title: 15004_Relapse_Ascites


title: Sample 34 vs 42, heavy polysomes vs heavy polysomes, reverse labeling slide B

status: Public on Jun 21 2012

type: RNA

city: Leicester

first: Kate

middle: Marie

last: Dudek

address: Hodgkin Building, Lancaster Road

department: Genomics Group

country: United Kingdom

institute: MRC Toxicology Unit

hyb_protocol: Samples combined (cy-3 labelled and cy-5 labelled). 4 µg tRNA and 40 µl Genisphere 2x enhanced hybridisation buffer added. Samples denatured at 95°C for 5 minutes and then incubated at 42°C. Complete MEEBO array is split over 2 slides (part A and part B), therefore, sample split and equal volume added to each slide. Slides hybridised for 16 hours at 42°C using Genetix hybridisation chamber. Following hybridisation slides were washed sequentially: wash 1: 1X SSC, 0.03% SDS for 5 minutes, wash 2: 0.2X SSC for 3 minutes, wash 3: 0.05X SSC for 3 minutes.

scan_protocol: Slides scanned on a 4200 Axon scanner and data acquired using GenePix Pro v.6.0.

data_processing: Result files were LOWESS normalised and tested for statistical significance using a two-labelled T test. Forward and reverse reactions were combined and each mRNA had a normalised log 2 value, indicative of fold change. The data for each of the 4 sub pools (monosome, light polysome, medium polysome and heavy polysome) was combined into one data matrix file so that the  normalised log 2 values could be analysed across the gradient.

molecule: total RNA

organism: Rattus norvegicus

source_name: Fractionated liver RNA, treated with 1120mg/kg of FP014SC for 15 days.

label_protocol: Equal amounts of RNA from each sub-pool were precipitated with 10 µl 3M NaOAc pH 5.2 and 275 µl 100% ethanol at -20°C overnight. Following centrifugation (12000xg, 10 minutes, 4°C) pellets were washed twice with 75% ethanol and resuspended in 10 µl water. We used a direct labelling technique to conjugate the reverse transcribed cDNA to cy dyes. The precipitated RNA was first primed with 8 µg/ul oligo dT25N2 and 1 µl 10 nM/µl random pentadecamers at 70°C for 8 minutes, then reverse transcribed and labelled at 50°C for 2 hours in the presence of dNTPs, Superscript III and Cy-3/Cy-5. The cDNA was hydrolysed through addition of 0.5M EDTA and 3M NaOH (70°C for 10 minutes) and then purified using Microcon YM-30 columns.

growth_protocol: Male Wistar rats, 209-248g, 8-10 weeks old. 12 hour light/dark cycle. Food and water provided ad libitum, 24 hours a day.

extract_protocol: Liver samples were lysed (15 mM Tris-HCl (pH 8.0), 300 mM NaCl and 15 mM MgCl2, plus inhibitors (1 mg/ml heparin 100 µg/ml cycloheximide and 80 U RNAsin)), added  to a 10-50% sucrose gradient and ultracentrifuged at 182,000x g for 2 hours. The gradient was aliquotted into 16 1ml fractions and added to Tri reagent (Sigma). RNA was extracted as per the manufacturer's instructions and then sub-pooled into fractions corresponding to monosomes, light polysomes, medium polysomes and heavy polysomes.

treatment_protocol: Rats were randomly assigned to groups on the basis of body weight. Dosing was performed intra-gastricallly by gavage. Treated rats received 2 x 560mg/kg of test compound per day for 15 days, controls received vehicle-only; in a dose volume of 10ml/kg. 20 hours after the final administration rats were sacrificed under chloroform anaesthesia and exsanguinated. Liver and kidneys were taken for analysis.

tag: treatment

tag: gender

value: Male

tag: strain

value: Wistar

tag: tissue

value: Liver

tag: fraction sub-pool

value: Heavy polysomes

source_name: Fractionated liver RNA, treated with vehicle-only.

value: treated with vehicle-only.


title: Sample 34 vs 42, heavy polysomes vs heavy polysomes, forward labeling slide B

value: treated with 1120mg/kg of FP014SC for 15 days.


title: 15003_Primary_Ovarian

type: genomic

city: Melbourne

first: Prof David

last: Bowtell PhD.

state: VIC

address: Locked Bag 1 A' Beckett St

department: Research Division

country: Australia

institute: PeterMacCallum Cancer Centre

description: Tumour tissue collected at relapse

hyb_protocol: Protocol per manufacturer's protocol

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner

data_processing: Raw CEL files were normalized using methods available in R package "aroma.affymetrix". Systematic biases including allelic-crosstalk and fragment length biases were removed using the methods available in this package. The resultant values were log2 transformed to obtain the normalized values.

label: Biotin

molecule: genomic DNA

organism: Homo sapiens

label_protocol: Protocol per manufacturer's protocol

growth_protocol: Frozen tissues were sectioned on a cryostat and lysed immediately

extract_protocol: Genomic DNA was isolated using the Qiagen Dneasy kit

value: Female

value: Tumour


title: Sample 34 vs 42, medium polysomes vs medium polysomes, reverse labeling slide B

value: Medium polysomes


title: MA-104 SARS CoV DeltaE 24hpi rep1

city: Cantoblanco

first: Juan

middle: Carlos

last: Oliveros

state: Madrid

address: Darwin 3

country: Spain

institute: CNB, CSIC

description: Gene expression data from MA-104 cells infected with SARS-CoV-DeltaE and collected at 24hpi

hyb_protocol: Following fragmentation, 10 µg of biotinylated cRNA were hybridized to Affymetrix GeneChips (Human Genome U133 plus 2.0) at 45ºC during 16 hours. Each sample was added to a hybridization solution containing 100mM 2-(N-morpholino)ethanesulfonic acid, 1 M Na+, 20mM of EDTA and 0,01% tween-20

scan_protocol: The arrays were stained with streptavidin-ficoeritrin and read at 1.56 μm in a GeneChip Scanner 3000 7G System (Affymetrix, Santa Clara, CA)

data_processing: GeneChip intensities were background-corrected, normalized and sumarized by RMA method, using the “Affy” package from Bioconductor.

label: biotin

organism: Chlorocebus aethiops

source_name: MA-104 cells, infected with SARS-CoV-DeltaE, 24hpi

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

growth_protocol: Subconfluent monolayers (90% confluency) of Vero E6 and MA-104 cells were infected at multiplicity of infection (moi) of 0.01 or 2 with the viruses rSARS-CoV-ΔE, and rSARS-CoV or rSARS-CoV-MA15-ΔE and rSARS-CoV-MA15. Culture supernatants were collected at different hours post-infection (hpi) and virus titer was determined as previously described.

extract_protocol: Total RNA was prepared using the RNeasy Mini Kit (Qiagen) according to the manufacturer´s instructions. RNA was quantified and the RNA quality was assessed with a 2100 Bioanalyzer (Agilent Technologies).

tag: infection

value: SARS CoV DeltaE

tag: cell line

tag: induce ifnβ

value: YES

tag: hours post infection

value: 24 hpi


title: Sample 34 vs 42, medium polysomes vs medium polysomes, reverse labeling slide A


title: 15004_Primary_Ovarian

description: Tumour tissue collected at relapse


title: Sample 34 vs 42, medium polysomes vs medium polysomes, forward labeling slide B


title: MA-104 SARS CoV 24hpi rep3

description: Gene expression data from MA-104 cells infected with SARS-CoV (WT) and collected at 24hpi

source_name: MA-104 cells, infected with SARS-CoV (WT), 24hpi

value: SARS CoV


title: 15005_Primary_Ovarian

description: Tumour tissue collected at relapse


title: Sample 34 vs 42, light polysomes vs light polysomes, reverse labeling slide B

value: Light polysomes


title: 15006_Primary_Ascites

description: Tumour tissue collected at primary surgery


title: 15005_Relapse_Ascites


title: Sample 34 vs 42, light polysomes vs light polysomes, reverse labeling slide A


title: MA-104 SARS CoV 24hpi rep2


title: Sample 34 vs 42, light polysomes vs light polysomes, forward labeling slide A


title: MA-104 SARS CoV 24hpi rep1


title: Sample 34 vs 42, medium polysomes vs medium polysomes, forward labeling slide A


title: Sample 34 vs 42, monosomes vs monosomes, reverse labeling slide B

value: Monosomes


title: Sample 34 vs 42, monosomes vs monosomes, reverse labeling slide A


title: Sample 34 vs 42, monosomes vs monosomes, forward labeling slide B


title: Sample 34 vs 42, monosomes vs monosomes, forward labeling slide A


title: Vero E6 Mock infected 15hpi rep1

description: Gene expression data from Vero E6 cells mock-infected and collected at 15hpi

source_name: Vero E6 cells, mock-infected, 15hpi

value: Mock infected

value: Vero E6

value: NO

value: 15 hpi


title: Sample 33 vs 44, heavy polysomes vs heavy polysomes, reverse labeling slide B

value: Male

value: Wistar

value: Liver


title: 15007_Primary_Ovarian


title: 15008_Primary_Ascites

description: Tumour tissue collected at relapse


title: 15009_Primary_Ascites

description: Tumour tissue collected at relapse


title: 4065_Primary_Ovarian

description: Tumour tissue collected at relapse


title: 15009_Primary_Ovarian


title: 4065_Relapse_Ascites


title: 15008_Primary_Ovarian


title: Sample 33 vs 44, heavy polysomes vs heavy polysomes, forward labeling slide B

value: treated with vehicle-only.

value: Heavy polysomes

value: treated with 1120mg/kg of FP014SC for 15 days.


title: Sample 34 vs 42, light polysomes vs light polysomes, forward labeling slide B


title: 15007_Primary_Ascites

value: Female

value: Tumour


title: Sample 33 vs 44, heavy polysomes vs heavy polysomes, forward labeling slide A


title: 5622_Primary_Ovarian

description: Tumour tissue collected at relapse


title: 6496_Illeal_mes_nod


title: 6496_Bladder_Peritoneum


title: Vero E6 Mock infected 15hpi rep2


title: Sample 33 vs 44, medium polysomes vs medium polysomes, reverse labeling slide B

value: Medium polysomes


title: Sample 33 vs 44, heavy polysomes vs heavy polysomes, reverse labeling slide A


title: Sample 33 vs 44, medium polysomes vs medium polysomes, forward labeling slide B


title: Sample 33 vs 44, medium polysomes vs medium polysomes, reverse labeling slide A


title: Sample 33 vs 44, medium polysomes vs medium polysomes, forward labeling slide A


title: Sample 33 vs 44, light polysomes vs light polysomes, reverse labeling slide B


title: Vero E6 Mock infected 15hpi rep3


title: Vero E6 SARS CoV DeltaE 15hpi rep2

description: Gene expression data from Vero E6 cells infected with SARS-CoV-DeltaE and collected at 15hpi

source_name: Vero E6 cells, infected with SARS-CoV-DeltaE, 15hpi

value: SARS CoV DeltaE


title: Vero E6 SARS CoV DeltaE 15hpi rep1


title: Sample 33 vs 44, light polysomes vs light polysomes, forward labeling slide B


title: Vero E6 SARS CoV 15hpi rep2

description: Gene expression data from Vero E6 cells infected with SARS-CoV (WT) and collected at 15hpi

source_name: Vero E6 cells, infected with SARS-CoV (WT), 15hpi

value: SARS CoV


title: Sample 33 vs 44, light polysomes vs light polysomes, forward labeling slide A

