title: VEH Bulge Rep. 2

city: New Haven

first: Valerie

last: Horsley

state: CT

address: 266 Whitney Avenue

department: Department of Molecular, Cellular and Developmental Biology

institute: Yale University

description: Hair follicle stem cells from vehicle-treated mice

hyb_protocol: Biotinylated, fragmented DNA was hybridized at 45oC for 17 hours to the Mouse Gene 1.0 ST Array (Affymetrix)

scan_protocol: Processed chips were read using a GeneChip Scanner 3000 7G (Affymetrix)

data_processing:
The data were analyzed using GeneSpring GX 11.0 software. (Agilent)
MoEX-1_0-st-v1.r2.pgf
MoEx-1_0-st-v1.r2.dt1.mm8.mps

source_name: Vehicle treated hair follicle stem cells

label_protocol: One round of amplification/labeling was performed on 20ng Total RNA using the Ovation Exon Module, Ovation Pico WT Asystem and Encore Biotin Module (Nugen) to generate biotinylated cDNA

growth_protocol: Hair follicle bulge stem cells were FACS-purified from P56 aged mouse skin based on dual expression of alpha6 integrin and CD34.

extract_protocol: Total RNA was extracted using Trizol LS and the Qiagen Rneasy Kit according to the manufacturer's protocol.

treatment_protocol: Mice were treated with 100 mg/kg CSA or a vehicle control by intraperitoneal injection for 3 days prior to tissue collection.

value: hair follicle bulge stem cell

tag: age

value: vehicle


title: Chop-/- DEN #3

status: Public on Sep 27 2013

type: RNA

city: Iowa City

first: David

middle: Thomas

last: Rutkowski

state: IA

address: 51 Newton Rd.

department: Anatomy and Cell Biology

country: USA

institute: University of Iowa Carver College of Medicine

hyb_protocol: 750ng of this product were mixed with Illumina hybridization buffer, placed onto Illumina mouseRef8 v2 BeadChips (Part No. BD-202-0202), and incubated at 58º C for 17h, with rocking, in an Illumina Hybridization Oven.  Following hybridization, the arrays were washed, blocked, then stained with streptavidin-Cy3 (Amersham/GE Healthcare, Piscataway, NJ) according to the Illumina Whole-Genome Gene Expression Direct Hybridization Assay protocol.

scan_protocol: Beadchips were scanned with the Illumina iScan System (ID #N054)

data_processing: Data were collected using the GenomeStudio software v2011.1. Default parameters within GenomeStudio were used.

label: Biotin

molecule: total RNA

organism: Mus musculus

source_name: whole liver RNA 9 months old

label_protocol: 100 nanograms total RNA was converted to amplified Biotin-aRNA  using the Epicentre TargetAmp-Nano Labeling Kit for Illumina Expression BeadChip (Illumina, Inc., San Diego, CA, Cat. #TAN07924) according to the manufacturer’s recommended protocol. The amplified Biotin-aRNA  product was purified through a QIAGEN RNeasy MinElute  Cleanup column (QIAGEN Cat #74204) according to modifications from Epicentre.

extract_protocol: Resected livers or liver tumors were flash frozen in liquid nitrogen. Total RNA was extracted from frozen material using Trizol.

tag: gender

value: male

tag: strain

tag: genotype

value: Chop-/-

tag: tissue

value: whole liver

tag: treatment

value: 25 mg/kg DEN


title: wild-type DEN tumor #2

source_name: liver tumor RNA 9 months old

value: wild-type

value: liver tumor


title: siIPMK + MMC experiment 3

city: Cambridge

first: Vihandha

last: Wickramasinghe

address: Hills Road

country: United Kingdom

institute: MRC Cancer Unit, Hutchison/MRC Research Centre

description:
Sample name: siP2_3_plus
Cells were treated with MMC for 24h

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing:
The data were normalized using quantile normalization with R package lumi
The dataset was filtered before normalization, to remove non-expressed probes to avoid adding noise to the data.

label: biotin

molecule: cytoplasmic RNA

organism: Homo sapiens

source_name: Cal51 cells

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

extract_protocol: RNA was extracted from cytoplasmic fraction of cells (obtained by digitonin permeabilisation) with QIAGEN RNeasy mini kit according to manufacturers instructions. RNA was treated with RNase free DNase (Qiagen) prior to elution. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Cells were transfected with Control siRNA or IPMK siRNA and cytoplasmic RNA was harvested 72 hours post-transfection. Some samples were treated with DNA crosslinking reagent mitomycin C (MMC) for 24h prior to harvest

tag: cell line

value: Breast carcinoma cell line Cal51

tag: genotype/variation

value: IPMK depletion

tag: agent

value: MMC


title: VEH Bulge Rep. 1

tag: cell type

value: Male


title: CSA Bulge Rep. 2

description: Hair follicle stem cells from CSA-treated mice

source_name: CSA treated hair follicle stem cells

value: CSA


title: WT_Light_r4

city: Palaiseau

first: Adeline

last: SIMON

address: 22 place de l'agronomie

country: France

institute: INRAE

description: This sample is of wild-type Botrytis cinerea B0510, subjected to a light stimulation. It is the fourth of four wild-type_light (WT_L) biological replicates used in this experiment, each from separate cultures.

hyb_protocol: Hybridization on microarrays were done by PartnerChip (http://www.partnerchip.fr/) using the procedures established by NimbleGen (Roche)  and the reagents from Invitrogen (Life technologies, France).

scan_protocol: Scanning was performed by PartnerChip (http://www.partnerchip.fr/) using NimbleScan.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the ANAIS website (http://anais.versailles.inra.fr/).

organism: Botrytis cinerea

source_name: Botrytis cinerea B0510_wild-type

label_protocol: Synthesis of double-stranded cDNA and Cy3-labeling were done by PartnerChip (http://www.partnerchip.fr/) using the procedures established by NimbleGen (Roche) and the reagents from Invitrogen (Life technologies, France)

growth_protocol: Wild type B05.10 and the deltaBcLTF1 mutant were grown for 3 days on solid CM before non-sporulating mycelia were transferred to solid CM covered with cellophane overlays. Cultures were incubated for 52 h in darkness, and then half of the cultures were transferred to white light. After 60 min all four cultures (WT-D; WT-L; deltaBcLTF1-D; deltaBcLTF1-L) were harvested.

extract_protocol: Total RNA was extracted using the Trizol procedure. Total RNA was treated with the DNA-free kit to remove any trace of DNA (Ambion - Applied Biosystems, France).

value: Wild-type

tag: light treatment

value: Light


title: WT_Light_r3

description: This sample is of wild-type Botrytis cinerea B0510, subjected to a light stimulation. It is the third of four wild-type_light (WT_L) biological replicates used in this experiment, each from separate cultures.


title: CSA Bulge Rep. 1


title: siIPMK + MMC experiment 1

description:
Sample name: siP2_1_plus
Cells were treated with MMC for 24h


title: wild-type DEN #4


title: siIPMK + MMC experiment 2

description:
Sample name: siP2_2_plus
Cells were treated with MMC for 24h


title: siIPMK no DNA Damage experiment 3

description: Sample name: siP2_3_minus

value: untreated


title: wild-type DEN #3


title: WT_Light_r1

description: This sample is of wild-type Botrytis cinerea B0510, subjected to a light stimulation. It is the first of four wild-type_light (WT_L) biological replicates used in this experiment, each from separate cultures.


title: siIPMK no DNA Damage experiment 2

description: Sample name: siP2_2_minus


title: wild-type DEN tumor #3


title: WT_Dark_r4

description: This sample is of wild-type Botrytis cinerea B0510, cultured in darkness. It is the fourth of four wild-type_dark (WT_D) biological replicates used in this experiment, each from separate cultures.

value: Dark


title: WT_Dark_r3

description: This sample is of wild-type Botrytis cinerea B0510, cultured in darkness. It is the third of four wild-type_dark (WT_D) biological replicates used in this experiment, each from separate cultures.


title: DeltaBcLTF1_Dark_r1

description: This sample is of Botrytis cinerea B0510 mutant deltaBcLTF1, cultured in darkness. It is the first of four deltaBcLTF1_dark (Delta_D) biological replicates used in this experiment, each from separate cultures.

source_name: Botrytis cinerea B0510_deltaBcLTF1

value: Mutant deltaBcLTF1


title: genomic DNA HCC tissue [0846-01E_T5]

type: genomic

city: Stony Brook

first: Jinyu

last: Li

state: NY

address: 101 Nicolls Rd

department: Cancer Center

institute: Stony Brook University

description: diseased liver

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol

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

data_processing:
BeadStudio software v3.2
matrix signal intensities value definition: Unmethylated and methylated signal intensities

label: Cy5 and Cy3

molecule: genomic DNA

source_name: genomic DNA HCC tissue

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from samples using Qiagen DNeasy Blood and Tissue Kit according to standard instructions

value: Female

tag: disease state

value: HCC

tag: tissue source

value: CHTN


title: wild-type PBS #2

value: male

value: whole liver

value: PBS


title: Prostate Secretion Fluid_Ca3

city: Istanbul

first: Mustafa

last: Ozen

address: Fatih

department: Medical Genetics

country: Turkey

institute: Istanbul University

hyb_protocol: Labeled RNAs are heat denatured and hybridized to Agilent 8x60K miRNA microarray V4 comprised of 1349 probes targeting a comprehensive selection of 1205 human and 144 virus miRNAs with control probes from Sanger miRBase (release 16) at 55o C for 20 hr.

scan_protocol: After hybridization and post-hybridization washes, the chip was scanned by Agilent Microarray Scanner with Surescan High Resolution Technology (Agilent Technologies, Santa Clara, CA).

data_processing: Scanned images were analyzed with Feature Extraction v10.7.3.1 (Agilent Technologies, CA) and Bioconductor software. Data are normalized by quantile normalization. P values and fold changes are calculated.

source_name: Prostate Secretion Fluid

label_protocol: 50 ng of total RNA from each sample are labeled with Cy3, via using “Agilent miRNA Labeling and Hyb Kit”.

extract_protocol: Total RNA was isolated from equal amounts of secretion samples collected from BPH and PCa patients using ”mirVana PARIS kit” (Ambion, Darmstadt, Germany) according to the manufacturer’s protocol.

tag: body fluid

value: Prostate Secretion Fluid

tag: collection method

value: Prostate massages


title: Prostate Secretion Fluid_Ca2


title: Prostate Secretion Fluid_Ca4


title: siCONTROL + MMC experiment 2

description:
Sample name: siCON_2_plus
Cells were treated with MMC for 24h

value: Breast carcinoma cell line Cal51

value: control


title: WT_Dark_r2

description: This sample is of wild-type Botrytis cinerea B0510, cultured in darkness. It is the second of four wild-type_dark (WT_D) biological replicates used in this experiment, each from separate cultures.


title: siIPMK no DNA Damage experiment 1

description: Sample name: siP2_1_minus

value: IPMK depletion


title: siCONTROL + MMC experiment 1

description:
Sample name: siCON_1_plus
Cells were treated with MMC for 24h

value: MMC


title: Chop-/- DEN #1

value: Chop-/-

value: 25 mg/kg DEN


title: Prostate Secretion Fluid_BPH4


title: siCONTROL no DNA Damage experiment 2

description: Sample name: siCON_2_minus

value: untreated


title: Chop-/- PBS #1


title: WT_Dark_r1

description: This sample is of wild-type Botrytis cinerea B0510, cultured in darkness. It is the first of four wild-type_dark (WT_D) biological replicates used in this experiment, each from separate cultures.

value: Wild-type

value: Dark


title: wild-type DEN #2

value: wild-type


title: siCONTROL no DNA Damage experiment 1

description: Sample name: siCON_1_minus


title: wild-type DEN tumor #1

value: liver tumor


title: wild-type PBS #1


title: Prostate Secretion Fluid_BPH2


title: siCONTROL no DNA Damage experiment 3

description: Sample name: siCON_3_minus


title: Prostate Secretion Fluid_BPH3


title: wild-type DEN #1


title: Prostate Secretion Fluid_BPH1


title: subject F_adherent fraction+TNF_1

status: Public on Sep 26 2013

city: Bologna

first: Simone

last: Rampelli

address: Via Belmeloro 6

country: Italy

institute: University of Bologna

hyb_protocol: Hybridization was carried out in the dark at 65 °C for 1.5 h, in a temperature-controlled system. After removal of the chamber, the slide was washed for 15 min in a prewarmed (65 °C) solution of 1X SSC/0.1% SDS with gentle shaking. Finally, the slide was spun at 800 rpm for 3 min.

