title: A2:LJ110 del pdhr LBo

description: A2:LJ110 del pdhr LBo

source_name: LJ110 del pdhr LBo

tag: background strain

tag: genetic modification

value: PdhR knockout mutant (LJ110deltapdhR)


title: Slice7_reps1-4

status: Public on Dec 21 2011

type: RNA

city: Duesseldorf

first: Andrea

last: Braeutigam

address: Universitaetsstrasse 1

department: Botany

country: Germany

institute: Heinrich Heine University Duesseldorf

description: Gene expression based on physical location in a leaf

scan_protocol: Arrays were scanned according to manufacturer's standard protocols.

data_processing: Transcripts were normalized to the 75th percentile within each array using the Agilent Gene spring program. For K-means clustering and hierachical clustering, four replicates were averaged.

molecule: total RNA

organism: Zea mays

source_name: third leaf, 18cm length

label_protocol: The cDNA and following antisense cRNA synthesis was performed according the one-color microarray-based gene expression analysis protocol (Agilent).

growth_protocol: Z. mays plants of the ecotype B73 were grown in the greenhouse for 14 to 15 days in clay pots in Floraton soil. Natural light, a shading system and artificial light were used to extend the daylight period to 16 hours at a photon flux density of approximately 500 μmol m-2 s-1. The humidity in the greenhouse was between 75 and 90%. The green house’s ventilation system kept the temperature at 24°C.

extract_protocol: The 3rd leaf was harvested at 18cm length measured from tip to emergence from the stem. Leaves were harvested by placing them atop a custom made leaf guillotine where they were snap frozen. By closing the lid, the leaf is cut into ten pieces of 2cm width, the last of which had not yet emerged.  Twenty plants were pooled for each biological replicate. The mRNA was isolated after the method of Logemann et al. (1987) and from the same plant material the enzyme activities and metabolites were measured of. The isolated RNA was purified with the RNeasy Purification Kit according to the producer’s instruction (Qiagen). The quality was checked with the Agilent 2100 Bioanalyzer using the RNA 6000 Nano Kit. The cDNA and following antisense cRNA synthesis was performed according the one-color microarray-based gene expression analysis protocol (Agilent ). An aliquot of 1.65 µg of this RNA was loaded on one-color microarrays with custom designed oligonucleotide probes (Agilent 025271).

treatment_protocol: No treatment was applied

tag: tissue

value: third leaf

tag: slice (slice1=oldest, slice10=youngest)


title: VitD/control 48h rep1

status: Public on Dec 20 2011

city: MADRID

first: Luis

last: LOMBARDIA

state: Madrid

address: Melchor Fernandez Almagro, 3

department: Molecualr Pathology Programme

country: Spain

institute: CNIO (Spanish National Cancer Center)

hyb_protocol: Hybridization conditions were as per Mirus' kit recommendations. Slides were pre-soaked (in buffer with 2X SSC, 0.05% SDS, 0.25% Sodium Borohydride) for 30min at 45ºC and pre-hybridized (in buffer with 5X SSC, 0.1% SDS, 1% BSA) at 42°C for 45min. Arrays were hybridized  overnight at 42°C simultaneously with Cy5- and Cy3-labeled samples previously denatured in 1X hybridization solution (provided in Mirus' kit). After incubation, slides were washed 2 x 5 min. each in 2X SSC, 0.1% SDS at hybridization temperature, 2 x 5 min. each in 1X SSC at hybridization temperature and finally 2 x 1 min each in 0.1X SSC at room temperature. Slides were briefly dip  in dH20 and dried by centrifugation at 500 rcf for 1 minute.

scan_protocol: The slides were scanned at a resolution of 10 µm with Agilent G2565BA Microarray Scanner (Agilent Technologies) and Cy3 and Cy5 fluorescent signals were quantified using Feature Extraction Software (Agilent Technologies).

data_processing: Raw data from microarray images were background subtracted and global Lowess normalized with Feature Extraction Software (Agilent Technologies).

organism: Homo sapiens

source_name: VitD treated cells 48h

label_protocol: One-step, direct labeling of 500 ng miRNA's extract has been carried out with the Label IT® miRNA Labeling Kit, Cy™3/Cy™5 (Mirus)  by following manufacturer instructions. Extracts from cells treated with 1,25(OH)2D3 or vehicle at each time point were compared in dye swapped hybridizations.

growth_protocol: A human colon cancer cell line, SW480-ADH, was cultured in DMEM plus 10% foetal bovine serum (Invitrogen, Paisley, UK).

extract_protocol: Cellular small RNA fractions were extracted with PureLink miRNA isolation kit (Invitrogen) by following manufacturer instructions. Quality of the RNA was determined with a 2100 Bioanalyzer (Agilent Technologies, Carlsbad, CA) and RNA amount was established by using a NanoDrop spectrophotometer (NanoDrop, Wilmington, DE).

treatment_protocol: Treatments with 1,25(OH)2D3 or isopropanol (vehicle) were performed in medium supplemented with charcoal-treated serum.

tag: cell line

tag: treatment

value: vitamin D

tag: time

source_name: Control cells 48h

value: control


title: Malignant_1

type: protein

city: Vienna

first: Parvez

last: Syed

address: Muthgasse 11

country: Austria

institute: Austrian Institution of Technology

hyb_protocol: The microarrays were blocked for 30 min with PBST+3% non-fat milk powder. Microarrays were washed with PBST, twice for 5 min. Serum diluted 1:10 in PBST was applied onto the microarray and incubated for 2 hours.  Microarrays were washed with PBST, twice for 5 min. Antihuman IgG conjugated with Alexa 532 was diluted  1:500 in PBST+3% non-fat milk powder and incubated for 30 min. Microarrays were washed with PBST, twice for 5 min.

scan_protocol: The processed microarray images were captured using an Axon Genepix 4000A microarray scanner

data_processing: For microarray data analyses in addition to R, BRB-ArrayTools Version: 3.6.0 - Stable Release

label: Alexa 532

molecule: protein

source_name: Carcinoma, intraductal, noninvasive

label_protocol: After the hybridization of human sera with the protein microarrays, secondary antibody (anti-human IgG) conjuagted with Alexa532 was used for detecting the sero-reactive proteins on the microarray

extract_protocol: The His-tag recombiant proteins were expressed in E. coli using autoinduction and purified using Ni-NTA agarose. Elution of the purified recombinant proteins was done using 50 mM Imidazole. These proteins were used for the generation of protein microarrays. The serum autoantibody profiling of the sera from breast cancer patients (benign & malignant) and healthy controls was done using the protein micrarrays

tag: disease state

value: Carcinoma, intraductal, noninvasive

tag: age


title: Malignant_2

source_name: Invasive ductal carcinoma

value: Invasive ductal carcinoma


title: Malignant_3


title: Benign_1

source_name: Borderline tumour (ovarian)

value: Borderline tumour (ovarian)


title: Slice5_reps1-4

hyb_protocol: An aliquot of 1.65 µg of this RNA was loaded on one-color microarrays with custom designed oligonucleotide probes (Agilent 025271)


title: VitD/control 24h rep2

source_name: Control cells 24h

source_name: VitD treated cells 24h


title: Slice8_reps1-4


title: Pt042A  Distal field_Buccal mucosa

type: genomic

city: Genova

first: PAOLA

last: SCARUFFI

state: GE

address: LARGO R. BENZI, 10

country: Italy

institute: "San Martino" Hospital

description:
DNA amplification kit: Sigma
aCGH analysis

hyb_protocol: Labeled DNAs were hybridized to Human Genome CGH 105K array platform (Agilent Technologies)following the "Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis protocol”, v. 5.0. Briefly, fluorescent-labeled reference and tumor DNAs (4 µg each) were mixed with 25 µg of human Cot-1 DNA (Invitrogen Life Technologies) and control targets (Agilent). Slides were hybridized in SureHyb gasket (Agilent Technologies) placed in rotisserie (20 RPM rotation speed) in hybridization oven at 65°C for 40 hrs. After hybridization, the slides were washed with Oligo aCGH Wash Buffer 1 (Agilent Technologies) at room temperature for 5 min, with Oligo aCGH Wash Buffer 2 (Agilent Technologies) at 37°C for 1 min, with the Stabilization and Drying Solution (Agilent) for 1 minute at room temperature.

scan_protocol: Slides were scanned immediately after washing by the Agilent G2565BA Scanner using two color scan setting for 2x105k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel 1 is set to Red & Green, Red PMT is set to 100%, Green PMT is set to 100%) . Microarray performance was assessed by QC metric tool.

data_processing: The scanned TIFF images were processed by Feature Extraction version 9.5.3.1 (Agilent Technologies). Data files were analyzed byAgilent CGH Analytics Software (version 3.5.14) according to ADM-2 algorithm. The quality of each experiment was assessed by QC metric tool.

molecule: genomic DNA

source_name: Distal field

label_protocol: DNA was amplified using GenomePlex Whole Genome Amplification Kit (Sigma-Aldrich) (DNA= 50ng) or Ovation WGA System kit (Nugen Technologies) (DNA<50ng). We followed the "Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis protocol”, v. 5.0 (Agilent Technologies). For each array, amplified test and reference DNAs (2 µg each) were labeled by Bioprime Labeling Kit (Invitrogen, Paisley, UK). Briefly,  amplified DNA was labeled with Cy3-dUTP or Cy5-dUTP (Perkin Elmer) (reference and test samples, respectively) using the Random-Primed Bioprime DNA Labeling kit (Invitrogen Life Technologies). Unincorporated nucleotides were removed on Microcon YM-30 filters (Millipore) according to the manufacturer’s protocol. Dye incorporations of post-labeling products were measured by ND-1000 spectrophotometer (NanoDrop Technologies) and the parameters that predicted successful hybridization were a minimum Cy3 incorporation of 0.5 pmol/ul and Cy5 incorporation of 0.3 pmol/ul.

extract_protocol: DNA was extracted using ArchivePure DNA (5-Prime) with some modifications: after protein precipitation the DNA was purified by phenol-chloroform extraction and collected by ethanol precipitation using 20 µg of glycogen (20 mg/ml). DNA quality was assessed by agarose gel and ND-1000 spectrophotometer (NanoDrop Technologies).