value: Light polysomes


title: Vero E6 SARS CoV DeltaE 15hpi rep3


title: Vero E6 SARS CoV 15hpi rep3


title: Sample 33 vs 44, monosomes vs monosomes, reverse labeling slide B

value: Monosomes


title: Sample 33 vs 44, light polysomes vs light polysomes, reverse labeling slide A


title: Sample 33 vs 44, monosomes vs monosomes, reverse labeling slide A


title: 6496_Right_ovary

description: Tumour tissue collected at relapse


title: Vero E6 SARS CoV 15hpi rep1


title: 5622_Relapse_Ascites


title: Sample 33 vs 44, monosomes vs monosomes, forward labeling slide B


title: 6496_Omentum

description: Tumour tissue collected at relapse

source_name: Omentum


title: Sample 33 vs 44, monosomes vs monosomes, forward labeling slide A


title: 6496_Left_ovary


title: Vero E6 Mock infected 07hpi rep3

description: Gene expression data from Vero E6 cells mock-infected and collected at 7hpi

source_name: Vero E6 cells, mock-infected, 7hpi

value: Mock infected

value: 7 hpi


title: Sample 32 vs 43, heavy polysomes vs heavy polysomes, reverse labeling slide B


title: 7899_Lymph_node


title: Sample 32 vs 43, heavy polysomes vs heavy polysomes, reverse labeling slide A


title: Vero E6 Mock infected 07hpi rep1

value: Vero E6

value: NO


title: Sample 32 vs 43, heavy polysomes vs heavy polysomes, forward labeling slide A

value: Male


title: Vero E6 Mock infected 07hpi rep2


title: Vero E6 SARS CoV DeltaE 07hpi rep3

description: Gene expression data from Vero E6 cells infected with SARS-CoV-DeltaE and collected at 7hpi

source_name: Vero E6 cells, infected with SARS-CoV-DeltaE, 7hpi


title: 7899_Colon_nodule


title: 7899_Ovary

source_name: Ovary


title: Sample 32 vs 43, medium polysomes vs medium polysomes, reverse labeling slide A

value: Wistar


title: Sample 32 vs 43, heavy polysomes vs heavy polysomes, forward labeling slide B

value: Liver


title: Sample 32 vs 43, medium polysomes vs medium polysomes, forward labeling slide B

value: treated with vehicle-only.


title: Vero E6 SARS CoV DeltaE 07hpi rep2


title: Sample 32 vs 43, medium polysomes vs medium polysomes, reverse labeling slide B


title: 15006_Primary_Ovarian


title: 7899_Omentum


title: Sample 32 vs 43, light polysomes vs light polysomes, reverse labeling slide B


title: Vero E6 SARS CoV DeltaE 07hpi rep1


title: Sample 32 vs 43, light polysomes vs light polysomes, reverse labeling slide A


title: Vero E6 SARS CoV 07hpi rep3

description: Gene expression data from Vero E6 cells infected with SARS-CoV (WT) and collected at 7hpi

source_name: Vero E6 cells, infected with SARS-CoV (WT), 7hpi


title: Sample 32 vs 43, monosomes vs monosomes, reverse labeling slide B


title: Sample 32 vs 43, light polysomes vs light polysomes, forward labeling slide A


title: Sample 32 vs 43, monosomes vs monosomes, reverse labeling slide A


title: Sample 32 vs 43, monosomes vs monosomes, forward labeling slide B


title: 4956_Relapse_Ascites


title: ADAM17 cKO skin, rep1

city: Freiburg

first: Claus-Werner

last: Franzke

address: Hauptstr. 7

department: Dermatology

country: Germany

institute: University of Freiburg

description:
6FrC_2
back skin P10_litter1

hyb_protocol: For each sample, 1.65 ug of Cy3-labeled cRNA was fragmented and hybridized to Agilent Whole Mouse Genome Oligo Microarrays (G4122F) for 17 hours at 65°C in a rotating Agilent hybridization oven.

scan_protocol: Microarrays were scanned using a DNA microarray scanner, Model G2565A (Agilent Technologies).

data_processing: Data extraction was conducted using Feature Extraction software Version 10.5 (Agilent Technologies). Normalization was performed according to the Agilent Feature Extraction One-Color Protocol. Threshold: 1.0 . Logbase: 2. Technology: Agilent.SingleColor.14850. Normalization: Shift to 75th percentile. Baseline Transformation: median of all samples. FlagSettings: Feature is not Uniform:A. Feature is a population outlier:A. Feature is Saturated:A. Feature is not above background:M. Feature is not positive and significant:M.

label: Cy 3

organism: Mus musculus

source_name: P10 mouse back skin, ADAM17 cKO

label_protocol: Cyanine-3 (Cy3)-labeled cRNA was prepared from 500ng RNA using the Quick Amp Labeling Kit, one-color (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using the Qiagen RNeasy Fibrous Tissue Mini Purification kit with on-column DNase I treatment following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

tag: strain/background

value: mix of 129Sv and C57BL/6

tag: genotype

value: conditional keratinocyte-specific ADAM17 knockout

value: back skin

tag: age

value: 10 days


title: Control skin, rep2

description:
8FrC_3
back skin P10_litter2

source_name: P10 mouse back skin, control

value: control


title: Sample 32 vs 43, monosomes vs monosomes, forward labeling slide A

value: treated with 1120mg/kg of FP014SC for 15 days.


title: 4956_Primary_Ovarian

description: Tumour tissue collected at relapse

value: Female

value: Tumour


title: Vero E6 SARS CoV 07hpi rep1

value: SARS CoV


title: Sample 32 vs 43, light polysomes vs light polysomes, forward labeling slide B

value: Light polysomes


title: Control skin, rep1

description:
4FrC_1
back skin P10_litter1


title: Vero E6 SARS CoV 07hpi rep2

value: 7 hpi


title: Caco-2 cells_10uM of HTy, rep3

status: Public on Jun 20 2012

city: Jaén

first: Gema

last: Pereira-Caro

state: Jaén

address: Ctra. Bailén Motril, km 18.5

institute: IFAPA

description: Gene expression data from Caco-2 cells/TC7 treated with 10 µM of Hydroxytyrol for 24 h

hyb_protocol: The final cRNA was checked for quality before fragmentation and hybridization onto a total of 20 arrays. Hybridization was done as described Affymetrix:Protocol:Hybridization-EukGE-WS2v4.

scan_protocol: Fluorescence intensity for each chip was captured with an Affymetrix HP GeneArray laser confocal scanner (Agilent Technologies). Affymetrix Microarray Suite version 5.0 (MAS 5.0, Affymetrix) was used to quantify each chip.

data_processing: Microarray data analysis (CEL files) were loaded into the DNA-Chip Analyzer software (dChip, version 5/8/08) for normalization, generation of expression values and statistical analysis. After normalization by the Invariant Set Normalization method, probe expression levels were evaluated using the Perfect Match-only model permitting to detect the genes differentially expressed after 24h of treatment with 10 μM of HTy and HTy-Et compared with untreated cells.

source_name: Caco-2 cells treated with 10 µM of HTy for 24 h

label_protocol: Double-stranded cDNA synthesis and generation of biotin-labelled cRNA was performed according to the manufacturer's protocol (Affymetrix Inc.).

growth_protocol: The human Caucasian colon adenocarcinoma cells Caco-2 (TC7 clonal cells) were grown in 75 cm2 flasks and maintained in Dulbecco modified Eagle’s medium (DMEM) (without phenol red) supplemented with 20% fetal calf serum, 1% (v/v) non-essential amino acids, 2 mmol/L glutamine, 100 IU/mL penicillin and 100 μg/L streptomycin in a humidified atmosphere of 5% CO2 and 95% air at 37 ºC. All cells used were between passages 50 and 60.

extract_protocol: Total RNA was isolated using the QIAGEN® RNeasy Mini KitQIAGEN® according to the manufacturer’s instructions (Qiagen). Quality of the resulting RNA was checked using the Agilent 2100 Bioanalyzer (Agilent Technologies) and RNA concentration was measured using a Nanodrop ND-1000 spectrophotometer system (Nanodrop Technologies).

treatment_protocol: Stock solutions (1 mM) of HTy and HTy-Et were prepared in 10% DMSO with deionized water. Then, 10 times diluted solutions were prepared from stock solutions by adding distilled water yielding the concentration 100 μM (1% DMSO) which were ultimately diluted with serum-free DMEM to prepare test solutions 10 µM (0.1% of DMSO). Concentrations were checked by HPLC to confirm complete dissolution in aqueous DMEM media. Caco-2 cells were treated with either 0 or 10 µM HTy-Et or 10µM HTy for 24 h.

tag: cell type

value: Epithelial

tag: disease state

value: Colon Adenocarcinoma

tag: clone

value: TC7 clonal cells

tag: agent

value: HTy


title: ADAM17 cKO skin, rep2

description:
9FrC_4
back skin P10_litter2


title: Caco-2 cells_10uM of HTy, rep1


title: Caco-2 cells_Control, rep2

description: Gene expression data from Caco-2 cells/TC7 (control cells)

source_name: Caco-2 cells


title: Caco-2 cells_Control, rep1


title: Caco-2 cells_10uM of EHTy, rep2

description: Gene expression data from Caco-2 cells/TC7 treated with 10 µM of Hydroxytyrosyl ethyl ether for 24 h

source_name: Caco-2 cells treated with 10 µM of EHTy for 24 h

value: EHTy


title: Caco-2 cells_Control, rep3


title: Caco-2 cells_10uM of EHTy, rep1


title: 8466_Primary_Ovarian


title: prostate_benign_pat5

city: Oulu

first: Markku

middle: H

last: Vaarala

address: Aapistie 5

department: Department of Surgery

country: Finland

institute: University of Oulu

hyb_protocol: Following fragmentation, biotinylated cRNA was hybridized to Affymetrix Human Genome U133 Plus 2 arrays. After being washed, the array was stained with streptavidin–phycoerythrin (Molecular Probes). Staining signal was amplified using biotinylated antistreptavidin  (Vector Laboratories) and second staining with streptavidin–phycoerythrin.  Following fragmentation, biotinylated cRNA was hybridized to Affymetrix Human Genome U133 Plus 2 arrays. After being washed, the array was stained with streptavidin–phycoerythrin (Molecular Probes). Staining signal was amplified using biotinylated antistreptavidin  (Vector Laboratories) and second staining with streptavidin–phycoerythrin.

scan_protocol: GeneChips were scanned using a GeneChip Scanner 3000.

data_processing: The expression data were analyzed using Affymetrix GeneChip Operating System Software. Signal intensities of all probe sets were scaled to the target value of 500. The data was further processed using Chipster v2.0.0 (http://chipster.csc.fi) software.

source_name: prostate benign tissue from radical prostatectomy specimen

label_protocol: Double-stranded DNA was synthesized from 8 ug of total RNA as template by means of the One-Cycle cDNA Synthesis Kit (Affymetrix) and T7-(dT)24 primer. The DNA was purified using GeneChip Sample Cleanup Module (Qiagen). In vitro transcription was performed to produce biotin-labeled cRNA using an in vitro transcription labeling kit (Affymetrix) according to manufacturer’s instructions. Biotinylated cRNA was cleaned with a GeneChip Sample Cleanup Module (Qiagen) and fragmented to 35–200 nucleotide.