scan_protocol: All arrays were scanned with ScanArray 5000 scanner (Perkin Elmer Life Sciences, Boston, MA, USA), at 10 μm resolution. In the experiments, the fluorescent images were obtained with different acquisition parameters on both laser power and photo-multiplier gain, in order to avoid saturation. Fluorescence intensities were quantitated by ScanArray Express 3.0 software, using the “Adaptive circle” option, letting diameters vary from 60 to 300 μm.

data_processing: Mean fluorescence intensities (IF) were normalized on the basis of the synthetic ligation control signal (Zip63): (a) outlier values (2.5-fold above or  below the average) were discarded; (b) a correction factor was calculated in order to set the average IF of the ligation control  to 50000 (n=6); (c) the correction factor was applied to both the probes and background IF values.

organism: human gut metagenome

source_name: fecal slurry TNF-treated HT29 cells adherent fraction, 1 h

label_protocol: In presence of a perfect match between a pair of specific probes (a 5'phosphorilated Common Probe and a 5'-Cy3-labelled Discriminating Oligo) and a DNA template (deriving from a previous PCR), a fluorescently labelled product is formed

extract_protocol: 16S rDNA was amplified by PCR. 16S rDNA amplicons were used as template for Ligase Detection Reaction (LDR) to form the fluorescenly labelled products.

tag: host

value: human, 30 years old female


title: siCONTROL + MMC experiment 3

description:
Sample name: siCON_3_plus
Cells were treated with MMC for 24h


title: subject F_fecal slurry

source_name: fecal slurry


title: subject F_adherent fraction+TNF_2


title: WT_Light_r2

description: This sample is of wild-type Botrytis cinerea B0510, subjected to a light stimulation. It is the second of four wild-type_light (WT_L) biological replicates used in this experiment, each from separate cultures.

value: Light


title: subject F_adherent fraction_1

source_name: fecal slurry HT29 cells adherent fraction, 1 h


title: subject E_adherent fraction+TNF_2

value: human, 28 years old male


title: subject E_adherent fraction+TNF_1


title: subject E_adherent fraction_2


title: subject F_adherent fraction_2


title: Chop-/- DEN #2

value: male

value: whole liver


title: subject E_fecal slurry


title: subject E_adherent fraction_1


title: subject D_adherent fraction+TNF_2

value: human, 27 years old male


title: subject D_adherent fraction+TNF_1


title: subject D_adherent fraction_2


title: subject D_fecal slurry


title: subject C_adherent fraction+TNF_2

value: human, 28 years old female


title: subject C_adherent fraction+TNF_1


title: subject D_adherent fraction_1


title: subject C_adherent fraction_2


title: subject C_adherent fraction_1


title: subject C_fecal slurry


title: subject B_adherent fraction_2

value: human, 33 years old female


title: subject B_adherent fraction+TNF_2


title: subject B_adherent fraction_1


title: subject B_adherent fraction+TNF_1


title: subject A_adherent fraction_2

value: human, 38 years old male


title: subject B_fecal slurry


title: subject A_adherent fraction+TNF_1


title: subject 207_adherent fraction+TNF_1

value: human, 2 months old male


title: subject 207_adherent fraction_2


title: subject 207_adherent fraction_1


title: subject 207_adherent fraction+TNF_2


title: subject A_adherent fraction_1


title: subject A_fecal slurry


title: subject 207_fecal slurry


title: subject 704_adherent fraction+TNF_1

value: human, 7 months old male


title: subject 704_adherent fraction_2


title: subject 704_adherent fraction_1


title: subject 603_adherent fraction+TNF_2

value: human, 6 months old female


title: subject 704_fecal slurry


title: subject 603_adherent fraction_1


title: subject 603_adherent fraction_2


title: subject 603_adherent fraction+TNF_1


title: subject 704_adherent fraction+TNF_2


title: subject A_adherent fraction+TNF_2


title: subject 603_fecal slurry


title: subject 6CF_adherent fraction+TNF_2

value: human, 6 months old male


title: subject 6CF_adherent fraction_1


title: subject 6CF_adherent fraction+TNF_1


title: subject 6CF_adherent fraction_2


title: subject 6CF_fecal slurry


title: subject 2SA_adherent fraction_2


title: subject 2SA_adherent fraction_1


title: subject 2SA_adherent fraction+TNF_1


title: subject 2SA_fecal slurry


title: subject 5GC_adherent fraction_1

value: human, 5 months old male


title: subject 5GC_adherent fraction+TNF_2


title: subject 4NG_adherent fraction+TNF_1

value: human, 4 months old male


title: subject 5GC_adherent fraction_2


title: subject 5GC_adherent fraction+TNF_1


title: subject 8PS_adherent fraction+TNF_2

value: human, 8 months old male


title: subject 4NG_adherent fraction+TNF_2


title: subject 5GC_fecal slurry


title: subject 8PS_adherent fraction+TNF_1


title: subject 2SA_adherent fraction+TNF_2


title: subject 4NG_fecal slurry


title: subject 4NG_adherent fraction_1


title: Chop-/- DEN #4

value: Chop-/-

value: 25 mg/kg DEN


title: subject 8PS_adherent fraction_2


title: subject 8AF_adherent fraction+TNF_2

value: human, 8 months old female


title: subject 8PS_fecal slurry


title: subject 8PS_adherent fraction_1


title: subject 8AF_adherent fraction+TNF_1


title: subject 7ARb_adherent fraction+TNF_2


title: subject 8AF_adherent fraction_1


title: subject 8AF_adherent fraction_2


title: subject 7ARb_adherent fraction_1


title: subject 8AF_fecal slurry


title: subject 7AR_adherent fraction+TNF_2


title: subject 7ARb_adherent fraction+TNF_1


title: subject 7ARb_adherent fraction_2


title: subject 7AR_adherent fraction+TNF_1


title: subject 3TT_adherent fraction+TNF_1

value: human, 3 months old male


title: subject 7AR_adherent fraction_2


title: subject 7AR_adherent fraction_1


title: Prostate Secretion Fluid_Ca1

value: Prostate Secretion Fluid

value: Prostate massages


title: subject 3TT_adherent fraction_1


title: subject 3TT_adherent fraction_2


title: subject 3TT_fecal slurry


title: subject 3TT_adherent fraction+TNF_2


title: subject 7AR_fecal slurry


title: MDA-MB-231, input DNA, treated by hypoxia and glucose deprivation

type: SRA

city: Boston

first: Xiaole

middle: Shirley

last: Liu

state: MA

address: 450 Brookline Avenue, CLS 11007

department: Department of Biostatistics and Computational Biology

institute: Dana-Farber Cancer Institute, Harvard School of Public Health

library_source: genomic

data_processing:
ChIP-seq reads were aligned to the hg19 genome assembly using Bowtie version 0.12.7 with the following parameters: bowtie -S -m 1 *.fastq  *.sam.
Sam format files were converted to bed format; mapped reads of treat and input files were randomly sampled to the same depth.
Peaks were called using MACS with p-value cutoff of 1e-7.
Genome_build: hg19
Supplementary_files_format_and_content: Wig files were generated using MACS; scores represent tag pileup over each position.Bed files of peak positions were also generated by MACS.

source_name: breast cancer cells

growth_protocol: All breast cancer cells were cultured according to Neve et al. (Cancer Cell 2006). Following retroviral or lentiviral infection, cells were maintained in the presence of puromycin (2 ug/ml) (Sigma).

extract_protocol:
ChIP was performed as previously described by Chen et al. (Cell 2008).
The ChIP-seq library was prepared using ChIP-Seq DNA Sample Prep Kit (Illumina) according to the manufacturer’s instructions.

treatment_protocol: For all hypoxia experiments, cells were maintained in an anaerobic chamber (Coy laboratory) with 0.1% O2. For glucose deprivation experiments, cells were maintained in DMEM without glucose medium (Gibco) with 10% FBS (Gibco) and 50 units/ml of penicillin/streptomycin.

value: triple negative breast cancer cells

tag: chip antibody


title: subject 7ARb_fecal slurry


title: subject 4NG_adherent fraction_2


title: whole lung with vehicle replicate B19

first: Alvin

middle: T.

last: Kho

address: 320 Longwood Avenue

department: Informatics Program

institute: Boston Children's Hospital

description:
whole lung with vehicle replicate B19
Lung_Veh_B19

hyb_protocol: 25 micrograms of each biotin-labeled cRNA was hybridized to an Affymetrix Mouse430_2 chip according to the manufacturer's protocol. Four biotinylated hybridization controls (BioB, BioC, BioD, and Cre) were included in each hybridization reaction to verify consistent hybridization efficiency. Hybridization is carried out according the Affymetrix GeneChip® Manual. Affymetrix hybridization ovens are used to incubate the arrays at a constant temperature of 45oC overnight. Preparation of microarrays for scanning is carried out with Affymetrix appropriate wash protocols matched to the specific chip type on a Model 450 Fluidics station. Affymetrix GeneChip Operating Software (GCOS) operating system controls the Fluidics station process.

scan_protocol: Standard Affymetrix protocol.

data_processing: All 16 sample CEL files were inputted into Bioconductor/R version 2.11.10 to derive Robust Multi-Array Average (RMA) normalized output using the rma() function in the affy library.

source_name: Whole lung, control

label_protocol: In vitro transcription (IVT) is performed using the GeneChip Expression Amplification Reagents kit- 30 reactions (P/N 900449) and is carried out according to the standard Affymetrix protocols and quantification of the IVT samples is carried out on a Bio-Tek UV Plate Reader.

growth_protocol: Described in PMID:19164857

extract_protocol: 10 micrograms of total RNA was used to generate target cRNA for hybridization toaccording to standard Affymetrix protocols.

treatment_protocol: Described in PMID:19164857

tag: microarray hybridization date

value: whole lung

value: vehicle

tag: whole organ harvested at


title: whole lung with vehicle replicate B14

description:
whole lung with vehicle replicate B14
Lung_Veh_B14

tag: strain


description:
whole lung with dexamethasone replicate B40
Lung_Dex_B40

source_name: Whole lung, DEX

value: dexamethasone


description:
whole lung with dexamethasone replicate B28
Lung_Dex_B28


title: whole lung with vehicle replicate B12

description:
whole lung with vehicle replicate B12
Lung_Veh_B12


description:
whole lung with dexamethasone replicate B31
Lung_Dex_B31


description:
whole cerebellum with vehicle replicate B79
CB_Veh_B79

source_name: Whole cerebellum, control

value: whole cerebellum


description:
whole cerebellum with vehicle replicate B78
CB_Veh_B78


description:
whole cerebellum with vehicle replicate B80
CB_Veh_B80


description:
whole lung with dexamethasone replicate B46
Lung_Dex_B46


title: whole lung with vehicle replicate B22

description:
whole lung with vehicle replicate B22
Lung_Veh_B22


description:
whole cerebellum with dexamethasone replicate B49
CB_Dex_B49

source_name: Whole cerebellum, DEX


description:
whole cerebellum with vehicle replicate B81
CB_Veh_B81


description:
whole cerebellum with dexamethasone replicate B39
CB_Dex_B39


description:
whole cerebellum with dexamethasone replicate B52
CB_Dex_B52


description:
whole cerebellum with dexamethasone replicate B50
CB_Dex_B50


title: F1_liver_calorie_restricted_biological_rep7

city: Madison

first: Jamie

last: Barger

state: WI

address: 510 Charmany Drive, Suite 263

institute: LifeGen Technologies, LLC

description: Gene expression data from mice consuming calorie restricted diet

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on the Affymetrix Mouse Genome 430 2.0 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray Scanner 3000

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

source_name: Liver, Calorie Restricted diet

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

growth_protocol: Male mice were purchased from Jackson Laboratory at six weeks of age and were individually housed and fed 84 kcal/week of a diet based on the AIN93M formulation for two weeks

