title: SCAT_RFIpl_20kg_rep8

description: Gene expression in 20 kg body weight pig subcutaneous adipose tissue with high residual feed intake

data_processing: All analyses were then performed using the R software version 2.10.0 (R Development Core Team, 2008). Raw spots intensities were first submitted to quality filtration based on 4 criteria: intensity, uniformity, saturation and outliers detection. Intensities of filtered spots were transformed into log2(Cy3), and data were normalized by median centering, i.e. subtracting the median value across all probes from all raw values for each sample to obtain experimentally consolidated gene expression values. Normalized data were submitted to an analysis of variance using the fixed effects of genetic line breed (RFIpl or RFIneg).

source_name: SCAT, high-RFI, 20kg body weight

growth_protocol: The low-RFI (RFIneg) and high-RFI (RFIpl) pigs were fed ad libitum.

value: SCAT

value: RFIpl


title: Cont (ABE)

status: Public on Jan 01 2014

type: RNA

city: Tokyo

first: zhu

last: yun

address: takanawa 4-21-12

country: Japan

institute: scinet company

hyb_protocol: The arrays were hybridized at 65℃ overnight

scan_protocol: The arrays were scaned using FLA-8000 (FUJIFILM).

data_processing: The signal intensities were quantified using ArrayGauge software (FUJIFILM). The ratio of the signal intensity for E2- or ABE-treated sample to that for the control sample was calculated for each gene, and then normalized using control genes .

molecule: total RNA

organism: Homo sapiens

source_name: Cont (ABE)

label_protocol: Five mg of total RNA was reverse-transcribed and labeled with cy3 (GE Healthcare) using SuperScript Indirect cDNA labeling system (Invitrogen).

extract_protocol: Total RNA was extracted using RNeasy plus mini kit (QIAGEN).

tag: cell type

value: breast cancer


title: NSCL/P sample 4

city: Sao Paulo

first: Lucas

last: Alvizi

state: Sao Paulo

address: Rua do Matao 277

department: Genetics and Evolutionary Biology

country: Brazil

institute: University of Sao Paulo

description: gene expression data from dental pulp stem cells extracted from deciduos tooth

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip®Human Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 and hybridized for 16 hr in the Affymetrix Hybridization Oven 640.

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

data_processing: Data were analyzed with Expression Console (Affymetrix) and normalized by RMA method.

label: biotin

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

growth_protocol: Cells were cultured in DMEM-F12 (Life Technologies) supplemented with 15% Foetal Bovine Serum (HyClone), 1% Non-essential aminoacids solution (Life Technologies), 1% penicillin-streptomycin solution (Life Technologies), in a humidified incubator at 37oC and 5% CO2. For storage, cells were frozen in medium containing 90% FBS and 10% DMSO (LGC Biotecnologia). Protocols are also described in Bueno et al, 2011 Stem Cell Reviews and Reports.

extract_protocol: Total RNA isolation was performed with NucleoSpin RNA II kit (Macherey-Nagel), following manufacturer’s recommendations. RNA quality and concentration were assessed using Nanodrop 1000 and agarose gel electrophoresis. Only RNA samples with absorbance ratio 260/280 > 1.8, preserved rRNA ratio (28S/18S) and no signs of degradation were used.

treatment_protocol: No specific treatment was used in cells cultures. Growing cells were used in the media described above.

tag: condition

value: Non-syndromic cleft lip/palate (NSCL/P)

tag: tissue

value: decidous teeth dental pulp

tag: gender

value: female


title: subcutaneousadiposetissue_RFIneg_115kg_rep3

city: Saint-Gilles

first: Annie

last: Vincent

address: domaine de la prise

country: France

institute: INRA

description: Gene expression in 115 kg body weight pig subcutaneous adipose tissue with low residual feed intake

hyb_protocol: Microarray hybridizations were carried out in Agilent’s SureHyb hybridization chambers containing 1.65 µg of Cy3-labeled cRNA sample per hybridization. Hybridization reactions were performed at 65°C for 17 h using Agilent’s Gene Expression Hybridization Kit

scan_protocol: After washing, microarrays were scanned at 5 µm/pixel resolution using the Agilent DNA Microarray Scanner G2505C, and images were analyzed with Agilent Feature Extraction Software (Version 10.7.3.1, protocol GE1_107_Sep09)

data_processing: All analyses were then performed using the R software version 2.10.0 (R Development Core Team, 2008). Raw spots intensities were first submitted to quality filtration based on 4 criteria: intensity, uniformity, saturation and outliers detection. Intensities of filtered spots were transformed into log2(Cy3), and data were normalized by median centering, i.e. subtracting the median value across all probes from all raw values for each sample to obtain experimentally consolidated gene expression values. Normalized data were submitted to an analysis of variance using the fixed effects of genetic line breed (RFIpl or RFIneg) or feed restriction effect (RFIpl or RFIplR)

organism: Sus scrofa

source_name: subcutaneous adipose tissue, low-RFI, 115kg body weight

label_protocol: Total RNA (150 ng) from each sample was labeled with Cy3 dye using the low RNA input linear amplification kit (Agilent Technologies) following the manufacturer’s instructions. Briefly, a two-step procedure was used to generate fluorescent complementary RNA (cRNA) by using T7 RNA polymerase. Samples were then purified with an RNeasy mini elute kit (Qiagen, Hilden, Germany)

growth_protocol: The low-RFI (RFIneg) and high-RFI (RFIpl) pigs were fed ad libitum. The high restricted-RFI pigs were fed at the low-RFI (RFIneg) feeding level.

extract_protocol: For total RNA extraction, samples of frozen tissues (80 to 100 mg each) were homogenized in Trizol reagent (Invitrogen, Cergy-Pontoise, France) using a TissueLyser (Qiagen) and were then treated as previously described (Vincent et al., 2012). RNA was finally purified using a silica-membrane technology under vacuum (Nucleospin 8 RNA kit, Macherey Nagel, Hoerdt, France)

value: subcutaneous adipose tissue

tag: strain

value: RFIneg

tag: feed condition

value: Ad libitum


title: monocytes_1 vs monocytes+platelets_1

city: Berlin

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

country: Germany

institute: Max-Planck-Institute for Infection Biology

description: biological replicate 1

hyb_protocol: After precipitation, purification and quantification of labeled samples, 1.25 µg of each labeled cRNA was fragmented and hybridized to whole human genome 4x44k multipack microarrays (AMADID 014850) according to the supplier’s protocol (Agilent Technologies).

scan_protocol: Scanning of microarrays was performed with 5 µm resolution and extended range using a G2565CA high resolution laser microarray scanner (Agilent Technologies).

data_processing: Raw microarray image data were analyzed with the Image Analysis / Feature Extraction software G2567AA (Version A.10.5.1, Agilent Technologies) using default settings and the GE2_105_Jan09 FE protocol. The extracted MAGE-ML files were further analyzed with the Rosetta Resolver Biosoftware, Build 7.2.2 SP1.31 (Rosetta Biosoftware). Ratio profiles comprising single hybridizations were combined in an error-weighted fashion to create ratio experiments. A 1.5–fold change expression cut-off for ratio experiments was applied together with anti-correlation of ratio profiles rendering the microarray analysis highly significant (P-value > 0.01), robust and reproducible.  The normalized ratio provided in the data table below is always cy5/cy3 log(REDsignal/GREENsignal) per feature (processed signals used). Color swap arrays comprise either test/ref for positive polarity and ref/test for negative polarity.

source_name: monocytes

label_protocol: RNA labeling was performed with the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)

growth_protocol: Human mononuclear cells and human platelets were obtained from buffy coat of umbilical cord blood. Monocytes were prepared by density gradient centrifugation on Biocoll separation solution and enriched by immunoaffinity selection (Monocyte Isolation Kit II; Miltenyi Biotec, Germany) and  platelets were centrifuged at 430 g for 20 min, platelet-rich plasma was removed and added to Tyrodes-HEPES buffer [HEPES 2.5 mmol/L, NaCl 150 mmol/L, KCl 1 mmol/L, NaHCO3 2.5 mmol/L, NaH2PO4 0.36 mmol/L, glucose (Glc) 5.5 mmol/L, BSA 1 mg/ml, pH 6.5]. After centrifuged (900 g for 10 min) and after removal of the supernatant, the resulting platelet pellet was resuspended and washed in Tyrodes-HEPES buffer (pH 7.4).

extract_protocol: Total RNA was extracted with TRIzol according the suppliers protocol (Invitrogen) using Glycogen as carrier.

treatment_protocol: Monocytes were cultured in high glucose DMEM medium with GlutaMax (supplemented with 5% heat inactivated fetal calf serum, penicillin (100 U/mL)-streptomycin (100 mg/mL), 1% MEM-vitamins and 1% nonessential amino acids; Invitrogen, Karlsruhe, Germany) at 37°C and 5% CO2 in 24 well plates for 2 hours. After that, freshly isolated platelets (monocyte to platelet, 1:100) were added. Half of the culture medium was changed with fresh complete medium every two days. After culture for 5 days, floating cells or platelets were washed out with warm PBS-1% FCS.

value: monocytes

source_name: monocytes and platelets co-culture

value: monocytes and platelets


title: SCAT_RFIpl_20kg_rep7


title: monocytes+platelets_2 vs monocytes_2

description: color-swap of biological replicate 2


title: 507596A01

type: genomic

city: Hangzhou

first: Ping

last: Yu

address: 359 Tiyuchang Road

country: China

institute: China National Rice Research Institute

description: test sample vs control sample

hyb_protocol: Labeled samples were co-hybridized with hybridization system(NimbleGen) according to the NimbleGen`s CGH user`s guide(see manufacture`s user guide)

scan_protocol: The arrays were scanned using MS200 scanner(NimbleGen) with 2µm resolution according to the NimbleGen`s CGH user`s guide(see manufacture`s user guide)

data_processing: Arrays were processed using Nimblegen's standard protocol for Nimblescan 2.5 CGH data extraction and analysis

molecule: genomic DNA

organism: Oryza sativa Indica Group

source_name: test DNA from leaf

label_protocol: Pairs of genomic DNA (1µg) was labeled with fluorescent dyes Cy5 (test samples) or Cy3(reference DNA) according to the NimbleGen`s CGH user`s guide(see manufacture`s user guide)

extract_protocol: Genomic DNA was extracted and purified from fresh young leaves using the Plant Genomic DNA Kit (TianGen)

tag: subspecies

value: Indica

tag: group

organism: Oryza sativa Japonica Group

source_name: reference DNA from leaf

value: Japonica

value: Temperate


title: NSCL/P sample 2

source_name: dental pulp stem cells extracted from deciduos tooth

value: male


title: NSCL/P sample 3


title: PC9GRM2_None_23hr

city: Minato-ku

first: Noriko

last: Gotoh

state: Tokyo

department: Institute of Medical Science

institute: The University of Tokyo

description: Gene expression after 23hr in PC9GRM2 with no treatment

hyb_protocol: Hybridization was carried out using the Gene Expression Hybridization Kit (Agilent Technologies), according to the manufacturer’s directions. Briefly, a cRNA sample (1.65 g) was subjected to fragmentation (30 min at 60 °C) and then hybridization on a 44K Agilent Whole Human Genome Oligo Microarray (G4112F) (Agilent Technologies). . RNA samples with an RNA integrity number (RIN) greater than 8 were used for further analysis. Hybridization was carried out on a 44K Agilent Whole Human Genome Oligo Microarray (G41112F) (Agilent Technologies).

scan_protocol: Microarrays were scanned by a dynamic autofocus microarray scanner (Agilent DNA Microarray Scanner, Agilent Technologies) under the default parameters (Green PMT was set to 100%, and the scan resolution was set to 5 um. Feature Extraction Software v9.1 (Agilent Technologies) was used to obtain a raw signal value and a quality flag (Present [P], Marginal [M], or Absent [A]).

data_processing: After aggregating all the scanned signals for the different time points, cell lines, and treatments into a single data matrix, quantile normalization (Bolstad et al., Bioinformatics, 2003) was applied to remove the between-experiment distributional biases due to assay artifacts by forcing the same percentile values on all of the processed data.

source_name: PC9GRM2, 23hr, no treatment

label_protocol: RNA samples were labeled using the Agilent Low RNA Input Linear Amplification Kit (Agilent Technologies) according to the manufacturer’s directions. Briefly, amplification and labeling of total RNA (500 ng) was performed using Cyanine 3-CTP.

growth_protocol: Parental PC9 cells were grown in RPMI1640 media supplemented with 10% fetal bovine serum. For the stablishment of gefitinib-resistance cell line (PC9GR), PC9 cells were treated with growth medium containing gefitinib at the concentrations 0.02-0.1 uM for 14-28 days, 0.005-0.02 uM for 14-28 days, and 0.1 uM for a range of exposure durations, yielding approximately 500 survived clones. Following further treatments of gefitinib and repeated clone refining with the indicated concentrations (0 uM, 0.1 uM and 1 uM), a total of 179 clones were screened out based on MTT assays that verified significant suppression of growth in the cancer populations after 7 days. Among the clones further refined that lacked the MET amplification and the EGFR T790M mutation, PC9GR was isolated as a line demonstrating one of the lowest dose responses and almost the same doubling time to PC9.