treatment_protocol: Samples were processed to obtain DAPI stained nuclei suspensions following the method of Otto et al., (Methods Cell Biol., 1994 Academic Press San Diego; 211-217) with modifications. High resolution DNA flow cytometry of these samples was used to obtain DNA content histograms and to evaluate the DNA Index (DI), as previously described in details (Donadini et al., 2010, Cell. Oncol. 32, 373-383). DNA diploid controls were represented by gender-specific human lymphocytes. The mean CV of the corresponding DNA diploid G0-G1 peaks was 1.2±0.2%. The DNA diploid (DI=1) and aneuploid sublines were sorted using a Cyflow Space FCM equipped with a PPCS unit (Partec GmbH) at the purity of about 99%.

tag: main site

value: Buccal mucosa

tag: histology

value: Non dysplastic

tag: smoke habit

value: Non Smoker

tag: age (years)

tag: dna index

tag: gender

value: Male

tag: dna amplification kit

value: Sigma

source_name: Human Genomic DNA: male Cat G147A Promega, Madison, WI


title: Pt022B Distal mucosa_Buccal mucosa

source_name: Distal mucosa

value: Female

source_name: Human Genomic DNA: female Cat G152A,Promega, Madison, WI


title: Malignant_5


title: Slice6_reps1-4


title: Pt008A Distal mucosa_Gingiva, left

label_protocol: DNA was amplified using GenomePlex Whole Genome Amplification Kit (Sigma-Aldrich) (DNA= 50ng). We followed the "Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis protocol”, v. 5.0 (Agilent Technologies). For each array, amplified test and reference DNAs (2 µg each) were labeled by Bioprime Labeling Kit (Invitrogen, Paisley, UK). Briefly,  amplified DNA was labeled with Cy3-dUTP or Cy5-dUTP (Perkin Elmer) (reference and test samples, respectively) using the Random-Primed Bioprime DNA Labeling kit (Invitrogen Life Technologies). Unincorporated nucleotides were removed on Microcon YM-30 filters (Millipore) according to the manufacturer’s protocol. Dye incorporations of post-labeling products were measured by ND-1000 spectrophotometer (NanoDrop Technologies) and the parameters that predicted successful hybridization were a minimum Cy3 incorporation of 0.5 pmol/ul and Cy5 incorporation of 0.3 pmol/ul.

value: Gingiva, left


title: Pt032B Distal mucosa_Tongue

value: Tongue

value: Smoker


title: Slice2_reps1-4


title: Pt032B Leukoplakia_Tongue (Front lesion)

source_name: Leukoplakia

value: Tongue (Front lesion)

value: Mild dysplastic leukoplakia


title: Slice3_reps1-4

value: third leaf


title: Slice4_reps1-4


title: VitD/control 24h rep1

value: vitamin D


title: Pt013A Distal mucosa_Buccal mucosa, cheek right

value: Buccal mucosa, cheek right


title: Pt024B Distal mucosa_Tongue


title: Pt029A Distal field_Buccal mucosa, cheek

value: Buccal mucosa, cheek


title: Pt014A Distal mucosa_Buccal mucosa, cheek left

value: Buccal mucosa, cheek left


title: secondary growth eOM1

city: Gainesville

first: Christopher

middle: Joseph

last: Martyniuk

state: FL

address: CEHT Mowry Road

department: Physiological Sciences

country: USA

institute: UF

description:
12007-8
secondary growth eOM sample 1

hyb_protocol: Agilent one color protocol; Microarrays were washed the following day according to the supplemental Agilent protocol “Preventing Ozone-Related Problems”.  Slides were washed in GE Wash Buffer 1 at room temperature for 1 min, followed by GE Wash Buffer 2 at 37ºC for 1 min, acetonitrile wash at room temperature for 1 min, and Stabilizing and Drying Solution wash at room temperature for 30 s.

scan_protocol: Microarrays were kept in the dark until scanned at 5 μm at both 10 and 100 PMT (Agilent G2505 B Microarray Scanner).  Agilent Feature Extraction Software (v9.5) formed a composite of the two scans and calculated parameters for Extended Dynamic Range.

data_processing: Normalized signal intensity provided here is LOESS Normalization using JMP Genomics v4.0 software

organism: Micropterus salmoides

source_name: ovary

label_protocol: Agilent one color protocol for Cy3

extract_protocol: Total RNA for microarray analysis was extracted from LMB ovary using RNA STAT-60 reagent (TEL-TEST Inc., Friendswood, TX, USA).

treatment_protocol: wild largemouth bass sampled each month over 1 year, ovary sample taken for microarray analysis on reprodcutive tissue, n=4/stage

value: ovary

tag: Sex

value: female

tag: Stage

value: secondary growth eOM


title: atresia AT1

description:
6206-12
atresia AT sample 1

value: atresia AT


title: atresia AT3

description:
8236-5
atresia AT sample 3


title: secondary growth eOM3

description:
12007-10
secondary growth eOM sample 3


title: secondary growth eOM2

description:
12007-9
secondary growth eOM sample 2


title: secondary growth lOM4

description:
21907-17
secondary growth lOM sample 4

value: secondary growth lOM


title: secondary growth lOM2

description:
21907-9
secondary growth lOM sample 2


title: secondary growth lOM1

description:
21907-7
secondary growth lOM sample 1


title: ovulation OV2

description:
1227-11
ovulation OV sample 2

value: ovulation OV


title: secondary growth eOM4

description:
12007-11
secondary growth eOM sample 4


title: ovulation OV1

description:
1227-6
ovulation OV sample 1


title: secondary growth lV1

description:
1196-16
secondary growth lV sample 1

value: secondary growth lV


title: secondary growth lV4

description:
1196-22
secondary growth lV sample 4


title: secondary growth lV3

description:
1196-20
secondary growth lV sample 3


title: secondary growth lV2

description:
1196-18
secondary growth lV sample 2


title: secondary growth lOM3

description:
21907-15
secondary growth lOM sample 3


title: ovulation OV4

description:
1227-19
ovulation OV sample 4


title: Slice1_reps1-4

tag: development

value: tip (oldest segment)


title: primary growth CA2

description:
10206-3
primary growth CA sample 2

tag: tissue

value: primary growth CA


title: secondary growth eV1

description:
11206-9
secondary growth eV sample 1

value: secondary growth eV


title: secondary growth eV3

description:
11206-14
secondary growth eV sample 3


title: ovulation OV3

description:
1227-14
ovulation OV sample 3


title: secondary growth eV2

description:
11206-12
secondary growth eV sample 2


title: atresia AT2

description:
11206-17
atresia AT sample 2


title: primary growth CA4

description:
10206-6
primary growth CA sample 4


title: primary growth CA3

description:
10206-4
primary growth CA sample 3


title: secondary growth eV4

description:
11206-18
secondary growth eV sample 4


title: day 1 adipogenic diff. (mRNA) BR1

city: Padova

first: Federica

last: Eduati

state: Italy

address: Via G. Gradenigo 6/B

institute: University of Padova

hyb_protocol: The labeled cDNA was hybridized on human oligo chips in a water bath for 16h at 42°C. Arrays were then washed in 2x SSC/ 0.1% SDS, 1x SSC, and 0.5x SSC, each at 42°C for 5 min prior to drying and scanning.

scan_protocol: Arrays scanned using the AXON 4000B scanner and the GENEPIX software

data_processing: Background subtraction as well as GENEPIX global mean and dye swap normalization were applied.

source_name: Mesenchymal stem cells harvested at day 1 after induction of differentiation

label_protocol: 15 µg RNA aliquots of each time point were fluorescently labelled with Cy3 or Cy5 during cDNA synthesis from total RNA using Superscript II Kit (Invitrogen) as manufacturers instructions. Samples purified using QIAGEN PCR purification kit before hybridization.

growth_protocol: hMADS cells were grown in Dulbecco's Modified Eagle's Medium (DMEM low glucose) containing 10% fetal calf serum (FCS), and 100 U/ml penicillin and streptomycin. After reaching 80% confluence, adherent cells were detached with 0.25% trypsin EDTA and seeded at a density of 4500 cells per cm2. hMADS cells were maintained in proliferation medium supplemented with 2 ng/ml fibroblast growth factor 2 (FGF2)

extract_protocol: Total RNA was isolated using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) or Tri-Reagent (Euromedex, Mundolsheim, France) according to the manufacturer's instructions.

treatment_protocol: Two days after confluence (referred to as day 0), cells were cultured in DMEM/Ham's F12 medium supplemented with 10 μg/ml transferrin, 0.86 μM insulin, 0.2 nM of triiodothyronine, 1 μM dexamethasone, 100 μM isobutyl-methylxanthine, and 100 nM rosiglitazone. Three days later, the medium was changed (dexamethasone and isobutyl-methylxanthine were omitted).