extract_protocol: RNA were isolated using QuickPrep Total RNA Extraction Kit (Amersham Biosciences) according to manufacturer’s instructions

tag: sample type

value: microdissected histologically confirmed

value: prostate


title: prostate_benign_pat4


title: prostate_benign_pat6


title: Sample 32 vs 43, medium polysomes vs medium polysomes, forward labeling slide A

source_name: Fractionated liver RNA, treated with vehicle-only.

tag: treatment

value: treated with vehicle-only.

value: Male

value: Wistar

value: Liver

value: Medium polysomes

source_name: Fractionated liver RNA, treated with 1120mg/kg of FP014SC for 15 days.


title: prostate_castrated_pat1

source_name: prostate tissue from castrated subject

tag: gleason pattern

value: random biopsy

value: 3 days surgical castration


title: prostate_cancer_pat5

source_name: prostate cancer tissue from radical prostatectomy specimen


title: prostate_cancer_pat4


title: prostate_castrated_pat2


title: 8466_Relapse_Ascites

tag: gender

value: Female

value: Tumour


title: explants treated sucessively with PMA/IO and LP299v (A-), biological rep1

city: Burjassot (Valencia)

first: Gaspar

last: Perez Martinez

state: Valencia

address: P.O. Box 73

department: Food Biotechnology

institute: Institute of Agrochemistry and Food Technology (CSIC)

description: Gene expression data from PMA/IO stimulated colonic intestinal mucosa with subsequent LP299v (A-)incubation

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using GeneChip scanner 3000 (Affymetrix). Affymetrix’s GeneChip Operating Software (GCOS, Affymetrix) was used to obtain and analyze images.

data_processing: Data were analyzed using dCHIP analysis software. Normalization was done using the Invariant Set Method and modeled using the PM/MM model.

source_name: human colonic intestinal explants, cultured first with PMA/IO for 3 hours and then with LP299v (A-) for 4 hours

label_protocol: 100 ng of total RNA was amplified and labelled according to the Affymetrix two-cycle protocol.

growth_protocol: human mucosal tissues were obtained at surgery from 3 patients with neoplasm. Full thickness colonic wall specimens distant from the tumor and without macroscopic or microscopic lesions were collected. Preparation for surgery was similar for all patients and included gut washes with electrolyte-polyethylene glycol solution and broad spectrum antibiotic therapy. Specimens were rinsed under a jet of saline and gently washed twice in sterile saline. Multiple mucosal samples weighing 25 – 35 mg each were separated from the underlying tissue and placed on culture filter plates with the luninal side uppermost. Intestinal explants were incubated in medium containing antibiotics (penicillin, streptomycin and genatmycin) for 1 h to eradicate indigenous flora.

extract_protocol: After incubation, tissues were harvested in RNAlater (Ambion), and stored at -80ºC for later RNA isolation. Total RNA was isolated from mucosal samples using RNeasy mini kit (Quiagen GmbH, Hilden) following manufacturer’s instructions.

treatment_protocol: Intestinal explants were incubated either with medium (Control) or with the combination of PMA/IO for 3 hours. Then, culture medium was changed and replaced with either medium without any stimulants (Control, inflamed) or medium containing probiotic bacteria (BL23, LP299v, LP299v A-) and incubated for 4 hours.

tag: tissue

value: colonic intestinal mucosa


title: 8479_Ascites

source_name: Ascites


title: 8794_Relapse_Ascites


title: explants treated sucessively with PMA/IO and BL23, biological rep3

description: Gene expression data from PMA/IO stimulated colonic intestinal mucosa with subsequent BL23 incubation

source_name: human colonic intestinal explants, cultured first with PMA/IO for 3 hours and then with BL23 for 4 hours


title: explants treated sucessively with PMA/IO and LP299v, biological rep2

description: Gene expression data from PMA/IO stimulated colonic intestinal mucosa with subsequent LP299v incubation

source_name: human colonic intestinal explants, cultured first with PMA/IO for 3 hours and then with LP299v for 4 hours


title: explants treated sucessively with PMA/IO and LP299v, biological rep3


title: 8479_Right_Ovary


title: 8794_Primary_Ovarian

description: Tumour tissue collected at relapse


title: 8479_Omentum

source_name: Omentum


title: Caco-2 cells_10uM of EHTy, rep3

value: Epithelial


title: Directly frozen tissue, biological rep3

description: Gene expression data from directly frozen colonic intestinal tissue after extirpation

source_name: human colonic intestinal tissue, immediately frozen after extirpation


title: explants treated sucessively with PMA/IO and BL23, biological rep2


title: Directly frozen tissue, biological rep1


title: DGM-00428 [gene_expr]

city: New York

first: Yael

last: Strulovici-Barel

state: NY

address: 1300 York Avenue

department: Department of Genetic Medicine

country: USA

institute: Weill Cornell Medical College

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

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

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.

source_name: small airway epithelium from healthy nonsmokers or healthy smokers

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1-2 microg total RNA (Expression Analysis Technical Manual, 701022 Rev.2, Affymetrix).

extract_protocol: Trizol extraction and RNAeasy clean-up of total RNA was performed according to the manufacturer's instructions.

tag: department of genetic medicine id

tag: smoking status

value: S


title: DGM-01142 [gene_expr]


title: explants treated sucessively with PMA/IO and BL23, biological rep1


title: Control explants without any treatment, biological rep3

description: Gene expression data from colonic intestinal explants cultured without any stimulation

source_name: human colonic intestinal explants cultured without any treament


title: DGM-00668 [gene_expr]


title: explants treated sucessively with PMA/IO and LP299v (A-), biological rep3


title: DGM-01980 [gene_expr]


title: DGM-01242 [gene_expr]


title: DGM-00702 [gene_expr]


title: explants treated  with PMA/IO biolocial rep2

description: Gene expression data from PMA/IO stimulated colonic intestinal mucosa with subsequent control medium incubation

source_name: human colonic intestinal explants, cultured first with PMA/IO for 3 hours and then with culture medium for 4 hours


title: explants treated sucessively with PMA/IO and LP299v (A-), biological rep2


title: 9954_Relapse_Ascites


title: Control explants without any treatment, biological rep2


title: 9965_Relapse_Ascites


title: 8479_Left_Ovary


title: prostate_cancer_pat6


title: explants treated sucessively with PMA/IO and LP299v, biological rep1


title: explants treated  with PMA/IO biolocial rep1


title: DGM-01910 [gene_expr]


title: Directly frozen tissue, biological rep2


title: DGM-01973 [gene_expr]


title: DGM-01775 [gene_expr]


title: Caco-2 cells_10uM of HTy, rep2

source_name: Caco-2 cells treated with 10 µM of HTy for 24 h

value: Colon Adenocarcinoma

tag: cell line

value: TC7 clonal cells


title: DGM-01790 [gene_expr]


title: Control explants without any treatment, biological rep1


title: DGM-01698 [gene_expr]


title: DGM-01556 [gene_expr]


title: DGM-01634 [gene_expr]


title: 9965_Primary_Ovarian

description: Tumour tissue collected at relapse


title: DGM-01642 [gene_expr]


title: DGM-01616 [gene_expr]


title: DGM-01547 [gene_expr]


title: explants treated  with PMA/IO biolocial rep3


title: DGM-01353 [gene_expr]


title: DGM-01349 [gene_expr]


title: DGM-01525 [gene_expr]


title: DGM-01530 [gene_expr]


title: DGM-01111 [gene_expr]


title: DGM-01172 [gene_expr]


title: DGM-01273 [gene_expr]


title: 9954_Primary_Ovarian

description: Tumour tissue collected at relapse


title: DGM-01267 [gene_expr]


title: DGM-01090 [gene_expr]


title: prostate_castrated_pat3


title: DGM-01254 [gene_expr]


title: DGM-01135 [gene_expr]


title: DGM-01107 [gene_expr]


title: DGM-01266 [gene_expr]


title: DGM-01284 [gene_expr]


title: DGM-01025 [gene_expr]


title: DGM-01050 [gene_expr]


title: DGM-01022 [gene_expr]


title: DGM-01015 [gene_expr]


title: DGM-01717 [gene_expr]

value: NS


title: DGM-01635 [gene_expr]


title: DGM-00564 [gene_expr]


title: DGM-01644 [gene_expr]


title: DGM-01011 [gene_expr]


title: DGM-00515 [gene_expr]


title: DGM-01585 [gene_expr]


title: DGM-01558 [gene_expr]


title: DGM-01275 [gene_expr]

source_name: small airway epithelium from healthy nonsmokers or smokers with COPD

tag: copd status

value: yes


title: DGM-00104 [gene_expr]


title: DGM-02088 [gene_expr]


title: DGM-00512 [gene_expr]


title: DGM-00382 [gene_expr]


title: DGM-00082 [gene_expr]


title: DGM-10287 [gene_expr]


title: DGM-10406 [gene_expr]


title: DGM-00683 [gene_expr]


title: DGM-01590 [gene_expr]


title: 13488700 - NLS-D4-2 vs NLS-M4-2

city: Lyon

first: Charles

middle: Patrick

last: Scutt

address: 46 allee d'Italie

department: RDP

country: France

institute: ENS de Lyon

description: Identification of target genes from three transcription factors involved in gynoecium development

hyb_protocol: NLS-M4-2 Cy5 / NLS-D4-2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 3.0, Cy3:pmt voltage 532nm,650V,laser power 100%, Cy5:635nm,pmt voltage 620V,laser power 100%

data_processing: The raw data comprised the logarithm of median feature pixel intensity at wavelength 635 nm (red) and 532 nm (green). No background was subtracted. An array-by-array normalization was performed to remove systematic biases. First, we excluded spots that were considered badly formed features by the experimenter (Flags=-100). Then we performed a global intensity-dependent normalization using the loess procedure (see Yang et al., 2002) to correct the dye bias. Finally, on each block, the log-ratio median is subtracted from each value of the log-ratio of the block to correct a print-tip effect on each metablock.

organism: Arabidopsis thaliana

label_protocol: labelling Cy3 and Cy5 direct, amplification=yes, aRNA 5 ug. Labelling protocol: 5 µg of aRNA (8µl) mixed with 2 µl of random nonamers 1µg/µl and 0.5 µl of RNAse Out 40 U/µl, denatured 10 min at 70 °C and chilled on ice. The followig components were added to the sample 4 µl of first strand buffer 5 X, 1 µl of 10 mM dNTP/2mM dCTP, 2 µl of 0.1 M DTT, 1.5 µl of Cy3-dCTP or Cy5-dCTP (Amersham Pharmacia Biotech, 25nmol tube, PA5502), 1 µl of SuperScript II RT 200U/µl. Then it was incubated at 42°C for 2.5 hours and chilled on ice. The sample was denaturated by adding 2 µl of NaOH 2.5M and incubated at 37 °C for exactly 15 min, then was added 10 µl of 2M MOPS and put on ice. The dyes were purified with the QIAquick PCR Purification Kit (QIAGEN).

growth_protocol: flowers - Peet-based compost, hygrometry 55-75%, Temp. 15-20°C Light 12000-14000 lux

treatment_protocol: Name:Solvant-4h_Gen45 - compound based treatment - compound addition,water+silwet:time 2min . Mock treatment : dipping of inflorescences 2 min in solvant (Silwet L77 0.01% and ethanol 0,1%). Plants are harvested after 4 hours.