extract_protocol: Total RNA was isolated from each sample by TRIzol® reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s directions. The quality of the total RNA was evaluated on a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).

treatment_protocol: After 48-hr starvation, each cell line were treated with 100 ng/ml EGF and/or 0.5 uM gefitinib. Cells were harvested at 26 time points during 24 hours.

value: non-small cell lung cancer cell line

tag: drug response

value: gefitinib-resistant cell line

tag: cell line

tag: time

tag: treatment

value: no treatment


title: PC9GRM2_None_22hr

description: Gene expression after 22hr in PC9GRM2 with no treatment

source_name: PC9GRM2, 22hr, no treatment


title: PC9GRM2_None_24hr

description: Gene expression after 24hr in PC9GRM2 with no treatment

source_name: PC9GRM2, 24hr, no treatment


title: SCAT_RFIpl_20kg_rep6

value: SCAT

value: RFIpl


title: SCAT_RFIpl_20kg_rep5


title: PC9GRM2_None_21hr

description: Gene expression after 21hr in PC9GRM2 with no treatment

source_name: PC9GRM2, 21hr, no treatment


title: NSCL/P sample 1

value: Non-syndromic cleft lip/palate (NSCL/P)


title: Nrf2 KO treated with cisplatin rep3

city: Seoul

first: Sang Geon

last: Kim

state: Seoul

address: San56-1, Sillim-dong, Kwanak-gu

department: College of Pharmacy

country: South Korea

institute: Seoul National University

description: Nrf2 KO treated with cisplatin rep3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Illumina BeadScan 500 System

data_processing: The data were quantile normalized using R (version 2.9.1) with BeadArray (version 1.12.1).

organism: Mus musculus

source_name: renal tissue from Nrf2 KO mice

label_protocol: Refer to the Illumina Gene Expression System Manual

growth_protocol: Animal were cared under the guidelines of the Institutional Animal Use and Care Committee at Seoul National University. Male C57BL/6 mice (9 weeks old) were purchased from Samtako Company (Osan, Korea), and housed at 20±2°C with 12-h light/dark cycles and a relative humidity of 50±5% (Tecniplast, Varese, Italy) under filtered, pathogen-free air, with food (Purina, Korea) and water available ad libitum.

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

treatment_protocol: WT and Nrf2 KO C57BL/6 mice (9 weeks old) were intraperitoneally injected with a single dose of cisplatin (15 mg/kg body weight) or vehicle (saline)

tag: genotype

value: Nrf2 KO

value: Male

tag: age

value: 9 weeks

value: kidney


title: 507594A01

description: test sample vs control sample


title: SCAT_RFIpl_20kg_rep4

value: Ad libitum


title: 507596A02

description: test sample vs control sample

value: Aus


title: SCAT_RFIpl_20kg_rep3


title: SCAT_RFIpl_20kg_rep2


title: Nrf2 KO treated with cisplatin rep1

description: Nrf2 KO treated with cisplatin rep1

value: intraperitoneally injected with a single dose of cisplatin (15 mg/kg body weight)


title: Nrf2 KO rep3

description: Nrf2 KO rep3

value: intraperitoneally injected with a single dose of vehicle (saline)


title: PC9GRM2_None_18hr

description: Gene expression after 18hr in PC9GRM2 with no treatment

source_name: PC9GRM2, 18hr, no treatment


title: PC9GRM2_None_19hr

description: Gene expression after 19hr in PC9GRM2 with no treatment

source_name: PC9GRM2, 19hr, no treatment


title: Nrf2 KO rep1

description: Nrf2 KO rep1


title: SCAT_RFIneg_20kg_rep8

description: Gene expression in 20 kg body weight pig subcutaneous adipose tissue with low residual feed intake

source_name: SCAT, low-RFI, 20kg body weight

value: RFIneg


title: SCAT_RFIneg_20kg_rep7


title: PC9GRM2_None_20hr

description: Gene expression after 20hr in PC9GRM2 with no treatment

source_name: PC9GRM2, 20hr, no treatment


title: Nrf2 KO treated with cisplatin rep2

description: Nrf2 KO treated with cisplatin rep2


title: WT treated with cisplatin rep3

description: WT treated with cisplatin rep3

source_name: renal tissue from WT mice

value: WT


title: SCAT_RFIneg_20kg_rep6


title: PC9GRM2_None_16hr

description: Gene expression after 16hr in PC9GRM2 with no treatment

source_name: PC9GRM2, 16hr, no treatment


title: WT treated with cisplatin rep2

description: WT treated with cisplatin rep2


title: PC9GRM2_None_13hr

description: Gene expression after 13hr in PC9GRM2 with no treatment

source_name: PC9GRM2, 13hr, no treatment


title: SCAT_RFIneg_20kg_rep5


title: Nrf2 KO rep2

description: Nrf2 KO rep2


title: SCAT_RFIpl_20kg_rep1

source_name: SCAT, high-RFI, 20kg body weight


title: SCAT_RFIneg_20kg_rep4


title: PC9GRM2_None_15hr

description: Gene expression after 15hr in PC9GRM2 with no treatment

source_name: PC9GRM2, 15hr, no treatment


title: PC9GRM2_None_12hr

description: Gene expression after 12hr in PC9GRM2 with no treatment

source_name: PC9GRM2, 12hr, no treatment


title: WT treated with cisplatin rep1

description: WT treated with cisplatin rep1


title: WT rep2

description: WT rep2


title: SCAT_RFIneg_20kg_rep1


title: PC9GRM2_None_10hr

description: Gene expression after 10hr in PC9GRM2 with no treatment

source_name: PC9GRM2, 10hr, no treatment


title: PC9GRM2_None_9hr

description: Gene expression after 9hr in PC9GRM2 with no treatment

source_name: PC9GRM2, 9hr, no treatment


title: PC9GRM2_None_11hr

description: Gene expression after 11hr in PC9GRM2 with no treatment

source_name: PC9GRM2, 11hr, no treatment


title: skeletalmuscle_RFIplR_115kg_rep8

description: Gene expression in 115 kg body weight pig Longissimus skeletal muscle with high residual feed intake restricted at low RFI feeding level

data_processing: All analyses were then performed using the R software version 2.10.0 (R Development Core Team, 2008a). Raw spots intensities were first submitted to quality filtration based on 4 criteria: intensity, uniformity, saturation and outliers detection. Intensities of filtered spots were transformed into log2(Cy3), and data were normalized by median centering, i.e. subtracting the median value across all probes from all raw values for each sample to obtain experimentally consolidated gene expression values. Normalized data were submitted to an analysis of variance using the fixed effects of genetic line breed (RFIpl or RFIneg) or feed restriction effect (RFIpl or RFIplR)

source_name: skeletalmuscle,  restricted high-RFI, 115kg body weight

growth_protocol: The low-RFI (RFIneg) and high-RFI (RFIpl) pigs were fed ad libitum. The restricted high-RFI pigs were fed at the low-RFI (RFIneg) feeding level.

value: Longissimus skeletal muscle

value: RFIplR

value: Restricted at RFIneg feeding level


title: WT rep1

description: WT rep1


title: PC9GRM2_None_17hr

description: Gene expression after 17hr in PC9GRM2 with no treatment

source_name: PC9GRM2, 17hr, no treatment

value: non-small cell lung cancer cell line

value: gefitinib-resistant cell line

value: no treatment


title: SCAT_RFIneg_20kg_rep2

value: SCAT


title: PC9GRM2_None_8hr

description: Gene expression after 8hr in PC9GRM2 with no treatment

source_name: PC9GRM2, 8hr, no treatment


title: LLC Tumor_Old_0.5Gyx3Proton, rep9

city: Boston

first: christine

middle: elaine

last: briggs

state: MA

address: 736 Cambridge Street

department: Center for Cancer Systems Biology

country: USA

institute: christine briggs

description: Old 0.5Gyx3 Proton LLC (70)

hyb_protocol: Following hybridization at 55C, the chips were washed.

scan_protocol: Standard Illumina scanning protocol using Illumina iScan.

data_processing: The data was checked with GenomeStudio (Illumina) for quality control. In GenomeStudio, data was background subtracted and rank invariant normalization was applied.

source_name: Old 0.5Gyx3 proton LLC tumor

label_protocol: Total RNA of 500ng per sample was amplified using Ambion TotalPrep (Ambion), and 1.5µg of the product was loaded onto the chips.

extract_protocol: RNA was isolated from mouse tumor tissue. Tumor chunks of 1 to 2mm in diameter were placed in TRIzol (Invitrogen, Carlsbad, CA) and homogenized using a Tissue Lyser II (Qiagen, Valencia, CA). Tissue with TRIzol was centrifuged at 1200g and 0.2ml of chloroform was added for 5min. Samples were centrifuged at 10,000g for 15min at 4°C. The aqueous phase with RNA was transferred to a 1.5ml eppendorf tube. Isopropyl alcohol (0.5ml) was added to each sample (room temperature) for 10min and samples were centrifuged at 10,000g for 10min at 4°C. RNA pellets were washed once with 75% ethanol and resuspended in 100μl RNase-free water. Quality and quantity of RNA were measured by an Agilent 2100 Bioanalyzer (Agilent Technologies, Inc., Santa Clara, CA).

value: Lewis lung carcinoma (LLC) tumor

value: male

value: old

value: 0.5Gyx3 proton irradiation


title: PC9GRM2_None_7hr

description: Gene expression after 7hr in PC9GRM2 with no treatment

source_name: PC9GRM2, 7hr, no treatment


title: SCAT_RFIneg_20kg_rep3

value: Ad libitum


title: LLC Tumor_Old_0.5Gyx3Proton, rep10

description: Old 0.5Gyx3 Proton LLC (71)


title: LLC Tumor_Old_0.5Gyx3Proton, rep8

description: Old 0.5Gyx3 Proton LLC (69)


title: LLC Tumor_Old_0.5Gyx3Proton, rep7

description: Old 0.5Gyx3 Proton LLC (6)


title: skeletalmuscle_RFIplR_115kg_rep7


title: 507594A02

description: test sample vs control sample

source_name: test DNA from leaf

value: Indica

source_name: reference DNA from leaf

value: Japonica

value: Temperate


title: PC9GRM2_None_6hr

description: Gene expression after 6hr in PC9GRM2 with no treatment

source_name: PC9GRM2, 6hr, no treatment


title: PC9GRM2_None_5hr

description: Gene expression after 5hr in PC9GRM2 with no treatment

source_name: PC9GRM2, 5hr, no treatment


title: LLC Tumor_Old_0.5Gyx3Proton, rep6

description: Old 0.5Gyx3 Proton LLC (5)


title: J2315_hfq2, biological rep2

city: Lisboa

first: Leonilde

middle: Morais

last: Moreira

address: A. Rovisco Pais

department: Bioengineering

country: Portugal

institute: Instituto Superior Tecnico

description: Mutation in the hfq2 gene

hyb_protocol: Following fragmentation, 2 µg of end-labeled fragmented cDNA were used in a 200-µl hybridization cocktail containing added hybridization controls and hybridized on arrays for 16 hours at 50ºC. Modified post-hybridization wash and double-stain protocols (FLEX450_0005; GeneChip HWS kit, Affymetrix) were used on an Affymetrix GeneChip Fluidics Station 450.

scan_protocol: Arrays were scanned on an Affymetrix GeneChip scanner 3000 7G.

data_processing: Scanned arrays were analyzed with Affymetrix Expression Console software for quality control. Subsequent analysis was carried out with DNA-Chip Analyzer 2010. First a digital mask was applied, leaving for analysis only the 8812 probe sets on the array representing Burkholderia cenocepacia J2315 transcripts. Then the 9 arrays were normalized to a baseline array with median CEL intensity by applying an Invariant Set Normalization Method. Normalized CEL intensities of the arrays were used to obtain model-based gene expression indices based on a Perfect Match (PM)-only model. Replicate data (triplicates) for each bacterial isolate was weighted gene-wise by using inverse squared standard error as weights. All genes compared were considered to be differentially expressed if the 90% lower confidence bound of the fold change between experiment and baseline was above 1.2.

organism: Burkholderia cenocepacia

source_name: J2315  Δhfq2 with 16h growth in LB medium

label_protocol: RNA was processed for use on Affymetrix custom dual species Burkholderia arrays, according to the manufacturer’s Prokaryotic Target Preparation Assay. Briefly, 10 ug of total RNA containing spiked in Poly-A RNA controls (GeneChip Expression GeneChip Eukaryotic Poly-A RNA Control Kit; Affymetrix, Santa Clara, CA) was used in a reverse transcription reaction with random primers (Invitrogen Life Technologies) to generate first-strand cDNA. After removal of RNA, 2 ug of cDNA were fragmented with DNase and end-labeled with biotin using terminal polynucleotidyl transferase (GeneChip WT Terminal Labeling Kit; Affymetrix). Size distribution of the fragmented and end-labeled cDNA, was assessed using an Agilent 2100 Bioanalyzer.