tag: cell type

value: primary hMADS

source_name: Mesenchymal stem cells harvested at day -3 before induction of differentiation


title: day 1 adipogenic diff. (mRNA) BR2

value: day 1 after induction of differentiation

value: 10 μg/ml transferrin, 0.86 μM insulin, 0.2 nM of triiodothyronine, 1 μM dexamethasone, 100 μM isobutyl-methylxanthine, and 100 nM rosiglitazone

value: day -3 before induction of differentiation


title: primary growth CA1

description:
10206-2
primary growth CA sample 1


title: primary growth PN3

description:
7196-5
primary growth  Pn sample 3

value: primary growth  Pn


title: day 2 adipogenic diff. (mRNA) BR1

source_name: Mesenchymal stem cells harvested at day 2 after induction of differentiation


title: day 10 adipogenic diff. (mRNA) BR2

source_name: Mesenchymal stem cells harvested at day 10 after induction of differentiation

value: 10 μg/ml transferrin, 0.86 μM insulin, 0.2 nM of triiodothyronine, 1 μM dexamethasone, 100 μM isobutyl-methylxanthine, and 100 nM rosiglitazone then dexamethasone and sobutyl-methylxanthine omitted at day 3


title: day 15 adipogenic diff. (mRNA) BR2

source_name: Mesenchymal stem cells harvested at day 15 after induction of differentiation


title: day 5 adipogenic diff. (mRNA) BR2

source_name: Mesenchymal stem cells harvested at day 5 after induction of differentiation


title: day 15 adipogenic diff. (mRNA) BR1

value: day 15 after induction of differentiation


title: day 10 adipogenic diff. (mRNA) BR1

value: day 10 after induction of differentiation


title: day 5 adipogenic diff. (mRNA) BR1

value: day 5 after induction of differentiation


title: day 2 adipogenic diff. (mRNA) BR2

value: day 2 after induction of differentiation


title: day 0 adipogenic diff. (mRNA) BR1

source_name: Mesenchymal stem cells harvested at day 0 before induction of differentiation


title: day -2 adipogenic diff. (mRNA) BR2

source_name: Mesenchymal stem cells harvested at day -2 before induction of differentiation


title: primary growth PN4

description:
7196-8
primary growth  Pn sample 4

value: ovary

value: female


title: primary growth PN2

description:
7196-4
primary growth  Pn sample 2


title: primary growth PN1

description:
7196-2
primary growth  Pn sample 1


title: day 0 adipogenic diff. (mRNA) BR2

value: day 0 before induction of differentiation


title: day -2 adipogenic diff. (mRNA) BR1

value: day -2 before induction of differentiation


title: PAO1 wild-type strain grown in NY+NO3 media, replicate 2

city: Rochester

first: Barbara

middle: H.

last: Iglewski

state: NY

address: 601 Elmwood Ave

department: Microbiology and Immunology

institute: University of Rochester

description: Gene expression data from cultures grown aerobically in NY+NO3 media

hyb_protocol: Hybridization was performed by using an Affymetrix Gen Chip System workstation equiped with Microarray Suite software (version 5.0), and a hybridization oven and fluidics workstation

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner.

data_processing: Transcript was detected using MAS software (version 5.0; Affymetrix) using default parameters.  Pairwise comparisons were performed with Data Mining Tools (version 3.0; Affymetrix).

label: biotin

organism: Pseudomonas aeruginosa

source_name: Pseudomonas aeruginosa wild-type strain PAO1

label_protocol: End-labeling of cDNA fragmented with Dnase I (Amersham) was done with Biotin-ddUTP and the Enzo BioArray terminal labeling kit (Affymetrix)

growth_protocol: growth was done aerobically shaking at 250rpm at 37 degrees Celcius in NY media supplemented with yeast extract until early stationary phase (OD600 ~1.2 )

extract_protocol: Tri-reagent (ambion was used to extract RNA; Residual DNA was removed with amplification grade DNAse I (Invitrogen) and RNA was concentrated using a MinElute kit (Qiagen).  RNA integrity was assessed using a Bioanalyzer (Agilent Technologies, Foster, City, CA).  cDNA synthesis, labeling, fragmentation, hybridization, and chip scanning was performed at the University of Rochester Core Facility.

treatment_protocol: in parallel samples, 100mM KNO3 was added to the growth media

tag: genotype/variation

value: wild-type

tag: growth media

value: NY+NO3 media


title: PAO1 wild-type strain grown in NY+NO3 media, replicate 3


title: PAO1 delta PA1006 strain grown in NY media, replicate 2

description: Gene expression data from cultures grown aerobically in NY media

source_name: Pseudomonas aeruginosa delta PA1006 mutant strain PAO1

value: delta PA1006/nbvF

value: NY media


title: PAO1 wild-type strain grown in NY+NO3 media, replicate 1


title: E. faecalis relArelQ double mutant, 30 min mupirocin treatment, replicate 2

first: Jessica

middle: K

last: Kajfasz

address: 1395 Center Drive

department: Oral Biology

institute: University of Florida

description: ΔrelAQ Mup30-2

hyb_protocol: The slides were hybridized to a mixture containing equal amounts of test and reference cDNA for 16 h at 42°C in a MAUI hybridization chamber (BioMicro Systems).  Hybridized slides were washed.

scan_protocol: Slides were scanned using a GenePix scanner (Axon Instruments, Inc., Union City, CA).

data_processing: Data were analyzed using software available at the J. Craig Venter Institute PFGRC website.  Single-channel images of the slides were loaded into Spotfinder and overlaid.  A spot grid was created according to PFGRC specifications and manually adjusted to fit all spots.  The Microarray Data Analysis System (MIDAS) software was used to normalize the spot intensity data using LOWESS and iterative log mean centering with default setting.  MIDAS also utilized In-Slide Replicate Analysis to average the intensities of the spots that were replicated on the microarray slide.  Spots that were missing or labeled as “bad” during the upstream processes in 50% of the slides were cut off in the output files, which also did not include control spots printed on the slides.  Statistical analysis was carried out with BRB array tools (http://linus.nci.nih.gov/BRB-ArrayTools.html) with a cutoff P value of 0.001.

organism: Enterococcus faecalis OG1RF

source_name: relAQ mutant treated with mupirocin for 30 min RNA

label_protocol: Once RNA was purified as described above, cDNA was generated from 2ug RNA per sample as described by the protocol available from the Pathogen Functional Genomics Research Center (PFGRC) using Invitrogen Superscript III Reverse Transcriptase (Invitrogen, Gaithersburg, MD) to increase cDNA yields. Purified cDNAs were coupled to Cy3 (experimental samples) or Cy5 (reference cDNA).

extract_protocol: To isolate RNA from E. faecalis, cells were harvested by centrifugation at 4°C and then treated with the RNA protect reagent (QIAGEN, Inc., Chatsworth, CA). Total RNA was isolated from homogenized E. faecalis cells by the hot acid-phenol method as described previously (Abranches, 2006).  RNA pellets were resuspended in nuclease-free H2O, and treated with DNase I (Ambion) at 37°C for 30 minutes.  RNA concentrations were determined using a Nanodrop ND-1000 Spectrophotometer (Thermo Fisher Scientific, Waltham, MA), and 1 µL samples were run on an agarose gel to verify RNA integrity.  The RNA was purified again using the RNeasy mini kit (Qiagen), including a second on-column DNase treatment that was performed as recommended by the supplier.

treatment_protocol: Mupirocin treatment for 30 min.

tag: strain

tag: genotype

value: relAQ mutant

tag: growth phase

value: early-log mupirocin stressed

tag: treatment

value: mupirocin

tag: treatment duration

value: 30 min

source_name: wild type mid-log RNA

growth_protocol: Cells were grown in Brain-Heart medium to OD600 of 0.5 in a 5% CO2 incubator at 37°C.

value: mid-log

tag: sample type

value: reference


title: E. faecalis relArelQ double mutant, 15 min mupirocin treatment, replicate 3

description: ΔrelAQ Mup15-3

source_name: relAQ mutant treated with mupirocin for 15 min RNA

treatment_protocol: Mupirocin treatment for 15 min.

value: 15 min


title: E. faecalis relArelQ double mutant, 30 min mupirocin treatment, replicate 4

description: ΔrelAQ Mup30-4


title: E. faecalis relArelQ double mutant, 15 min mupirocin treatment, replicate 4

description: ΔrelAQ Mup15-4


title: E. faecalis relArelQ double mutant, 30 min mupirocin treatment, replicate 3

description: ΔrelAQ Mup30-3


title: E. faecalis relArelQ double mutant, 15 min mupirocin treatment, replicate 2

description: ΔrelAQ Mup15-2


title: E. faecalis relArelQ double mutant, 15 min mupirocin treatment, replicate 1

description: ΔrelAQ Mup15-1


title: Control-grown E. faecalis relArelQ double mutant, replicate 4

description: ΔrelAQ Ctrl-4

source_name: relAQ mutant early-log RNA

value: early-log non-stressed


title: Control-grown E. faecalis relArelQ double mutant, replicate 3

description: ΔrelAQ Ctrl-3


title: PAO1 delta PA1006 strain grown in NY+NO3 media, replicate 1


title: PAO1 wild-type strain grown in NY media, replicate 1


title: PAO1 delta PA1006 strain grown in NY media, replicate 1


title: PAO1 wild-type strain grown in NY media, replicate 2


title: E. faecalis relArelQ double mutant, 30 min mupirocin treatment, replicate 1

description: ΔrelAQ Mup30-1


title: PAO1 delta PA1006 strain grown in NY+NO3 media, replicate 2


title: PAO1 delta PA1006 strain grown in NY+NO3 media, replicate 3


title: Control-grown E. faecalis relArelQ double mutant, replicate 2

description: ΔrelAQ Ctrl-2


title: Control-grown E. faecalis relArelQ double mutant, replicate 1

description: ΔrelAQ Ctrl-1


title: breast, post AFI treatment (H20_1950)

city: Houston

first: Suzanne

last: Fuqua

state: Texas

address: 1 Baylor Plaza

institute: Baylor College of Medicine

description:
RE1_H20_1950_U133Plus2.0.CEL
Gene expression data from human breast cancer

hyb_protocol: Standard Affymetix protocol for 3' IVT design

scan_protocol: Scanner GCS3000 7G

data_processing: Expression were estimated using BRB Array Tools software, GCRMA method

source_name: Human breast, post AFI treatment

label_protocol: 3' IVT express

extract_protocol: Trizol extraction

treatment_protocol: After a baseline tumor biopsy, patients were randomized to receive Anastrazole/fulvestrant(AF) or anastrazole/Fulvestrant/Gefitinib (AFG) for 3 weeks, then a second biopsy was obtained. After that all patients received the AFG treatment.