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

treatment_protocol: Starting at 8 weeks of age, mice were maintained on the control diet or were fed a 25% calorie restricted diet (Bio-Serv; Frenchtown, NJ, USA; Catalog# F05314)

tag: gender

value: male

value: liver


title: F1_liver_control_biological_rep3

description: Gene expression data from mice consuming control diet

source_name: Liver, Control diet

tag: tissue


title: F1_liver_calorie_restricted_biological_rep2


title: DBA_liver_calorie_restricted_biological_rep8


title: F1_liver_control_biological_rep8


title: DBA_liver_calorie_restricted_biological_rep6


title: F1_liver_control_biological_rep7


title: DBA_liver_calorie_restricted_biological_rep5


title: F1_liver_calorie_restricted_biological_rep3


title: F1_liver_calorie_restricted_biological_rep1


title: F1_liver_calorie_restricted_biological_rep4


title: F1_liver_control_biological_rep5


title: F1_liver_control_biological_rep6


title: DBA_liver_calorie_restricted_biological_rep7


title: DBA_liver_control_biological_rep6


title: F1_liver_control_biological_rep4


title: DBA_liver_control_biological_rep4


title: F1_liver_calorie_restricted_biological_rep5


title: F1_liver_control_biological_rep2


title: DBA_liver_calorie_restricted_biological_rep2


title: F1_liver_calorie_restricted_biological_rep8


title: DBA_liver_control_biological_rep8


title: DBA_liver_control_biological_rep5


title: DBA_liver_calorie_restricted_biological_rep1


title: DBA_liver_calorie_restricted_biological_rep4


title: F1_liver_control_biological_rep1


title: F1_liver_calorie_restricted_biological_rep6


title: DBA_liver_control_biological_rep3


title: DBA_liver_calorie_restricted_biological_rep3


title: DBA_liver_control_biological_rep1


title: CBA_liver_calorie_restricted_biological_rep5

value: CBA/J


title: CBA_liver_calorie_restricted_biological_rep8


title: CBA_liver_calorie_restricted_biological_rep2


title: CBA_liver_calorie_restricted_biological_rep7


title: CBA_liver_calorie_restricted_biological_rep6


title: DBA_liver_control_biological_rep2


title: CBA_liver_control_biological_rep8


title: CBA_liver_control_biological_rep6


title: CBA_liver_calorie_restricted_biological_rep3


title: C3H_liver_calorie_restricted_biological_rep8


title: CBA_liver_calorie_restricted_biological_rep4


title: CBA_liver_calorie_restricted_biological_rep1


title: C3H_liver_calorie_restricted_biological_rep2


title: DBA_liver_control_biological_rep7


title: CBA_liver_control_biological_rep3


title: CBA_liver_control_biological_rep7


title: CBA_liver_control_biological_rep1


title: C3H_liver_calorie_restricted_biological_rep3


title: CBA_liver_control_biological_rep5


title: CBA_liver_control_biological_rep2


title: C3H_liver_calorie_restricted_biological_rep5


title: C3H_liver_calorie_restricted_biological_rep7


title: C3H_liver_control_biological_rep8


title: C3H_liver_control_biological_rep6


title: C3H_liver_calorie_restricted_biological_rep6


title: C3H_liver_calorie_restricted_biological_rep4


title: CBA_liver_control_biological_rep4


title: C3H_liver_calorie_restricted_biological_rep1


title: C3H_liver_control_biological_rep7


title: Cbotulinum_CJ5-1

city: Atlanta

first: Brian

middle: H

last: Raphael

state: GA

address: 1600 Clifton Road

department: Enteric Diseases Laboratory Branch

institute: Centers for Disease Control and Prevention

hyb_protocol: Labeled DNA was hybridized to arrays for 14 hrs at 42C

scan_protocol: Genepix 4000B

data_processing: log10 (average of triplicate 635 nm signal intensity/average signal intensity for all empty spots on array)

organism: Clostridium botulinum A

label_protocol: 1 ug of genomic DNA was labeled with Cy5 random primers using Klenow fragemnt

growth_protocol: Bacteria were grown for 24 hours in TPGY medium

extract_protocol: genomic DNA extraction

tag: isolate


title: Cbotulinum_CJ4-1


title: C3H_liver_control_biological_rep5


title: C3H_liver_control_biological_rep4


title: Lymph_node_healthy_sample_9

city: Glasgow

first: Manikhandan

middle: A V

last: Mudaliar

state: Scotland

address: Room B528, Sir Graeme Davies Building, 120 University Place

department: College of Medical, Veterinary and Life Sciences

institute: University of Glasgow

hyb_protocol: Probe quality and fragmentation were confirmed using Bioanalyser 2100 prior to microarray hybridisation. Fragmented and labelled probes were hybridised for 18 hours onto Affymetrix GeneChip Canine Genome 2.0 Array (cat. 900725, Affymetrix) using GeneChip Hybridization, Wash, and Stain Kit (cat. 900720, Affymetrix).

scan_protocol: Microarrays were scanned using Genechip Scanner 3000 7G.

data_processing: The data in the matrix table were generated in the Affymetrix Expression Console and normalised using RMA method in Partek GS 6.5. Microarray data were generated from all the 35 canine samples (25 DLBCL and 10 healthy). However, data from 2 canine DLBCL samples (EU121 Sample 07 1 26-10-09.CEL and EU121 Sample 17 1 27-10-09.CEL) did not meet our required quality and were removed from further analysis.  Only data from 33 (23 DLBCL and 10 healthy) samples were used for analysis.

organism: Canis lupus familiaris

source_name: Lymph node, harvested from dogs euthanized for non-lymphoma conditions

label_protocol: 50ng RNA from each sample were used to generate complementary DNA strands using Ovation RNA Amplification System V2 (cat. 3100-12, Nugen) and 3.75ug of each cDNA were fragmented and biotin labelled using Encore™ Biotin Module (cat. 4200-12, Nugen).

extract_protocol: RNA extraction was performed in two balanced random batches by polytron homogenisation of tissue in Trizol (cat. 15596-026, Invitrogen) followed by phenol chloroform extraction. RNAs were quantitated and qualified using Nanodrop ND8000 (Thermo Scientific) and 2100 Bioanalyser (Agilent). Prior to cDNA probe generation RNAs were subjected to sample clean up and DNAse I treatment using RNEasy Micro (Qiagen) before repeat quantitation and qualification.

tag: case id

value: Healthy

tag: current medications

value: Not Available

tag: previous chemo (yes or no)

tag: Sex

tag: breed

tag: rna integrity number


title: Lymph_node_healthy_sample_7

tag: disease state


title: B6_liver_calorie_restricted_biological_rep3


title: C3H_liver_control_biological_rep3


title: B6_liver_calorie_restricted_biological_rep4


title: Lymph_node_healthy_sample_8


title: B6_liver_calorie_restricted_biological_rep5


title: Lymph_node_healthy_sample_10


title: B6_liver_calorie_restricted_biological_rep6


title: Lymph_node_healthy_sample_6


title: C3H_liver_control_biological_rep2


title: B6_liver_calorie_restricted_biological_rep8


title: mouse Irf8 KO / b-cat(Ex3), biological rep3

city: Berlin

first: Marina

last: Scheller

address: Robert-Rössle-Str. 10

country: Germany

institute: MDC Berlin

description: Gene expression changes associated with progression of Irf8–/– CML-like disease into blast crisis after β-catenin activation

hyb_protocol: Biotinylated cDNA (3µg) were hybridized to Mouse Genome 430 PM peg arrays for 18 hr at 45°C according to Nugen protocol. GeneChips were washed and stained using Affymetrix GeneTitan® system

scan_protocol: Scanning using an Affymetrix GeneTitan® system.

data_processing: Sample processing and array hybridization were performed at a Genomics Core Facility – Kompetenzzentrum Fluoreszente Bioanalytik (KFB) - Regensburg, Germany.

source_name: Mus Musculus

label_protocol: Generation of amplified SPIA® cDNA were prepared from <20 ng total RNA using NUGEN Amplification System (Nugen Pico WTA System) according to the manufacturer's instructions.

extract_protocol: Total RNA from cells was extracted using RNeasy mini or micro kit from (Qiagen, Hilden, Germany) according to the manufacturer's instructions.

treatment_protocol: Sorted GMPs were collected by centrifugation at 4°C and put immediately for RNA extraction on ice.

tag: genotype

value: Irf8 KO / b-cat(Ex3)

tag: cell type

value: GMP (Granulocyte Macrophage Progenitor) cells


title: Lymph_node_healthy_sample_4


title: B6_liver_calorie_restricted_biological_rep2


title: Lymph_node_healthy_sample_3


title: B6_liver_control_biological_rep8


title: B6_liver_control_biological_rep7


title: B6_liver_calorie_restricted_biological_rep7


title: B6_liver_control_biological_rep5


title: B6_liver_control_biological_rep6


title: mouse Irf8 KO / b-cat(Ex3), biological rep4


title: Lymph_node_healthy_sample_5


title: B6_liver_calorie_restricted_biological_rep1


title: MDA-MB-231,shXBP1,Hypoxia+Glucose deprivation,biological rep 2

description: Gene expression data from MDA-MB-231 cell line under treated condition with XBP1 knockdown

hyb_protocol: The biotin labeled cRNA was fragmented, and hybridized to Affymetrix human U133 plus 2.0 expression array according to the standard Affymetrix protocol.

data_processing: Raw gene expression values were obtained using Affymetrix GeneChip software and further analyzed using the Robust Multichip Average (RMA) algorithm in the Bioconductor affy package 1.30.0.

label_protocol: Biotin labeled cRNA was prepared from 1 ug of total RNA according to the standard Affymetrix protocol.

growth_protocol: All breast cancer cells were cultured according to Neve et al (Cancer Cell 2006). Following retroviral or lentiviral infection, cells were maintained in the presence of puromycin (2 ug/ml) (Sigma).

extract_protocol: Total RNA was extracted by using RNeasy mini kit with on column DNase digestion (QIAGEN).

treatment_protocol: For all hypoxia experiments, cells were maintained in an anaerobic chamber (Coy laboratory) with 0.1% O2. For glucose deprivation experiments, cells were maintained in DMEM without glucose medium (Gibco) with 10% FBS (Gibco) and 50 units/ml of penicillin/streptomycin. MDA-MB-231/T47D cells infected with control shRNA or XBP1 shRNA lentiviruses grown in glucose free medium were treated in 0.1% O2 in a hypoxia chamber for 24h.

tag: cell line


title: Lymph_node_healthy_sample_2


title: B6_liver_control_biological_rep4


title: MDA-MB-231,shCtrl,Hypoxia+Glucose deprivation,biological rep 2

description: Gene expression data from MDA-MB-231 cell line under treated condition without XBP1 knockdown


title: mouse Irf8 KO / b-cat(Ex3), biological rep1


title: B6_liver_control_biological_rep1


title: B6_liver_control_biological_rep3


title: B6_liver_control_biological_rep2


title: mouse Irf8 KO, biological rep3

value: lrf8 KO


title: MDA-MB-231,shCtrl,Hypoxia+Glucose deprivation,biological rep 1

source_name: MDA-MB-231 cell line under treated condition without XBP1 knockdown


title: mouse Irf8 KO / b-cat(Ex3), biological rep2


title: Lymph_node_biopsy_DLBCL_sample_23

source_name: Lymph node biopsy, diffuse large B-cell lymphoma (DLBCL)

value: DLBCL

value: No

tag: age (yrs)

value: F/S

value: Golden Retriever


title: Lymph_node_healthy_sample_1


title: MDA-MB-231,shXBP1,Hypoxia+Glucose deprivation,biological rep 1

source_name: MDA-MB-231 cell line under treated condition with XBP1 knockdown


title: Lymph_node_biopsy_DLBCL_sample_25

value: West Highland White Terrier


title: T47D,shXBP1,Hypoxia+Glucose deprivation,biological rep 2

description: Gene expression data from T47D cell line under treated condition with XBP1 knockdown


title: Lymph_node_biopsy_DLBCL_sample_24

value: Yes

tag: if yes chemo protocol

value: CHOP(started 20Oct07)

tag: time since last treatment (days)

value: M/N

value: Labrador Retriever


title: 129_liver_calorie_restricted_biological_rep8

tag: strain

value: male


title: T47D,shXBP1,Hypoxia+Glucose deprivation,biological rep 1

source_name: T47D cell line under treated condition with XBP1 knockdown


title: mouse Irf8 KO, biological rep2


title: 129_liver_calorie_restricted_biological_rep6

tag: gender

value: liver


title: mouse GMP ctrl, biological rep3

value: control MxCre–Ctnnb1(Ex3)fl/+


title: mouse GMP ctrl, biological rep2


title: mouse GMP ctrl, biological rep4


title: mouse Irf8 KO, biological rep1


title: Lymph_node_biopsy_DLBCL_sample_21

value: Doberman Pinscher


title: T47D,shCtrl,Hypoxia+Glucose deprivation,biological rep 2

description: Gene expression data from T47D cell line under treated condition without XBP1 knockdown


title: T47D,shCtrl,Hypoxia+Glucose deprivation,biological rep 1

source_name: T47D cell line under treated condition without XBP1 knockdown


title: Lymph_node_biopsy_DLBCL_sample_20

value: Not Available


title: 129_liver_calorie_restricted_biological_rep7

tag: tissue


title: Lymph_node_biopsy_DLBCL_sample_18

value: CHOP(started 24Mar08)CCNU/L-Aspar/Pred (started 28Apr08)

value: Siberian Husky


title: WHI3x4 over-expressor in YPE replicate1

first: Ying

last: Cai

state: New York

address: Life Sciences Building Rm 363

department: Molecular Genetics and Microbiology

description: Biological replicate 1 of 2. log phase WHI3x4 deletion in YEP+3% ethanol

hyb_protocol: Labeled samples were hybridized to the Agilent Yeast (V2) Gene Expression Microarray, 8x15K, using Agilent Gene Expression Hybridization Kits (CAT#5188-5242) following manufacturer’s instructions

scan_protocol: Scanned on an Agilent DNA microarray scanner, Model#: G2505B. Images were quantified using Agilent Feature Extraction Software (version 9.5.3.1).