growth_protocol: Bacterial strains were grown in 150 ml L medium contained into 250 ml Erlenmyer flasks at 37ºC, 250 r.p.m. for 16 h

extract_protocol: Total RNA extraction was carried out using the using the miRVana miRNA extraction kit (Ambion), and total RNA was enriched with the small-sized RNAs fraction, following manufacturer’s recommendation

treatment_protocol: Bacterial cells were resuspended in RNAlater reagent (Ambion).

tag: isolate

value: J2315  Δhfq2


title: skeletalmuscle_RFIplR_115kg_rep5


title: J2315_hfq2, biological rep3

description: Mutation in the hfq2 gene


title: LLC Tumor_Old_0.5Gyx3Proton, rep5

description: Old 0.5Gyx3 Proton LLC (4)


title: J2315_hfq, biological rep3

description: Mutation in the hfq gene

source_name: J2315 hfq::Tp with 16h growth in LB medium

value: J2315 hfq::Tp


title: J2315_hfq, biological rep2

description: Mutation in the hfq gene


title: LLC Tumor_Old_0.5Gyx3Proton, rep4

description: Old 0.5Gyx3 Proton LLC (3)


title: PC9GRM2_None_4hr

description: Gene expression after 4hr in PC9GRM2 with no treatment

source_name: PC9GRM2, 4hr, no treatment


title: 507594A03

description: test sample vs control sample


title: skeletalmuscle_RFIplR_115kg_rep3

value: Longissimus skeletal muscle


title: skeletalmuscle_RFIplR_115kg_rep4

value: RFIplR


title: J2315_hfq, biological rep1

description: Mutation in the hfq gene


title: J2315_hfq2, biological rep1

description: Mutation in the hfq2 gene


title: PC9GRM2_None_2hr

description: Gene expression after 2hr in PC9GRM2 with no treatment

source_name: PC9GRM2, 2hr, no treatment


title: skeletalmuscle_RFIplR_115kg_rep2

value: Restricted at RFIneg feeding level


title: skeletalmuscle_RFIplR_115kg_rep1


title: PC9GRM2_None_1hr

description: Gene expression after 1hr in PC9GRM2 with no treatment

source_name: PC9GRM2, 1hr, no treatment

value: non-small cell lung cancer cell line


title: LLC Tumor_Old_0.5Gyx3Proton, rep2

description: Old 0.5Gyx3 Proton LLC (1)


title: LLC Tumor_Old_0.5Gyx3Proton, rep3

description: Old 0.5Gyx3 Proton LLC (2)


title: J2315, biological rep3

description: Wild-type clinical strain

source_name: J2315 wild-type with 16h growth in LB medium


title: skeletalmuscle_RFIpl_115kg_rep7

description: Gene expression in 115 kg body weight pig Longissimus skeletal muscle with high residual feed intake

source_name: skeletalmuscle, high-RFI, 115kg body weight

value: RFIpl


title: J2315, biological rep1

description: Wild-type clinical strain


title: skeletalmuscle_RFIpl_115kg_rep8


title: skeletalmuscle_RFIpl_115kg_rep6


title: PC9GRM2_IRS_24hr

description: Gene expression after 24hr in PC9GRM2 treated with gefinitib

source_name: PC9GRM2, 24hr, gefinitib

value: gefitinib-resistant cell line

value: gefinitib


title: J2315, biological rep2

description: Wild-type clinical strain


title: PAO1_LB-37C_tech02

city: Charlottesville

first: Mariette

last: Barbier

state: VA

address: 345 Crispell Drive

department: Microbiology, Immunology and Cancer Biology

institute: University of Virginia

hyb_protocol: aRNA was fragmented using 5x fragmentation buffer and the total amount of fragmented biotinylated aRNA used per chip was 6.5 µg. Biotinylated aRNA was then spotted in triplicate on P. aeruginosa GeneChips® (Affymetrix) following the procedure established by the manufacturer. The hybridization and washing steps were performed in the Affymetrix Array facility at the Helmoltz Center for Infection Research (HZI) in Braunschweig, Germany (Dr. Roberts Geffers).

scan_protocol: standard Affymetrix

data_processing: The analyses of the arrays were performed using Bioconductor microarray analysis suite (Gentleman, 2004). The quality of all chips was assessed by fitting a linear model to the probe level data using the fitPLM function from the affyPLM package. Expression values were computed using the Robust Multichip Average algorithm. As the number of replicates was low, differentially expressed genes were identified using the Rank Products algorithm (Irizarry, 2003). The value of 0.05 was accepted as a cut-off for pfp.

organism: Pseudomonas aeruginosa PAO1

source_name: PAO1 grown at 37°C in LB

label_protocol: Biotinylated dUTP was incorporated during the cDNA synthesis step.

growth_protocol: All bacteria were grown to mid-exponential phase in lysogeny broth with shaking at 22°C or 37°C

extract_protocol: Cells were stabilized with RNA protect (Qiagen) and total RNA was purified using the RNeasy mini-kit (Qiagen).  Purified total RNA was amplified using the MessageAmpII Bacteria kit (Ambion).

tag: temperature


title: PAO1_LB-37C_tech03


title: PC9GRM2_None_3hr

description: Gene expression after 3hr in PC9GRM2 with no treatment

source_name: PC9GRM2, 3hr, no treatment

value: no treatment


title: PC9GRM2_IRS_23hr

description: Gene expression after 23hr in PC9GRM2 treated with gefinitib

source_name: PC9GRM2, 23hr, gefinitib


title: skeletalmuscle_RFIpl_115kg_rep5


title: PAO1_LB-37C_tech01


title: skeletalmuscle_RFIpl_115kg_rep4


title: LLC Tumor_Old, rep17

description: Old Acute Proton LLC (113)

source_name: Old 0Gy proton LLC tumor

value: Lewis lung carcinoma (LLC) tumor

value: male


title: PC9GRM2_None_0.5hr

description: Gene expression after 0.5hr in PC9GRM2 with no treatment

source_name: PC9GRM2, 0.5hr, no treatment


title: LLC Tumor_Old, rep19

description: Old Acute Proton LLC (115)

value: old


title: LLC Tumor_Old, rep16

description: Old Acute Proton LLC (112)


title: LLC Tumor_Old, rep18

description: Old Acute Proton LLC (114)


title: LLC Tumor_Old_0.5Gyx3Proton, rep1

description: Old 0.5Gyx3 Proton LLC (0)

source_name: Old 0.5Gyx3 proton LLC tumor

value: 0.5Gyx3 proton irradiation


title: PC9GRM2_None_0hr

description: Gene expression after 0hr in PC9GRM2 with no treatment

source_name: PC9GRM2, 0hr, no treatment


title: PC9GRM2_IRS_20hr

description: Gene expression after 20hr in PC9GRM2 treated with gefinitib

source_name: PC9GRM2, 20hr, gefinitib


title: PC9GRM2_IRS_22hr

description: Gene expression after 22hr in PC9GRM2 treated with gefinitib

source_name: PC9GRM2, 22hr, gefinitib


title: LLC Tumor_Old, rep14

description: Old Acute Proton LLC (110)


title: LLC Tumor_Old, rep15

description: Old Acute Proton LLC (111)


title: PC9GRM2_IRS_21hr

description: Gene expression after 21hr in PC9GRM2 treated with gefinitib

source_name: PC9GRM2, 21hr, gefinitib


title: skeletalmuscle_RFIpl_115kg_rep3

value: Ad libitum


title: PAO1_LB-22C_tech02

source_name: PAO1 grown at 22°C in LB


title: skeletalmuscle_RFIpl_115kg_rep2


title: PAO1_LB-22C_tech03


title: PC9GRM2_None_14hr

description: Gene expression after 14hr in PC9GRM2 with no treatment

source_name: PC9GRM2, 14hr, no treatment


title: skeletalmuscle_RFIpl_115kg_rep1


title: LLC Tumor_Old, rep13

description: Old Acute Proton LLC (109)


title: LLC Tumor_Old, rep12

description: Old Acute Proton LLC (108)


title: PC9GRM2_IRS_18hr

description: Gene expression after 18hr in PC9GRM2 treated with gefinitib

source_name: PC9GRM2, 18hr, gefinitib


title: PAOSX in M9G, biological rep3

city: Evreux

first: Sylvie

last: Chevalier

address: 55, rue Saint Germain

institute: University of Rouen

description: sigX deletion mutant

hyb_protocol: Hybridizations were performed at the Mc Gill University and Genome Quebec Innovation Centre (www.genomequebec.mcgill.ca)

scan_protocol: Scanning was done using a Genearray Scanner at the Mac Gill University and the Genome Quebec Innovation Centre (www.genomequebec.mcgill.ca)

data_processing:
The data were analyzed with Flexarray 1.3 Software developped by Genome Quebec Innovation Centre at McGill University
Data were processed using the robust multiarray average algorithm (RMA) for normalization, background correction and expression value calculation (log2)

organism: Pseudomonas aeruginosa

source_name: mutant isogenic

label_protocol: cDNA were synthetized, fragmented and labelled according to the standard affymetrix protocol for prokaryotic target from 10µg of RNA (GeneChip® Expression Analysis Technical Manual, affymetrix, P/N 702232 Rev. 3)

growth_protocol: Bacteria were grown overnight at 37°C on a rotary shaker (180 rpm) in mineral M9 medium containing 0.2% of dextrose (M9G). Cultures were inoculated at an initial OD580 of 0.08 in fresh M9G medium, and allowed to grow to mid log phase (OD580=0.4) before RNA extraction.

extract_protocol: RNA were extracted by the classical hot acid-phenol method.

value: PAOSX


title: skeletalmuscle_RFIneg_115kg_rep6

description: Gene expression in 115 kg body weight pig Longissimus skeletal muscle with low residual feed intake

source_name: skeletalmuscle, low-RFI, 115kg body weight

value: RFIneg


title: PC9GRM2_IRS_17hr

description: Gene expression after 17hr in PC9GRM2 treated with gefinitib

source_name: PC9GRM2, 17hr, gefinitib


title: PAO1_LB-22C_tech01


title: skeletalmuscle_RFIneg_115kg_rep5


title: PAOSX in M9G, biological rep1

description: sigX deletion mutant


title: WT rep3

description: WT rep3

source_name: renal tissue from WT mice

value: WT

value: Male

value: 9 weeks

value: kidney

value: intraperitoneally injected with a single dose of vehicle (saline)


title: skeletalmuscle_RFIneg_115kg_rep7

value: Longissimus skeletal muscle


title: LLC Tumor_Old, rep11

description: Old Acute Proton LLC (107)


title: skeletalmuscle_RFIneg_115kg_rep4


title: LLC Tumor_Old, rep10

description: Old 0Gy acute Proton LLC (106)


title: PC9GRM2_IRS_19hr

description: Gene expression after 19hr in PC9GRM2 treated with gefinitib

source_name: PC9GRM2, 19hr, gefinitib

value: non-small cell lung cancer cell line


title: PC9GRM2_IRS_16hr

description: Gene expression after 16hr in PC9GRM2 treated with gefinitib

source_name: PC9GRM2, 16hr, gefinitib

value: gefitinib-resistant cell line


title: LLC Tumor_Old, rep9

description: Old 0Gyx3 Proton LLC (98)


title: PAOSX in M9G, biological rep2

description: sigX deletion mutant


title: PC9GRM2_IRS_15hr

description: Gene expression after 15hr in PC9GRM2 treated with gefinitib

source_name: PC9GRM2, 15hr, gefinitib

value: gefinitib


title: LLC Tumor_Old, rep8

description: Old 0Gyx3 Proton LLC (97)

source_name: Old 0Gy proton LLC tumor


title: H103 in M9G, biological rep3

description: Wild type strain

source_name: wild type strain


title: skeletalmuscle_RFIneg_115kg_rep3


title: H103 in M9G, biological rep2

description: Wild type strain


title: PC9GRM2_IRS_14hr

description: Gene expression after 14hr in PC9GRM2 treated with gefinitib

source_name: PC9GRM2, 14hr, gefinitib


title: PC9GRM2_IRS_13hr

description: Gene expression after 13hr in PC9GRM2 treated with gefinitib

source_name: PC9GRM2, 13hr, gefinitib


title: skeletalmuscle_RFIneg_115kg_rep2


title: H103 in M9G, biological rep1

description: Wild type strain


title: skeletalmuscle_RFIneg_115kg_rep1


title: LLC Tumor_Old, rep7

description: Old 0Gyx3 Proton LLC (96)


title: LLC Tumor_Old, rep6

description: Old 0Gyx3 Proton LLC (95)


title: skeletalmuscle_RFIplR_115kg_rep6

description: Gene expression in 115 kg body weight pig Longissimus skeletal muscle with high residual feed intake restricted at low RFI feeding level

source_name: skeletalmuscle,  restricted high-RFI, 115kg body weight

value: RFIplR

value: Restricted at RFIneg feeding level


title: PC9GRM2_IRS_11hr

description: Gene expression after 11hr in PC9GRM2 treated with gefinitib

source_name: PC9GRM2, 11hr, gefinitib


title: LLC Tumor_Old, rep5

description: Old 0Gyx3 Proton LLC (94)

value: Lewis lung carcinoma (LLC) tumor

value: male


title: skeletalmuscle_RFIpl_20kg_rep6

description: Gene expression in 20 kg body weight pig Longissimus skeletal muscle with high residual feed intake

source_name: skeletalmuscle,high-RFI, 20kg body weight

value: RFIpl


title: LLC Tumor_Old, rep4

description: Old 0Gyx3 Proton LLC (93)

value: old


title: LLC Tumor_Old, rep3

description: Old 0Gyx3 Proton LLC (92)


title: PC9GRM2_IRS_10hr

description: Gene expression after 10hr in PC9GRM2 treated with gefinitib

source_name: PC9GRM2, 10hr, gefinitib


title: PC9GRM2_IRS_9hr

description: Gene expression after 9hr in PC9GRM2 treated with gefinitib

source_name: PC9GRM2, 9hr, gefinitib


title: skeletalmuscle_RFIpl_20kg_rep8

value: Ad libitum


title: skeletalmuscle_RFIpl_20kg_rep5


title: Control PLC/PRF/5, Rep4

city: Beijing

first: Feng

last: Zhang

address: Tiantan xili 2# NIFDC

institute: National Institutre for Food and Drug Control

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45°C on GeneChip Wheat Genome Array in the Affymetrix Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the affymetrix scanner 3000 7G.The scanned images were first assessed by visual inspection then analyzed to generate raw data files saved as CEL files using the default setting of AGCC.