value: AFG

value: post

tag: response

value: PR

value: pos

value: neg

tag: baseline age (years)

tag: baseline tumor size (cm)

tag: patient id (to identify the 2 chips from the same patient)


title: breast, pre AFI treatment (H18_1930)

description:
RE1_H18_1930_U133Plus2.0.CEL
Gene expression data from human breast cancer

source_name: Human breast, pre AFI treatment

value: pre


title: breast, post AFI treatment (H19_1935)

description:
RE1_H19_1935_U133Plus2.0.CEL
Gene expression data from human breast cancer

value: SD


title: E. faecalis relQ mutant, 30 min mupirocin treatment, replicate 4

description: ΔrelQ Mup30-4

source_name: relQ mutant treated with mupirocin for 30 min RNA

value: relQ mutant

value: wild-type


title: E. faecalis relQ mutant, 30 min mupirocin treatment, replicate 1

description: ΔrelQ Mup30-1


title: E. faecalis relQ mutant, 30 min mupirocin treatment, replicate 2

description: ΔrelQ Mup30-2


title: breast, pre AFI treatment (H17_1910)

description:
RE1_H17_1910_U133Plus2.0.CEL
Gene expression data from human breast cancer


title: E. faecalis relQ mutant, 15 min mupirocin treatment, replicate 4

description: ΔrelQ Mup15-4

source_name: relQ mutant treated with mupirocin for 15 min RNA


title: breast, post AFI treatment (H5_1332)

description:
RE1_H5_1332_U133Plus2.0.CEL
Gene expression data from human breast cancer


title: E. faecalis relQ mutant, 30 min mupirocin treatment, replicate 3

description: ΔrelQ Mup30-3


title: E. faecalis relQ mutant, 15 min mupirocin treatment, replicate 2

description: ΔrelQ Mup15-2


title: breast, post AFI treatment (H10_1594)

description:
RE1_H10_1594_U133Plus2.0.CEL
Gene expression data from human breast cancer

value: PD


title: E. faecalis relQ mutant, 15 min mupirocin treatment, replicate 1

description: ΔrelQ Mup15-1

value: early-log mupirocin stressed


title: breast, pre AFI treatment (H2_1279)

description:
RE1_H2_1279_U133Plus2.0.CEL
Gene expression data from human breast cancer


title: breast, post AFI treatment (H13_1647)

description:
RE1_H13_1647_U133Plus2.0.CEL
Gene expression data from human breast cancer

value: CR


title: breast, pre AFI treatment (H11_1610)

description:
RE1_H11_1610_U133Plus2.0.CEL
Gene expression data from human breast cancer


title: Control-grown E. faecalis relQ mutant, replicate 4

description: ΔrelQ Ctrl-4

source_name: relQ mutant early-log RNA


title: breast, post AF treatment (H24_2259)

description:
RE1_H24_2259_U133Plus2.0.CEL
Gene expression data from human breast cancer

source_name: Human breast, post AF treatment

value: AF

value: missing


title: day 15 adipogenic diff. (miRNA) BR2

hyb_protocol: The labeled miRNAs were hybridized on miRNA chips for 16 h at 64 °C in a HS 400 Pro Hybridization Station (Tecan, Grödig, Austria). All hybridizations were repeated with reversed dye assignment (dye-swap).

scan_protocol: Arrays scanned using the software GENEPIX

label_protocol: 5 µg RNA aliquots of each time point were fluorescently labeled using a miRCURY LNA microRNA Power Labeling Kit (Exiqon, Vedbaek, Denmark) according to manufacturer´s instructions

growth_protocol: hMADS cells were grown in Dulbecco's Modified Eagle's Medium (DMEM low glucose) containing 10% fetal calf serum (FCS), and 100 U/ml penicillin and streptomycin. After reaching 80% confluence, adherent cells were detached with 0.25% trypsin EDTA and seeded a density of 4500 cells per cm2. hMADS cells were maintained in proliferation medium supplemented with 2 ng/ml fibroblast growth factor 2 (FGF2)

value: primary hMADS

tag: time

value: day 15 after induction of differentiation

value: 10 μg/ml transferrin, 0.86 μM insulin, 0.2 nM of triiodothyronine, 1 μM dexamethasone, 100 μM isobutyl-methylxanthine, and 100 nM rosiglitazone then dexamethasone and sobutyl-methylxanthine omitted at day 3

source_name: Mesenchymal stem cells harvested at day -3 before induction of differentiation


title: E. faecalis relQ mutant, 15 min mupirocin treatment, replicate 3

description: ΔrelQ Mup15-3

value: mupirocin

value: 15 min

value: mid-log

value: reference


title: breast, post AF treatment (H14_1659)

description:
RE1_H14_1659_U133Plus2.0.CEL
Gene expression data from human breast cancer

value: post

value: pos

value: neg


title: breast, pre AFI treatment (H3_1296)

description:
RE1_H3_1296_U133Plus2.0.CEL
Gene expression data from human breast cancer

value: AFG

value: pre


title: breast, post AF treatment (H4_1328)

description:
RE1_H4_1328_U133Plus2.0.CEL
Gene expression data from human breast cancer

value: SD


title: breast, post AFI treatment (H6_1346)

description:
RE1_H6_1346_U133Plus2.0.CEL
Gene expression data from human breast cancer


title: Control-grown E. faecalis relQ mutant, replicate 3

description: ΔrelQ Ctrl-3

value: relQ mutant

value: early-log non-stressed

value: wild-type


title: day 10 adipogenic diff. (miRNA) BR2

source_name: Mesenchymal stem cells harvested at day 10 after induction of differentiation

value: day -3 before induction of differentiation


title: breast, pre AF treatment (H12_1628)

description:
RE1_H12_1628_U133Plus2.0.CEL
Gene expression data from human breast cancer

source_name: Human breast, pre AF treatment

value: AF


title: breast, pre AF treatment (H1_1278)

description:
RE1_H1_1278_U133Plus2.0.CEL
Gene expression data from human breast cancer


title: breast, post AF treatment (H16_1717)

description:
RE1_H16_1717_U133Plus2.0.CEL
Gene expression data from human breast cancer

value: PR


title: Control-grown E. faecalis relQ mutant, replicate 2

description: ΔrelQ Ctrl-2


title: day 10 adipogenic diff. (miRNA) BR1

value: primary hMADS

value: day 10 after induction of differentiation

value: 10 μg/ml transferrin, 0.86 μM insulin, 0.2 nM of triiodothyronine, 1 μM dexamethasone, 100 μM isobutyl-methylxanthine, and 100 nM rosiglitazone then dexamethasone and sobutyl-methylxanthine omitted at day 3


title: breast, pre AF treatment (H23_2233)

description:
RE1_H23_2233_U133Plus2.0.CEL
Gene expression data from human breast cancer

value: missing


title: day 5 adipogenic diff. (miRNA) BR2

source_name: Mesenchymal stem cells harvested at day 5 after induction of differentiation


title: day 15 adipogenic diff. (miRNA) BR1

source_name: Mesenchymal stem cells harvested at day 15 after induction of differentiation


title: E. faecalis relA mutant, 30 min mupirocin treatment, replicate 4

description: ΔrelA Mup30-4

source_name: relA mutant treated with mupirocin for 30 min RNA

value: relA mutant

value: early-log mupirocin stressed

value: mupirocin

value: 30 min

value: mid-log

value: reference


title: E. faecalis relA mutant, 30 min mupirocin treatment, replicate 3

description: ΔrelA Mup30-3


title: Control-grown E. faecalis relQ mutant, replicate 1

description: ΔrelQ Ctrl-1


title: breast, post AF treatment (H8_1389)

description:
RE1_H8_1389_U133Plus2.0.CEL
Gene expression data from human breast cancer

value: post

value: PD

value: pos

value: neg


title: day 5 adipogenic diff. (miRNA) BR1

value: day 5 after induction of differentiation

value: day -3 before induction of differentiation


title: breast, pre AF treatment (H15_1682)

description:
RE1_H15_1682_U133Plus2.0.CEL
Gene expression data from human breast cancer

value: AF

value: pre

value: PR


title: day 2 adipogenic diff. (miRNA) BR2

source_name: Mesenchymal stem cells harvested at day 2 after induction of differentiation

value: primary hMADS

value: 10 μg/ml transferrin, 0.86 μM insulin, 0.2 nM of triiodothyronine, 1 μM dexamethasone, 100 μM isobutyl-methylxanthine, and 100 nM rosiglitazone


title: breast, pre AFI treatment (H9_1575)

description:
RE1_H9_1575_U133Plus2.0.CEL
Gene expression data from human breast cancer

value: AFG


title: day 2 adipogenic diff. (miRNA) BR1

value: day 2 after induction of differentiation


title: E. faecalis relA mutant, 30 min mupirocin treatment, replicate 2

description: ΔrelA Mup30-2

value: relA mutant

value: early-log mupirocin stressed

value: mupirocin

value: wild-type


title: E. faecalis relA mutant, 30 min mupirocin treatment, replicate 1

description: ΔrelA Mup30-1

value: 30 min

value: mid-log

value: reference


title: E. faecalis relA mutant, 15 min mupirocin treatment, replicate 4

description: ΔrelA Mup15-4

source_name: relA mutant treated with mupirocin for 15 min RNA

value: 15 min


title: E. faecalis relA mutant, 15 min mupirocin treatment, replicate 3

description: ΔrelA Mup15-3

source_name: wild type mid-log RNA


title: day 0 adipogenic diff. (miRNA) BR2

source_name: Mesenchymal stem cells harvested at day 0 before induction of differentiation


title: day 1 adipogenic diff. (miRNA) BR1

source_name: Mesenchymal stem cells harvested at day 1 after induction of differentiation


title: day 0 adipogenic diff. (miRNA) BR1

value: day 0 before induction of differentiation


title: CP70 treated with PXD101, biological replicate 3

city: London

first: Wei

last: Dai

address: Du Cane Road

department: Sugery and Cancer

country: United Kingdom

institute: Imperial College London

hyb_protocol: The NuGEN hybridization v1.0 protocol was followed for hybridising labelled DNA to standard GeneChips with 11 micron feature size. This hybridisation protocol is derived from the NuGEN FL-Ovation cDNA Biotin Module v2 user guide and the Affymetrix GeneChip Expression Analysis Technical Manual.

scan_protocol: The Affymetrix GeneChip scanner 3000 running GCOS software

data_processing: The data were analyzed in R (version 2.10.1) using Affy package and quantile normalization as the normalisation method.