data_processing: Agilent Feature Extraction Software (v 9.5.3.1) was used for background subtraction and LOWESS normalization. Saturated and outlier spots were removed. The log ratios were averaged for the same probe.

organism: Saccharomyces cerevisiae

source_name: WHI3x4 cells

label_protocol: Samples were labeled using Agilent Quick Amp Labeling Kit (CAT#5190-0444) following manufacturer’s instructions

growth_protocol: Cells were grown in YEP medium supplemented with different carbon sources as indicated at 30°C to log phase for harvest.

extract_protocol: Total RNA extracted using Yeast RiboPure Kit (CAT#AM1926) following manufacturer's instructions.

tag: strain background

tag: growth medium

value: YEP+3% ethanol


title: 129_liver_calorie_restricted_biological_rep2


title: Lymph_node_biopsy_DLBCL_sample_22

tag: case id

value: DLBCL

tag: current medications

value: Standard Poodle


title: 129_liver_calorie_restricted_biological_rep5


title: Lymph_node_biopsy_DLBCL_sample_19

tag: previous chemo (yes or no)

value: No

tag: Sex

value: F/S

value: Vizsla


title: 129_liver_calorie_restricted_biological_rep4


title: mouse GMP ctrl, biological rep1

value: GMP (Granulocyte Macrophage Progenitor) cells


title: 129_liver_calorie_restricted_biological_rep3


title: 6 day old embryo vitrified 4

city: Valencia

first: M. Desemparats

last: Saenz-de-Juano

state: Valencia

address: Camino de Vera s/n

department: Animal Science

country: Spain

institute: Universidad Politécnica Valencia

description: Gene expression of 6 day old blastocyst after transfer and vitrification

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was mixed with Agilent fragmentation buffer and Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, Agilent hybridization buffer was added and hybridized to a Rabbit Agilent Custom Gene Expression Oligo Microarrays (G4102A) 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.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm). Feature_extraction: The scanned images were analyzed with Feature Extraction Software 10,7,3,1 (Agilent) using default parameters (protocol GE1_107 and Grid: 037293_D_F_20111104).

data_processing: Data were normalized using intra-array median subtraction and log2 transformation

molecule: polyA RNA

organism: Oryctolagus cuniculus

source_name: 6 day old embryo, vitrified

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng of total RNA or 5 ng of polyA RNA using the One-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol:
Fetal Placentas: Total RNA extracted using Trizol (Invitrogen) following manufacturer's instructions
6 day old embryos: polyA RNA was extracted using Dynabeads Micro mRNA (Life technologies)

treatment_protocol: The vitrification procedure was carried out in two steps at 20ºC.  In the first step, embryos were placed for 2 min in a vitrification solution consisting of 12.5% dimethyl sulphoxide (DMSO) and 12.5% ethylene glycol (EG) in DPBS supplemented with 0.2% of BSA.  In the second step, embryos were suspended for 30 seconds in a solution of 20% DMSO and 20% EG in DPBS supplemented with 0.2% of BSA.  Then, embryos suspended in vitrification medium were loaded into 0.25 ml plastic straws and two sections of DPBS were added at either end of each straw, separated by air bubbles.  Finally, straws were sealed and plunged directly into liquid nitrogen.  Warming was performed by horizontally placing the straw 10 cm from liquid nitrogen for 20-30 seconds and when the crystallisation process began, the straws were immersed in a water bath at 20ºC for 10-15 seconds.

tag: treatment

value: vitrified

tag: developmental stage

value: 6 day old blastocyst


title: Lymph_node_biopsy_DLBCL_sample_16

tag: disease state

value: rimadyl

value: M/N

tag: breed

value: Labrador Retriever

tag: rna integrity number


title: WHI3x4 over-expressor in YPE replicate2

description: Biological replicate 2 of 2. log phase WHI3x4 deletion in YEP+3% ethanol

tag: genotype


title: 6 day old embryo vitrified 3


title: Lymph_node_biopsy_DLBCL_sample_15

tag: age (yrs)

value: German Shepherd


title: whi3 deletion in YPE replicate2

description: Biological replicate 2 of 2. log phase whi3 deletion in YEP+3% ethanol

source_name: whi3 cells


title: whi3 deletion in YPE replicate1

description: Biological replicate 1 of 2. log phase whi3 deletion in YEP+3% ethanol


title: 129_liver_control_biological_rep8

value: male

value: liver


title: 6 day old embryo vitrified 1


title: whi3 deletion in YPD replicate2

description: Biological replicate 2 of 2. log phase whi3 deletion in YEP+2% glucose

value: YEP+2% glucose


title: 6 day old embryo vitrified 2


title: Lymph_node_biopsy_DLBCL_sample_12

value: Yes

tag: if yes chemo protocol

value: Dox/Cytoxan/Pred(started 17Apr08)

tag: time since last treatment (days)


title: 6 day old embryo control 4

description: Gene expression of 6 day old blastocyst after transfer

source_name: 6 day old embryo, control

value: control


title: 129_liver_calorie_restricted_biological_rep1

tag: strain

tag: gender


title: Lymph_node_biopsy_DLBCL_sample_14

value: DLBCL

value: doxycycline

value: M

value: Golden Retriever


title: 129_liver_control_biological_rep7

tag: tissue


title: Lymph_node_biopsy_DLBCL_sample_13

value: CHOP(started 26Mar08)


title: WHI3x4 over-expressor in YPD replicate1

description: Biological replicate 1 of 2. log phase WHI3x4 deletion in YEP+2% glucose

tag: strain background

tag: growth medium


title: 6 day old embryo control 2


title: 129_liver_control_biological_rep6


title: 6 day old embryo control 3


title: WHI3x4 over-expressor in YPD replicate2

description: Biological replicate 2 of 2. log phase WHI3x4 deletion in YEP+2% glucose


title: 129_liver_control_biological_rep5


title: whi3 deletion in YPD replicate1

description: Biological replicate 1 of 2. log phase whi3 deletion in YPD


title: 129_liver_control_biological_rep2


title: C3H_liver_control_biological_rep1


title: Lymph_node_biopsy_DLBCL_sample_10

tag: case id

tag: current medications

value: Not Available

value: No

value: F/S


title: 6 day old embryo control 1

value: 6 day old blastocyst


title: 129_liver_control_biological_rep3


title: Lymph_node_biopsy_DLBCL_sample_11

tag: previous chemo (yes or no)

tag: Sex

value: M/N

value: Labrador Retriever


title: Fetal placenta vitrified 4

description: Gene expression of fetal placenta derived from vitrified transferred embryos

source_name: Fetal placenta, 14 days, vitrified

tag: treatment

value: vitrified

tag: developmental stage

value: 14 day fetal placenta


title: Fetal placenta vitrified 3


title: Fetal placenta vitrified 2


title: 129_liver_control_biological_rep4

description: Gene expression data from mice consuming control diet

value: male

value: liver


title: Lymph_node_biopsy_DLBCL_sample_9

tag: disease state

value: Yes

value: Dox/Pred (started 08Nov07)CCNU/L-Aspar/Pred (started 03Jun08)

tag: breed

value: Labrador X


title: with IL-11+FGF2_replicate 1

first: Raed

last: Abu Dawud

address: Föhrertstr. 15

department: Immunology

institute: Berlin-Brandenburg Center for Regenerative Therapies

description:
replicate 1
SAMPLE 7

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: The data were normalised using Genome Studio.

source_name: with IL-11+FGF2_replicate 1

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

growth_protocol: embryonic stem cells grown on matrigel in N2B27 medium supplemented with cytokines.

extract_protocol: RNA was extracted and DNAseI were performed using the QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with agarose gel.

treatment_protocol: bFGF supplement (24ng/ml), IL-11 treatment 10ng/ml.

tag: cell line

value: hESC line H1


title: Fetal placenta vitrified 1


title: Fetal placenta control 3

description: Gene expression of fetal placenta derived from control transferred embryos

source_name: Fetal placenta, 14 days, control

value: control


title: Lymph_node_biopsy_DLBCL_sample_5

value: DLBCL

tag: age (yrs)

tag: rna integrity number


title: with IL-11_replicate 1

description:
replicate 1
SAMPLE 5

source_name: with IL-11_replicate 1


title: Fetal placenta control 4


title: without FGF2_replicate 2

description:
replicate 2
SAMPLE 3

source_name: without FGF2_replicate 2


title: 129_liver_control_biological_rep1

source_name: Liver, Control diet


title: Lymph_node_biopsy_DLBCL_sample_3

value: tramadol

tag: if yes chemo protocol

value: CHOP(started 08Apr08)

tag: time since last treatment (days)

value: German Shepard X


title: Lymph_node_biopsy_DLBCL_sample_8

value: rimadyl

value: No

value: F/S

value: Golden Retriever


title: with FGF2_replicate 1

description:
replicate 1
SAMPLE 2

source_name: with FGF2_replicate 1


title: without FGF2_replicate 1

description:
replicate 1
SAMPLE 1

source_name: without FGF2_replicate 1


title: Lymph_node_biopsy_DLBCL_sample_2

value: M/N

value: Bloodhound


title: Lymph_node_biopsy_DLBCL_sample_1

value: Miniature Schnauzer


title: NE_Replicate 1

city: Beltsville

first: Duk Kyung

last: Kim

state: MD

address: Bldg. 1043, BARC-East

institute: USDA, ARS

description: Biological replicate 1 of 2

hyb_protocol: With the use of Agilent’s Gene Expression Hybridization Kit (Cat# 5188-5242), 825ng of cyanine 3-labeled and cyanine 5-labeled linearly amplified cRNA was added to individual hybridization cocktails and then fragmented. At hybridization each well contained one cy3 and one cy5 labeled sample and control per pair.  The hybridization cocktail is then dispensed into the wells of gasket slides (4 samples/slide: Cat# G2534-60012) on top of which a Chicken 4x44K Gene Expression Microarray, (Cat# G2519F, AMADID 015068) was placed.  This microarray “sandwich” was then sealed in a hybridization chamber.  The microarrays were hybridized at 65°C rotating at 10 RPMs for 17 hours.  Slides were washed in Agilent’s Gene Expression Wash Buffers according to manufacturer recommendations.

scan_protocol: The microarrays were scanned on the Agilent Microarray Scanner.  Scanner data extraction and analysis was performed using Feature Extraction software version 10.7.3.1.

data_processing: Data quality was evaluated by reviewing ten standard QC metrics generated by the Agilent Technologies Feature Extraction Software version 10.7.3.1. Microarrays were determined to be free of any large artifacts (≥ 10% of total surface area) that could have affected the quality of the data.

organism: Gallus gallus

label_protocol: Using Agilent’s 2-Color Quick Amp Labeling Kit, (Cat# 5190-0444), 0.5 to 1 ug of RNA (Agilent suggested: total RNA input range 50 ng - 2 μg) and Spike-In (2-Color RNA Spike-In Kit Cat# 5188-5279) were denatured in the presence of a T7 promoter primer.  Reverse Transcriptase was used to reverse-transcribe the mRNA.  cDNA was used as a template for in vitro transcription where a T7 RNA polymerase simultaneously amplified target material and incorporated cyanine 3- or cyanine 5-labeled CTP.  Labeled cRNA was purified using spin columns from the Qiagen RNeasy Mini Kit and the quantity and quality of the cRNA was determined by Nanodrop ND-1000 UV-VIS spectrophotometer.