data_processing: The data were normalized using Robust Multi-array Average(RMA) .

label: Biotin

source_name: Control samples for PLC/PRF/5

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 200ng total RNA (3' IVT Express Kit User Manual, 2008, Affymetrix).

growth_protocol: PLC/PRF/5 cells were growed in DMEM/M199 medium containing 10% FBS. After HEV or medium inoculation, cells was cultured with a sustaining medium (DMEM/M199 containing 2% FBS)

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

treatment_protocol: For test cells, PLC/PRF/5 cells were inoculated with HEV stock for 6 hour, and then washed with serum free DMEM/M199 for three times. After washing, cells were maintained with sustaining medium for sixty days. Sustaining medium was replaced with fresh medium weekly. At the end of inoculation, cells was resolved with Trizol and total RNA was extracted for microarray assays. For the control cells, HEV stock for inoculation  was displaced with serum free DMEM/M199.


title: Control PLC/PRF/5, Rep5


title: LLC Tumor_Old, rep2

description: Old 0Gyx3 Proton LLC (91)


title: LLC Tumor_Old, rep1

description: Old 0Gyx3 Proton LLC (73)


title: skeletalmuscle_RFIpl_20kg_rep7


title: Control PLC/PRF/5, Rep2


title: Control PLC/PRF/5, Rep1


title: skeletalmuscle_RFIpl_20kg_rep4


title: PC9GRM2_IRS_7hr

description: Gene expression after 7hr in PC9GRM2 treated with gefinitib

source_name: PC9GRM2, 7hr, gefinitib


title: Control PLC/PRF/5, Rep3


title: LLC Tumor_Adolescent_0.5Gyx3Proton, rep9

description: Young 0.5Gyx3 Proton LLC (153)

source_name: Young 0.5Gyx3 proton LLC tumor

value: young

value: 0.5Gyx3 proton irradiation


title: LLC Tumor_Adolescent_0.5Gyx3Proton, rep10

description: Young 0.5Gyx3 Proton LLC (154)


title: PC9GRM2_IRS_6hr

description: Gene expression after 6hr in PC9GRM2 treated with gefinitib

source_name: PC9GRM2, 6hr, gefinitib


title: PC9GRM2_IRS_8hr

description: Gene expression after 8hr in PC9GRM2 treated with gefinitib

source_name: PC9GRM2, 8hr, gefinitib


title: PC9GRM2_IRS_5hr

description: Gene expression after 5hr in PC9GRM2 treated with gefinitib

source_name: PC9GRM2, 5hr, gefinitib


title: skeletalmuscle_RFIpl_20kg_rep3


title: HEV inoculated PLC/PRF/5, Rep5

source_name: PLC/PRF/5 inoculated with HEV virus stock from monkey feces

value: inoculated with HEV from monkey feces


title: skeletalmuscle_RFIpl_20kg_rep2


title: LLC Tumor_Adolescent_0.5Gyx3Proton, rep8

description: Young 0.5Gyx3 Proton LLC (152)


title: PC9GRM2_IRS_4hr

description: Gene expression after 4hr in PC9GRM2 treated with gefinitib

source_name: PC9GRM2, 4hr, gefinitib


title: HEV inoculated PLC/PRF/5, Rep4


title: LLC Tumor_Adolescent_0.5Gyx3Proton, rep7

description: Young 0.5Gyx3 Proton LLC (150)


title: LLC Tumor_Adolescent_0.5Gyx3Proton, rep5

description: Young 0.5Gyx3 Proton LLC (148)


title: PC9GRM2_IRS_3hr

description: Gene expression after 3hr in PC9GRM2 treated with gefinitib

source_name: PC9GRM2, 3hr, gefinitib


title: skeletalmuscle_RFIpl_20kg_rep1


title: HEV inoculated PLC/PRF/5, Rep3


title: LLC Tumor_Adolescent_0.5Gyx3Proton, rep6

description: Young 0.5Gyx3 Proton LLC (149)


title: skeletalmuscle_RFIneg_20kg_rep7

description: Gene expression in 20 kg body weight pig Longissimus skeletal muscle with low residual feed intake

source_name: skeletalmuscle, low-RFI, 20kg body weight

value: RFIneg


title: LLC Tumor_Adolescent_0.5Gyx3Proton, rep4

description: Young 0.5Gyx3 Proton LLC (147)


title: skeletalmuscle_RFIneg_20kg_rep4


title: HEV inoculated PLC/PRF/5, Rep1


title: PC9GRM2_IRS_1hr

description: Gene expression after 1hr in PC9GRM2 treated with gefinitib

source_name: PC9GRM2, 1hr, gefinitib


title: HEV inoculated PLC/PRF/5, Rep2


title: skeletalmuscle_RFIneg_20kg_rep6


title: OCI-AML3_500 nM JQ1_8 hours

city: Houston

first: Kapil

last: Bhalla

state: TX

address: 1400 Holcombe Blvd., Unit 428

institute: MD Anderson Cancer Center

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

scan_protocol: Scanning of the chip is conducted using an Affymetrix GeneChip® Scanner 3000 7G with autoloader.

data_processing: The primary analysis was performed using Affymetrix Expression Console Software using default analysis settings.

source_name: OCI-AML3, treated, 500 nM JQ1, 8 hours

label_protocol: Cy3 labeled cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Roche High Pure RNA isolation kit with on-column DNAse I digestion. Elution in RNAse free water.

value: lymphocyte


title: PC9GRM2_IRS_2hr

description: Gene expression after 2hr in PC9GRM2 treated with gefinitib

source_name: PC9GRM2, 2hr, gefinitib


title: LLC Tumor_Adolescent_0.5Gyx3Proton, rep3

description: Young 0.5Gyx3 Proton LLC (146)


title: OCI-AML3_untreated_8 hours

source_name: OCI-AML3, untreated cells, 8 hours


title: skeletalmuscle_RFIneg_20kg_rep5


title: PC9GRM2_IRS_0.5hr

description: Gene expression after 0.5hr in PC9GRM2 treated with gefinitib

source_name: PC9GRM2, 0.5hr, gefinitib


title: skeletalmuscle_RFIneg_20kg_rep3


title: PC9GRM2_IRS_0hr

description: Gene expression after 0hr in PC9GRM2 treated with gefinitib

source_name: PC9GRM2, 0hr, gefinitib


title: skeletalmuscle_RFIneg_20kg_rep1


title: LLC Tumor_Adolescent_0.5Gyx3Proton, rep2

description: Young 0.5Gyx3 Proton LLC (145)


title: PC9GRM2_EGF_IRS_24hr

description: Gene expression after 24hr in PC9GRM2 treated with EGF and gefitinib

source_name: PC9GRM2, 24hr, EGF and gefitinib

value: EGF and gefitinib


title: PC9GRM2_IRS_12hr

description: Gene expression after 12hr in PC9GRM2 treated with gefinitib

source_name: PC9GRM2, 12hr, gefinitib


title: LLC Tumor_Adolescent_0.5Gyx3Proton, rep1

description: Young 0.5Gyx3 Proton LLC (144)


title: liver_RFIplR_115kg_rep5

description: Gene expression in 115 kg body weight pig liver with high residual feed intake restricted at RFIneg feeding level

source_name: liver,  restricted high-RFI, 115kg body weight

value: liver


title: liver_RFIplR_115kg_rep6


title: skeletalmuscle_RFIneg_20kg_rep2

value: Longissimus skeletal muscle


title: PC9GRM2_EGF_IRS_22hr

description: Gene expression after 22hr in PC9GRM2 treated with EGF and gefitinib

source_name: PC9GRM2, 22hr, EGF and gefitinib

value: non-small cell lung cancer cell line

value: gefitinib-resistant cell line


title: LLC Tumor_Adolescent, rep17

description: Young 0Gy acuteProton LLC (163)

source_name: Young 0Gy proton LLC tumor


title: LLC Tumor_Adolescent, rep15

description: Young 0Gy acuteProton LLC (160)


title: LLC Tumor_Adolescent, rep18

description: Young 0Gy acuteProton LLC (164)


title: TR146 oral epithelial cell line treated with interferon gamma

city: Davis

first: Michael

last: George

state: CA

address: 451 Health Sciences Drive

department: Medical Microbiology and Immunology

institute: University of California, Davis

description: Gene expression data from healthy uninfected rhesus macaque tongue epithelium

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip U133Plus2 3' IVT arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000

data_processing: The data were analyzed with dChip, version 2010

source_name: Cancer Research UK

label_protocol: Biotinylated cRNA were prepared according to the standard protocols described in the Affymetrix Gene Expression Analysis Technical Manual

growth_protocol: TR146 cells were grown at 37°C in two 6-well cell culture dishes in DMEM/F12 media supplemented 10% FBS, and 1% antibiotic/antimycotic cocktail

extract_protocol: RNA was extracted with the Qiagen Rneasy kit according to the manufacturer's instructions.

treatment_protocol: TR146 cells were grown to ~80% confluence before replacing media with media supplemented with 20 mM IFN gamma or, in mock-treated cultures, buffer only.  Cells were then incubated at 37°C for 24 hr. before harvesting by centrifugation.  Six independent experiments utilizing IFN gamma-treated and mock-treated control cultures were performed and the RNA extracts from each set of 6 were pooled prior to microarray processing.

tag: source

value: human head/neck cancer

value: interferon gamma


title: B01183

city: Kingston

first: Madhuri

last: Koti

state: Ontario

address: Botterell Hall, Stuart Street

department: Biomedical and Molecular Sciences

country: Canada

institute: Queen's University

hyb_protocol: 500 nanograms of total RNA was used for cDNA synthesis using GeneChip 3′ IVT Express Kit (Affymetrix Inc, Santa Clara, CA USA.)

scan_protocol: Scanning and probe quantification of the gene chips was performed on an AffymetrixGeneChip Scanner 3000 as per the manufacturer's instructions.

data_processing: Normalization of the microarray data was conducted using MAS5 algorithm from the affy Bioconductor package.

source_name: Tumor

label_protocol: GeneChip Two-Cycle Target Labeling and Control Reagents (Affymetrix, Santa Clara, CA)

growth_protocol: Fresh frozen tumour samples stored at -80 C.