source_name: Ovarian Cisplatin resisant cell line CP70 treated with PXD101

label_protocol: The RNA was amplified using the WT-Ovation Pico target pre v 1.0 protocol which was derived from the NuGEN WT-Ovation Pico RNA Amplication system (WTO_Pico_UserGuide) and the NuGEN FL-Ovation cNDA Biotin Module v2 (FLBv2_User_Guide).

growth_protocol: Cell line was grown in RPMI-1640 supplemented with glutamine (2mM) and 10% fetal bovine serum in humidified 5% CO2 in air incubators at 37 ̊C.

extract_protocol: RNA was extracted and purified from cell lines using the Qiagen RNAeasy kit according to standard instructions.

treatment_protocol: A2780/cp70 +Decitabine: A2780/cp70 cells were treated at 50% confluence with 0.1 µM Decitabine for 48 h with Decitabine being replaced after 24h. Cells were harvested 96 h following drug removal. A2780/cp70 +PXD101: A2780/cp70 cells were treated at 50% confluence with 0.1 µM PXD101 for 48 h. Cells were harvested 96 h following drug removal.   A2780/cp80 +Decitabine+PXD101: A2780/cp70 cells were treated at 50% confluence with 0.1 µM Decitabine for 48 h with 0.1 µM PXD101 being added for an additional 24 hours following the initial 24 hour DAC treatment. Cells were harvested 96 h following drug removal.

tag: cell line


title: CP70 treated with Decitabine and PXD101, biological replicate 3

source_name: Ovarian Cisplatin resisant cell line CP70 treated with Decitabine and PXD101


title: day 1 adipogenic diff. (miRNA) BR2

value: day 1 after induction of differentiation

value: day -3 before induction of differentiation


title: day -2 adipogenic diff. (miRNA) BR1

source_name: Mesenchymal stem cells harvested at day -2 before induction of differentiation


title: E. faecalis relA mutant, 15 min mupirocin treatment, replicate 2

description: ΔrelA Mup15-2


title: day -2 adipogenic diff. (miRNA) BR2

value: day -2 before induction of differentiation


title: Control-grown E. faecalis relA mutant, replicate 2

description: ΔrelA Ctrl-2

source_name: relA mutant early-log RNA

value: early-log non-stressed


title: CP70 treated with PXD101, biological replicate 2


title: CP70 treated with Decitabine and PXD101, biological replicate 2


title: CP70 treated with Decitabine, biological replicate 3

source_name: Ovarian Cisplatin resisant cell line CP70 treated with Decitabine


title: CP70, biological replicate 3

source_name: Ovarian Cisplatin resistant cell line CP70


title: CP70 treated with Decitabine, biological replicate 1


title: E. faecalis relA mutant, 15 min mupirocin treatment, replicate 1

description: ΔrelA Mup15-1


title: Control-grown E. faecalis relA mutant, replicate 3

description: ΔrelA Ctrl-3


title: Control-grown E. faecalis relA mutant, replicate 4

description: ΔrelA Ctrl-4


title: A2780, biological replicate 3

source_name: Ovarian Cisplatin sensitive cell line A2780


title: CP70 treated with Decitabine, biological replicate 2


title: CP70 treated with PXD101, biological replicate 1


title: CP70 treated with Decitabine and PXD101, biological replicate 1


title: CP70, biological replicate 2


title: CP70, biological replicate 1


title: Control-grown E. faecalis relA mutant, replicate 1

description: ΔrelA Ctrl-1


title: E. faecalis OG1RF wild type, 30 min mupirocin treatment, replicate 3

description: OG1RF Mup30-3

source_name: wild-type treated with mupirocin for 30 min RNA


title: A2780, biological replicate 2


title: A2780, biological replicate 1


title: E. faecalis OG1RF wild type, 30 min mupirocin treatment, replicate 2

description: OG1RF Mup30-2


title: E. faecalis OG1RF wild type, 30 min mupirocin treatment, replicate 4

description: OG1RF Mup30-4


title: Nrf2b DMSO Rep2

city: Hamilton

first: Andrew

middle: G.

last: McArthur

state: Ontario

address: 1280 Main Street West

department: Biochemistry & Biomedical Sciences

country: Canada

institute: McMaster University

description: Gene expression with Nrf2b MO, DMSO exposure at 48 hpf. RNA sampled at 52 hpf

hyb_protocol: Cy3 labeled samples were hybridized to the Agilent 4x44K zebrafish microarray at the Genome Technology Core of the Whitehead Institute (Cambridge, MA), following the Agilent protocols.

scan_protocol: Hybridization results were scanned using a Agilent DNA Micorarray Scanner.

data_processing: Raw array data obtained from the Whitehead Institute were extracted using Agilent's feature extraction software using background detrending (spatial and multiplicative). Prior to normalization, Cy3 values below 5 were set to 5. The data were then normalized using the non-linear scaling method based on rank invariant probes. After normalization but before statistical analyses, probes not significantly above background in all microarrays were removed.

organism: Danio rerio

source_name: Injection of Nrf2b MO at 1-4 cell stage. DMSO exposure at 48 hpf. RNA sampled at 52 hpf.

label_protocol: The RNA samples were labeled with Cy3 using the Agilent Low Input Quick Amp Labeling kit, following the manufacturer's instructions.

growth_protocol: Zebrafish (Danio rerio) from the Tupfel/Long fin mutation wild-type strain (TL) were used in all experiments. Fish were maintained and embryos were collected under standard light and temperature conditions as previously described.

extract_protocol: At 52 hpf, embryos were fixed in RNA Later and stored at -80°C. RNA was extracted using RNA STAT-60, following the manufacturer's instruction.

treatment_protocol: Embryos at the 1-4 cell stage were injected with 3-5 nl of a control morpholino (MO) or gene-specific MO to knockdown Nrf2a, Nrf2b, or a Nrf2a+b combination. At 48 hpf, triplicate groups of 5 embryos were exposed to 2 µM of tert butyl hydroquinone or 2% DSMO for 4 hours.

value: pooled embryos

tag: developmental stage

value: 52 hpf


title: Nrf2b DMSO Rep3

value: Tupfel/Long fin mutation wild-type strain (TL)

tag: tissue


title: E. faecalis OG1RF wild type, 15 min mupirocin treatment, replicate 2

description: OG1RF Mup15-2

source_name: wild-type treated with mupirocin for 15 min RNA


title: E. faecalis OG1RF wild type, 30 min mupirocin treatment, replicate 1

description: OG1RF Mup30-1


title: E. faecalis OG1RF wild type, 15 min mupirocin treatment, replicate 3

description: OG1RF Mup15-3


title: MCF10A-HER23_3d cultures_SHP2 miR1_1

city: Basel

first: Tim

last: Roloff

address: Maulbeerstrasse 66

department: Functional Genomics

country: Switzerland

institute: FMI

hyb_protocol: Affymetrix Human Gene 1.0 st v1 GeneChip arrays were hybridized following the GeneChip Whole Transcript (WT) Sense Target Labeling Assay Manual (Affymetrix) with a hybridization time of 16h. The Affymetrix Fluidics protocol FS450_0007 was used for washing.

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

data_processing: CEL files were read into R (v2.10) using the R/Bioconductor (v2.4) package oligo (v1.8) and normalized probeset level expression values were calculated with the command rma and the R/Bioconductor annotation package pd.hugene.1.0.st.v1

label: Biotin

label_protocol: 100ng total RNA was processed according to the GeneChip Whole Transcript (WT) Double-Stranded Target Assay Manual from Affymetrix (GeneChip Whole Transcription Sense Target Labeling technical manual, Rev. 2).

growth_protocol: Three-dimensional cultures of MCF10A-HER2/3 cells expressing inducible CTRL miR, SHP2 miR1 or SHP2 miR2 for 15 days. Cells were grown in DMEM/F12 medium containg EGF, insulin, cholera toxin, hydrocortisone, horse serum and PS

extract_protocol: After 15 days of three-dimensional cultures a standard TRIZOL extraction method was used to obtain total RNA from MCF10A-HER2/3 cells in the presence or absence of SHP2

treatment_protocol: Doxycycline, added the day after seeding the cells in three-dimensional cultures and refreshed every 2 days

tag: transfection

value: SHP2 miR1


title: MCF10A-HER23_3d cultures_SHP2 miR2_2

value: SHP2 miR2


title: MCF10A-HER23_3d cultures_SHP2 miR1_2


title: E. faecalis OG1RF wild type, 15 min mupirocin treatment, replicate 4

description: OG1RF Mup15-4

value: early-log mupirocin stressed


title: MCF10A-HER23_3d cultures_SHP2 miR2_1


title: BT474 xenograft_SHP2 miR2_2

source_name: BT474 tumors

growth_protocol: BT474 cells were injected orthotopically into the fat pad of mammary gland 2/3 of imuunodeficient mice. After tumor development, we depleted SHP2 for 30 days in vivo.

extract_protocol: Tumors were dissected and total RNA was isolated with a standard TRIZOL extraction method.

treatment_protocol: Doxycycline in drinking water (2 g per liter). The treatment started after tumor development and continued until the end of the experiment (day 30). The drinking water containing doxycycline was refreshed every two days.


title: MCF10A-HER23_3d cultures_CTRL miR_1

value: CTRL miR


title: Nrf2a_2b DMSO Rep3

description: Gene expression with Nrf2a and Nrf2b MO, DMSO exposure at 48 hpf. RNA sampled at 52 hpf

source_name: Injection of Nrf2a and Nrf2b MO at 1-4 cell stage. DMSO exposure at 48 hpf. RNA sampled at 52 hpf.


title: Control-grown E. faecalis OG1RF wild type, replicate 4

description: OG1RF Ctrl-4

source_name: wild-type early-log RNA

value: wild-type


title: Nrf2b DMSO Rep1


title: Control-grown E. faecalis OG1RF wild type, replicate 3

description: OG1RF Ctrl-3


title: Nrf2a_2b DMSO Rep1


title: Nrf2a DMSO Rep3

description: Gene expression with Nrf2a MO, DMSO exposure at 48 hpf. RNA sampled at 52 hpf

source_name: Injection of Nrf2a MO at 1-4 cell stage. DMSO exposure at 48 hpf. RNA sampled at 52 hpf.