tag: Arabidopsis thaliana (columbia)  - dev.stage (Boyes et al. Plant Cell 2001):6.00

treatment_protocol: Name:DEX-4h_Gen45 - compound based treatment - compound addition,dexamethasone:quantity 0.01mM time 2min . Dipping of inflorescences 2 min in dexamethasone (once at 10(u)M diluted in Silwet L77 0.01% and ethanol 0,1%). Plants are harvested after 2 hours.


title: 13488701 - NLS-M4-2 vs NLS-D4-2

hyb_protocol: NLS-D4-2 Cy5 / NLS-M4-2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13366253 - NLS-M4-1 vs NLS-D4-1

hyb_protocol: NLS-D4-1 Cy5 / NLS-M4-1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

tag: Arabidopsis thaliana (columbia)  mutant (35S::NLS-VP16GR) - dev.stage (Boyes et al. Plant Cell 2001):6.00,boyes


title: 13488704 - SPT-C2-1 vs SPT-CD2-1

hyb_protocol: SPT-CD2-1 Cy5 / SPT-C2-1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

treatment_protocol: Name:DEX+CYC-2h_Gen45 - compound based treatment - compound addition,cycloheximide:quantity 0.01mM time 2min . Dipping of inflorescences 2 min in both dexamethasone (once at 10(u)M diluted in Silwet L77 0.01% and ethanol 0,1%) and cycloheximide (twice at 10(u)g/ml (with 1h in between) diluted in Silwet L77 0.01% and DMSO 0.01%). Plants are harvested after 2 hours.

treatment_protocol: Name:CYC-2h_Gen45 - compound based treatment - compound addition,cycloheximide:quantity 0.01mM time 2min . Dipping of inflorescences 2 min in cycloheximide (twice at 10(u)g/ml (with 1h in between) diluted in Silwet L77 0.01% and DMSO 0.01%). Plants are harvested after 2 hours.


title: 13488708 - SPT-C2-2 vs SPT-CD2-2

hyb_protocol: SPT-CD2-2 Cy5 / SPT-C2-2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

treatment_protocol: no treatment


title: IR-KO_Rep2

city: Rokkasho

first: Takashi

last: Sugihara

state: Aomori

address: 2-121 Hacchazawa

department: Radiobiology

country: Japan

institute: Institute for Environmental Sciences

description: Gene expression at 3 dyas after IR ot NonIR

hyb_protocol: Cy3-labelled cRNA (specific activity >9.0 pmol Cy3/ug cRNA) was fragmented at 40°C for 120 minutes in a reaction volume of 100 ml containing 1x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome Oligo Microarrays (G4122F) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting for 4x44k array slides, (Scan resolution 5 um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 11.0 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Irradiated-ATM-KO Replicative2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.4 ug RNA using the Quickamp lebeling kit (Agilent) according to the manufacturer's instructions (Agilent Technologies, Santa Clara, CA) 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-1000 Spectrophotometer.

extract_protocol: RNA was prepared using Trizol (Invitrogene) following the manufacturer's recommendations.  The RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Firstly, ATM-KO and ATM-WT were irradiated at 4.32 Gy, and their cultures were incubated for 72 hours at 37 ºC in a humidified incubator with 5% CO2.

value: embryonic fibroblasts


title: 13501428 - SPT-CD2-3 vs SPT-C2-3

hyb_protocol: SPT-C2-3 Cy5 / SPT-CD2-3 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: IR-KO_Rep3

source_name: Irradiated-ATM-KO Replicative3


title: 13488712 - SPT-CD2-2 vs SPT-C2-2

hyb_protocol: SPT-C2-2 Cy5 / SPT-CD2-2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13488713 - SPT-CD2-1 vs SPT-C2-1

hyb_protocol: SPT-C2-1 Cy5 / SPT-CD2-1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13366247 - NLS-D4-1 vs NLS-M4-1

hyb_protocol: NLS-M4-1 Cy5 / NLS-D4-1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

tag: Arabidopsis thaliana (columbia)  mutant (35S::NLS-VP16GR) - dev.stage (Boyes et al. Plant Cell 2001):6.00


title: 13501834 - SPT-C2-3 vs SPT-CD2-3

hyb_protocol: SPT-CD2-3 Cy5 / SPT-C2-3 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: IR-KO_Rep1

source_name: Irradiated-ATM-KO Replicative1


title: NonIR-WT_Rep2

source_name: Nonirradiated-ATM-WT Replicative2


title: NonIR-KO_Rep3

source_name: Nonirradiated-ATM-Ko Replicative3


title: NonIR-WT_Rep3

source_name: Nonirradiated-ATM-WT Replicative3


title: NonIR-KO_Rep2

source_name: Nonirradiated-ATM-KO Replicative2


title: IR-WT_Rep2

source_name: Irradiated-ATM-WT Replicative2


title: NonIR-KO_Rep1

source_name: Nonirradiated-ATM-KO Replicative1


title: NonIR-WT_Rep1

source_name: Nonirradiated-ATM-WT Replicative1


title: IR-WT_Rep1

source_name: Irradiated-ATM-WT Replicative1


title: SIVF017 NSC, rep3

city: CARDIFF

first: Peter

last: Giles

address: Heath Park

institute: Cardiff University

description:
NSC_46
Replicate 3 of 3.

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: A modified version of the standard Illumina protocol to also acquire per bead array data.

data_processing: The data were normalized using a background subtraction and quantile normalization with Illumina BeadStudio.

source_name: Human ES cell line SIVF017, NSC progeny

label_protocol: Biotinylated cRNA were prepared with the Ambion TotalPrep RNA amplification kit for Illumina arrays.

growth_protocol:
HD human ES cell lines used: SI-187 (XY, 51 CAG, passages 12-25, Stemride, Chicago), SIVF020 HD (XX, 48 CAG , passage 15-28, Sydney IVF Stem Cells, Australia), SIVF018 (XX, 46 CAG, passage 18-30, Sydney IVF Stem Cells, Australia), Huez2.3 (XX, 44 CAG, passages 25-47, IGBMC, Stratsbourg), VUB05 (XY, 44 CAG, passages 35-130, AZ-VUB, Belgium), SIVF017 (XY, 40 CAG, passages 18-35, Sydney IVF Stem Cells, Australia).
Wild type human ES cell lines used: SA-01 (XY, passages 30-83, Cellartis AB, Sweden), VUB01 (XY, passages 80-90, AZ-VUB, Belgium) H9 (XX, passages 40–60, WiCell Research Institute), huES24 (XY, passages 35-60, Harvard University, Massachusetts), and WT4 (XY, passage 50-65, Kings College, London).

Embryonic stem cell lines were maintained on a layer of mitotically inactivated murine embryonic STO fibroblasts (ATCC) for a variable number of passages. Manual dissection was routinely used to passage the cells rather than enzymatic methods. The hES cells were cultured in DMEM/F12 glutamax supplemented with 20% knockout serum ment, 1 mM nonessential amino acids, 1% penicillin/streptomycin, 0.55 mM 2-mercaptoethanol and 5 ng/ml recombinant human FGF2 (all from Invitrogen, Cergy Pontoise, France). Cultures were fed daily and passaged every 5-7 days.

extract_protocol: RNA was extracted using the QIAGEN RNeasy mini kit including on-column DNase treatment in accordance with the prescribed protocol provided with the kit. Quality control was performed with the Agilent Bioanalyzer.

treatment_protocol: Neural differentiation was based on dual SMAD inhibition. Human ES cells were manually detached from the feeder-layer, collected in differentiation medium composed of N2B27 medium supplemented with FGF2 (5ng/ml, Invitrogen, Cergy Pontoise, France) and transferred for 6 hours to low-attachment plate. Cells were then seeded on polyornithine and laminin (12 hours coating, 300 ng/cm² and 100μg/cm² respectively; Sigma, St. Louis, Missouri, USA) coated tissue culture plates. Differentiation medium was changed after 24, then every other day. Human recombinant Noggin (300 ng/ml, Peprotech, London, UK) and SB431542 (20μM, Tocris Biosciences, Ellisville, Missouri, USA) were added from day 0 and on for every medium change until rosette neural stem cell (R-NSC) arose, usually at day 8 to 10. R-NSC was manually collected at day 10-12, trypsinized using 0.05% trypsin (Invitrogen, Cergy Pontoise, France) and seeded at 100,000 cells per cm2 in polyornithine and laminin coated tissue culture plates in N2B27 medium supplemented with FGF2 (10ng/mL), EGF (10ng/mL R&D systems, Minneapolis, USA) and BDNF (10ng/mL Peprotech, London, UK) (passage 1). Cells were maintained in the same medium and passaged every 2-3 days for no more than 25 passages.

tag: hd genotype

value: HD

value: ES cell-derived neural stem cell (NSC) progeny

value: male


title: IR-WT_Rep3

source_name: Irradiated-ATM-WT Replicative3


title: SIVF017 NSC, rep2

description:
NSC_44
Replicate 2 of 3.

tag: cell type


title: WT4 NSC, rep3

description:
NSC_42
Replicate 3 of 3.

source_name: Human ES cell line WT4, NSC progeny

value: wild type


title: WT4 NSC, rep2

description:
NSC_41
Replicate 2 of 3.


title: SIVF017 NSC, rep1

description:
NSC_43
Replicate 1 of 3.


title: SIVF018 NSC, rep1

description:
NSC_31
Replicate 1 of 3.

source_name: Human ES cell line SIVF018, NSC progeny


title: WT4 NSC, rep1

description:
NSC_39
Replicate 1 of 3.


title: SIVF020 NSC, rep1

description:
NSC_35
Replicate 1 of 3.

source_name: Human ES cell line SIVF020, NSC progeny

value: female


title: SIVF020 NSC, rep2

description:
NSC_36
Replicate 2 of 3.


title: SIVF018 NSC, rep3

description:
NSC_33
Replicate 3 of 3.


title: VUB05 NSC, rep3

description:
NSC_23
Replicate 3 of 4.

source_name: Human ES cell line VUB05, NSC progeny


title: Huez2.3 NSC, rep4

description:
NSC_30
Replicate 4 of 4.

source_name: Human ES cell line Huez2.3, NSC progeny


title: Huez2.3 NSC, rep1

description:
NSC_26
Replicate 1 of 4.


title: VUB05 NSC, rep2

description:
NSC_22
Replicate 2 of 4.


title: Huez2.3 NSC, rep3

description:
NSC_29
Replicate 3 of 4.


title: SIVF020 NSC, rep3

description:
NSC_38
Replicate 3 of 3.


title: VUB05 NSC, rep4

description:
NSC_25
Replicate 4 of 4.


title: SI-187 NSC, rep4

description:
NSC_20
Replicate 4 of 4.

source_name: Human ES cell line SI-187, NSC progeny


title: SIVF018 NSC, rep2

description:
NSC_32
Replicate 2 of 3.


title: Huez2.3 NSC, rep2

description:
NSC_27
Replicate 2 of 4.


title: SI-187 NSC, rep3

description:
NSC_19
Replicate 3 of 4.


title: VUB05 NSC, rep1

description:
NSC_21
Replicate 1 of 4.