extract_protocol: RNA was extracted as usiing Qiagen Rneasy mini kit as per the manufacturer's protocol

value: Ovary

tag: Stage

value: IIIc

tag: classification

value: chemotherapy sensitive


title: liver_RFIplR_115kg_rep7

tag: tissue

value: RFIplR

value: Restricted at RFIneg feeding level


title: LLC Tumor_Adolescent, rep16

description: Young 0Gy acuteProton LLC (161)

value: Lewis lung carcinoma (LLC) tumor

tag: gender

value: male

value: young


title: PC9GRM2_EGF_IRS_20hr

description: Gene expression after 20hr in PC9GRM2 treated with EGF and gefitinib

source_name: PC9GRM2, 20hr, EGF and gefitinib


title: D00443

value: III

value: chemotherapy resistant


title: B01360


title: PC9GRM2_EGF_IRS_23hr

description: Gene expression after 23hr in PC9GRM2 treated with EGF and gefitinib

source_name: PC9GRM2, 23hr, EGF and gefitinib

value: EGF and gefitinib


title: B01440


title: 1706

value: IIIa


title: LLC Tumor_Adolescent, rep14

description: Young 0Gy acuteProton LLC (159)


title: liver_RFIplR_115kg_rep8

value: liver

tag: strain


title: PC9GRM2_EGF_IRS_21hr

description: Gene expression after 21hr in PC9GRM2 treated with EGF and gefitinib

source_name: PC9GRM2, 21hr, EGF and gefitinib

value: non-small cell lung cancer cell line


title: PC9GRM2_EGF_IRS_19hr

description: Gene expression after 19hr in PC9GRM2 treated with EGF and gefitinib

source_name: PC9GRM2, 19hr, EGF and gefitinib

value: gefitinib-resistant cell line


title: untreated TR146 oral epithelial cell line

value: human head/neck cancer


title: LLC Tumor_Adolescent, rep13

description: Young 0Gy acuteProton LLC (158)


title: PC9GRM2_EGF_IRS_18hr

description: Gene expression after 18hr in PC9GRM2 treated with EGF and gefitinib

source_name: PC9GRM2, 18hr, EGF and gefitinib


title: PC9GRM2_EGF_IRS_16hr

description: Gene expression after 16hr in PC9GRM2 treated with EGF and gefitinib

source_name: PC9GRM2, 16hr, EGF and gefitinib


title: 1625

value: IIIb


title: liver_RFIplR_115kg_rep3

tag: feed condition


title: PC9GRM2_EGF_IRS_17hr

description: Gene expression after 17hr in PC9GRM2 treated with EGF and gefitinib

source_name: PC9GRM2, 17hr, EGF and gefitinib


title: LLC Tumor_Adolescent, rep11

description: Young 0Gy acuteProton LLC (156)


title: PC9GRM2_EGF_IRS_15hr

description: Gene expression after 15hr in PC9GRM2 treated with EGF and gefitinib

source_name: PC9GRM2, 15hr, EGF and gefitinib


title: liver_RFIpl_115kg_rep7

description: Gene expression in 115 kg body weight pig liver with high residual feed intake

source_name: liver, high-RFI, 115kg body weight

value: RFIpl

value: Ad libitum


title: PC9GRM2_EGF_IRS_13hr

description: Gene expression after 13hr in PC9GRM2 treated with EGF and gefitinib

source_name: PC9GRM2, 13hr, EGF and gefitinib


title: 1359

value: Ovary

value: IIIc


title: 1776


title: liver_RFIplR_115kg_rep2

value: RFIplR

value: Restricted at RFIneg feeding level


title: liver_RFIplR_115kg_rep1


title: 1355

value: IIa

value: chemotherapy sensitive


title: LLC Tumor_Adolescent, rep10

description: Young 0Gy acuteProton LLC (155)

value: Lewis lung carcinoma (LLC) tumor

value: male

value: young


title: PC9GRM2_EGF_IRS_14hr

description: Gene expression after 14hr in PC9GRM2 treated with EGF and gefitinib

source_name: PC9GRM2, 14hr, EGF and gefitinib

value: EGF and gefitinib


title: 1605

value: IIb

value: chemotherapy resistant


title: 1296

value: II


title: LLC Tumor_Adolescent, rep12

description: Young 0Gy acuteProton LLC (157)


title: liver_RFIpl_115kg_rep6

value: liver


title: liver_RFIplR_115kg_rep4


title: LLC Tumor_Adolescent, rep8

description: Young 0Gyx3 Proton LLC (141)


title: LLC Tumor_Adolescent, rep9

description: Young 0Gyx3 Proton LLC (142)


title: liver_RFIpl_115kg_rep8


title: 1299

value: IIIb


title: LLC Tumor_Adolescent, rep7

description: Young 0Gyx3 Proton LLC (140)


title: PC9GRM2_EGF_IRS_12hr

description: Gene expression after 12hr in PC9GRM2 treated with EGF and gefitinib

source_name: PC9GRM2, 12hr, EGF and gefitinib

value: non-small cell lung cancer cell line

value: gefitinib-resistant cell line


title: liver_RFIpl_115kg_rep4

value: RFIpl

value: Ad libitum


title: liver_RFIpl_115kg_rep5


title: LLC Tumor_Adolescent, rep6

description: Young 0Gyx3 Proton LLC (139)


title: 1587

value: Ovary

value: IIIc


title: LLC Tumor_Adolescent, rep4

description: Young 0Gyx3 Proton LLC (137)


title: PC9GRM2_EGF_IRS_9hr

description: Gene expression after 9hr in PC9GRM2 treated with EGF and gefitinib

source_name: PC9GRM2, 9hr, EGF and gefitinib


title: liver_RFIpl_115kg_rep3


title: PC9GRM2_EGF_IRS_11hr

description: Gene expression after 11hr in PC9GRM2 treated with EGF and gefitinib

source_name: PC9GRM2, 11hr, EGF and gefitinib


title: PC9GRM2_EGF_IRS_10hr

description: Gene expression after 10hr in PC9GRM2 treated with EGF and gefitinib

source_name: PC9GRM2, 10hr, EGF and gefitinib


title: 1703


title: liver_RFIpl_115kg_rep2


title: liver_RFIpl_115kg_rep1


title: 1381

value: IIIa


title: PC9GRM2_EGF_IRS_7hr

description: Gene expression after 7hr in PC9GRM2 treated with EGF and gefitinib

source_name: PC9GRM2, 7hr, EGF and gefitinib


title: 1308

source_name: Tumor

value: chemotherapy sensitive


title: LLC Tumor_Adolescent, rep3

description: Young 0Gyx3 Proton LLC (136)

source_name: Young 0Gy proton LLC tumor

value: Lewis lung carcinoma (LLC) tumor


title: 1304


title: LLC Tumor_Adolescent, rep1

description: Young 0Gyx3 Proton LLC (134)

value: male


title: liver_RFIneg_115kg_rep7

description: Gene expression in 115 kg body weight pig liver with low residual feed intake

source_name: liver, low-RFI, 115kg body weight

value: RFIneg


title: liver_RFIneg_115kg_rep8


title: PC9GRM2_EGF_IRS_6hr

description: Gene expression after 6hr in PC9GRM2 treated with EGF and gefitinib

source_name: PC9GRM2, 6hr, EGF and gefitinib

value: EGF and gefitinib


title: liver_RFIneg_115kg_rep5


title: 1561

value: IIb


title: PC9GRM2_EGF_IRS_4hr

description: Gene expression after 4hr in PC9GRM2 treated with EGF and gefitinib

source_name: PC9GRM2, 4hr, EGF and gefitinib


title: 1680

value: IIc

value: chemotherapy resistant


title: LLC Tumor_Adolescent, rep2

description: Young 0Gyx3 Proton LLC (135)

value: young


title: CD11b DC Xbp1 KO (DC conditional KO), biological replicate 2

city: Ghent

first: Sophie

last: Janssens

address: Technologiepark 927

department: VIB Inflammation Research Center

country: Belgium

institute: University of Ghent-VIB

description: Splenic CD11b DC from Xbp1 KO

hyb_protocol: Standard Affymetrix protocol. cDNA was hybrised on Affymetrix GeneChip Mouse Gene 1.0 ST Arrays (GPL6246).

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data were processed using Bioconductor. Normalisation was done by RMA.
probe_group_file: MoGene-1_0-st-v1.r4.pgf
meta-probeset_file: MoGene-1_0-st-v1.r4.mps

source_name: CD11b, KO

label_protocol: Affymetrix WT Terminal Labeling Kit

growth_protocol: Spleens were isolated from WT and KO mice (age around 8 weeks). Spleen was minced and digested with Liberase TM (0.02mg/ml; Roche) and Dnase I recombinant (0.01 U/µl; Roche) for 30 min at 37°C in HBSS followed by lysis of red blood cells. CD3+ and CD19+ cells were depleted using anti-CD3 FITC and anti-CD19 FITC antibodies and anti-FITC microbeads (Miltenyi Biotec). T- and B-depleted splenocytes were stained with CD11c-PE Texas red, CD8a-PeCy5, CD11b-PeCy7, MHCII-APC-Cy7, CD24-Pacific blue and live/dead marker conjugated to Amcyan. CD8+ cDCs were isolated by cell sorting gating on FSC/SSC/singlets/alive/FITC-/ MHCII+/ CD24hi/ CD8+/ CD11cint-hi whereas CD11b+ cDCs were isolated by gating on FSC/ SSC/ singlets/ alive/FITC-/ MHCII+/ CD24lo-int/ CD11b+/ CD11chi. Cell sorting was performed on a FACSAria (BD Biosciences).

extract_protocol: RNEasy Plus Micro Kit (QIAGEN)

treatment_protocol: Not applicable

value: Spleen

value: Xbp1 KO


title: liver_RFIneg_115kg_rep6

value: liver


title: PC9GRM2_EGF_IRS_5hr

description: Gene expression after 5hr in PC9GRM2 treated with EGF and gefitinib

source_name: PC9GRM2, 5hr, EGF and gefitinib

value: non-small cell lung cancer cell line

value: gefitinib-resistant cell line


title: LLC Tumor_Adolescent, rep5

description: Young 0Gyx3 Proton LLC (138)


title: 1627

value: Ovary


title: liver_RFIneg_115kg_rep4

value: Ad libitum


title: PC9GRM2_EGF_IRS_3hr

description: Gene expression after 3hr in PC9GRM2 treated with EGF and gefitinib

source_name: PC9GRM2, 3hr, EGF and gefitinib


title: CD11b DC wild type, biological replicate 3

description: Splenic CD11b DC from WT

source_name: CD11b, WT

value: WT


title: liver_RFIneg_115kg_rep2


title: PC9GRM2_EGF_IRS_2hr

description: Gene expression after 2hr in PC9GRM2 treated with EGF and gefitinib

source_name: PC9GRM2, 2hr, EGF and gefitinib


title: CD11b DC Xbp1 KO (DC conditional KO), biological replicate 3

description: Splenic CD11b DC from Xbp1 KO


title: 1224

value: Unavailable

value: chemotherapy sensitive


title: 1157

value: IIIc


title: liver_RFIneg_115kg_rep3

value: RFIneg


title: PC9GRM2_EGF_IRS_0.5hr

description: Gene expression after 0.5hr in PC9GRM2 treated with EGF and gefitinib

source_name: PC9GRM2, 0.5hr, EGF and gefitinib

value: EGF and gefitinib


title: 1101

value: IV


title: CD11b DC wild type, biological replicate 2

description: Splenic CD11b DC from WT


title: 1188

value: III


title: CD11b DC wild type, biological replicate 1

description: Splenic CD11b DC from WT


title: CD11b DC Xbp1 KO (DC conditional KO), biological replicate 1

description: Splenic CD11b DC from Xbp1 KO


title: liver_RFIneg_115kg_rep1


title: 1100

value: chemotherapy resistant


title: PC9GRM2_EGF_IRS_1hr

description: Gene expression after 1hr in PC9GRM2 treated with EGF and gefitinib

source_name: PC9GRM2, 1hr, EGF and gefitinib


title: PC9GRM2_EGF_23hr

description: Gene expression after 23hr in PC9GRM2 treated with EGF

source_name: PC9GRM2, 23hr, EGF

value: EGF


title: 1240


title: CD8 DC Xbp1 KO (DC conditional KO), biological replicate 1

description: Splenic CD8 DC from Xbp1 KO

source_name: CD8 DC, KO

value: Spleen


title: CD8 DC Xbp1 KO (DC conditional KO), biological replicate 3

description: Splenic CD8 DC from Xbp1 KO

value: Xbp1 KO


title: liver_RFIpl_20kg_rep7

description: Gene expression in 20 kg body weight pig liver with high residual feed intake

data_processing: All analyses were then performed using the R software version 2.10.0 (R Development Core Team, 2008a). Raw spots intensities were first submitted to quality filtration based on 4 criteria: intensity, uniformity, saturation and outliers detection. Intensities of filtered spots were transformed into log2(Cy3), and data were normalized by median centering, i.e. subtracting the median value across all probes from all raw values for each sample to obtain experimentally consolidated gene expression values. Normalized data were submitted to an analysis of variance using the fixed effects of genetic line breed (RFIpl or RFIneg).

source_name: liver, high-RFI, 20kg body weight

value: liver

value: RFIpl


title: CD8 DC Xbp1 KO (DC conditional KO), biological replicate 2

description: Splenic CD8 DC from Xbp1 KO


title: PC9GRM2_EGF_IRS_0hr

description: Gene expression after 0hr in PC9GRM2 treated with EGF and gefitinib

source_name: PC9GRM2, 0hr, EGF and gefitinib

value: non-small cell lung cancer cell line

value: gefitinib-resistant cell line


title: PC9GRM2_EGF_20hr

description: Gene expression after 20hr in PC9GRM2 treated with EGF

source_name: PC9GRM2, 20hr, EGF


title: PC9GRM2_EGF_21hr

description: Gene expression after 21hr in PC9GRM2 treated with EGF

source_name: PC9GRM2, 21hr, EGF


title: liver_RFIpl_20kg_rep6

value: Ad libitum


title: liver_RFIpl_20kg_rep5


title: 1413

source_name: Tumor

value: Ovary


title: CD8 DC wild type, biological replicate 3

description: Splenic CD8 DC from WT

source_name: CD8 DC, WT

value: WT


title: 1351

value: chemotherapy sensitive


title: PC9GRM2_EGF_22hr

description: Gene expression after 22hr in PC9GRM2 treated with EGF

source_name: PC9GRM2, 22hr, EGF


title: CD8 DC wild type, biological replicate 1

description: Splenic CD8 DC from WT


title: Ts_8

city: Taipei

first: Tzu-Hao

last: Chang

address: 250 Wu-Xin Street

department: Graduate Institute of Biomedical Informatics

country: Taiwan

institute: Taipei Medical University

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: The arrays were scanned to a target intensity of 500 by a GeneArray Scanner, and patterns of hybridization were detected as light emitted from the fluorescent reporter groups incorporated into the target and hybridized to oligonucleotide probes.