title: E. faecalis OG1RF wild type, 15 min mupirocin treatment, replicate 1

description: OG1RF Mup15-1

value: mupirocin

source_name: wild type mid-log RNA


title: Control-grown E. faecalis OG1RF wild type, replicate 2

description: OG1RF Ctrl-2

value: mid-log


title: MCF10A-HER23_3d cultures_CTRL miR_2


title: Control-grown E. faecalis OG1RF wild type, replicate 1

description: OG1RF Ctrl-1

value: reference


title: Nrf2a DMSO Rep2


title: BT474 xenograft_SHP2 miR1_7


title: BT474 xenograft_SHP2 miR1_6


title: BT474 xenograft_SHP2 miR2_1


title: BT474 xenograft_SHP2 miR2_3


title: BT474 xenograft_SHP2 miR1_2


title: IGROV1 NSP, biological replicate 2

description: ovarian cancer cell line IGROV1, NSP cell

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

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

data_processing: BeadStudio software methylation module 1.0.5

label: Cy5 and Cy3

source_name: ovarian cancer cell line IGROV1

label_protocol: Standard Illumina Protocol

growth_protocol: Cell lines were grown in RPMI-1640 supplemented with glutamine (2mM) and 10% fetal bovine serum in humidified 5% CO2 in air incubators at 37 ̊C.

extract_protocol: DNA was extracted and purified from cell lines using the Qiagen QIAamp DNA Kit according to standard instructions.


title: BT474 xenograft_SHP2 miR1_5


title: BT474 xenograft_SHP2 miR1_3


title: Nrf2a DMSO Rep1


title: BT474 xenograft_SHP2 miR1_1


title: Control MO DMSO Rep1

description: Gene expression with control MO, DMSO exposure at 48 hpf. RNA sampled at 52 hpf

source_name: Injection of control MO at 1-4 cell stage. DMSO exposure at 48 hpf. RNA sampled at 52 hpf.


title: IGROV1 SP biological replicate 2

description: ovarian cancer cell line IGROV1, SP cell


title: BT474 xenograft_CTRL miR_5


title: Control MO DMSO Rep3


title: BT474 xenograft_CTRL miR_4


title: Control MO DMSO Rep2


title: BT474 xenograft_SHP2 miR1_4


title: BT474 xenograft_CTRL miR_6


title: U87_in-direct_co-culture_rep3

city: Ljubljana

first: Kristina

last: Gruden

address: Vecna pot 111

department: Department of Biotechnology and Systems Biology

country: Slovenia

institute: National Institute of Biology

description: biological replicate 3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol (BeadStudio).

data_processing: The data were log2 transformed and normalised using robust spline normalisation with lumi package in R statistical environment.

source_name: U87 cell culture

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

growth_protocol: Human MSCs derived from bone marrow were purchased from Lonza Bioscience, Walkersville Inc. (MSC-4: 6F4085). After resuscitation cells were plated and grown according to manufacturers recommendations. Briefly, hMSC were grown in Dulbecco medium (DMEM, Sigma 5921,) and 10% fetal bovine serum (FBD, PPL), supplemented with 100 U penicilin, 1000 U streptomycin, 2mM L-Glutamine, Na-Pyruvate and non-essential amino acids. During cultivation (37°C, 5% CO2) medium changes were carried out three times weekly. Cells were passaged after reaching 75% confluence and plated at density 5000 cells/cm2. Human brain tumor cell line (U87-MG) was purchased from the American Type Culture Collection –ATCC (Manassas, VA, USA). Cells were cultured in the same medium as hMSC cells. They were passaged at 75% confluency and seeded at a density 15 000 cells/cm2. All experiments were further performed in a medium containing 10% serum. hMSC of passage 7 and glioma cell lines of passage 40 were used in the experiments. The co-culture experiments were set up in duplicates using 6-well Transwell inserts (Costar, Cornig incorporated, NY) with 0.4 um pore size. On the bottom of the well the hMSC were plated at the density of 105 cells in 2 ml, whereas the U87-MG cells were always plated in the insert at the density of 80 000 cells/mL. Cells were always left to adhere for 3h before being put together for 72 h.

extract_protocol: Total RNA was isolated from three biological replicates of monocultures and indirect co-cultures of MSC and U87-MG cells using Trizol reagent (Invitrogen Limited, Paisley, Scotland UK) following manufacturer’s instructions. RNA was column purified with RNeasy Mini Kit (Qiagen,UK) and integrity confirmed using the Agilent 2100 Bioanalyzer (Agilent Technologies, USA).

treatment_protocol: Cells were not treated in any way. In co-culture experiments, cells were left to grow in separate chambers of Boyden chambers for 72 h, as described above.

tag: cell line passage

tag: duration of cultivation

tag: type of cultivation plate

value: Boyden chamber top chamber (co-culture)


title: hMSC4_in-direct_co-culture_rep3

description: biological replicate 3

source_name: MSC-4 cell culture

tag: stem cell clone

value: Boyden chamber bottom chamber (co-culture)


title: U87_monoculture_rep3

description: biological replicate 3

value: Boyden chamber top chamber (single culture)


title: hMSC4_in-direct_co-culture_rep2

description: biological replicate 2


title: U87_in-direct_co-culture_rep2

description: biological replicate 2


title: hMSC4_monoculture_rep3

description: biological replicate 3

value: Boyden chamber bottom chamber (single culture)


title: IGROV1 NSP, biological replicate 1

value: ovarian cancer cell line IGROV1, NSP cell


title: Porcine, control, biological, rep1

city: Wuhan

first: Liu

last: Shuqing

state: Hubei province

address: No.1,Shizishan Street · Hongshan District

country: China

institute: Huazhong agricultural university

description: Gene expression data from Porcine alveolar Macrophages isolated from control pigs at 28 d.p.i.

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 the Hewlett-Packard GeneArray Scanner G2500A.

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

organism: Sus scrofa

source_name: Porcine alveolar Macrophages isolated from control pigs, 28 dpi

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

growth_protocol: Six 28 days old healthy pigs were obtained, Three pigs  were  inoculated intratracheally with 2 ml of  4.5×108 colony forming units of HPS4 strain MD0322. other three pigs were intratracheally challenged with 2 ml PBS as control. All pigs were slaughtered at 28 dpi.

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

treatment_protocol: Bronchoalveolar lavage of the lungs was performed with 100mL aliguots of sterile PBS containing genamicin at 70 μg/mL(Sigma).Then lavage fluids were centrifuged at 230 ×g for 15 min, and cells were washed twice with Dulbecco’s Modified Eagle’s Medium (DMEM) containing gentamicin (50μg/mL).

value: Alveolar Macrophage


title: Porcine, control, biological, rep3


title: hMSC4_monoculture_rep2

description: biological replicate 2


title: U87_monoculture_rep2

description: biological replicate 2


title: IGROV1 SP, biological replicate 1

value: ovarian cancer cell line IGROV1, SP cell


title: BT474 xenograft_CTRL miR_3


title: BT474 xenograft_CTRL miR_2


title: Porcine, HPS4 infection, biological rep2

description: Gene expression data from Porcine alveolar Macrophages isolated from HPS4 infection pigs at 28 d.p.i.

source_name: Porcine alveolar Macrophages isolated from HPS4 infection pigs, 28 dpi


title: Porcine, HPS4 infection, biological rep3


title: Primary tumour 7

description: Primary ovarian tumour tissue

source_name: Primary ovarian tumour tissue

value: ovarian tumour tissue


title: Porcine, control, biological, rep2


title: Relapse tumour 7

description: Relapse ovarian tumour tissue

source_name: Relapse ovarian tumour tissue


title: hMSC4_in-direct_co-culture_rep1

description: biological replicate 1


title: BT474 xenograft_CTRL miR_1


title: U87_in-direct_co-culture_rep1

description: biological replicate 1


title: hMSC4_monoculture_rep1

description: biological replicate 1


title: U87_monoculture_rep1

description: biological replicate 1


title: Primary tumour 6

description: Primary ovarian tumour tissue


title: HVS-CD4-ITK-R335W_unstim_rep2

first: Karl

last: Koehrer

address: Universitaetsstr. 1

department: BMFZ

institute: University of Duesseldorf

description: T cells, CD4 positive, ITK R335W mutant

hyb_protocol: Samples were hybridized using Hybridization Kit materials (Affymetrix) according to the WT Terminal Labeling Protocol (P/N 702808 Rev.1, Affymetrix); Fluidics Protocol FS450_0007

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data processing was done using GeneSpring GX 11 software (Agilent). ExonPLIER16 summarization was applied to core probe set intensities.
HuGene-1_0-st-v1.r4.mps
HuGene-1_0-st-v1.r4.pgf