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

tag: age

value: day 20

value: Intestinal IEL

tag: strain

value: Broiler

value: necrotic enteritis

value: non-infected control


title: with IL-11+FGF2_replicate 2

description:
replicate 2
SAMPLE 8

source_name: with IL-11+FGF2_replicate 2

value: hESC line H1


title: Lymph_node_biopsy_DLBCL_sample_4

source_name: Lymph node biopsy, diffuse large B-cell lymphoma (DLBCL)

value: DLBCL

value: Yes

value: GS(started 04Jan07)

value: Whippet


title: NE_Replicate 2

description: Biological replicate 1 of 2 (Dye-exchange of Replicate 1)

tag: tissue


title: vascular stromal fraction of mesenteric adipose tissue of ob/ob mice, treated with propolis for 12 wks, biological rep 1

status: Public on Sep 25 2013

city: Ebetsu

first: Hiroshi

last: Kitamura

address: 582 Midorimachi, Bunkyodai

department: School of Veterinary Medicine

country: Japan

institute: Rakuno Gakuen University

description:
vascular stromal fraction of mesenteric adipose tissue of ob/ob mice, treated with propolis (100mg/kg, ip, twice a week) for 12 weeks
Mesenteric adipose tissue cut as small pieces were digested with collagenase. After centrifugation, cell pellet was treated with ACK solution to hemolyse. After removal of cell debris, resultant cells were subjected to microaray analysis.

hyb_protocol: 0.6 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 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome Oligo Microarrays (G4852A) for 17 hours at 65Â°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 37Â°C GE Wash buffer 2 (Agilent), then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing:
The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (GE1_107_Sep09 and Grid:028005_D_F_20120201) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
Normalized signal intensity calculated using GeneSpring 12.1GX. Setting is : Advanced Flag Import (Feature is not positive and significant, Not Detected; Feature in not Uniform, Compromised; Feature is not above background, Not Detected; Feature is Saturated, Compromised; Feature is a population outlier, Compromised), Normalization Option (Threshold raw signals to 1.0; Normaliation algorithm, Percentile Shift; Percentile target, 75), Preprocess Baseline Options (Do not perform baseline transformation)

source_name: vascular stromal fraction of mesenteric adipose tissue of ob/ob mice, treated with propolis for 12 weeks

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug RNA using the One-Color Low Input Quick Amp WT Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

extract_protocol: Total cellular RNA was prepared with TRIzol reagent according to a manual.

treatment_protocol: Male ob/ob mice were treated with Brazilian propolis (100mg/kg, ip, twice a week) of vehicle (involving low concntration of DMSO and ethanol) for 12 weeks

tag: gender

value: male

value: propolis (100mg/kg, twice a week)

tag: time

value: 12 weeks


title: Fetal placenta control 2

value: control

value: 14 day fetal placenta


title: vascular stromal fraction of mesenteric adipose tissue of ob/ob mice, treated with propolis for 12 wks, biological rep 3


title: vascular stromal fraction of mesenteric adipose tissue of ob/ob mice, treated with propolis for 12 wks, biological rep 2


title: vascular stromal fraction of mesenteric adipose tissue of ob/ob mice, treated with vehicle for 12 wks, biological rep 2

description:
vascular stromal fraction of mesenteric adipose tissue of ob/ob mice, treated with vehicle for 12 weeks
Mesenteric adipose tissue cut as small pieces were digested with collagenase. After centrifugation, cell pellet was treated with ACK solution to hemolyse. After removal of cell debris, resultant cells were subjected to microaray analysis.

value: vehicle


title: Fetal placenta control 1


title: vascular stromal fraction of mesenteric adipose tissue of ob/ob mice, treated with vehicle for 12 wks, biological rep 1

source_name: vascular stromal fraction of mesenteric adipose tissue of ob/ob mice, treated with vehicle for 12 weeks


title: NE_Replicate 4

description: Biological replicate 2 of 2 (Dye-exchange of Replicate 2)


title: vascular stromal fraction of mesenteric adipose tissue of ob/ob mice, treated with vehicle for 12 wks, biological rep 3


title: with IL-11 _replicate 2

description:
replicate 2
SAMPLE 6

source_name: with IL-11 _replicate 2


title: PMA-treated U937 1

description: PMA-treated U937 1

hyb_protocol: Hybridization, washing, and staining were performed according to the Affymetrix standard method.

scan_protocol: GeneChips were scanned using a GeneChip Scanner 3000.

data_processing: CHP and CEL files were obtained using an Affymetrix Expression Console software packaging. affymetrix-algorithm-name: rma-exon-core

source_name: PMA-treated U937 1

label_protocol: Biotinylated cDNA were prepared using a Sense Target Labeling kit according to the standard Affymetrix protocol from 1 micro gram of total RNA.

growth_protocol: RPMI1640 supplemented with 10%FCS, 37C, 5%CO2 Passage: three times/week

extract_protocol: Total RNA were extracted with TRIzol. Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: phorbol 12-myristate 13-acetate (30nM) or vehicle (DMSO, 1/1000 volume) for 3 days

tag: agent

value: PMA

tag: time point

value: 3 days


title: SAE 12523357 Prep. 1 L.p. JR32 Cy3 vs. Prep. 1 uninfected Cy5 t48

city: Cologne

first: Ludwig

last: Eichinger

address: Joseph-Stelzmann-Strasse 52

institute: Institute for Biochemistry 1

description: DNA microarrays containing 5,423 non-redundant ESTs from the D. discoideum cDNA project (Urushihara et al., 2004), partial sequences of 450 selected genes, probes of the SpotReport-10 Array Validation System (Stratagene, La Jolla, USA) and appropriate positive and negative controls were produced in-house using standard protocols. Briefly, probes were amplified by two 100µl PCR reactions in 96-well microtiter plates using standard primers (M13F2: 5’-GTAAAACGACGGCCAGTG-3’, M13R2: 5’-C6-Aminolink-ACCATGATTACGCCAAGC-3’) for the cloned ESTs and gene-specific primers for the selected genes and the positive controls. After analysis by agarose gel electrophoresis (10µl of each reaction), the two reactions were combined, precipitated, solubilised in 11µl 25% DMSO, 1µl separated again by agarose gel electrophoresis and evaluated (Farbrother et al., 2002). Probes were transferred with the proteineer dp pipetting robot (Bruker, Germany) into 384-well microarray plates with cylindrical wells (Abgene, Hamburg, Germany) and printed onto UltraGaps slides (Corning, New York, USA) at 18°C and 45% humidity with a BioRobotics MicroGrid 600 microarray robot (Genomic Solutions, Huntingdon, UK) using MicroSpot 2500 microarraying pins. Each probe was spotted in duplicate, positive and negative controls were spotted 6, 24, 192 or 286 times and the SpotReport controls 96 times. The microarray is composed of three grids with 16 subarrays each and 14,620 spots in total. The complete microarray dataset is available at GEO, accession number GPL1972.

hyb_protocol: Cy3 and Cy5 labelled targets were mixed, ethanol precipitated and dissolved in 65 µl of hybridisation buffer (Noegel et al., 1985) with 500 µg/ml Fish sperm DNA (Roche, Mannheim, Germany) and 2 µM Oligo dA 18-mer. The hybridisation mix was heated to 80 °C for 10 min, applied to the microarray under a cover-slip and incubated in a hybridisation chamber (Corning, New York, USA) for 15 hours at 37°C. Post-hybridisation washes were performed twice with 2x SSC, 0.1% SDS and once with 0.1x SSC, 0.1% SDS for 5 min each, five times with 0.1x SSC and once with with 0.01x SSC for 5 sec each and dried by centrifugation at 235xg for 5 min. See also Farbrother et al., Cell. Microbiol., 3:438-456, 2006.

scan_protocol: Signal detection was performed with the ScanArray 4000XL confocal laser scanner (PerkinElmer Life Sciences, Wellesley, USA). Images for Cy3 and Cy5 were obtained, spots were detected and quantified with ScanArray Express v2.2 (PerkinElmer Life Sciences), then manually inspected and if necessary corrected. See also Farbrother et al., Cell. Microbiol., 3:438-456, 2006.

data_processing:
For each individual comparison, six microarrays were hybridised and analysed. Two imagepairs were produced per microarray slide, one with high laser intensity so that signals for most probes and also some saturated signals were obtained and a second one with lower laser intensity so that none of the signals was saturated. This way the dynamic range of the measurement was expanded. To handle the import and export of microarray data to different analysis programs an Excel Add-In, Array tools, was programmed in Visual Basic. Upon import of two data files of the same microarray scanned with different laser powers, the saturated spots of the high laser power scan were replaced by non-saturated spots from the low laser power scan. In addition, the import also performed data filtering by flagging SpotReport controls, negative controls, empty spots, spots where only spotting solution was printed and spots whose intensities were below or equal to zero as "Bad". Fluorescence ratios were normalised by LOWESS-normalisation using R1.6.2 (BioConductor, http://www.bioconductor.org/). The normalized M values (M = log2 (Intensityexperiment/Intensitycontrol) were transferred into a new worksheet for significance analysis of microarrays (SAM) analysis (Tusher et al., 2001). At the transfer all probes spotted in higher replicates were reduced to double spots by averaging. Furthermore all probes that were flagged "Found" in less than half of the spots, were excluded from SAM analysis. Differentially regulated genes were identified using the one-class SAM method calculating 1000 permutations. The SAM program not only identifies the differentially regulated genes, but also predicts the number of false positives. These are the genes that are falsely reported as differentially expressed. This feature was used in all microarray experiments to set the significance level such, that the 90th percentile of the false discovery rate (FDR) was minimal.
See also Farbrother et al., Cell. Microbiol., 3:438-456, 2006.

organism: Dictyostelium discoideum

source_name: Prep. 1, uninfected, t48

label_protocol: Fairplay indirect labelling kit.

extract_protocol: RNA was isolated using the protocol for the isolation of cytoplasmic RNA of the RNeasy mini kit (Qiagen AG).