data_processing: The CEL files were generated using Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings. Signal intensities were derived from CEL files and Signal intensity derived from the CEL files, using GCRMA method.

source_name: primary surgical treatment

label_protocol: biotin

growth_protocol: Frozen tissue samples were embedded, and sections were cut and mounted on slides. The slides were stained with H&E to ensure that at least 70% of the cellular content was comprised of epithelial ovarian cancer cells.

treatment_protocol: Frozen rissues

value: ovarian cancer cells

tag: tissue subtype

value: serous

tag: advanced disease stage

value: stage III

tag: recurrence status

value: recurrence

tag: survival/death

value: survival


title: liver_RFIpl_20kg_rep4


title: Ts_4

value: death


title: CD8 DC wild type, biological replicate 2

description: Splenic CD8 DC from WT


title: Ts_47

value: non-recurrence


title: Cxcr5 positive CD4+ T cells

city: Bethesda

first: Lai

last: Wei

state: MD

address: 10 Center Dr. Room 2B47

institute: NIH/NEI/NCCAM

hyb_protocol: Labeled RNA was hybrizized onto arrays using GeneChip® Hybridization, Wash, and Stain Kit

scan_protocol: GeneChip Operating Software (GCOS v1.1) was used.

data_processing:
Data was summarized using RMA algorithm within GeneSpring 11.0.
probe group file: MoGene-1_0-st-v1.r4.pgf
meta-probeset file: MoGene-1_0-st-v1.r4.mps

source_name: CD4+ T cells

label_protocol: 2 ug total RNA was labeled using Ambion® WT Expression Kit and GeneChip® WT Terminal Labeling and Controls Kit

growth_protocol: Naïve CD4+CD25-CD44lowCD62Lhigh T cells from C57BL6 mice were FACS-sorted and activated with plate-bound anti-CD3e (clone, 2C11) and anti-CD28 (clone, 37.51) under neutral conditions.

extract_protocol: Total RNA was extracted with TRIzol reagent (Invitrogen).

treatment_protocol: 24 hours after activation, cells were infected by retroviruses control empty vector (Empty-RV-GFP). One days after infection, GFP cells were FACS sorted.

tag: cell type

value: CD4+ T cells

tag: genotype/variation

value: Cxcr5 positive


title: PC9GRM2_EGF_19hr

description: Gene expression after 19hr in PC9GRM2 treated with EGF

source_name: PC9GRM2, 19hr, EGF

tag: drug response

tag: cell line

tag: time

tag: treatment

value: EGF


title: Ts_46

value: stage II


title: Ts_5

value: stage IV


title: empty vector transfected CD4+ T cells

description: RV

value: empty vector transfected


title: PC9GRM2_EGF_16hr

description: Gene expression after 16hr in PC9GRM2 treated with EGF

source_name: PC9GRM2, 16hr, EGF

value: non-small cell lung cancer cell line

value: gefitinib-resistant cell line


title: liver_RFIpl_20kg_rep2

value: liver

value: RFIpl

value: Ad libitum


title: liver_RFIneg_20kg_rep8

description: Gene expression in 20 kg body weight pig liver with low residual feed intake

source_name: liver, low-RFI, 20kg body weight

value: RFIneg


title: Cxcr5 negative CD4+ T cells

value: Cxcr5 negative


title: liver_RFIpl_20kg_rep1


title: PC9GRM2_EGF_IRS_8hr

description: Gene expression after 8hr in PC9GRM2 treated with EGF and gefitinib

source_name: PC9GRM2, 8hr, EGF and gefitinib

value: EGF and gefitinib


title: PC9GRM2_EGF_18hr

description: Gene expression after 18hr in PC9GRM2 treated with EGF

source_name: PC9GRM2, 18hr, EGF


title: liver_RFIneg_20kg_rep7


title: Ascl2 vector transfected CD4+ T cells,  biological rep2

value: Ascl2 vector transfected


title: PC9GRM2_EGF_17hr

description: Gene expression after 17hr in PC9GRM2 treated with EGF

source_name: PC9GRM2, 17hr, EGF


title: Ascl2 vector transfected CD4+ T cells,  biological rep1


title: Ts_43

value: ovarian cancer cells

value: serous

value: survival


title: Ts_45

value: non-recurrence


title: liver_RFIneg_20kg_rep5


title: PC9GRM2_EGF_13hr

description: Gene expression after 13hr in PC9GRM2 treated with EGF

source_name: PC9GRM2, 13hr, EGF

value: EGF


title: empty vector transfected CD4+ T cells,  biological rep2

value: CD4+ T cells


title: Ts_37

value: stage III


title: PC9GRM2_EGF_15hr

description: Gene expression after 15hr in PC9GRM2 treated with EGF

source_name: PC9GRM2, 15hr, EGF


title: liver_RFIneg_20kg_rep6


title: liver_RFIpl_20kg_rep8

source_name: liver, high-RFI, 20kg body weight


title: Ts_41


title: PC9GRM2_EGF_10hr

description: Gene expression after 10hr in PC9GRM2 treated with EGF

source_name: PC9GRM2, 10hr, EGF


title: liver_RFIneg_20kg_rep4


title: liver_RFIneg_20kg_rep3


title: Ts_3

value: recurrence


title: PC9GRM2_EGF_11hr

description: Gene expression after 11hr in PC9GRM2 treated with EGF

source_name: PC9GRM2, 11hr, EGF

value: non-small cell lung cancer cell line


title: Ts_39


title: PC9GRM2_EGF_12hr

description: Gene expression after 12hr in PC9GRM2 treated with EGF

source_name: PC9GRM2, 12hr, EGF

value: gefitinib-resistant cell line


title: liver_RFIneg_20kg_rep2

value: liver


title: Gata6-KO heart, CRE, biological rep3

city: Cincinnati

first: Bruce

middle: J

last: Aronow

state: OH

address: 240 Albert Sabin Way

department: Biomedical Informatics, Developmental Biology

institute: Cincinnati Children's Hospital Medical Center

description: total heart mRNA gene expression as a function of Gata4 or Gata6 knockout

hyb_protocol: Affymetrix Mouse Genes ST 1.0 microarray standard conditions

scan_protocol: Affymetrix Expression Console

data_processing:
Expression values were subjected to RMA normalization using Affymetrix CDF probeset definition and GeneSpringGX v7.3.1.
Relative expression levels for each probeset was calculated in reference to the median of its value in Gata4Flox and Gata6Flox non-CRE control samples. These data are on the Series record.

source_name: Gata6-KO heart, CRE, biological rep3

label_protocol: Ambion WT labeling kit

growth_protocol: Six-ten week old mice were used for all experiments, and were housed under pathogen-free conditions.

extract_protocol: Harvested hearts were homogenized in Trizol and RNA from homogenates was isolated via ethanol precipitation.

treatment_protocol: Cre expression by the MHCalpha transgene leading to Gata4-flox or Gata6-flox gene deletion during late cardiac development.

value: heart

tag: genotype

tag: age

value: 8 week adult mice


title: Gata6-KO heart, CRE, biological rep2

source_name: Gata6-KO heart, CRE, biological rep2


title: empty vector transfected CD4+ T cells,  biological rep1

value: empty vector transfected


title: Ts_36


title: PC9GRM2_EGF_9hr

description: Gene expression after 9hr in PC9GRM2 treated with EGF

source_name: PC9GRM2, 9hr, EGF


title: PC9GRM2_EGF_8hr

description: Gene expression after 8hr in PC9GRM2 treated with EGF

source_name: PC9GRM2, 8hr, EGF


title: liver_RFIpl_20kg_rep3

city: Saint-Gilles

first: Annie

last: Vincent

institute: INRA

description: Gene expression in 20 kg body weight pig liver with high residual feed intake

hyb_protocol: Microarray hybridizations were carried out in Agilent’s SureHyb hybridization chambers containing 1.65 µg of Cy3-labeled cRNA sample per hybridization. Hybridization reactions were performed at 65°C for 17 h using Agilent’s Gene Expression Hybridization Kit

scan_protocol: After washing, microarrays were scanned at 5 µm/pixel resolution using the Agilent DNA Microarray Scanner G2505C, and images were analyzed with Agilent Feature Extraction Software (Version 10.7.3.1, protocol GE1_107_Sep09)

label_protocol: Total RNA (150 ng) from each sample was labeled with Cy3 dye using the low RNA input linear amplification kit (Agilent Technologies) following the manufacturer’s instructions. Briefly, a two-step procedure was used to generate fluorescent complementary RNA (cRNA) by using T7 RNA polymerase. Samples were then purified with an RNeasy mini elute kit (Qiagen, Hilden, Germany)

growth_protocol: The low-RFI (RFIneg) and high-RFI (RFIpl) pigs were fed ad libitum.

value: RFIpl

value: Ad libitum


title: PC9GRM2_EGF_7hr

description: Gene expression after 7hr in PC9GRM2 treated with EGF

source_name: PC9GRM2, 7hr, EGF


title: PC9GRM2_EGF_24hr

description: Gene expression after 24hr in PC9GRM2 treated with EGF

source_name: PC9GRM2, 24hr, EGF


title: Gata4-KO heart, CRE, biological rep3

source_name: Gata4-KO heart, CRE, biological rep3


title: Ts_34

source_name: primary surgical treatment


title: Ts_35


title: Ts_32


title: Gata4-KO heart, CRE, biological rep1

source_name: Gata4-KO heart, CRE, biological rep1


title: Gata6-KO heart, CRE, biological rep1

source_name: Gata6-KO heart, CRE, biological rep1


title: Gata6-flox heart, non-CRE, biological rep1


title: Wild type Exponential, biological rep 1

city: Rochester

first: Paul

last: Dunman

state: NY

address: 601 Elmwood Avenue

department: Microbiology and Immunology

institute: University of Rochester

description: Gene expression data from mid-exponential phase wildtype 98-37-09 cells

hyb_protocol: 1.5 ug of cDNA were hybrized for 16 hr at 45C on an A. baumannii Affymetrix GeneChip.  GeneChips were washed and stained in an Affymetrix Fluidics Station using ProKaryotic GE-wash2 protocol.

scan_protocol: GeneChips were scanned in an Affymetrix 7G GeneArray Scanner

data_processing: The data were analyzed with Microarray Suite version 5.0 using Affymetrix default analysis settings.

organism: Acinetobacter baumannii

source_name: Acinetobacter baumannii mid-exponential

label_protocol: cDNA was synthesized, fragmented and biotinylated according to the manufacturer's protocol for prokaryotic antisense labeling (Affymetrix)

growth_protocol: Cells were grown to mid-exponential phase (Optical Density 600nm of 0.4-0.5) in LB broth at 37C with aeration (225 rpm in a rotary shaker)

extract_protocol: Total bacterial RNA was isolated using Rneasy kits according to the manufacturer's recommendations (Qiagen)

treatment_protocol: Once reaching mid exponential phase 1:1 acetone-ethanol was added to inhibit cellular ribonucleases

tag: sample

value: Whole cell

value: Wild type

tag: growth phase

value: Mid-exponential


title: PC9GRM2_EGF_6hr

description: Gene expression after 6hr in PC9GRM2 treated with EGF

data_processing: After aggregating all the scanned signals for the different time points, cell lines, and treatments into a single data matrix, quantile normalization (Bolstad et al., Bioinformatics, 2003) was applied to remove the between-experiment distributional biases due to assay artifacts by forcing the same percentile values on all of the processed data.