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix) according to the WT Terminal Labeling Protocol (P/N 702808 Rev.1, Affymetrix)

growth_protocol: After Herpesvirus Saimiri transformation of human primary T cells: RPMI 1640 (Life Technologies) and Panserin 401 (PAN Biotech) mixed in a ratio 1:1, supplemented with 10% FCS (PAN Biotech), 100 µg/mL gentamicin and 10 U/mL IL-2 (Roche)

extract_protocol: Column-based RNA extraction

tag: cell type

value: HVS-transformed T cells

tag: genotype/variation

value: ITK R335W mutant , homozygous


title: Porcine, HPS4 infection, biological rep1


title: Relapse tumour 6

description: Relapse ovarian tumour tissue


title: HVS-CD4-control_unstim_rep3

description: T cells, CD4 positive, control

value: ITK wild type


title: HVS-CD4-ITK-R335W_unstim_rep1

description: T cells, CD4 positive, ITK R335W mutant


title: Primary tumour 5

description: Primary ovarian tumour tissue


title: Primary tumour 4

description: Primary ovarian tumour tissue


title: Relapse tumour 5

description: Relapse ovarian tumour tissue


title: HVS-CD4-control_unstim_rep2

description: T cells, CD4 positive, control


title: Cell transfected with Pax8 siRNA rep2

city: Napoli

first: Lucio

last: Nitsch

address: Via Pansini 5

department: Biologia e Patologia Cellulare e Molecolare

institute: Unversity of Naples Federico II

description: RNA from cells 72hrs after transfection

hyb_protocol: According to Affymetrix protocol described in GeneChip® Expression Analysis Technical Manual at http://www.affymetrix.com

data_processing:
Gene-level signals were generated from CEL files by GeneSpring v.11.5 software (Agilent Technologies Inc.), using the Probe Logarithmic Intensity Error (PLIER16) summarization algorithm
RaGene-1_0-st-v1.r4.pgf

organism: Rattus norvegicus

source_name: FRTL-5 differentiated thyroid cells silenced for Pax8

growth_protocol: FRTL-5 cells were grown in Coon’s modified F-12 medium (Euroclone) supplemented with 5% calf serum and a six-hormone mixture

extract_protocol: Total RNA was extracted 72 hours after transfection using TRIzol reagent (Invitrogen) and treated with RNase-free DNase I (Applied Biosystem)

treatment_protocol: FRTL-5 cells were transfected in triplicate with 100 nM Pax8 siGENOME siRNA (siPax8 samples) or siGENOME Non-Targeting #3 (DHARMACON) as scramble (ntPax8 control samples) using DharmaFECT 1 transfection reagent, following the manufacturer’s protocol.

tag: knockdown

value: silenced for Pax8


title: HVS-CD4-ITK-R335W_unstim_rep3

description: T cells, CD4 positive, ITK R335W mutant


title: Relapse tumour 4

description: Relapse ovarian tumour tissue

tag: sample type


title: Cell transfected with Pax8 siRNA rep3

description: RNA from cells 72hrs after transfection

scan_protocol: According to Affymetrix protocol described in GeneChip® Expression Analysis Technical Manual at http://www.affymetrix.com


title: Primary tumour 3

description: Primary ovarian tumour tissue


title: Relapse tumour 3

description: Relapse ovarian tumour tissue


title: Control rep3

first: Nancy

last: Benight

address: 1100 Bates Street

scan_protocol: Standard Illumina scanning protocol

data_processing: Cubic Spline using Illumina Beadchip Studio

organism: Mus musculus

source_name: whole colon

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

extract_protocol: RNA was extracted using Qiagen's Rneasy Mini kit and the protocol with extra washes.  Quantity and quality were verified using Nanodrop

tag: treatment

value: Control

tag: strain

tag: gender

value: Male

value: colon


title: control 1 (saline-treated at P4 and 7)

first: Morgan

middle: L

last: Kleiber

address: Biological and Geological Sciences Building

department: Biology

institute: University of Western Ontario

hyb_protocol: 5.5 ug of single-stranded cDNA was hybridized for 16 hours at 45 degrees C to the array.  Liquid handling steps were performed by a GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 using Command Console v1.1

data_processing: The data were analyzed with Partek Genomics Suite software v6.6.  Probes  were quantile-normalized using the GeneChip-Robust Multiarray Averaging and log2 transformed. All other settings were left as default.

source_name: brain, total RNA from 3 saline-treated males

label_protocol: Single-stranded cDNA was synthesized using 200 ng of total RNA using Ambion WE Expression Kit for Affymetrix GeneChip Whole Transcript WT Expression Arrays and labelled using the Affymetrix GeneChip WT Terminal Labeling kit.

growth_protocol: Mice were raised in standard same-sex housing conditions (14/10-hour light/dark cycle, 40-60% humidity,21°C to 24°C temperature).  Mice were sacrificed at postnatal day 60.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions and cleaned using RNeasy Mini kit (QIAGEN).  RNA quality and quantity was analyzed by Agilent 2100 Bioanalyzer and a NanoDrop ND-1000 spectrophotometer.  Equal ug of total brain RNA were pooled from three male mice (from different litters) to minimize litter effect noise.

treatment_protocol: Mice were injected subcutaneously with 20% ethanol in 0.15M saline (or 0.15M saline alone as a control) at postnatal days 4 and 7.  Dosages represented two 2.5 g/kg ethanol doses spaced two hours apart on each day.  During treatment, the mother was removed from the cage and replaced following the completion of all injections.  To avoid litter effects, mice were sex and weight-matched within litters (ie, control and ethanol-treated mice were parented by the same dam).  Mice were weaned at postnatal day 25 and housed in same-sex colonies of 2-4 individuals per cage.  At postnatal day 60, mice were sacrificed by CO2 asphyxiation and whole brain tissue were dissected using RNAse-free tools.  Brains were snap-frozen in liquid nitrogen and stored at -80 degrees C until RNA isolation.

value: ethanol


title: Control cells transfected with Non-Targeting siRNA rep1

description: RNA from cells 72hrs after transfection

source_name: FRTL-5 differentiated thyroid control cells

label_protocol: According to Affymetrix protocol described in GeneChip® Expression Analysis Technical Manual at http://www.affymetrix.com

value: non-targeting siRNA control


title: Relapse tumour 1

description: Relapse ovarian tumour tissue


title: HVS-CD4-control_unstim_rep1

description: T cells, CD4 positive, control


title: DSS rep6

value: Dextran Sulfate Sodium


title: Control rep4


title: Control cells transfected with Non-Targeting siRNA rep2

description: RNA from cells 72hrs after transfection


title: Control cells transfected with Non-Targeting siRNA rep3

description: RNA from cells 72hrs after transfection


title: Primary tumour 2

description: Primary ovarian tumour tissue


title: PEO23

description: ovarian cancer cell line isolated from patient after chemotherpay

value: ovarian cancer cell line


title: DSS rep5


title: ethanol 4 (ethanol-treated at P4 and 7)

source_name: brain, total RNA from 3 ethanol-treated males

value: control


title: Relapse tumour 2

description: Relapse ovarian tumour tissue


title: Cell transfected with Pax8 siRNA rep1

description: RNA from cells 72hrs after transfection


title: Nrf2a_2b DMSO Rep2

source_name: Injection of Nrf2a and Nrf2b MO at 1-4 cell stage. DMSO exposure at 48 hpf. RNA sampled at 52 hpf.

value: Tupfel/Long fin mutation wild-type strain (TL)

value: pooled embryos

value: 52 hpf


title: ethanol 2 (ethanol-treated at P4 and 7)


title: DSS rep4


title: DSS + MTA rep6

value: Dextran Sulfate Sodium + Methylthioadenosine


title: Human Rectal Carcinoma Replicate 8

city: Beijing

first: Ming-Rong

last: Wang

address: 17 Panjiayuan Nanli, Chaoyang District, Beijing, China

institute: Cancer Institute (Hospital), Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China

description: Biological replicate 8 of 8.Human Rectal Carcinoma Biopsy Tissue

hyb_protocol: Reference DNA probes and adenoma/carcinoma DNA probes was combined and Human Cot-1 DNA (Invitrogen), 10 Blocking Agent and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, then samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential.

scan_protocol: Scanned on an Agilent G2565BA Scanner

data_processing:
Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1).
Agilent Genomic Workbench Lite Edition 6.5 was used to normalize and analyze the probe data.

source_name: Human Rectal Carcinoma Biopsy Tissue

label_protocol:
500 ng the reference commercial genomic DNA (promega) and the same amount of adenoma/carcinoma DNA were digested with Alu I (promega) and RSA I (promega) following Agilent's instructions (Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis Protocol Version 6.1, August 2009)
The digested DNA fragments were labeled with cyanine-3 dUTP or cyanine-5 dUTP using Agilent Genomic DNA Enzymatic Labeling Kit (Agilent p/n 5190-0449). Then Microcon YM-30 (Millipore) was used to clear up the labeled probes.

extract_protocol: Genomic DNA extracted using Qiagen DNeasy Blood & Tissue Kit following manufacturer's instructions

treatment_protocol: Biopsy tissue was obtained by colonoscopy and stored at -80 ℃ until DNA extraction.

value: Carcinoma

tag: age

tag: Sex

tag: location

value: Rectal

source_name: Commercial Human Genomic DNA: Male

tag: company

value: Promega

tag: catalog


title: PEO14

description: ovarian cancer cell line isolated from patient before chemotherpay


title: Human Rectal Carcinoma Replicate 7

description: Biological replicate 7 of 8.Human Rectal Carcinoma Biopsy Tissue

tag: tissue

value: Femaie

source_name: Commercial Human Genomic DNA: Female


title: Human Rectal Carcinoma Replicate 5

description: Biological replicate 5 of 8.Human Rectal Carcinoma Biopsy Tissue


title: Human Rectal Carcinoma Replicate 6

description: Biological replicate 6 of 8.Human Rectal Carcinoma Biopsy Tissue


title: Primary tumour 1

description: Primary ovarian tumour tissue

value: ovarian tumour tissue


title: DSS + MTA rep5


title: DSS + MTA rep4


title: Human Rectal Carcinoma Replicate 4

description: Biological replicate 4 of 8.Human Rectal Carcinoma Biopsy Tissue


title: Control rep2

value: Control


title: PEO4, biological replicate 2

source_name: ovarian cancer cell line isolated from patient after chemotherpay


title: PEA2


title: DSS rep1

value: Male


title: PEO1, biological replicate 1

source_name: ovarian cancer cell line isolated from patient before chemotherpay


title: Human Rectal Adenoma Replicate 8

description: Biological replicate 8 of 8.Human Rectal Adenoma Biopsy Tissue

source_name: Human Rectal Adenoma Biopsy Tissue

value: Adenoma


title: Human Rectal Carcinoma Replicate 1

description: Biological replicate 1 of 8.Human Rectal Carcinoma Biopsy Tissue


title: Human Rectal Carcinoma Replicate 2

description: Biological replicate 2 of 8.Human Rectal Carcinoma Biopsy Tissue


title: Human Rectal Adenoma Replicate 5

description: Biological replicate 5 of 8.Human Rectal Adenoma Biopsy Tissue


title: PEA1


title: PEO1, biological replicate 2


title: MCP6

description: ovarian cancer cell line A2780 derivative  MCP6, resistant to cisplatin