tag: strain/background

value: Legionella pneumophila JR32

value: 48h post infection


title: SAE 12523227 Prep. 1 L.p. JR32 Cy5 vs. Prep. 1 uninfected Cy3 t48

tag: treatment


title: PMA-treated HL60 3

description: PMA-treated HL60 3

source_name: PMA-treated HL60 3


title: with FGF2_replicate 2

description:
replicate 2
SAMPLE 4

source_name: with FGF2_replicate 2


title: PMA-treated THP-1 1

description: PMA-treated THP-1 1

source_name: PMA-treated THP-1 1


title: SAE 12523246 Prep. 3 L.p. JR32 Cy5 vs. Prep. 3 uninfected Cy3 t48

source_name: Prep. 3, uninfected, t48


title: PMA-treated U937 3

description: PMA-treated U937 3

source_name: PMA-treated U937 3


title: DMSO-treated THP-1 1

description: DMSO-treated THP-1 1

source_name: DMSO-treated THP-1 1

value: DMSO


title: PMA-treated HL60 1

description: PMA-treated HL60 1

source_name: PMA-treated HL60 1


title: SAE 12522855 Prep. 2 L.p. JR32 Cy3 vs. Prep. 2 uninfected Cy5 t48

source_name: Prep. 2, uninfected, t48


title: NE_Replicate 3

description: Biological replicate 2 of 2

value: day 20

value: Intestinal IEL

value: Broiler

value: necrotic enteritis

value: non-infected control


title: DMSO-treated HL60 3

description: DMSO-treated HL60 3

source_name: DMSO-treated HL60 3


title: SAE 12523244 Prep. 2 L.p. JR32 Cy5 vs. Prep. 2 uninfected Cy3 t48


title: DMSO-treated U937 2

description: DMSO-treated U937 2

source_name: DMSO-treated U937 2


title: SAE 12523245 Prep. 3 L.p. JR32 Cy3 vs. Prep. 3 uninfected Cy5 t48


title: DMSO-treated U937 3

description: DMSO-treated U937 3

source_name: DMSO-treated U937 3


title: SAE 12523032 Prep. 1 L.p. JR32 Cy5 vs. Prep. 1 uninfected Cy3 t1

source_name: Prep. 1, uninfected, t1

source_name: Prep. 1, L.p. JR32, t1

value: 1h post infection


title: PMA-treated THP-1 3

description: PMA-treated THP-1 3

source_name: PMA-treated THP-1 3


title: PMA-treated HL60 2

description: PMA-treated HL60 2

source_name: PMA-treated HL60 2


title: DMSO-treated HL60 2

description: DMSO-treated HL60 2

source_name: DMSO-treated HL60 2


title: DMSO-treated U937 1

description: DMSO-treated U937 1

source_name: DMSO-treated U937 1


title: DMSO-treated THP-1 3

description: DMSO-treated THP-1 3

source_name: DMSO-treated THP-1 3


title: PMA-treated THP-1 2

description: PMA-treated THP-1 2

source_name: PMA-treated THP-1 2


title: PMA-treated U937 2

description: PMA-treated U937 2

source_name: PMA-treated U937 2


title: DMSO-treated HL60 1

description: DMSO-treated HL60 1

source_name: DMSO-treated HL60 1


title: MPI-902

city: Regensburg

first: Christian

middle: W

last: Kohler

state: Bavaria

address: Am BioPark 9

department: Institute of Functional Genomics

institute: University of Regensburg

hyb_protocol: Affymetrix hybridization was carried on U133A GeneChips according to the manufacturer's recommendations. In brief, 15 microgram of Biotin-labelled and fragmented cRNA were mixed with 20x GeneChip Eukaryotic Hybridization Control (Affymetrix) and supplemented with B2 control oligonucletide, salmon sperm DNA, acetylated bovine serum albumin and hybridization buffer and water making up a total volume of 300 microliter

scan_protocol: After hybridization of night (16 hours, 45° C) the hybridization mixture was removed from the GeneChip and washing and staining of the GeneChips was performed in a fluidics station (Affymetrix). The detection of the Biotin-labeled cRNA was mediated by a streptavidin-phycoerythrin complex. The measurement of the fluorescence intensity was carried out in an Agilent scanner (GA2500)

data_processing: Probe level normalization was done using the calibration and variance stabilization method by Huber et al. (Bioinformatics 2002, PMID: 12169536). Probe-set summarization was performed using the median polish method on the normalised data (Irizarry et al. Nucleic Acids Research 2003, PMID: 12582260)

source_name: tumor

label_protocol: For Affymetrix GeneChip hybridization, 5 microgram of total RNA was employed to generate a double-stranded cDNA with the help of the INVITROGEN Superscript kit. After removal of small molecular components (Affymetrix Clean-up Module), Biotin-labelled cRNA was synthesized by application of the ENZO Labeling kit (T7 RNA polymerase). The concentration of the produced cRNA was determined photometrically (NanoDrop) and the size range of the labelled products was evaluated by BioAnalyzer (Agilent) measurement before and after fragmentation

extract_protocol: RNA was isolated using RNeasy Mini Kit (QIAGEN) and the concentration was determined photometrically (NanoDrop). The quality of the RNA was assessed based on the presence of the tht 18S and 28S tRNA by analysis of an aliquot in the Agilent BioAnalyzer (Agilent)

value: diffuse large B-Cell lymphoma

tag: dlbcl molecular subtype

value: unclassified

tag: molecular diagnosis

value: non-mBL


title: MPI-905


title: FrMPI-905

hyb_protocol: Straight after a RNA quality measurement and with a known RNA concentration for each sample, 300ng were able to be hybridised with our custom-designed Reporter Probe (each with a specific 5’-end colour code signal) and Capture Probe (marked with biotin at the 3’ end). !Sample_scan_protocol = After overnight hybridisation the samples were ready to load to the PrepStation where they were washed with a two-step magnetic bead-purification process and loaded in the 12-well cartridges. Afterwards the cartridges were loaded to the Digital Analyzer (DA, nCounter, NanoString Technologies Inc., Seattle, WA, USA). The DA resolution was set to high, meaning that 280 fields of view (FOV) were counted per sample. A comma-separated-value (.csv) file was obtained after processing.

scan_protocol: Straight after a RNA quality measurement and with a known RNA concentration for each sample, 300ng were able to be hybridised with our custom-designed Reporter Probe (each with a specific 5’-end colour code signal) and Capture Probe (marked with biotin at the 3’ end). After overnight hybridisation the samples were ready to load to the PrepStation where they were washed with a two-step magnetic bead-purification process and loaded in the 12-well cartridges. Afterwards the cartridges were loaded to the Digital Analyzer (DA, nCounter, NanoString Technologies Inc., Seattle, WA, USA). The DA resolution was set to high, meaning that 280 fields of view (FOV) were counted per sample. A comma-separated-value (.csv) file was obtained after processing.

data_processing: Data processing was done using the R-package NanoStringNorm (Waggot et al, Bioinformatics 2012). Final data normalization was performed using the quantile normalization (Bolstadt et al, Bioinformatics 2003)

extract_protocol: Formalin-fixed paraffin-embedded material was cut in five 10μm-thick pieces per sample. Extraction of RNA was done according to the manufacturer’s instructions (ExpressArt FFPE Clear RNAready Kit, AmpTec, Hamburg, Germany). Fresh-frozen blocks’ RNA was extracted as described in Hummel et al, NEJM 2006). The RNA quality was analyzed with the Agilent RNA 6000 Nano Chips (Agilent Technologies, Santa Clara, California, USA) following the product’s protocol.  Further material quality control is present after RNA processing at the nCounter instrument for digital multiplexed gene expression due to the company’s recommendations.

value: mature aggressive B-cell lymphomas

tag: sample type

value: frozen tissue


title: MPI-900

value: germinal center B-cell-like (GCB)


title: MPI-881

value: activated B-cell (ABC)-like


title: Lymph_node_biopsy_DLBCL_sample_6

source_name: Lymph node biopsy, diffuse large B-cell lymphoma (DLBCL)

tag: case id

tag: disease state

value: DLBCL

tag: current medications

tag: previous chemo (yes or no)

value: No

tag: Sex

value: M

tag: breed

value: Border Collie X


title: MPI-885

value: mBL


title: MPI-875


title: MPI-895


title: SAE 12523045 Prep. 3 L.p. JR32 Cy5 vs. Prep. 3 uninfected Cy3 t3

source_name: Prep. 3, uninfected, t3

source_name: Prep. 3, L.p. JR32, t3

value: Legionella pneumophila JR32

value: 3h post infection


title: SAE 12523235 Prep. 1 L.p. JR32 Cy3 vs. Prep. 1 uninfected Cy5 t3

source_name: Prep. 1, uninfected, t3

source_name: Prep. 1, L.p. JR32, t3


title: SAE 12523035 Prep. 3 L.p. JR32 Cy5 vs. Prep. 3 uninfected Cy3 t1

source_name: Prep. 3, uninfected, t1

source_name: Prep. 3, L.p. JR32, t1


title: MPI-901


title: SAE 12523234 Prep. 2 L.p. JR32 Cy5 vs. Prep. 2 uninfected Cy3 t1

source_name: Prep. 2, uninfected, t1

source_name: Prep. 2, L.p. JR32, t1


title: SAE 12523036 Prep. 1 L.p. JR32 Cy5 vs. Prep. 1 uninfected Cy3 t3


title: SAE 12523046 Prep. 1 L.p. JR32 Cy5 vs. Prep. 1 uninfected Cy3 t6

source_name: Prep. 1, uninfected, t6

source_name: Prep. 1, L.p. JR32, t6

value: 6h post infection


title: SAE 12523033 Prep. 2 L.p. JR32 Cy3 vs. Prep. 2 uninfected Cy5 t1


title: SAE 12523043 Prep. 2 L.p. JR32 Cy3 vs. Prep. 2 uninfected Cy5 t3

source_name: Prep. 2, uninfected, t3

source_name: Prep. 2, L.p. JR32, t3


title: SAE 12523047 Prep. 2 L.p. JR32 Cy3 vs. Prep. 2 uninfected Cy5 t6

source_name: Prep. 2, uninfected, t6

source_name: Prep. 2, L.p. JR32, t6


title: MPI-869


title: DMSO-treated THP-1 2

description: DMSO-treated THP-1 2

source_name: DMSO-treated THP-1 2

value: DMSO

value: 3 days

tag: cell line


title: SAE 12523184 Prep. 3 L.p. JR32 Cy3 vs. Prep. 3 uninfected Cy5 t6

source_name: Prep. 3, uninfected, t6

source_name: Prep. 3, L.p. JR32, t6


title: SAE 12523044 Prep. 3 L.p. JR32 Cy3 vs. Prep. 3 uninfected Cy5 t3

source_name: Prep. 3, uninfected, t3


title: SAE 12523231 Prep. 1 L.p. JR32 Cy3 vs. Prep. 1 uninfected Cy5 t1

source_name: Prep. 1, uninfected, t1

source_name: Prep. 1, L.p. JR32, t1

value: 1h post infection


title: SAE 12523354 Prep. 1 L.p. JR32 Cy3 vs. Prep. 1 uninfected Cy5 t6


title: SAE 12523355 Prep. 2 L.p. JR32 Cy5 vs. Prep. 2 uninfected Cy3 t6


title: SAE 12523034 Prep. 3 L.p. JR32 Cy3 vs. Prep. 3 uninfected Cy5 t1


title: SAE 12523236 Prep. 2 L.p. JR32 Cy5 vs. Prep. 2 uninfected Cy3 t3


title: FrMPI-902

source_name: tumor

tag: tissue

value: unclassified


title: FrMPI-901

value: GCB

value: non-mBL


title: FrMPI-900

value: mature aggressive B-cell lymphomas

value: frozen tissue


title: FrMPI-895


title: FrMPI-885


title: FrMPI-873


title: FrMPI-875


title: FrMPI-881

value: ABC


title: MPI-863

value: diffuse large B-Cell lymphoma


title: FrMPI-864


title: FrMPI-869


title: MPI-865

value: activated B-cell (ABC)-like


title: MPI-864


title: MPI-859

value: germinal center B-cell-like (GCB)

value: intermediate


title: MPI-858


title: MPI-860


title: FrMPI-859


title: FrMPI-860


title: MPI-847


title: MPI-848


title: MPI-849


title: FrMPI-858


title: FrMPI-852


title: FrMPI-865


title: MPI-845


title: MPI-846


title: FrMPI-863


title: FrMPI-850


title: FrMPI-848


title: MPI-680

value: mBL


title: FrMPI-847


title: MPI-618


title: MPI-475


title: MPI-619


title: MPI-621


title: FrMPI-846


title: MPI-831


title: FrMPI-845


title: FrMPI-842


title: FrMPI-849


title: FrMPI-840


title: FrMPI-831


title: FrMPI-812


title: FrMPI-822


title: MPI-698_tissue

hyb_protocol: Affymetrix hybridization was carried out on U133A GeneChips according to the manufacturer's recommendations. In brief, 15 microgram of biotin-labelled and fragmented cRNA were mixed with 20x GeneChip Eukaryotic Hybridization Control (Affymetrix) and supplemented with B2 control oligonucletide, salmon sperm DNA, acetylated bovine serum albumin and hybridization buffer and water making up a total volume of 300 microliter. Hybridization was performed overnight (16 hours, 45° C).

scan_protocol: After hybridization, the hybridization mixture was removed from the GeneChip, and washing and staining of the GeneChips were performed in a fluidics station (Affymetrix). The detection of the biotin-labeled cRNA was mediated by a streptavidin-phycoerythrin complex. The measurement of the fluorescence intensity was carried out in an Agilent scanner (GA2500).

data_processing: Probe level normalization was done using the calibration and variance stabilization method by Huber et al. (Bioinformatics 2002, PMID: 12169536). Probe-set summarization was performed using the median polish method on the normalised data (Irizarry et al. Nucleic Acids Research 2003, PMID: 12582260).