source_name: PC9GRM2, 6hr, EGF

tag: tissue


title: Gata4-KO heart, CRE, biological rep2

source_name: Gata4-KO heart, CRE, biological rep2


title: Ts_31

value: ovarian cancer cells

value: serous

value: survival


title: Gata6-flox heart, non-CRE, biological rep2


title: Ts_2

value: death


title: RNase T2-mutant Exponential, biological rep 2

description: Gene expression data from mid-exponential phase ACJ7 (A1S_3026 mutation) cells

value: RNase T2 mutant


title: liver_RFIneg_20kg_rep1

address: domaine de la prise

description: Gene expression in 20 kg body weight pig liver with low residual feed intake

source_name: liver, low-RFI, 20kg body weight

extract_protocol: For total RNA extraction, samples of frozen tissues (80 to 100 mg each) were homogenized in Trizol reagent (Invitrogen, Cergy-Pontoise, France) using a TissueLyser (Qiagen) and were then treated as previously described (Vincent et al., 2012). RNA was finally purified using a silica-membrane technology under vacuum (Nucleospin 8 RNA kit, Macherey Nagel, Hoerdt, France)

tag: strain

value: RFIneg


title: PC9GRM2_EGF_5hr

description: Gene expression after 5hr in PC9GRM2 treated with EGF

source_name: PC9GRM2, 5hr, EGF

value: non-small cell lung cancer cell line

value: EGF


title: Wild type Exponential, biological rep 2


title: Ts_26

value: stage III

value: recurrence


title: Gata4-flox heart, non-CRE, biological rep2

value: heart

value: 8 week adult mice


title: RNase T2-mutant Exponential, biological rep 1


title: PC9GRM2_EGF_4hr

description: Gene expression after 4hr in PC9GRM2 treated with EGF

source_name: PC9GRM2, 4hr, EGF

value: gefitinib-resistant cell line


title: PC9GRM2_EGF_3hr

description: Gene expression after 3hr in PC9GRM2 treated with EGF

source_name: PC9GRM2, 3hr, EGF


title: Ts_28

value: non-recurrence


title: PC9GRM2_EGF_1hr

description: Gene expression after 1hr in PC9GRM2 treated with EGF

source_name: PC9GRM2, 1hr, EGF


title: PC9GRM2_EGF_0.5hr

description: Gene expression after 0.5hr in PC9GRM2 treated with EGF

source_name: PC9GRM2, 0.5hr, EGF


title: WT heart, CRE, biological rep2

source_name: Wt Gata4, Wt Gata6, heart, CRE transgenic, biological rep2

value: CRE


title: Gata4-flox heart, non-CRE, biological rep1


title: PC9GRM2_EGF_2hr

description: Gene expression after 2hr in PC9GRM2 treated with EGF

source_name: PC9GRM2, 2hr, EGF


title: WT heart, CRE, biological rep1

source_name: Wt Gata4, Wt Gata6, heart, CRE transgenic, biological rep1


title: VPA mHSC at 64 hours_Repeat1

city: Brussels

first: Inge

last: Mannaerts

address: Laarbeeklaan 103

department: Liver Cell Biology Lab

institute: Vrije Universiteit Brussel

description: BalbC; primary hepatic stellate cells, early timepoints; treated with HDAC-inhibitor

hyb_protocol: Hybridization for 16h at 45°C on mouse Gene 1.0 ST arrays (Affymetrix)

scan_protocol: Scanned on a 2-µm Affymetrix 3000 GeneScanner

data_processing:
All image files were generated using the Affymetrix GeneChip command console (AGCC)
The raw data were analyzed with RMA sketch using the standard settings for Gene 1.0 ST arrays of Expression Console in the AGCC software (affymetrix).

source_name: Primary mouse hepatic stellate cells, cultured for 64 hours, treated with 2.5 mM VPA

label_protocol: DNA is labeled by terminal deoxynucleotidyl transferase (TDT) with the Affymetrix DNA Labeling reagent that is covalently linked to biotin (GeneChip WT terminal Labeling kit, Affymetrix)

growth_protocol: Freshly isolated mouse hepatic stellate cells were isolated from BalbC mice and cultured in DMEM supplemented with 10 % FBS, 0.1% PenStrep and 0.1% Ultraglutamine

extract_protocol: RNA isolation with GeneJet RNA purification kit (Thermo) according to manufacturer' s protocol

treatment_protocol: 2 hours after seeding, unattached cells were washed away and valproic acid treatment was started (2.5 mM), T=0

tag: background strain

value: BalbC

value: primary hepatic stellate


title: Ts_23

value: ovarian cancer cells

tag: tissue subtype


title: Ts_20

value: serous

tag: advanced disease stage


title: Ts_21

tag: recurrence status

value: survival


title: Ts_24

tag: survival/death


title: PC9GRM2_EGF_0hr

city: Minato-ku

first: Noriko

last: Gotoh

institute: The University of Tokyo

description: Gene expression after 0hr in PC9GRM2 treated with EGF

hyb_protocol: Hybridization was carried out using the Gene Expression Hybridization Kit (Agilent Technologies), according to the manufacturer’s directions. Briefly, a cRNA sample (1.65 g) was subjected to fragmentation (30 min at 60 °C) and then hybridization on a 44K Agilent Whole Human Genome Oligo Microarray (G4112F) (Agilent Technologies). . RNA samples with an RNA integrity number (RIN) greater than 8 were used for further analysis. Hybridization was carried out on a 44K Agilent Whole Human Genome Oligo Microarray (G41112F) (Agilent Technologies).

scan_protocol: Microarrays were scanned by a dynamic autofocus microarray scanner (Agilent DNA Microarray Scanner, Agilent Technologies) under the default parameters (Green PMT was set to 100%, and the scan resolution was set to 5 um. Feature Extraction Software v9.1 (Agilent Technologies) was used to obtain a raw signal value and a quality flag (Present [P], Marginal [M], or Absent [A]).

source_name: PC9GRM2, 0hr, EGF

label_protocol: RNA samples were labeled using the Agilent Low RNA Input Linear Amplification Kit (Agilent Technologies) according to the manufacturer’s directions. Briefly, amplification and labeling of total RNA (500 ng) was performed using Cyanine 3-CTP.


title: VPA mHSC at 64 hours_Repeat2

tag: cell type


title: Control mHSC at 64 hours_Repeat3

description: BalbC; primary hepatic stellate cells, early timepoints

source_name: Primary mouse hepatic stellate cells, cultured for 64 hours


title: PC9_None_24hr

description: Gene expression after 24hr in PC9 with no treatment

source_name: PC9, 24hr, no treatment

value: gefitinib-sensitive cell line

value: no treatment


title: PC9_None_23hr

description: Gene expression after 23hr in PC9 with no treatment

source_name: PC9, 23hr, no treatment


title: Ts_19

source_name: primary surgical treatment

value: death


title: VPA mHSC at 64 hours_Repeat3


title: PC9_None_22hr

description: Gene expression after 22hr in PC9 with no treatment

source_name: PC9, 22hr, no treatment

value: non-small cell lung cancer cell line


title: PC9GRM2_EGF_14hr

description: Gene expression after 14hr in PC9GRM2 treated with EGF

source_name: PC9GRM2, 14hr, EGF

value: EGF


title: PC9_None_21hr

description: Gene expression after 21hr in PC9 with no treatment

source_name: PC9, 21hr, no treatment


title: Ts_15

value: stage I


title: Ts_17

value: recurrence


title: Ts_11

value: stage III


title: Tm_97

value: mucinous


title: Ts_14


title: Control mHSC at 16 hours_Repeat2

source_name: Primary mouse hepatic stellate cells, cultured for 16 hours


title: Control mHSC at 16 hours_Repeat1


title: Control mHSC at 64 hours_Repeat2


title: PC9_None_20hr

description: Gene expression after 20hr in PC9 with no treatment

source_name: PC9, 20hr, no treatment


title: VPA mHSC at 4 hours_Repeat3

source_name: Primary mouse hepatic stellate cells, cultured for 4 hours, treated with 2.5 mM VPA


title: PC9_None_17hr

description: Gene expression after 17hr in PC9 with no treatment

source_name: PC9, 17hr, no treatment


title: PC9_None_18hr

description: Gene expression after 18hr in PC9 with no treatment

source_name: PC9, 18hr, no treatment


title: Tm_96

value: stage II


title: Control mHSC at 4 hours_Repeat2

source_name: Primary mouse hepatic stellate cells, cultured for 4 hours


title: Control mHSC at 4 hours_Repeat3


title: PC9_None_16hr

description: Gene expression after 16hr in PC9 with no treatment

source_name: PC9, 16hr, no treatment


title: PC9_None_15hr

description: Gene expression after 15hr in PC9 with no treatment

source_name: PC9, 15hr, no treatment


title: PC9_None_13hr

description: Gene expression after 13hr in PC9 with no treatment

source_name: PC9, 13hr, no treatment


title: VPA mHSC at 4 hours_Repeat2


title: PC9_None_19hr

description: Gene expression after 19hr in PC9 with no treatment

source_name: PC9, 19hr, no treatment


title: Control mHSC at 64 hours_Repeat1

source_name: Primary mouse hepatic stellate cells, cultured for 64 hours


title: VPA mHSC at 4 hours_Repeat1


title: PC9_None_14hr

description: Gene expression after 14hr in PC9 with no treatment

source_name: PC9, 14hr, no treatment


title: Tm_98


title: SAM_waterdeficit-rewatering_rep1

city: Uppsala

first: Clement

last: Lafon-Placette

address: Almas Allé 5

country: Sweden

institute: SLU

description: SAM DNA methylation after 9 days in moderate watere deficit floowed by 5 days in non-limiting water conditions

hyb_protocol: DNA hybridization was conducted in Imaxio (Clermont-Ferrand, France) according to Agilent Technologies instructions. Briefly, Cy5- and Cy3-labeled DNAs were pooled in ddH2O before addition of Hybridization mix (Agilent Technologies), incubation at 95°C for 3 min and then at 37°C for 30 min. Samples were loaded onto the arrays and hybridized at 67°C for 40 hours at 20 rpm in Agilent hybridization chambers. Arrays were then washed according to the protocol at room temperature.

scan_protocol: Microarray slides were scanned with G2505C scanner (Agilent Technologies, France) and raw signal data were extracted using Feature Extraction 10.7 software. Reproducibility and reliability of each single microarray was assessed using Quality Control report data (Feature Extraction, Agilent Technologies).

data_processing: For CH3 microarray, data normalization, performed by Feature Extraction software, was used to correct cyanine bias with the linear method: the mean signal of probes selected for quality criteria (signal above background, non-outlier and whose ranks are similar between the two dyes) allowed the normalization of all probes values. For each probe, Cy5/Cy3 log ratio was then calculated. Data filtering was based on Feature Extraction flag criteria: non outlier population; not saturated, uniform and significant Cy3 and Cy5 probe signal; Cy3 and Cy5 probe signal above background. A probe signal was considered as “well above background” if g/rBGSubSignal was greater than 2.6 g/rBG_SD. To pass the filtering, a probe needed to pass all flag criteria for all replicates of at least one experimental condition (Control, Water Deficit or Re-irrigation). After this data filtering, 441214 probes were available. To determine if there were sequences differentially methylated, a probe signal fold change of 2 between at least 2 experimental conditions was chosen as a threshold. To reduce the number of false positive, additional filtering criteria were used: probes with mean signal between experimental conditions below 5% mean signal of total probes were eliminated; per condition and per dye, probes with signal below 10% mean signal of total probes were also eliminated. Probes needed a GC content comprised between 20% and 80% and a Tm comprised between 60°C and 85°C. Finally, when focusing on genes and 0.5 kb upstream/downstream regions, only unique probes (matching with one locus on v2.0 P. trichocarpa genome with an identity threshold of 50 nt out of 60) were selected.

organism: Populus x canadensis

source_name: SAM, water deficit followed by rewatering, MeDIP DNA,  replicate 1

label_protocol: For each sample, labeled DNA was generated according to Agilent Technologies recommendations. Briefly, near 500 ng of input control and immunoprecipitated (IP) methylated DNA were labeled using Genomic DNA Enzymatic Labeling Kit (Agilent Technologies, France). The use of random primers and the exo-Klenow fragment allowed the differential labeling of input control and IP methylated DNA with cyanine 3-labeled dUTP and cyanine 5-labeled dUTP respectively. Labeled DNA was purified using 30 kDa Amicon columns (Millipore, Molsheim, France). Quality control of synthesized labeled DNA was based on DNA and Cy5/Cy3 concentration measurement. For each sample, a yield of 2.5 µg of labeled DNA and a specific activity of 7-20 pmolCy5/gDNA and 18-25 pmolCy3/gDNA were chosen as quality minimum thresholds.

growth_protocol: Unrooted dormant stem cuttings of Populus × euramericana (P. deltoides × P. nigra) ‘Carpaccio’ genotype were obtained from INRA nursery (Nancy, France in 2008). Ten-years old mother plants are cut off each spring. Cuttings were 22 cm long and 0.5-2 cm wide and were harvested in February from plants grown in INRA nursery. Unrooted cuttings (20 for 101-74 and 12 for each hybrid) were then stocked 1 month in 2°C cold dark room. Before potting, cuttings soaked in water in vertical position to favor rooting. Rooted cuttings of Populus × euramericana (P. deltoides × P. nigra) ‘Carpaccio’ genotype (6 cuttings per treatment: ‘Control’, ‘Water deficit’ and ‘Re-irrigation’) were planted in 20L pots containing a mixture of peat and sand (50/50, v/v) amended with magnesian chalk (60 g/100 L) and fertilized with a low releasing fertilizer (Nutricote T100, 13/13/13/2, N/P/K/Mg + trace elements). Plants were placed in a greenhouse (Nancy, France in April 2008) exposed to natural daylight (ranging from 350 to 900 μmol m−2 s−1) and where temperature was maintained in the range 19–26 °C with humidity oscillating between 50 and 75%. Plants were watered to field capacity three times a day for 5 weeks, until plant height was between 0.6 and 0.9 m.

