementation (GnRH antagonist, androgen receptor antagonist, and Estradiol), bio rep 3

value: Irradiated rat testes, with FSH supplementation (GnRH antagonist, androgen receptor antagonist, and estradiol)


title: Irradiated testes with FSH supplementation (GnRH antagonist, androgen receptor antagonist, and Estradiol), bio rep 2


title: BAG6_08_06_AV

description: Phosphate Limited

source_name: Mesosom Enclosure 6; Experimental day 8; Time 6h


title: Irradiated testes with FSH supplementation (GnRH antagonist, androgen receptor antagonist, and Estradiol), bio rep 5


title: genotype: Embrapa48 - time: 018 - Treated or untreated: Mock - rep3

value: Mock


title: genotype: Embrapa48 - time: 024 - Treated or untreated: SBR - rep2


title: Irradiated testes with FSH supplementation (GnRH antagonist, androgen receptor antagonist, and Estradiol), bio rep 1


title: genotype: Embrapa48 - time: 018 - Treated or untreated: Mock - rep1


title: BAG5_15_06_AP

description: High phosphate enrichment

source_name: Mesosom Enclosure 5; Experimental day 15; Time 6h


title: genotype: Embrapa48 - time: 018 - Treated or untreated: SBR - rep2


title: Irradiated testes with FSH supplementation (GnRH antagonist, androgen receptor antagonist, and Estradiol), bio rep 4


title: 0-135

source_name: human skin


title: BAG5_12_06_NA

description: High phosphate enrichment

source_name: Mesosom Enclosure 5; Experimental day 12; Time 6h


title: 0-90

value: PN


title: genotype: Embrapa48 - time: 018 - Treated or untreated: SBR - rep1


title: genotype: Embrapa48 - time: 012 - Treated or untreated: Mock - rep3

source_name: (genotype: Embrapa48 - time: 012 - Treated or untreated: Mock)


title: E. coli O157:H7 EDL933 in LB at 37oC at 7 hrs incubation

description: RNA extracted from E. coli EDL933 cells grown for 7 hrs in LB at 37ºC

source_name: rna extracted from e. coli o157: H7 EDL933 cells grown (7 hrs incubation) in LB at 37ºC

value: control


title: BAG5_11_06_NA

description: High phosphate enrichment

source_name: Mesosom Enclosure 5; Experimental day 11; Time 6h

value: natural planktonic community exiting on Raunefjorden, Western Norway coast


title: BAG5_10_06_NA

description: High phosphate enrichment

source_name: Mesosom Enclosure 5; Experimental day 10; Time 6h


title: BAG5_09_06_NA

description: High phosphate enrichment

source_name: Mesosom Enclosure 5; Experimental day 9; Time 6h


title: BAG5_08_06_AV

description: High phosphate enrichment

source_name: Mesosom Enclosure 5; Experimental day 8; Time 6h


title: Irradiated rat testes, with hormonal ablation, biological rep 11

source_name: Irradiated rat testes, with hormonal ablation (GnRH antagonist and the androgen receptor antagonist flutamide)


title: 0-88


title: genotype: IR24 - time: 0 hai - rep3

source_name: shoot (genotype: IR24 - time: 0 hai)

value: 0 hai

value: Xanthomonas oryzae pv. oryzae


title: 0-87

value: skin

value: PP


title: Irradiated rat testes, with hormonal ablation, biological rep 10

value: Irradiated rat testes, with hormonal ablation (GnRH antagonist and the androgen receptor antagonist flutamide)


title: Irradiated rat testes, with hormonal ablation, biological rep 9

value: testes


title: genotype: Embrapa48 - time: 012 - Treated or untreated: Mock - rep1


title: 0-89


title: 0-79


title: Irradiated rat testes, with hormonal ablation, biological rep 6

value: LBNF1 rat


title: 0-78


title: Irradiated rat testes, with hormonal ablation, biological rep 8

value: 25~27 weeks old


title: 0-286

value: AD