label_protocol: For Affymetrix GeneChip hybridization, 5 microgram of total RNA was employed to generate a double-stranded cDNA with the help of the Invitrogen SuperScript kit. After removal of small molecular components (Affymetrix Clean-up Module), biotin-labelled cRNA was synthesized by application of the ENZO Labeling kit (T7 RNA polymerase). The concentration of the produced cRNA was determined photometrically (NanoDrop), and the size range of the labelled products was evaluated by BioAnalyzer (Agilent) measurement before and after fragmentation.

extract_protocol: RNA was isolated using the RNeasy Mini Kit (QIAGEN), and the concentration was determined photometrically (NanoDrop). The quality of the RNA was assessed based on the presence of the 18S and 28S tRNA by analysis of an aliquot in the Agilent BioAnalyzer (Agilent).

tag: gender

value: female

tag: age

value: non-Burkitt diffuse large B-cell lymphoma

value: pos

value: neg

value: IG-MYC

value: double


title: FrMPI-795


title: FrMPI-783


title: MPI-407_tissue

value: male


title: FrMPI-756

value: GCB


title: MPI-700_tissue

value: triple


title: FrMPI-698

value: mature aggressive B-cell lymphomas


title: Pop5 210 clone1

city: Seattle

first: Maitreya

middle: J.

last: Dunham

state: WA

address: Foege Building, S403B, Box 355065

department: Genome Sciences

institute: University of Washington

description: Pop5 210 clone1 vs. FY4

hyb_protocol: Reference: MDAgilentDNA.pdf

scan_protocol: Pixel Size : 5 Scan Date : 2011-12-06 Scan Time : 10:13:04 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505C Scanning software : ChipScan Scanning software version : A.8.3.1

data_processing:
Extraction Software : Agilent Feature Extractor
Extraction Software Version : 10.5.1.1
Datafile type : Agilent result file
The normalization algorithm was the Agilent default.

label_protocol: Reference: MDAgilentDNA.pdf

extract_protocol:
Extracted molecule : DNA
Extraction method : Nib and Grab (see supplemental methods)

tag: strain

tag: genotype

value: prototroph

source_name: Pop5 210 clone1

value: Pop5 210 clone1

tag: sex/mating type

value: MATa


title: FrMPI-680

value: frozen tissue


title: FrMPI-716


title: Pop7 201 clone1

description: Pop7 201 clone1 vs. FY4

scan_protocol: Pixel Size : 5 Scan Date : 2011-09-06 Scan Time : 10:52:53 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505C Scanning software : ChipScan Scanning software version : A.8.3.1

source_name: Pop7 201 clone1

value: Pop7 201 clone1


title: Pop6 211 clone1

description: Pop6 211 clone1 vs. FY4

source_name: Pop6 211 clone1

value: Pop6 211 clone1


title: FrMPI-700

value: intermediate


title: FrMPI-841

value: ABC

value: non-mBL


title: Pop4 210 clone1

description: Pop4 210 clone1 vs. FY4

scan_protocol: Pixel Size : 5 Scan Date : 2013-06-07 Scan Time : 09:21:47 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505C Scanning software : ChipScan Scanning software version : A.8.3.1

value: Pop4 210 clone1


title: Pop3 210 clone10

description: Pop3 210 clone10 vs. FY4

scan_protocol: Pixel Size : 5 Scan Date : 2012-09-01 Scan Time : 10:46:41 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505C Scanning software : ChipScan Scanning software version : A.8.3.1

source_name: Pop3 210 clone10

value: Pop3 210 clone10


title: Pop2 210 clone1

description: Pop2 210 clone1 vs. FY4

scan_protocol: Pixel Size : 5 Scan Date : 2011-11-01 Scan Time : 08:18:57 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505C Scanning software : ChipScan Scanning software version : A.8.3.1

source_name: Pop2 210 clone1

value: Pop2 210 clone 1


title: Pop3 210 clone1

description: Pop3 210 clone1 vs. FY4

scan_protocol: Pixel Size : 5 Scan Date : 2011-09-13 Scan Time : 10:33:54 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505C Scanning software : ChipScan Scanning software version : A.8.3.1

source_name: Pop3 210 clone1

value: Pop3 210 clone 1


title: FrMPI-626


title: FrMPI-621

value: mBL


title: FrMPI-619

value: GCB


title: FrMPI-618


title: MCF7/Aro D4A+Fulvestrant+GDNF, biological rep 3

city: Basel

first: Tim

last: Roloff

address: Maulbeerstrasse 66

department: Functional Genomics

country: Switzerland

institute: FMI

description: Sample name: MCF7-Aro_F+G_3

hyb_protocol: Affymetrix GeneChip arrays were hybridized following the GeneChip Whole Transcript (WT) Sense Target Labeling Assay Manual (Affymetrix) with a hybridization time of 16h. The Affymetrix Fluidics protocol FS450_0007 was used for washing.

scan_protocol: Scanning was performed with Affymetrix GCC Scan Control v. 3.0.0.1214 on a GeneChip® Scanner 3000 with autoloader.

data_processing: Probesets were summarized and probeset-level values normalized withjustRMA() function from R (version 2.10.0) / Bioconductor (version 2.5) package affy using the CDF environment HuGene-1_0-st-v1.r3.cdf (as provided by Bioconductor) and annotation HuGene-1_0-st-v1.na31.hg19.transcript.csv from Netaffx (www.netaffx.com).

source_name: Breast cancer cell line

label_protocol: RNA was processed according to the GeneChip Whole Transcript (WT) Double-Stranded Target Assay Manual from Affymetrix (GeneChip Whole Transcription Sense Target Labeling technical manual, Rev. 2).

growth_protocol: MCF7 aromatase expressing cells (MCF7/Aro) were cultured in MEM EBS (Amimed). Supplements included 10 % FCS, 2mmol/L L-glutamine, 100IU/ml penicillin, 100ug/ml streptomycin, 1mmol/L sodium pyruvate and 1% nonessential amino acids.

extract_protocol: RNA from MCF7/Aro-treated cells (triplicate experiments) was obtained using Rneasy Mini Kit (Qiagen) and hybridized to Affymetrix Human Gene 1.0 Array according to the standard Affymetrix protocols.

treatment_protocol: Cells were steroid deprived using MEM EBS phenol red-free medium (Amimed) supplemented with 10% charcoal-stripped FCS (Hyclone) for 2-4 days before to initiate treatment. Treatments with DMSO as control or with the ER pathway inhibitors Letrozole and Fulvestrant (100nM) were done 60-90 minutes before to perform the stimulation with the ligands: 1nM D4A (estrogen precursor androstenedione), 10ng/ml GDNF (Ret ligand GDNF) or EtOH as control. Treatments of MCF7/Aro cells were initiated 2 days post-seeding and the cells were treated with inhibitors and ligands every second day for 6 days.

tag: treatment

tag: time

value: 6 days


title: FrMPI-590

value: mature aggressive B-cell lymphomas

tag: dlbcl molecular subtype

value: unclassified

tag: molecular diagnosis


title: FrMPI-593

tag: sample type


title: FrMPI-589


title: FrMPI-586


title: MCF7/Aro D4A+Fulvestrant+GDNF, biological rep 2

description: Sample name: MCF7-Aro_F+G_2

value: MCF7 aromatase expressing cells (MCF7/Aro)


title: MCF7/Aro D4A+Fulvestrant, biological rep 3

description: Sample name: MCF7-Aro_F_3


title: MCF7/Aro D4A+Fulvestrant+GDNF, biological rep 1

description: Sample name: MCF7-Aro_F+G_1


title: FrMPI-584


title: Ctla4-/- T cells rep1

city: Worcester

first: Joonsoo

last: Kang

address: 368 Plantation St. ASC9-1047

institute: UMass Medical School

hyb_protocol: Hybridization was performed using the Affymetrix WT Terminal Labeling and Hybridization Kit. Briefly, 27 microlitres of fragmented and labeled cDNA was mixed with 73 microlitres of Hybridization mix (+2X Hybridization buffer + BSA+ Herring Sperm DNA). Hybridization was performed at 45C for 16 hours.

scan_protocol: Chips were scanned with Affymetix GeneChip Scanner 3000 7G

data_processing: Affymetrix Expression Console (v1.1) was used to check for quality and consistency and to generate normalized data using the RMA algorithm.

source_name: Activated CD4+ Ctla4-/- T cells from LN

label_protocol: Fragmentation and labeling was performed with the Affymetrix WT Terminal Labeling and Hybridization Kit

growth_protocol: CD4+CD25neg cells were sorted on a MoFlo sorter. Purity was confirmed to be >95%.

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

tag: strain background

tag: genotype/variation

value: 3 weeks

value: Lymph node T cells

tag: cell type

value: sorted CD4+CD25neg T cells


title: FrMPI-407

value: frozen tissue


title: FrMPI-528


title: Ctla4-/- T cells rep2


title: MCF7/Aro D4A+Fulvestrant, biological rep 1

description: Sample name: MCF7-Aro_F_1


title: DKO T cells rep2

source_name: Activated CD4+ DKO T cells from LN


title: DKO T cells rep1


title: MCF7/Aro D4A+Fulvestrant, biological rep 2

description: Sample name: MCF7-Aro_F_2


title: FrMPI-084


title: FrMPI-347


title: MCF7/Aro D4A+Letrozole+GDNF, biological rep 3

description: Sample name: MCF7-Aro_L+G_3


title: MCF7/Aro D4A+GDNF, biological, rep 3

description: Sample name: MCF7-Aro_D+G_3


title: MCF7/Aro D4A+Letrozole+GDNF, biological rep 2

description: Sample name: MCF7-Aro_L+G_2


title: MCF7/Aro D4A+Letrozole, biological rep 2

description: Sample name: MCF7-Aro_L_2


title: MCF7/Aro D4A+Letrozole+GDNF, biological rep 1

description: Sample name: MCF7-Aro_L+G_1


title: MCF7/Aro D4A+Letrozole, biological rep 1

description: Sample name: MCF7-Aro_L_1


title: FrMPI-043


title: MCF7/Aro D4A+GDNF, biological, rep 2

description: Sample name: MCF7-Aro_D+G_2


title: MPI-905

hyb_protocol: Straight after a RNA quality measurement and with a known RNA concentration for each sample, 300ng were able to be hybridised with our custom-designed Reporter Probe (each with a specific 5’-end colour code signal) and Capture Probe (marked with biotin at the 3’ end).

scan_protocol: After overnight hybridisation the samples were ready to load to the PrepStation where they were washed with a two-step magnetic bead-purification process and loaded in the 12-well cartridges. Afterwards the cartridges were loaded to the Digital Analyzer (DA, nCounter, NanoString Technologies Inc., Seattle, WA, USA). The DA resolution was set to high, meaning that 280 fields of view (FOV) were counted per sample. A comma-separated-value (.csv) file was obtained after processing.

value: FFPE tissue


title: MPI-902


title: MPI-901


title: MCF7/Aro D4A, biological rep 2

description: Sample name: MCF7-Aro_D_2


title: MCF7/Aro D4A+Letrozole, biological rep 3

description: Sample name: MCF7-Aro_L_3


title: MCF7/Aro D4A+GDNF, biological, rep 1

description: Sample name: MCF7-Aro_D+G_1


title: MPI-875


title: MCF7/Aro EtOH+GDNF, biological rep 3

description: Sample name: MCF7-Aro_E+G_3

value: EtOH+GDNF


title: MPI-873

value: non-mBL


title: MCF7/Aro D4A, biological rep 3

description: Sample name: MCF7-Aro_D_3


title: MCF7/Aro D4A, biological rep 1

description: Sample name: MCF7-Aro_D_1


title: MPI-895


title: MPI-881

value: ABC


title: MPI-885


title: MPI-865


title: MPI-900


title: MPI-869


title: SAE 12523185 Prep. 3 L.p. JR32 Cy5 vs. Prep. 3 uninfected Cy3 t6

tag: strain/background

value: Legionella pneumophila JR32

tag: time point

value: 6h post infection


title: MPI-864


title: MCF7/Aro EtOH, biological rep 3

description: Sample name: MCF7-Aro_E_3

tag: cell line

value: EtOH


title: MPI-860

tag: tissue


title: MCF7/Aro EtOH+GDNF, biological rep 2

description: Sample name: MCF7-Aro_E+G_2


title: MCF7/Aro EtOH+GDNF, biological rep 1

description: Sample name: MCF7-Aro_E+G_1


title: MCF7/Aro EtOH, biological rep 1

description: Sample name: MCF7-Aro_E_1


title: MPI-850

value: intermediate


title: MPI-852

value: GCB


title: MPI-848


title: MCF7/Aro EtOH, biological rep 2

description: Sample name: MCF7-Aro_E_2

value: 6 days


title: MPI-859

value: mature aggressive B-cell lymphomas


title: Identification of miR-27b target genes in PC3

city: Chiba

first: Naohiko

last: Seki

state: Chiba

address: 1-8-1, Inohana

institute: Chiba University

hyb_protocol: Agilent two-color gene expression hyb/wash protocol

scan_protocol: Microarray slides were scanned in an Agilent Technologies G2505C Microarray Scanner at 3 micron resolution. Images were quantified using Agilent Feature Extraction software version 10.7.3.1

data_processing: Agilent Feature Extraction Software version 10.7.3.1 was used for background subtraction and LOWESS normalization.

source_name: control miRNA transfected cell line

label_protocol: Agilent two-color Low RNA Input Linear Amplification Kit labeling protocol

growth_protocol: Normal cell culture medium RPMI 1640 or DMEM.