title: Subject 5 timepoint 4

city: Bad Krozingen

first: Thomas

middle: G

last: Nuehrenberg

state: Baden-Württemberg

address: Südring 15

department: Klinik für Kardiologie II

institute: Universitäts-Herzzentrum Freiburg • Bad Krozingen

hyb_protocol: according to manufacturers instruction (febit biomed)

scan_protocol: Geniom Wizard software on standard Microsoft Windows Workstation PC

data_processing:
summarizing of technical replica by median and VSN normalization. Following BG correction, negative values were corrected to 1
cut off for normalized data: 7; according to the manufacturer
normalized BG corrected intensity values* Easy to use protocol for Geniom RT Analyzer

source_name: purified thrombocytes

label_protocol: MPEA, microfluidic primer extension assay Biotin labeling

extract_protocol: Total RNA including miRNA was extracted from the isolated leukocyte depleted platelet pellets using the miRNeasy Mini Kit (Catalog No: 217004, Qiagen GmbH, Hilden, Germany) according to the manufacturer's recommendations. The eluted RNA was stored at -80°C

treatment_protocol: ASA: Acetylsalicylic Acid single dose 500 mg

tag: subject

tag: timepoint


title: Subject 5 timepoint 5

value: ASA


title: Subject 5 timepoint 2


title: Subject 5 timepoint 1


title: Subject 4 timepoint 4


title: Subject 4 timepoint 3


title: DGM-00583 [genotype]

hyb_protocol: Following labelling, 50 nanograms of DNA were hybridized for 16 hr at 50C on Affymetrix GeneChip Genome-Wide Human SNP Array 5.0 . GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

data_processing:
The data were analyzed with Partek Genomics Suite software, version 6.2 using default analysis settings and global scaling as normalization method.
CHP files were created from CEL files after running BRLMM_p

source_name: Blood from healthy nonsmokers or healthy smokers

label_protocol: DNA labeling was done according to the standard Affymetrix protocol from 50 nanograms total DNA (Affymetrix® Genome-Wide Human SNP Nsp/Sty Assay 5.0, 702419 Rev.1, Affymetrix).

extract_protocol: DNA was extracted from blood samples using the Autogen FX robotic system in according to the manufacturer's instructions


title: SA01 NSC, rep4

description:
NSC_15
Replicate 4 of 4.

source_name: Human ES cell line SA01, NSC progeny


title: DGM-00544 [genotype]


title: Subject 4 timepoint 5


title: Subject 4 timepoint 2


title: SI-187 NSC, rep2

description:
NSC_17
Replicate 2 of 4.


title: SA01 NSC, rep1

description:
NSC_12
Replicate 1 of 4.


title: SI-187 NSC, rep1

description:
NSC_16
Replicate 1 of 4.


title: SA01 NSC, rep3

description:
NSC_14
Replicate 3 of 4.


title: H9 NSC, rep2

description:
NSC_8
Replicate 2 of 4.

source_name: Human ES cell line H9, NSC progeny


title: SA01 NSC, rep2

description:
NSC_13
Replicate 2 of 4.


title: DGM-00702 [genotype]


title: Subject 4 timepoint 1


title: H9 NSC, rep4

description:
NSC_10
Replicate 4 of 4.


title: H9 NSC, rep1

description:
NSC_7
Replicate 1 of 4.


title: H9 NSC, rep3

description:
NSC_9
Replicate 3 of 4.


title: VUBO1 NSC, rep4

description:
NSC_5
Replicate 4 of 4.

source_name: Human ES cell line VUB01, NSC progeny


title: Subject 3 timepoint 5


title: Subject 3 timepoint 3


title: Subject 3 timepoint 4


title: Subject 3 timepoint 2


title: DGM-00663 [genotype]


title: Subject 2 timepoint 5


title: DGM-00641 [genotype]


title: Subject 2 timepoint 4


title: VUBO1 NSC, rep2

description:
NSC_3
Replicate 2 of 4.


title: SIVF020 ES, rep3

description:
ES_52
Replicate 3 of 3.

source_name: Human ES cell line SIVF020

value: embryonic stem (ES) cells


title: RIP SGC7901-NM-has-miR-625

city: Xi'an

first: sijun

last: Hu

address: Changle Road

country: China

institute: Xijing Hospital

hyb_protocol: Standard CapitalBio Methods

scan_protocol: Arrays scanned using a confocal scanner LuxScanTM 10K/A (CapitalBio), and the data of obtained images were extracted with the LuxScan3.0 software (CapitalBio)

data_processing: After background correction and removal of bad spots, A space and intensity-dependent normalization based on a LOWESS program was employed (Yang,Y.H.,et al., space and intensity-dependant normalization, Nucleic Acids Research, 2002,30:e15).

label_protocol: Fluorescent dye (Cy5 and Cy3-dCTP, Amersham Pharmacia Biotech, Piscataway, NJ) labeled DNA was produced through Eberwine's linear RNA amplification method.and subsequent enzymatic reaction. the amplified RNA (aRNA) was purified with NucleoSpin Extract II (MN). We took a cDNA labeling approach with Klenow enzyme after reverse transcription

extract_protocol: Total RNAs were isolated using the Trizol method (Invitrogen)

treatment_protocol: infection with has-miR-625 lentivirus, RIP with Ago2, total RNA purification

value: Human gastric cancer cells SGC7901-NM

value: infection with has-miR-625 lentivirus

tag: antibody

treatment_protocol: infection with has-miR-625 lentivirus, cell lysate (input), total RNA purification

value: none (input)


title: ileum infected pig, 6dpi, rep4

city: Campanillas

first: Rocio

last: Bautista

state: Malaga

address: C/ Severo Ochoa, 34. Parque Tecnologico

department: Edificio de Bioinnovacion

institute: Universidad de Malaga

description: Gene expression data from  mucosa ileum 6 day post infection with Salmonella typhimurium.

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

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

data_processing: The data were pre-processed using the robus multi-array analysis (RMA) included in affy library Bioconductor package (v. 2.5) using R version 2.7.0.

organism: Sus scrofa

source_name: ileum intestinal sections

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

extract_protocol: RNA extraction was done using the Rnesy Mini Kit according to manofacturer instructions

value: mucosa of the ileum

tag: treatment group

value: 6 days post Samonella typhimurium infection

tag: age

value: ~ 4 weeks old


title: ileum infected pig, 6dpi, rep3


title: VUBO1 NSC, rep3

description:
NSC_4
Replicate 3 of 4.


title: DGM-00413 [genotype]

value: S


title: SIVF020 ES, rep2

description:
ES_51
Replicate 2 of 3.


title: VUBO1 NSC, rep1

description:
NSC_1
Replicate 1 of 4.


title: RIP control SGC7901-NM-NC

treatment_protocol: infection with control lentivirus, RIP with Ago2, total RNA purification

tag: treatment

value: infection with control lentivirus

source_name: Input(NC)

treatment_protocol: infection with control lentivirus, cell lysate (input), total RNA isolation


title: SIVF020 ES, rep1

description:
ES_49
Replicate 1 of 3.

tag: gender


title: DGM-00428 [genotype]


title: Subject 2 timepoint 3


title: ileum infected pig, 6dpi, rep1

tag: tissue


title: Subject 2 timepoint 2


title: DGM-01283 [genotype]

tag: department of genetic medicine id

value: NS


title: Subject 2 timepoint 1


title: SIVF018 ES, rep3

description:
ES_48
Replicate 3 of 3.

source_name: Human ES cell line SIVF018


title: Subject 1 timepoint 4


title: Subject 1 timepoint 5


title: DGM-00785 [genotype]

tag: smoking status


title: ileum infected pig, 2dpi, rep3

description: Gene expression data from  mucosa ileum 2 day post infection with Salmonella typhimurium.

value: 2 days post Samonella typhimurium infection


title: Subject 1 timepoint 3


title: ileum infected pig, 2dpi, rep4


title: ileum infected pig, 1dpi, rep4

description: Gene expression data from  mucosa ileum 1 day post infection with Salmonella typhimurium.

value: 1 day post Samonella typhimurium infection


title: ileum infected pig, 2dpi, rep1


title: DGM-00774 [genotype]


title: Subject 1 timepoint 1


title: ileum infected pig, 2dpi, rep2


title: SIVF017 ES, rep1

description:
ES_41
Replicate 1 of 3.

source_name: Human ES cell line SIVF017

tag: cell line

value: HD


title: ileum infected pig, 1dpi, rep3


title: SIVF018 ES, rep2

description:
ES_47
Replicate 2 of 3.

value: male


title: DGM-00568 [genotype]


title: SIVF017 ES, rep2

description:
ES_42
Replicate 2 of 3.


title: WT4 ES, rep3

description:
ES_40
Replicate 3 of 3.

source_name: Human ES cell line WT4

value: wild type


title: ileum infected pig, 1dpi, rep2


title: WT4 ES, rep1

description:
ES_37
Replicate 1 of 3.


title: wild-type strain cultured for 360 min_4 (TT/2011)

city: Hyogo

first: Akeo

last: Shinkai

address: 1-1-1, Kouto, Sayo

department: SPring-8 Center

institute: RIKEN Harima Institute

description: wild-type strain cultivated for 360 min_4

hyb_protocol: 3'-terminal-labeled cDNA (2 micro g) was hybridized to a TTHB8401a520105F GeneChip (Affymetrix, Santa Clara, CA). The array was incubated for 16 h at 50°C in a solution comprising 180 mM MES, pH 6.6, 40 mM EDTA, 0.02% Tween 20, 7% dimethyl sulfoxide, 20 micro g of herring sperm DNA (Promega), 0.1 mg of bovine serum albumin (BSA), the recommended amount of Eukaryotic Hybridization Control (Affymetrix), and Control Oligo B2 for the alignment signal (Affymetrix), and then the array was automatically washed and stained with streptavidin-phycoerythrin (Invitrogen) by using a GeneChip Fluidics Station, 450XP (Affymetrix).

scan_protocol: The Probe Array was scanned with a GeneChip Scanner 3000 (Affymetrix).

data_processing: The expression levels were summarized by one-step Tukey’s biweight algorithm and normalized by global scaling method using GeneChip Operating Software, version 1.4 (Affymetrix, Santa Clara, CA). The trimmed mean target intensity of each array was arbitrarily set to 500.

organism: Thermus thermophilus HB8

source_name: T. thermophilus HB8, wild-type, rich medium, 360 min

label_protocol: cDNA was synthesized with SuperScript II (Invitrogen) reverse transcriptase in the presence of RNase inhibitor SUPERase (Ambion) and 6 base random primers (Invitrogen). The cDNA was fragmented with 1.2 units of DNase I (GE Healthcare Bio-Science Corp.) at 37°C for 10 min, and after inactivation at 98°C for 10 min, the cDNA fragments were labeled with GeneChip DNA Labeling Reagent (Affymetrix, Santa Clara, CA), using terminal transferase according to the manufacturer’s instructions (Affymetrix).

growth_protocol: The wild-type T. thermophilus HB8 strain was pre-cultured at 70°C for 16 h in 4 ml of TT medium containing 0.8% polypeptone, 0.4% yeast extract, 0.2% NaCl, 0.4 mM CaCl2, and 0.4 mM MgCl2, which was adjusted to pH 7.2 with NaOH. The cells were inoculated into 1 liter of the same medium to a final OD600nm of 0.005 and then cultivated at 70°C for 360 min (OD600nm =~ 1.4).