extract_protocol: Shoot apical meristem from 3 individuals (about 150 mg fresh weight per extraction) of the ‘Carpaccio’ P. × euramericana genotype for each treatment (‘Control’, ‘Water deficit’ and ‘Re-irrigation’) were grounded into a fine powder in liquid N2 and used for DNA extraction. CTAB DNA extraction protocol was used (Doyle & Doyle, 1987). Chemicals were purchased from Sigma-Aldrich (Saint-Quentin Fallavier, France). Briefly, for each water treatment, 150 mg of shoot apical meristem powder were solubilised in 1.5 mL of a pre-heated lysis buffer composed of 100 mM Tris-HCl (pH 8.0), 20 mM EDTA (pH 8.0), 2% (w/v) CTAB, 1.4 M NaCl, 0.2% (v/v) β-mercaptoethanol, 4% (w/v) PVP, 0.1 mg/mL Proteinase K. Samples were incubated at 60°C for 1h on a rotator. DNA was isolated after 2 chloroform/isoamyl alcohol (24:1) (v/v) extractions, RNase A digestion and isopropanol precipitation. DNA pellets were solubilised in ultrapure water and concentrations were estimated with Nanodrop quantification.   DNA was then sonicated using a VC 505 Vibra-Cell sonicator (Fisher Scientific, Illkirch, France) to obtain fragments ranging from 0.2 to 0.8 kb. Methylated DNA was immunoprecipitated according to (Weng et al., 2009). Briefly, 11 µg of sonicated DNA were diluted in 250 µL of IP buffer 1X composed of 10 mM Na3PO4 (pH 7.0), 140 mM NaCl, 0.05% Triton X-100 and denaturated during 10 min in boiling water. After 10 min of cooling in ice, 4 µg of DNA were kept at -20°C to be used as input control for microarray analysis. The 7 µg of DNA left were incubated overnight with 10 µg of mouse monoclonal anti-5mC antibodies (1 µg/µL; Eurogentec, France) on a rotator in a 4°C cold room. The DNA-antibodies mixture was coupled with Dynabeads Protein G (InVitrogen, Cergy-Pontoise, France) during 2 hours at 4°C. Beads were washed 4 times with IP Buffer 1X using a magnetic rack (Invitrogen, France). Methylated DNA was eluted by digesting antibodies overnight with 5 µL of Proteinase K (20 mg/mL; Sigma-Aldrich, France) in 250 µL of a digestion buffer composed of 50 mM Tris (pH 8.0), 10 mM EDTA pH 8.0, 0.5% SDS at 50°C on a rotator. DNA was isolated with 1 phenol/chloroform/isoamyl alcohol (25:24:1) (v/v/v) and 2 chloroform/isoamyl alcohol (24:1) (v/v) extractions using phase lock gel heavy tubes (Eppendorf, Le Pecq, France) and ethanol precipitation. DNA pellets were solubilised in ultrapure water and concentrations were estimated with Nanodrop quantification.

treatment_protocol: Soil water availability was determined following relative extractable water (REW), which was maintained in the range of 80-86% (minimum-maximum) for the fully watered treatment and 17–23% for the water deficit by controlled watering every morning. A moderate water deficit was applied for 14 days to the cuttings (‘water deficit’) while cuttings in ‘control’ condition remained fully watered. For the ‘Re-irrigation’ treatment, a moderate water deficit was applied for 9 days and for the 5 following days cuttings were fully watered.

value: shoot apical meristem

value: Carpaccio

value: 5 weeks

tag: sample type

value: MeDIP DNA

value: water deficit followed by rewatering

source_name: SAM, water deficit followed by rewatering, total DNA,  replicate 1


title: Tm_95

source_name: primary surgical treatment

value: ovarian cancer cells

value: non-recurrence


title: Tm_110

value: survival


title: SAM_waterdeficit_rep1

description: SAM DNA methylation after 14 days in moderate watere deficit

source_name: SAM, water deficit, MeDIP DNA, replicate 1

value: water deficit

source_name: SAM, water deficit, total DNA, replicate 1


title: Tm_107


title: Tm_106


title: PC9_None_11hr

description: Gene expression after 11hr in PC9 with no treatment

source_name: PC9, 11hr, no treatment

growth_protocol: Parental PC9 cells were grown in RPMI1640 media supplemented with 10% fetal bovine serum. For the stablishment of gefitinib-resistance cell line (PC9GR), PC9 cells were treated with growth medium containing gefitinib at the concentrations 0.02-0.1 uM for 14-28 days, 0.005-0.02 uM for 14-28 days, and 0.1 uM for a range of exposure durations, yielding approximately 500 survived clones. Following further treatments of gefitinib and repeated clone refining with the indicated concentrations (0 uM, 0.1 uM and 1 uM), a total of 179 clones were screened out based on MTT assays that verified significant suppression of growth in the cancer populations after 7 days. Among the clones further refined that lacked the MET amplification and the EGFR T790M mutation, PC9GR was isolated as a line demonstrating one of the lowest dose responses and almost the same doubling time to PC9.

extract_protocol: Total RNA was isolated from each sample by TRIzol® reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s directions. The quality of the total RNA was evaluated on a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).

tag: drug response

value: gefitinib-sensitive cell line

value: no treatment


title: Major_0h_250712

city: Barcelona

first: Sandra

last: Peiró

address: Aiguader 88

department: Programa de Recerca en Càncer

country: Spain

institute: IMIM-Hospital del Mar

hyb_protocol: Sample was hybridized to Mouse Gene 1.0 ST Array (Affymetrix) using a GeneChip Hybridization Oven 645

scan_protocol: GeneChip was scanned using Affymetrix GeneChip Scanner 7G

data_processing: The data were analyzed using the RMA algorithm and then LIMMA was applied to calculate significant differential expression between conditions

source_name: Total RNA from NMuMG cells stable transfected with a vector containing Major satellite sequences

label_protocol: 100-300 ng of total RNA were amplified and labeled using the WT Sense Target labeling system and control reagents (Affymetrix)

extract_protocol: RNeasy Kit QIAGEN

tag: cell line

value: NMuMG

value: vector with major satellite sequences


title: SAM_nonlimiting_rep1

description: SAM DNA methylation after 14 days in non-limiting water conditions

source_name: SAM, non-limiting water, MeDIP DNA, replicate 1

value: non-limiting water

source_name: SAM, non-limiting water, total DNA, replicate 1


title: Control mHSC at 4 hours_Repeat1

description: BalbC; primary hepatic stellate cells, early timepoints

value: BalbC

value: primary hepatic stellate


title: Te_93

value: endometrioid

value: stage II


title: Major_8h_250213

hyb_protocol: Sample was hybridized to Mouse Gene 1.0 ST Array (Affymetrix) using a GeneChip Hybridization Oven 646

source_name: Total RNA from NMuMG cells stable transfected with a vector containing Major satellite sequences treated 8 hours with TGFbeta

value: vector with major satellite sequences + TGFbeta


title: Te_92

value: stage I


title: PC9_None_10hr

description: Gene expression after 10hr in PC9 with no treatment

source_name: PC9, 10hr, no treatment

value: non-small cell lung cancer cell line

tag: time


title: Te_90

value: stage IV


title: CandidautilisWT_YPX5_24hr_rep2

city: Yokohama-shi

first: Hideyuki

last: Tamakawa

state: Kanagawa

address: 1-13-5, Fukuura, Kanazawa-ku

department: Central Laboratories for Key Technologies

institute: KIRIN Co., Ltd.

description:
XYLOSE5
Gene expression after 24hr in Candida utilis WT cell grown on xylose.

hyb_protocol: 0.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 20 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 20 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Kirin Candida utilis Oligo Microarrays (custom array) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565) using the one color scan setting for 8x15k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software Version 9.5.3.1 (Agilent) using default parameters (protocol GE1-QCM_Feb07 and Grid: 022762_D_F_20090126) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. Signal intensities were normalized using 75% quantile normalization.

organism: Cyberlindnera jadinii

source_name: Candida utilis WT, YPX5, 24hr

label_protocol: Five hundred ng of mRNA were labeled using the Quick Amp Labeling Kit, One-Color (Agilent Technologies) according to the manufacturer's instructions.

growth_protocol: Yeast cells were pre-cultured with shaking at 30°C for 3 days in 50 ml of YPD2 (10 g/L yeast extract, 20 g/L peptone, and 20 g/L glucose). Cells were harvested and inoculated at starting OD600 nm of 0.1 in 50 ml of YPD5 (10 g/L yeast extract, 20 g/L peptone, and 20 g/L glucose) or YPX5 (10 g/L yeast extract, 20 g/L peptone, and 50 g/L xylose), and grown with gentle stirring at 30°C under semi-aerobic conditions (sampling time: 10.5 or 24 hrs, respectively).

extract_protocol: Total RNA was extracted using glass beads and purified using an RNeasy column (Qiagen).

value: wild-type

tag: growth medium

value: xylose

value: 24 hr


title: PC9_None_9hr

description: Gene expression after 9hr in PC9 with no treatment

source_name: PC9, 9hr, no treatment

tag: treatment


title: Control_8h_250712

hyb_protocol: Sample was hybridized to Mouse Gene 1.0 ST Array (Affymetrix) using a GeneChip Hybridization Oven 643

source_name: Total RNA from NMuMG cells stable transfected with a control vector treated 8n hours with TFGbeta

value: control vector + TGFbeta


title: CandidautilisWT_YPX5_24hr_rep3

description:
XYLOSE6
Gene expression after 24hr in Candida utilis WT cell grown on xylose.

tag: genotype


title: Tm_102

value: ovarian cancer cells

value: mucinous

value: non-recurrence

value: survival


title: CandidautilisWT_YPX5_24hr_rep1

description:
XYLOSE4
Gene expression after 24hr in Candida utilis WT cell grown on xylose.


title: CandidautilisTMS174_YPX5_24hr_rep2

description:
XYLOSE8
Gene expression after 24hr in Candida utilis TMS174 (xylose-fermenting strain) cell grown on xylose.

source_name: Candida utilis TMS174, YPX5, 24hr


title: Major_0h_250213

hyb_protocol: Sample was hybridized to Mouse Gene 1.0 ST Array (Affymetrix) using a GeneChip Hybridization Oven 644

value: NMuMG

value: vector with major satellite sequences


title: Te_91

value: stage III

value: recurrence

value: death


title: PC9_None_6hr

description: Gene expression after 6hr in PC9 with no treatment

source_name: PC9, 6hr, no treatment

value: gefitinib-sensitive cell line

value: no treatment


title: Tm_101


title: PC9_None_12hr

description: Gene expression after 12hr in PC9 with no treatment

source_name: PC9, 12hr, no treatment

value: non-small cell lung cancer cell line


title: Major_8h_250712

hyb_protocol: Sample was hybridized to Mouse Gene 1.0 ST Array (Affymetrix) using a GeneChip Hybridization Oven 647

value: vector with major satellite sequences + TGFbeta


title: Control_8h_250213

hyb_protocol: Sample was hybridized to Mouse Gene 1.0 ST Array (Affymetrix) using a GeneChip Hybridization Oven 642


title: PC9_None_7hr

description: Gene expression after 7hr in PC9 with no treatment

source_name: PC9, 7hr, no treatment


title: PC9_None_5hr

description: Gene expression after 5hr in PC9 with no treatment

source_name: PC9, 5hr, no treatment


title: PC9_None_8hr

description: Gene expression after 8hr in PC9 with no treatment

source_name: PC9, 8hr, no treatment


title: Control_0h_250712

hyb_protocol: Sample was hybridized to Mouse Gene 1.0 ST Array (Affymetrix) using a GeneChip Hybridization Oven 641

source_name: Total RNA from NMuMG cells stable transfected with a control vector

value: control vectore


title: Te_89

source_name: primary surgical treatment

value: endometrioid

value: stage I


title: Control_0h_250213

hyb_protocol: Sample was hybridized to Mouse Gene 1.0 ST Array (Affymetrix) using a GeneChip Hybridization Oven 640

value: control vector


title: Te_87

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

value: ovarian cancer cells


title: CandidautilisWT_YPD5_10.5hr_rep3

description:
XYLOSE3
Gene expression after 10.5hr in Candida utilis WT cell grown on glucose.

source_name: Candida utilis WT, YPD5, 10.5hr

value: wild-type

value: glucose


title: PC9_None_3hr

description: Gene expression after 3hr in PC9 with no treatment

source_name: PC9, 3hr, no treatment


title: PC9_None_1hr

description: Gene expression after 1hr in PC9 with no treatment

source_name: PC9, 1hr, no treatment


title: Te_79

value: non-recurrence

value: survival


title: Te_77

value: stage II


title: Te_69


title: PC9_IRS_24hr

description: Gene expression after 24hr in PC9 treated with gefinitib

source_name: PC9, 24hr, gefinitib

value: gefinitib


title: CandidautilisWT_YPD5_10.5hr_rep2

description:
XYLOSE2
Gene expression after 10.5hr in Candida utilis WT cell grown on glucose.


title: PC9_None_4hr

description: Gene expression after 4hr in PC9 with no treatment

source_name: PC9, 4hr, no treatment