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

treatment_protocol: microRNA or siRNA transfection using Lipofectamine RNAiMAX (Invitrogen).

value: prostate cancer

tag: transfection or treatment

value: control

source_name: miR-27b transfected cell line


title: Identification of miR-23b target genes in PC3

source_name: miR-23b transfected cell line


title: Differentially expressed genes by wogonin treatment in FaDu

source_name: DMSO treatment cell lines

value: FaDu

value: head and neck squamous cell carcinoma

value: DMSO

source_name: wogonin treated cell line

value: wogonin


title: MPI-846

value: FFPE tissue

value: unclassified


title: Identification of miR-29a target genes in SAS

value: SAS

source_name: miR-29a transfected cell line


title: Differentially expressed genes by wogonin treatment in SAS


title: Identification of miR-24 target genes in PC3

source_name: miR-24 transfected cell line


title: MPI-842

source_name: tumor

value: ABC

value: non-mBL


title: MPI-841


title: Differentially expressed genes by knocking down of LAMB3 in SAS

source_name: control siRNA transfected cell line

source_name: si-LAMB3 transfected cell line


title: Identification of miR-375 target genes in FaDu

source_name: miR-375 transfected cell line


title: MPI-831


title: MPI-847


title: SAT_subject18_resveratrol

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

hyb_protocol: Hybridization and washing of the Affymetrix GeneChip Human Gene 1.1 ST peg arrays were performed on a GeneTitan Instrument according to the manufacturer's recommendations.

scan_protocol: Arrays were scanned on an Affymetrix GeneTitan instrument (Affymetrix, Santa Clara, CA).

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.20.4).

source_name: abdominal subcutaneous adipose tissue biopsy, after 30 days intervention with resveratrol

label_protocol: One hundred nanogram of RNA was used for whole transcript cDNA synthesis with the Ambion WT expression kit [catalog number 4411974] (Applied Biosystems/Life Technologies, Nieuwekerk a/d IJssel, The Netherlands).

growth_protocol: The current work was conducted as part of a previously published randomized double-blind crossover study (Timmers et al., Cell Metab 2011 Nov 2;14(5):612-22. PMID: 22055504 (GSE32357)). Nine healthy obese men (age 45–65 years; BMI 30-35 kg/m2) participated in a double-blind randomized cross-over study. Exclusion criteria were unstable body weight (weight gain or loss > 3 kg in the last three months), total body fat (%) < 25%, fasting plasma glucose > 6.1 mmol/l, hemoglobin < 7.8 mmol/l, engagement in programmed exercise > 2 hours total per week, impaired kidney and/ or hepatic function, first- or second-degree family member with type 2 diabetes mellitus, any medical condition requiring treatment and/or medication use, intake of dietary supplements except vitamins and minerals, unwilling to restrict high-resveratrol-containing foods, current alcohol consumption > 20 grams/day, participation in another biomedical study within 1 month before the first screening visit, a contraindication to MRI scanning. All subjects were informed about the nature of the study and written informed consent was obtained before study participation. The local Medical Ethical Committee of Maastricht University Medical Centre approved the study protocol.

extract_protocol: Adipose tissue biopsies were taken in the morning of day 30 after an overnight fast. Biopsies were obtained, immediately frozen in isopentane at its melting point, and stored at -80C until analysis. Total RNA was extracted from frozen adipose tissue specimens using TRIzol reagent (Invitrogen, Breda, the Netherlands) and puriﬁed on columns using the Qiagen RNeasy Micro Kit (Qiagen, Venlo, Netherlands). RNA quantity was measured with the ND-100 spectrophotometer (Isogen Life Science, Ijsselstein, the Netherlands), and RNA integrity was analysed on an Agilent 2100 BioAnalyzer (Agilent Technologies, Amsterdam, The Netherlands) using nanochips according to manufacturer's instructions.

treatment_protocol: The design of the study was a randomized cross-over design with two different treatments: placebo and resVida (150mg/day trans-resveratrol [99.9%; provided by DSM Nutritional Products, Ltd.]) with a 4-week washout period. Subjects were instructed to take the first supplement on the day after baseline measurements (d1) and the last supplement in the evening on day 29. In the morning of day 30, after 36h in the respiration chamber, a microdialysis test was conducted to measure adipose tissue and skeletal muscle lipolysis before and for 6 hours after ingestion of a high-fat liquid test meal. At the end of the microdialysis test, a subcutaneous adipose tissue biopsy was taken.

tag: race

value: Caucasian

tag: gender

value: male

tag: age

value: 61 years

tag: disease status

value: healthy, obese

value: white adipose

value: resveratrol

tag: subject


title: Identification of miR-145 target genes in DU145

value: prostate cancer

source_name: miR-145 transfected cell line


title: Differentially expressed genes by knocking down of CAV2 in 786O

value: renal cell carcinoma

value: control

source_name: si-CAV2 transfected cell line


title: SAT_subject16_resveratrol

value: 50 years

tag: treatment


title: MPI-822

value: mature aggressive B-cell lymphomas

tag: dlbcl molecular subtype


title: SAT_subject18_placebo

source_name: abdominal subcutaneous adipose tissue biopsy, after 30 days intervention with placebo

value: placebo


title: Differentially expressed genes by knocking down of LAMB3 in FaDu

value: FaDu

value: head and neck squamous cell carcinoma


title: SAT_subject16_placebo


title: SAT_subject15_placebo


title: Identification of miR-145 target genes in LNCap

value: LNCap


title: MPI-812

value: FFPE tissue

value: ABC


title: SAT_subject15_resveratrol

value: Caucasian


title: Identification of miR-145 target genes in PC3


title: SAT_subject11_placebo

value: male

value: 52 years


title: Differentially expressed genes by genistein treatment in DU145

source_name: non treatment cell line

value: no treatment

source_name: genistein treated cell line

value: genistein


title: MPI-700

value: GCB

value: intermediate


title: MPI-795

value: non-mBL


title: Differentially expressed genes by knocking down of CAV2 in A498

value: renal cell carcinoma

value: control


title: MPI-698

value: mature aggressive B-cell lymphomas


title: SAT_subject11_resveratrol

value: healthy, obese

value: white adipose

value: resveratrol


title: SAT_subject9_resveratrol

value: 60 years


title: SAT_subject9_placebo

value: placebo


title: MPI-621

value: FFPE tissue

value: mBL


title: SAT_subject8_resveratrol

value: Caucasian

value: male

value: 51 years


title: SAT_subject8_placebo


title: Differentially expressed genes by genistein treatment in PC3

value: prostate cancer

value: no treatment

value: genistein


title: MPI-626

value: GCB

value: intermediate


title: SAT_subject5_placebo

value: 63 years


title: MPI-590

value: mature aggressive B-cell lymphomas

value: unclassified


title: MPI-407


title: MPI-584

value: non-mBL


title: MPI-528


title: MPI-618


title: MPI-586


title: MPI-619


title: H99_Proline+Urea

city: Durham

first: Aubrey

last: Frazzitta

state: North Carolina

address: 0557 Duke Hospital South Research Drive

department: Medicine

institute: Duke University Medical Center

hyb_protocol: Hybridization was performed at the Duke University Microarray Facility following the Hybridization protocol (http://www.genome.duke.edu/cores/microarray/).

scan_protocol: Slides were scanned at the Duke University Microarray Facility using an Axon Genepix 4000B scanner (http://www.genome.duke.edu/cores/microarray/).

data_processing:
Data was analyzed using JMP genomics (SAS institute, Cary NC) and initial background subtraction was performed. Data were normalized using the Array Normalization process in JMP.
JMP Genomics computed LSMeans estimate of normalized log2-transformed signal intensities. In our ANOVA setting there is a filter specified to remove rows with 20% or more missing data--this resulted in eliminating ~ 400 genes relative to our platform.

label: Cy3, Cy5

organism: Cryptococcus neoformans

source_name: yeast culture

label_protocol: Labeling was performed at the Duke University Microarray Facility following the 1 Round Amp Labeling protocol for spotted arrays (http://www.genome.duke.edu/cores/microarray/).

growth_protocol: YCB + Proline media was inoculated with strains H99, ure1Δ, and amt1/2Δ and grown overnight at 30°C. Cells were washed in sterile water and resuspended in 25 mL of either YCB + Proline (0.25 g/L) or YCB + Proline (0.25 g/L) + Urea (0.25 g/L). All media were made at pH 5±0.1. The cultures were grown for 1 hour at 30°C, pelleted, and frozen at -80°C. RNA was isolated from each culture and compared in a dye-swap experiment. Two biological replicates of the experiment were performed.

extract_protocol: RNA for all samples was obtained from lyophilized cells using the TriZol extraction protocol (Invitrogen, Carlsbad, CA) followed by purification using the Qiagen RNeasy kit (Qiagen, Valencia, CA).

tag: strain

tag: nitrogen

value: Proline + Urea (0.25g/L)


title: amt1amt2_Proline+Urea

value: amt1 and amt2 deletion mutant


title: amt1amt2_Proline

value: Proline


title: H99_Proline


title: MPI-043

tag: sample type

value: FFPE tissue


title: MPI-475


title: ure1_Proline+Urea

value: ure1 deletion mutant


title: ure1_Proline


title: SAT_subject5_resveratrol

value: Caucasian

value: healthy, obese

value: white adipose

value: resveratrol


title: SAT_subject1_placebo

value: male

value: 45 years

value: placebo


title: MPI-084

value: GCB

value: mBL


title: SAT_subject2_resveratrol

value: 43 years


title: SAT_subject2_placebo


title: SAT_subject1_resveratrol


title: MPI-347

value: mature aggressive B-cell lymphomas

value: ABC


title: Y4184snf1_46

city: Wilmington

first: Seung-Pyo

last: Hong

state: DE

address: Experimental Station, E328/B47B

department: BCS&E

institute: DuPont Central Research and Development

description: This sample is of Yarrowia lipolytica Y4184 snf1 mutant. It is the second of three biological replicates used in this experiment, each from separate cultures.

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

data_processing: Data were normalized using RMA, and then averaged over the 4 replicated probes.

organism: Yarrowia lipolytica

source_name: Yarrowia lipolytica Y4184 delta_snf1

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol: Yarrowia lipoltica Y4184 strains were grown to mid-log phase (O.D.600nm 2.0) anerobically at 30°C in synthetic dextrose medium (2% glucose, 0.67% Yeast Nitrogen base without amino acids and with ammonium sulfate).

extract_protocol: A 10 ml aliquot from each culture was harvested by centrifugation at 2,000 x g for 2 min. The cell pellet was immediately frozen in liquid nitrogen and stored at -80 ˚C. Total RNA was prepared from cell pellets using TRIzol reagent (Life Technologies, Carlsbad, CA). Cell breakage was carried out using a Mini-Beadbeater 8 (BSP, Bartlesville, OK). The extracted total RNA was then purified using a Qiagen RNeasy kit.

treatment_protocol: Yarrowia lipoltica Y4184 snf1 strains were grown to mid-log phase (O.D.600nm 2.0) anerobically at 30°C in synthetic dextrose medium (2% glucose, 0.67% Yeast Nitrogen base without amino acids and with ammonium sulfate).

tag: genotype/variation

value: snf1 deletion