extract_protocol: Cells were collected from 25 ml of the culture medium, and then crude RNA was extracted by the addition of 1.4 ml of a solution comprising 5 mM Tris-HCl, pH 7.5, 5 mM EDTA, 0.25% SDS, and 50% of water-saturated phenol. This mixture was incubated at 65°C for 5 min, chilled on ice for 5 min, and then centrifuged at 4°C. Then, 750 micro l of TRIZOL LS (Invitrogen, Carlsbad, CA) was added to 0.2 ml of the aqueous phase. After incubation for 5 min at room temperature, the RNA was extracted with 0.2 ml of chloroform. The extraction was repeated with 0.5 ml of chloroform, and the aqueous phase was precipitated with isopropanol. The pellet was dissolved in 0.2 ml of nuclease-free water, precipitated with ethanol, and then resuspended in 0.2 ml of water. The RNA was treated with DNase I (Ambion, Austin, TX) at 37°C for 20 min in a 25-micro l reaction mixture. The reaction was terminated by the addition of 1 micro l of 0.5 M EDTA, followed by incubation at 70°C for 5 min. Thereafter, the RNA was precipitated with ethanol in the presence of 1% glycogen and 1 M NH4OAc.

tag: genotype

value: wild-type


title: wild-type strain cultured for 360 min_3 (TT/2011)

description: wild-type strain cultivated for 360 min_3


title: ileum non_infected pig, rep4

description: Gene expression data from ileum non infected

value: non infected


title: DGM-00080 [genotype]


title: ileum non_infected pig, rep2


title: ileum infected pig, 6dpi, rep2


title: Huez2.3 ES, rep4

description:
ES_36
Replicate 4 of 4.

source_name: Human ES cell line Huez2.3

value: embryonic stem (ES) cells

value: female


title: WT4 ES, rep2

description:
ES_38
Replicate 2 of 3.


title: DGM-00268 [genotype]


title: ileum non_infected pig, rep1


title: SIVF017 ES, rep3

description:
ES_44
Replicate 3 of 3.


title: wild-type strain cultured for 360 min_3 (TT/2010)

description: wild-type strain cultivated for 360 min_1

growth_protocol: The wild-type T. thermophilus HB8 strain was pre-cultured at 70°C for 16 h in 4 ml of TT medium containing 0.8% polypeptone, 0.4% yeast extract, 0.2% NaCl, 0.4 mM CaCl2, and 0.4 mM MgCl2, which was adjusted to pH 7.2 with NaOH. The cells (2 ml) were inoculated into 1 liter of the same medium and then cultivated at 70°C for 360 min.

extract_protocol: Cells were collected from 50 ml of the culture medium, and then crude RNA was extracted by the addition of 1.4 ml of a solution comprising 5 mM Tris-HCl, pH 7.5, 5 mM EDTA, 0.25% SDS, and 50% of water-saturated phenol. This mixture was incubated at 65°C for 5 min, chilled on ice for 5 min, and then centrifuged at 4°C. Then, 750 micro l of TRIZOL LS (Invitrogen, Carlsbad, CA) was added to 0.2 ml of the aqueous phase. After incubation for 5 min at room temperature, the RNA was extracted with 0.2 ml of chloroform. The extraction was repeated with 0.5 ml of chloroform, and the aqueous phase was precipitated with isopropanol. The pellet was dissolved in 0.2 ml of nuclease-free water, precipitated with ethanol, and then resuspended in 0.2 ml of water. The RNA was treated with DNase I (Ambion, Austin, TX) at 37°C for 20 min in a 25-micro l reaction mixture. The reaction was terminated by the addition of 1 micro l of 0.5 M EDTA, followed by incubation at 70°C for 5 min. Thereafter, the RNA was precipitated with ethanol in the presence of 1% glycogen and 1 M NH4OAc.


title: wild-type strain cultured for 360 min_1 (TT/2011)


title: Subject 3 timepoint 1


title: DGM-00123 [genotype]

tag: ethnicity

value: Afr


title: Huez2.3 ES, rep2

description:
ES_34
Replicate 2 of 4.


title: Huez2.3 ES, rep1

description:
ES_33
Replicate 1 of 4.


title: colon infected pig, 6dpi, rep2

description: Gene expression data from  mucosa colon 6 day post infection with Salmonella typhimurium.

source_name: colon intestinal sections

value: mucosa of the colon


title: wild-type strain cultured for 360 min_2 (TT/2011)

description: wild-type strain cultivated for 360 min_2


title: Huez2.3 ES, rep3

description:
ES_35
Replicate 3 of 4.


title: wild-type strain cultured for 360 min_2 (TT/2010)


title: colon infected pig, 6dpi, rep3


title: ileum non_infected pig, rep3

value: mucosa of the ileum


title: wild-type strain cultured for 360 min_1 (TT/2010)


title: VUB05 ES, rep4

description:
ES_32
Replicate 4 of 4.

source_name: Human ES cell line VUB05


title: colon infected pig, 6dpi, rep1

value: 6 days post Samonella typhimurium infection


title: VUB05 ES, rep2

description:
ES_30
Replicate 2 of 4.


title: PfmR-deficient strain_360_3

description: PfmR-deficient strain cultivated for 360 min_3

source_name: T. thermophilus HB8, PfmR deletion mutant, rich medium, 360 min

growth_protocol: The PfmR-deficient T. thermophilus HB8 strain was pre-cultured at 70°C for 16 h in 4 ml of TT medium containing 0.8% polypeptone, 0.4% yeast extract, 0.2% NaCl, 0.4 mM CaCl2, and 0.4 mM MgCl2, which was adjusted to pH 7.2 with NaOH. The cells (1.6 ml) were inoculated into 1 liter of the same medium and then cultivated at 70°C for 360 min.

value: PfmR-deficient


title: PfmR-deficient strain_360_2

description: PfmR-deficient strain cultivated for 360 min_2


title: PfmR-deficient strain_360_1

description: PfmR-deficient strain cultivated for 360 min_1


title: colon infected pig, 2dpi, rep4

description: Gene expression data from  mucosa colon 2 day post infection with Salmonella typhimurium.

value: ~ 4 weeks old


title: colon infected pig, 2dpi, rep2


title: VUB05 ES, rep3

description:
ES_31
Replicate 3 of 4.


title: colon infected pig, 2dpi, rep3


title: colon infected pig, 2dpi, rep1


title: colon infected pig, 1dpi, rep4

description: Gene expression data from  mucosa colon 1 day post infection with Salmonella typhimurium.


title: Embryo Irx3-/-;Irx5-/- rep 01

city: San Francisco

first: Nathalie

last: Gaborit

address: 1650 Owens Street

institute: the J. David Gladstone Institute

description:
Gene expression data from Irx3-/-;Irx5-/- embryos
Irx3-/-;Irx5-/-_01.CEL

hyb_protocol: 2.5ug of fragmented cDNA were hybridized to Affymetrix GeneChip mouse gene 1.0 ST.

scan_protocol: the arrays were scanned using the scan protocol GCS3000

data_processing:
Arrays were normalized together for array-specific effects using Affymetrix “Robust Multi-Array” (RMA) normalization, as implemented in the R affy package. For statistical analyses, all probe sets where none of the groups had an average log2 intensity greater than 3.0 were removed. Linear models were fitted for each gene using the limma package in R/Bioconductor, which was also used to calculate moderated t-statistics and the associated P-values. The FDR-adjusted P-values were adjusted for multiple testing by controlling for false-discovery rate using the Benjamini-Hochberg method.
The array values are given as log2(normalized array intensity), where average probeset expression level is typically between 7 and 8 (and where 8.0 = 2x the expression level of 7.0). Differential expression p-values and fdr-adjusted p-values are calculated as described above.

source_name: mouse embryo of Irx3-/-;Irx5-/- genotype

label_protocol: Biotynilated cDNA were prepared using NuGEN WT-Ovation FFPE System V2 and NuGEN Encore Biotin Module (NuGene) protocols, from 1ng total RNA

extract_protocol: Total RNA was isolated using PicoPure RNA Isolation Kit (Arcturus Bioscience) and quality was assessed with Agilent RNA 6000 Pico Chips on a Bioanalyzer (Agilent).

tag: genotype/variation

value: heart

tag: developmental stage

value: embryo


title: Embryo Irx5-/- rep 03

description:
Gene expression data from Irx5-/- embryos
Irx5-/-_03.CEL

source_name: mouse embryo of Irx5-/- genotype


title: VUB05 ES, rep1

description:
ES_28
Replicate 1 of 4.

tag: hd genotype


title: colon infected pig, 1dpi, rep2


title: SI-187 ES, rep3

description:
ES_26
Replicate 3 of 4.

source_name: Human ES cell line SI-187

tag: cell type


title: Embryo Irx3-/-;Irx5-/- rep 04

description:
Gene expression data from Irx3-/-;Irx5-/- embryos
Irx3-/-;Irx5-/-_04.CEL


title: SA01 ES, rep4

description:
ES_21
Replicate 4 of 4.

source_name: Human ES cell line SA01


title: Subject 1 timepoint 2

source_name: purified thrombocytes

tag: subject


title: SI-187 ES, rep2

description:
ES_25
Replicate 2 of 4.


title: colon infected pig, 6dpi, rep4


title: SI-187 ES, rep1

description:
ES_23
Replicate 1 of 4.


title: Embryo Irx3-/-;Irx5-/- rep 02

description:
Gene expression data from Irx3-/-;Irx5-/- embryos
Irx3-/-;Irx5-/-_02.CEL


title: SA01 ES, rep3

description:
ES_20
Replicate 3 of 4.


title: Embryo Irx3-/-;Irx5-/- rep 03

description:
Gene expression data from Irx3-/-;Irx5-/- embryos
Irx3-/-;Irx5-/-_03.CEL


title: SI-187 ES, rep4

description:
ES_27
Replicate 4 of 4.


title: Spheres_1

city: Torino

first: Paolo

last: Provero

address: Via Nizza 52

department: Molecular Biotechnology and Health Sciences

country: Italy

institute: University of Turin

description:
Hy3: 1_Exiqon_14173987_S01.txt
Hy5: 0_Exiqon_14173987_S01.txt

hyb_protocol: The hybridization was performed according to the miRCURY LNA array manual using a Tecan HS4800 hybridization station (Tecan, Austria).

scan_protocol: The miRCURY LNA array microarray slides were scanned using the Agilent G2565BA Microarray Scanner System (Agilent Technologies, Inc., USA).

data_processing: Image analysis was carried out using the ImaGene 9.0 software (BioDiscovery, Inc., USA). The quantified signals were background corrected and normalized using the global Lowess (LOcally WEighted Scatterplot Smoothing) regression algorithm in Bioconductor.

source_name: ESFT spheres

label_protocol: Total RNA from sample and reference was labelled with Hy3 and Hy5 fluorescent label, respectively, using the miRCURY LNA Array power labelling kit (Exiqon, Denmark) following the procedure described by the manufacturer.

growth_protocol: Primary ESFT spheres were cultured in IMDM (Gibco), supplemented with 20% KO serum (Gibco), pen/strep (Gibco), 10 ug/ml LIF (Millipore), 10 ng/mL of recombinant human epidermal growth factor (Invitrogen), 10 ng/mL of recombinant human basic fibroblast growth factor (Invitrogen). Adherent cells were derived from spheres and cultured in  IMDM, 10% FCS and pen/strep for 7 days.

extract_protocol: Total RNA was isolated using Trifast (Peqlab) according to the manufacturer’s recommendations.

value: primary Ewing’s sarcoma family tumor (ESFT)

tag: spheres/adherent

value: spheres

source_name: Human Universal Reference RNA from Ambion

tag: sample type

value: reference


title: Spheres_2

description:
Hy3: 1_Exiqon_14173988_S01.txt
Hy5: 0_Exiqon_14173988_S01.txt


title: Adherent_1

description:
Hy3: 1_Exiqon_14173989_S01.txt
Hy5: 0_Exiqon_14173989_S01.txt

source_name: ESFT adherent cells

value: adherent


title: SIVF018 ES, rep1

description:
ES_46
Replicate 1 of 3.

value: HD

value: male


title: DGM-00683 [genotype]

source_name: Blood from healthy nonsmokers or healthy smokers

value: S


title: Adherent_2

description:
Hy3: 1_Exiqon_14173990_S01.txt
Hy5: 0_Exiqon_1417399Hy5: 0_S01.txt


title: colon non_infected pig, rep4

description: Gene expression data from colon non infected

tag: treatment group

value: non infected


title: DGM-00512 [genotype]


title: colon infected pig, 1dpi, rep3

value: 1 day post Samonella typhimurium infection

tag: age


title: SA01 ES, rep2

description:
ES_18
Replicate 2 of 4.

value: wild type

value: embryonic stem (ES) cells


title: SA01 ES, rep1

description:
ES_17
Replicate 1 of 4.


title: TC252_control

description:
Hy3: 1_Exiqon_14241678_S01.txt
Hy5: 1_Exiqon_14241678_S01.txt

source_name: TC252 cells, control vector

growth_protocol: Cell lines were cultured in RPMI (Gibco) supplemented with 10% FCS (Gibco) and pen/strep (Gibco).

treatment_protocol: Cells were infected as previously described (PMID:14584050, 17786951, 18381423).  For stable knock-down of Tarbp2 (V3LHS_300582), the pGIPZ lentiviral system from Open Biosystems was used. For stable knock-down of Tarbp2 (V3LHS_300582), the pGIPZ lentiviral system from Open Biosystems was used.

value: Ewing sarcoma cells

value: control

source_name: pool of all samples in the series

value: mix of A673, TC252, and STA-ET-8.2

value: half of samples shTARBP2, half of samples control


title: STA-ET-8.2_shTARBP2

description:
Hy3: 1_Exiqon_14241680_S01.txt
Hy5: 1_Exiqon_1424168Hy5: 1_S01.txt

source_name: STA-ET-8.2 cells, shTARBP2


title: STA-ET-8.2_control

description:
Hy3: 1_Exiqon_1424168Hy3: 1_S01.txt
Hy5: 1_Exiqon_14241681_S01.txt

source_name: STA-ET-8.2 cells, control vector


title: Jejunum infected pig, 6dpi, rep3

description: Gene expression data from  mucosa jejunum 6 day post infection with Salmonella typhimurium.

source_name: jejunum intestinal sections

value: mucosa of the jejunum

value: 6 days post Samonella typhimurium infection

value: ~ 4 weeks old


title: H9 ES, rep3

description:
ES_10
Replicate 3 of 4.

source_name: Human ES cell line H9

value: female


title: H9 ES, rep1

description:
ES_8
Replicate 1 of 4.


title: DGM-00382 [genotype]


title: DGM-10287 [genotype]


title: Jejunum infected pig, 6dpi, rep4


title: colon non_infected pig, rep3

source_name: colon intestinal sections

value: mucosa of the colon


title: H9 ES, rep4

description:
ES_11
Replicate 4 of 4.


title: A673_control

description:
Hy3: 1_Exiqon_14241677_S01.txt
Hy5: 1_Exiqon_14241677_S01.txt

source_name: A673 cells, control vector

value: reference


title: VUBO1 ES, rep3

description:
ES_4
Replicate 3 of 4.

source_name: Human ES cell line VUB01


title: Embryo Irx5-/- rep 01

description:
Gene expression data from Irx5-/- embryos
Irx5-/-_01.CEL

source_name: mouse embryo of Irx5-/- genotype

value: heart

value: embryo


title: colon non_infected pig, rep2


title: TC252_shTARBP2

description:
Hy3: 1_Exiqon_14241679_S01.txt
Hy5: 1_Exiqon_14241679_S01.txt

source_name: TC252 cells, shTARBP2


title: Embryo Irx5-/- rep 02

description:
Gene expression data from Irx5-/- embryos
Irx5-/-_02.CEL


title: H9 ES, rep2

description:
ES_9
Replicate 2 of 4.


title: A673_shTARBP2

description:
Hy3: 1_Exiqon_14241676_S01.txt
Hy5: 1_Exiqon_14241676_S01.txt

source_name: A673 cells, shTARBP2


title: VUBO1 ES, rep4

description:
ES_5
Replicate 4 of 4.

value: male


title: Embryo Irx3-/-;Irx5+/- rep 04

description:
Gene expression data from Irx5-/- embryos
Irx3-/-;Irx5+/-_04.CEL

source_name: mouse embryo of Irx3-/-;Irx5+/- genotype


title: DGM-00104 [genotype]

value: S


title: colon non_infected pig, rep1

value: non infected


title: Embryo Irx3-/-;Irx5+/- rep 03

description:
Gene expression data from Irx3-/-;Irx5+/- embryos
Irx3-/-;Irx5+/-_03.CEL


title: Embryo Irx5+/- rep 02

description:
Gene expression data from Irx5+/- embryos
Irx5+/-_02.CEL

source_name: mouse embryo of Irx5+/- genotype


title: Embryo Irx5+/- rep 01

description:
Gene expression data from Irx5+/- embryos
Irx5+/-_01.CEL


title: VUBO1 ES, rep2

description:
ES_3
Replicate 2 of 4.

value: wild type


title: Embryo Irx3-/-;Irx5+/- rep 01

description:
Gene expression data from Irx3-/-;Irx5+/- embryos
Irx3-/-;Irx5+/-_01.CEL


title: Embryo Irx3-/-;Irx5+/- rep 02

description:
Gene expression data from Irx3-/-;Irx5+/- embryos
Irx3-/-;Irx5+/-_02.CEL


title: colon infected pig, 1dpi, rep1

description: Gene expression data from  mucosa colon 1 day post infection with Salmonella typhimurium.

value: 1 day post Samonella typhimurium infection


title: Embryo Irx5+/- rep 03

description:
Gene expression data from Irx5+/- embryos
Irx5+/-_03.CEL


title: Jejunum infected pig, 2dpi, rep3

description: Gene expression data from  mucosa jejunum 2 day post infection with Salmonella typhimurium.

value: 2 days post Samonella typhimurium infection


title: Jejunum infected pig, 6dpi, rep2


title: Rev Flip-3

city: Houston

first: David

middle: S

last: Loose

state: TX

address: 6431 Fannin St, MSB 4.130

department: Integrative Biology & Pharm

institute: University of Texas

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Scanned at factor 3 on Illumina Beadstation

data_processing: Genome studio expression module v 1.6.0. Normalized samples were quantile normalized and background subtracted and with FDR control

source_name: total liver RNA, 0.5 mg/g 5'-AMP injected 12 hours mouse3

label_protocol: Standard Illumina amplification and biotin labeling

extract_protocol: standard Illumina protocol

value: liver

tag: treatment

tag: time

value: 12 hours post-injection

tag: genetic background


title: STA_CD133-

description:
Hy3: 1_Exiqon_14172551_S01.txt
Hy5: 0_Exiqon_14172551_S01.txt

hyb_protocol: The hybridization was performed according to the miRCURY™ LNA array manual using a Tecan HS4800 hybridization station (Tecan, Austria).

scan_protocol: The miRCURY™ LNA array microarray slides were scanned using the Agilent G2565BA Microarray Scanner System (Agilent Technologies, Inc., USA).

data_processing: Image analysis was carried out using the ImaGene 9.0 software (BioDiscovery, Inc., USA). The quantified signals were background corrected and normalized using the global Lowess (LOcally WEighted Scatterplot Smoothing) regression algorithm.

source_name: STA-ET-8.2 cells, CD133- fraction

label_protocol: Total RNA from sample and reference was labelled with Hy3™ and Hy5™ fluorescent label, respectively, using the miRCURY™ LNA Array power labelling kit (Exiqon, Denmark) following the procedure described by the manufacturer.

growth_protocol: STA-ET-8.2 cells lines were cultured in RPMI (Gibco) supplemented with 10% FCS (Gibco) and pen/strep (Gibco).

value: STA-ET-8.2 cells

value: negative

source_name: Pool of all samples in the series


title: VUBO1 ES, rep1

description:
ES_2
Replicate 1 of 4.

value: embryonic stem (ES) cells

tag: gender


title: Jejunum infected pig, 2dpi, rep2

tag: tissue

value: mucosa of the jejunum

value: ~ 4 weeks old


title: MSC_EWSFLI1_CD133-

description:
Hy3: 1_Exiqon_14172548_S01.txt
Hy5: 0_Exiqon_14172548_S01.txt

source_name: EWS-FLI1 expressing human pediatric mesenchymal stem cells, CD133- fraction

growth_protocol: Human pediatric mesenchymal stem cells (hpMSC) were isolated and cultured as previously described (PMID: 14584050, 17786951, 18381423).

treatment_protocol: Human pediatric mesenchymal stem cells were infected as previously described (PMID:14584050, 17786951, 18381423).


title: MSC_ESFT_sample_2_CD133-

description:
Hy3: 1_Exiqon_14172550_S01.txt
Hy5: 0_Exiqon_14172550_S01.txt

source_name: Primary Ewing sarcoma sample 2, CD133- fraction

growth_protocol: Primary ESFT sphere were cultured in IMDM (Gibco), supplemented with 20% KO serum (Gibco), pen/strep (Gibco), 10 ug/ml LIF (Millipore), 10 ng/mL of recombinant human epidermal growth factor (Invitrogen), 10 ng/mL of recombinant human basic fibroblast growth factor (Invitrogen).

value: primary Ewing sarcoma cells


title: Rev Flip-4

source_name: total liver RNA, 0.5 mg/g 5'-AMP injected 12 hours mouse4

value: female


title: Jejunum infected pig, 2dpi, rep4


title: Rev Flip-2

source_name: total liver RNA, 0.5 mg/g 5'-AMP injected 12 hours mouse2


title: Jejunum infected pig, 2dpi, rep1

source_name: jejunum intestinal sections


title: Jejunum infected pig, 6dpi, rep1

description: Gene expression data from  mucosa jejunum 6 day post infection with Salmonella typhimurium.

value: 6 days post Samonella typhimurium infection


title: Rev Flip-1

source_name: total liver RNA, 0.5 mg/g 5'-AMP injected 12 hours mouse1


title: AIHM-4

source_name: total liver RNA, 0.5 mg/g 5'-AMP injected 6 hours mouse4

value: 6 hours post-injection


title: Jejunum infected pig, 1dpi, rep4

description: Gene expression data from  mucosa jejunum 1 day post infection with Salmonella typhimurium.


title: AIHM-2

source_name: total liver RNA, 0.5 mg/g 5'-AMP injected 6 hours mouse2


title: Jejunum infected pig, 1dpi, rep2


title: MSC_ESFT_sample_1_CD133-

description:
Hy3: 1_Exiqon_14172549_S01.txt
Hy5: 0_Exiqon_14172549_S01.txt

source_name: Primary Ewing sarcoma sample 1, CD133- fraction

value: reference


title: Jejunum infected pig, 1dpi, rep3


title: Acute Lymphoblastic Leukemia Patient 10

city: Kuala Lumpur

first: Zubaidah

last: Zakaria

address: Jalan Pahang

department: Haematology Unit

country: Malaysia

institute: Institute for Medical Research

hyb_protocol: The labeled and experimental and reference DNAs were then mixed with the presence of Cot-1 DNA and blocking agent. Following centrifugation, the sample mixture were resuspended in 260ul 2X HI-RPM hybridization buffer, heated to 95°C for 5 minutes and incubated for 30 minutes at 37°C to block repetitive elements on the DNA samples. Then, samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. Hybridization was performed for 40 hours at 65°C using Agilent hybridization station. After hybridization, slides were washed sequentially.

scan_protocol: Slides were scanned on an Agilent G2505B scanner.

data_processing: Images were quantified using Agilent Feature Extraction Software v10.7.3.1. Deep analysis, comparison and visualization of the raw genomic data were performed using Agilent’s DNA Analytics v.4.0.76 software.

source_name: PALL_bone marrow

label_protocol: 3 μg of digested reference genomic DNA and test genomic DNA was differentially labeled using the Genomic DNA Enzymatic Labeling Kit (Agilent Technologies). Initially, the DNA was denatured in the presence of the random primer at 95ºC for 3 minutes in a thermomixer and then quickly cooled in ice. The labeling occurred with the addition of fluorescent dye dUTP-cyanine 3 (Reference DNA) and dUTP-cyanine 5 (Test DNA). Incubation took place for 2 hours at 37ºC in a water bath. The unincorporated nucleotides were removed using Microcon YM-30 filter units (Millipore) and the purified labeled DNA was eluted with 1 x TE Buffer pH 8.0.

extract_protocol: Extraction of genomic DNA with high molecular weight was performed using QIAamp DNA extraction kit (Qiagen) according to the manufacturer's instructions.

value: Male

value: 10.8 years

tag: disease state

value: pediatric acute lymphoblastic leukemia (pALL)

tag: risk assessment

value: standard risk

value: bone marrow

source_name: Human male genomic DNA (Promega P/N G147A)


title: Jejunum infected pig, 1dpi, rep1

value: 1 day post Samonella typhimurium infection


title: MSC_ESFT_sample_1_CD133+

description:
Hy3: 1_Exiqon_14172545_S01.txt
Hy5: 0_Exiqon_14172545_S01.txt

source_name: Primary Ewing sarcoma sample 1, CD133+ fraction

value: positive


title: STA_CD133+

description:
Hy3: 1_Exiqon_14172547_S01.txt
Hy5: 0_Exiqon_14172547_S01.txt

source_name: STA-ET-8.2 cells, CD133+ fraction

value: STA-ET-8.2 cells


title: MSC_ESFT_sample_2_CD133+

description:
Hy3: 1_Exiqon_14172546_S01.txt
Hy5: 0_Exiqon_14172546_S01.txt

source_name: Primary Ewing sarcoma sample 2, CD133+ fraction


title: Acute Lymphoblastic Leukemia Patient 11

value: 5.9 years

value: medium risk


title: Jejunum non_infected pig, rep3

description: Gene expression data from jejunum non infected

value: mucosa of the jejunum

value: non infected


title: MSC_EWSFLI1_CD133+

description:
Hy3: 1_Exiqon_14172544_S01.txt
Hy5: 0_Exiqon_14172544_S01.txt

source_name: EWS-FLI1 expressing human pediatric mesenchymal stem cells, CD133+ fraction


title: G1-Control-3

source_name: total liver RNA control mouse3

value: liver

value: control


title: AIHM-1

source_name: total liver RNA, 0.5 mg/g 5'-AMP injected 6 hours mouse1

value: female


title: Acute Lymphoblastic Leukemia Patient 6

value: 8.3 years


title: Acute Lymphoblastic Leukemia Patient 7

value: 6.3 years

value: reference


title: Acute Lymphoblastic Leukemia Patient 8

value: Female

value: 4.1 years

source_name: Human female genomic DNA (Promega P/N G152A)


title: Jejunum non_infected pig, rep2

value: ~ 4 weeks old


title: Jejunum non_infected pig, rep4


title: Jejunum non_infected pig, rep1


title: AIHM-3

source_name: total liver RNA, 0.5 mg/g 5'-AMP injected 6 hours mouse3

value: 6 hours post-injection


title: Acute Lymphoblastic Leukemia Patient 9

value: 9.3 years

value: pediatric acute lymphoblastic leukemia (pALL)

value: high risk

value: bone marrow


title: G1-Control-1

source_name: total liver RNA control mouse1


title: G1-Control-2

source_name: total liver RNA control mouse2


title: Acute Lymphoblastic Leukemia Patient 5

hyb_protocol: The labeled experimental and reference DNAs were then mixed with the presence of Cot-1 DNA and blocking agent. Following centrifugation, the sample mixture was resuspended in 260ul 2X HI-RPM hybridization buffer, heated to 95°C for 5 minutes and incubated for 30 minutes at 37°C to block repetitive elements on the DNA samples. Then, samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. Hybridization was performed for 40 hours at 65°C using an Agilent hybridization station. After hybridization, slides were washed sequentially.

data_processing: Images were quantified using Agilent Feature Extraction Software v10.7.3.1. Deep analysis, comparison and visualization of the raw genomic data were performed using Agilent’s DNA Analytics v4.0.76 software. The ADM2 algorithm with a threshold of 6.0 was used.

source_name: PALL bone marrow

extract_protocol: Extraction of genomic DNA with high molecular weight was performed using the QIAamp DNA extraction kit (Qiagen) according to the manufacturer's instructions.

value: male

value: 7.1 years

source_name: Human male genomic DNA

extract_protocol: Promega (P/N G147A)


title: fibroblasts patient HHC 5852 low glucose and IFN-γ (100 IU/mL) for 4 days

status: Public on Jun 19 2012

city: Leiden

first: Marieke

last: Griffioen

address: Albinusdreef 2

department: Hematology

country: Netherlands

institute: Leiden University Medical Center

description: female patient with myelodysplastic syndrome refractory anemia with excess of blasts type 2 in remission after transplantation with allogeneic hematopoietic stem cells

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized in R

source_name: fibroblasts cultured from a skin derived biopsy in DMEM with low glucose and IFN-γ (100 IU/mL) for 4 days

label_protocol: Biotinylated cRNA were prepared with the Ambion TotalPrep RNA Amp kit for Illumina arrays

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

tag: source tissue

value: skin

tag: individual

value: patient HHC 5852

value: fibroblasts


title: EBV-transformed B-cells patient MRJ 3087

description: female patient with chronic myeloid leukemia in remission prior to transplantation with allogeneic hematopoietic stem cells

source_name: B-cells immortalized by Epstein Barr Virus

value: peripheral blood

value: female

value: patient MRJ 3087

value: EBV-transformed B-cells


title: fibroblasts patient MRJ 3087 low glucose and IFN-γ (100 IU/mL) for 4 days

description: female patient with chronic myeloid leukemia in remission after transplantation with allogeneic hematopoietic stem cells


title: Meljuso melanoma cell line

description: patient with melanoma

source_name: Immortalized cells from a melanoma

value: melanoma

value: patient with melanoma

tag: cell line

value: Meljuso melanoma cell line


title: Acute Lymphoblastic Leukemia Patient 4

value: 5.6 years

source_name: Human female genomic DNA

extract_protocol: Promega (P/N G152A)

value: reference


title: Acute Lymphoblastic Leukemia Patient 3

value: pediatric acute lymphoblastic leukemia (pALL)

value: 4.3 years


title: fibroblasts patient AAG 4766 low glucose and IFN-γ (100 IU/mL) for 4 days

description: female patient with acute myeloid leukemia in remission after transplantation with allogeneic hematopoietic stem cells

value: patient AAG 4766


title: fibroblasts patient MRJ 3087 low glucose

source_name: fibroblasts cultured from a skin derived biopsy in DMEM with low glucose

value: patient with chronic myeloid leukemia in remission after transplantation with allogeneic hematopoietic stem cells

value: low glucose


title: fibroblasts patient HKR 7645 low glucose

description: male patient with myelofibrose in remission after transplantation with allogeneic hematopoietic stem cells

value: skin

value: male

value: patient HKR 7645


title: fibroblasts patient AAG 4766 low glucose

value: patient with acute myeloid leukemia in remission after transplantation with allogeneic hematopoietic stem cells

value: fibroblasts


title: mature dendritic cells donor USQ 5957

description: male healthy individual

source_name: mature dendritic cells cultured from CD14+ monocytes with GM-CSF and IL-4 for 7 days. TNF-α, IL-1β, IL-6, prostaglandin E2 and IFN-γ was added during the final 2 days for maturation.

value: peripheral blood

value: healthy individual

value: donor USQ 5957

value: mature dendritic cells


title: fibroblasts patient HKR 7645 low glucose and IFN-γ (100 IU/mL) for 4 days

value: patient with myelofibrose in remission after transplantation with allogeneic hematopoietic stem cells


title: Acute Lymphoblastic Leukemia Patient 1

value: bone marrow

value: 2.7 years


title: fibroblasts patient HHC 5852 low glucose

value: female

value: patient with myelodysplastic syndrome refractory anemia with excess of blasts type 2 in remission after transplantation with allogeneic hematopoietic stem cells

value: patient HHC 5852


title: Acute Lymphoblastic Leukemia Patient 2

value: pediatric acute lymphoblastic leukemia (pALL)

value: 4 years

value: reference


title: mature dendritic cells patient MRJ 3087

value: patient with chronic myeloid leukemia in remission prior to transplantation with allogeneic hematopoietic stem cells

value: patient MRJ 3087


title: immature dendritic cells patient MRJ 3087

source_name: immature dendritic cells cultured from CD14+ monocytes with GM-CSF and IL-4 for 7 days

value: immature dendritic cells


title: mature dendritic cells donor SVH 4762

description: female healthy individual

value: donor SVH 4762


title: WT organoid + RanKL

city: London

first: Vivian

last: Li

address: 1 Midland Road

institute: The Francis Crick Institute

description: wildtype organoids treated with RankL

hyb_protocol: The synthezied cRNA was then purified with RNeasy mini kit (Qiagen). 825ng of the corresponding Cy3 and Cy5 cRNA was fragmentated at 60°C for 30 min in the presence of blocking agent and fragmentation buffer (Agilent), then combined with 55ul 2X hybridization buffer (Agilent) and applied to 4X44k human expression microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequentially

scan_protocol: Scanned on an Agilent G2505 DNA microarray scanner.

data_processing: Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization. Ratios are given in log10.

source_name: Organoid from wildtype mouse small intestine

label_protocol: 1µg of total RNA were primed with 1.2 µl of T7 promoter primer at 65°C for 10 min together with control spike A/B, then reversed transcribed at 40°C for 2hrs in the presence of MMLV RTase (Agilent), and dNTP mix. It was then followed by the cRNA transcription at 40°C for 2hrs in the presence of T7 RNA polymerase, inorganic pyrophosphatase, NTP mix, DTT, PEG and Cy3/Cy5-labeled-CTP.

growth_protocol: Intestinal organoids were cultured in vitro in crypt culture medium (EGF, Noggin, R-spondin) according to Sato et al, Nature, 2009

extract_protocol: Total RNA extracted using RNeasy mini kit (Qiagen) following manufacturer's instructions.

treatment_protocol: Intestinal organoids were cultured in the presence or absence of RanKL according to the materials and methods

value: organoids treated with RankL

value: organoids w/o treatment


title: immature dendritic cells donor USQ 5957

description: male healthy individual

value: peripheral blood

value: male

value: healthy individual

value: donor USQ 5957


title: WT organoid + RanKL (dyeswap)

description: Dye swap of Sample1.