title: MCP1

description: ovarian cancer cell line A2780 derivative MCP1, resistant to cisplatin


title: Human Rectal Adenoma Replicate 7

description: Biological replicate 7 of 8.Human Rectal Adenoma Biopsy Tissue


title: Human Rectal Carcinoma Replicate 3

description: Biological replicate 3 of 8.Human Rectal Carcinoma Biopsy Tissue


title: DSS rep3

value: colon


title: PEO4, biological replicate 1


title: CP70

description: ovarian cancer cell line A2780 derivative CP70, resistant to cisplatin


title: DSS rep2


title: DSS + MTA rep2


title: Human Rectal Adenoma Replicate 6

description: Biological replicate 6 of 8.Human Rectal Adenoma Biopsy Tissue


title: Control rep1


title: A2780p6

description: ovarian cancer cell line A2780 derivative A2780p6, sensitive to cisplatin


title: DSS + MTA rep3


title: Human Rectal Adenoma Replicate 2

description: Biological replicate 2 of 8.Human Rectal Adenoma Biopsy Tissue


title: Human Rectal Adenoma Replicate 4

description: Biological replicate 4 of 8.Human Rectal Adenoma Biopsy Tissue


title: A2780p5

description: ovarian cancer cell line A2780 derivative A2780p5, sensitive to cisplatin


title: Human Rectal Adenoma Replicate 1

description: Biological replicate 1 of 8.Human Rectal Adenoma Biopsy Tissue


title: CCRFCEM vs. TE671 Exp2

city: Athens

first: George

middle: I

last: Lambrou

state: Attiki

address: Thivon & Levadeias

department: First Department of Pediatrics

country: Greece

institute: National and Kapodistrian University of Athens

description:
The CCRF-CEM (ALL) cell line was used as the model, it was obtained from the European Collection of Cell Cultures (ECACC). The CCRF-CEM cell line, a CD4+ (Miranda, Wolf et al. 1996) and CD34+ presenting cell line (Naujokat, Sezer et al. 2000)
The cell line has been observed to undergone minor changes after long-term culture, except for the presence of dense granules in the nucleoli (Uzman, Foley et al. 1966). Finally, the CCRF-CEM cell line has been reported to manifest autocrine catalase activity which participates to its mechanisms of growth and progression (Sandstrom and Buttke 1993).
The TE-671 (RMS) cell lines were used as the model, both obtained from the European Collection of Cell Cultures (ECACC).
However, it is today known that this cell line is parental if not identical to the RD rhabdomyosarcoma cell line. However, several reports still refer to this cell line as medulloblastoma.

hyb_protocol: Hybridization was performed with the CyScribe Post-Labeling kit (RPN5660, GE Healthcare, former Amersham Inc.) as described by the manufacturer. The fluorescent dyes used were Cy3 and Cy5. cDNAs were purified with PCR product clean-up kit (# 28104, QIAGEN Inc.). Slides were activated at 55o C for 30 min in 1% BSA. Samples were applied on the slides, and let to hybridize overnight at 55o C. The following day, slides were washed in 200 ml 0.1× SSC and 0,1% SDS for 3× 5 min, in 200 ml 0.1× SSC for 2× 5 min  and in 200 ml ddH2O for 30 sec. Slides were dried by centrifugation at 1500 rpm for 3 min and scanned with a microarray scanner.

scan_protocol: Slides were scanned with a microarray scanner (ScanArray 4000XL) (Perkin Elmer Inc. MA, former GSI Lumonics, USA). Images were generated with ScanArray microarray acquisition software (GSI Lumonics, USA). Image analysis and raw data acquisition were performed with the ImaGene® software from BioDiscovery (California, USA).

data_processing:
Data collection
Microarray data pre-processing analysis was performed with ImaGene® v.6.0 Software (BioDiscovery Inc, CA) and ARMADA software (National Hellenic Research Foundation, Athens Greece). Data were collected from exported text file and data pre-processing was performed using the Microsoft Excel® environment. Data were processed in two ways: The first included the separation of each channel (Cy3 and Cy5), and the second included pre-processing of the ratio between the two samples.
Data preprocessing and Background Correction
A common preprocessing stage was applied to the raw data (the median intensity value in each channel) of both platforms. Specifically, the well performing version of the robust loess-based background correction (rLsBC) approach, as proposed by Sifakis et al. (2011) was applied. rLsBC assumes that the background noise affects the spot intensities in a multiplicative manner. Instead of using the measurements of the local (feature-related) background for the correction, rLsBC utilizes the regression estimate of the logarithmic background distribution BR,G according to the logarithmic foreground intensity FR,G for each channel (R: Red and G: Green). Thus, rLsBC provides a robust estimation of the channel-specific background noise, utilized to background-correct the logarithmic foreground intensities: FcR,G = FR,G - BlR,G where FcR,G  is the logarithmic background-corrected foreground intensity, and BlR,G the robust estimate of background noise, for each channel. The absolute background-corrected foreground intensity f_c^(R,G) for each channel is then calculated as: f_c^(R,G)=2^(F_c^(R,G) ).
Normalization
The background corrected signal intensities were further normalized in order to mitigate the effect of extraneous, non-biological variation in the measured gene expression levels. Normalization was performed by using six different methods: a) No further processing after background correction, b) log2 transformation, c) LOWESS normalization, d) division with the Global Median (median of the 50% percentile), e) subtraction of Global Median (the median of the 50% percentile) and f) Rank Invariant with running Median. Finally, the Rank Invariant normalization method was chosen for further processing and analysis. The rank invariant normalization approach followed included the robust version of the intensity-dependent scatter-plot smoother Loess with a quadratic polynomial model, and a smoothing parameter equal to 10%, which was considered appropriate for the relatively small number of probes attached in the microarrays.
Data integration
We performed data integration at a lower level as previously described. Specifically, the preprocessed datasets of each array were combined into one unified dataset, in which standard statistical procedures were applied. Nonetheless, whenever applicable to the nature of the present study, some of the key issues needed to be addressed, such as preprocessing, preparation and annotation of the individual datasets, complied to previously reported guidelines.
Filtering
As low signal intensity measurements are less reliable in terms of the impact of noise on them than high gene expression measurements, an intensity-dependent filtering with an absolute threshold value of 10 was used in each channel, in order to exclude low quality features. In addition, Signal-to-Noise Ratio was used as:  , where μR,G and μB is the mean value intensity for the respective channel (Cy3 or Cy5) and mean background intensity, respectively; and σB is the background mean signal standard deviation. A threshold of 2 was set as a cut-off value, meaning that spot intensity for at least one channel should be twice as much as that of the background.
Analysis
The data were further analyzed in order to identify the differentially expressed genes (DEGs) and the groups of genes that share common expression characteristics. Analysis steps were conducted in the Matlab® computing environment.
Identification of Differentially Expressed Genes
Furthermore, each gene was tested for its significance in differential expression using a z-test. Genes were considered to be significantly differentially expressed if they obtained a p-value <0.05. The False Discovery Rate (FDR) was calculated as previously described. There was a FDR of 1% for p<0.05 for the IntelliGene microarray chip. The DE genes per experiment were identified at a confidence level of 95%.

source_name: CCRFCEM T-cell acute lymphoblastic leukemia cell line

label_protocol: For the assay of mRNA levels two sets of microarray chips were used: cDNA microarray chips (4.8k genes) obtained from TAKARA (IntelliGene™ II Human CHIP 1) (36). Hybridization was performed with the CyScribe Post-Labeling kit (GE Healthcare former Amersham Inc. Buckinghamshire UK) as described by the manufacturer. The fluorescent dyes used were Cy3 and Cy5. The RNA extracted from the CCRF-CEM cells was stained with Cy3 (reference) and RNA from the TE-671 cell line with Cy5 (experiment). cDNAs were purified with QIAGEN PCR product clean-up kit. Slides were activated at 55oC for 30 min in 1% BSA. Samples were applied on the slides, and let to hybridize overnight at 55oC. The following day, slides were washed in 200 ml 0.1x SSC and 0.1% SDS for 3x5 min, in 200 ml 0.1x SSC for 2x5 min and in 200 ml ddH2O for 30 sec. Slides were dried by centrifugation at 1500 rpm for 3 min and scanned with a ScanArray 4000XL microarray scanner (Perkin Elmer Inc. MA, former GSI Lumonics, USA).

growth_protocol: The CCRFCEM cell line was seeded at time -24h and left overnight to grow. After 24h (time: 0h) sample was taken in order to perform measurements and every 24h thereafter. CCRF-CEM cells were grown in RPMI-1640 medium supplemented with 2 mM L-Glutamine and Streptomycin/Penicillin 100 U/ml (Gibco), 20% FBS (Gibco) at 37oC, 5% CO2 and ~100% humidity. Cells were allowed to grow to ~1.500x10^3 cells/μl for CCRF-CEM. Cells were harvested with centrifugation at 1000 rpm for 10 min. Supernatant was discarded and cells were washed with pre-warmed 1x PBS, re-centrifuged at 1000 rpm for 10 min and pellet was kept for further processing.

extract_protocol: RNA was isolated with TRIzol (Invitrogen Inc., Grand Island NY) according to the manufacturer’s instructions. The amount of RNA isolated was measured with a SmartSpec 3000 spectrophotometer (BioRad, Berkley CA) and RNA integrity was estimated by 2% agarose gel electrophoresis. At least 40 μg of RNA from each sample was used. DNase treatment (RQ1 DNAse, Promega, Fitchburg WI) followed, as described by the manufacturer. Finally, RNA samples were further purified using the RNA-Easy Mini Kit (QIAGEN, Hilden D) and RNA amounts and integrity were determined again as above. Samples with a 1.8 to 2.0 A260/A280 ratio were selected. In addition, those that empirically showed a twice as bright 28S band than the 18S band on the gel were utilized.

treatment_protocol: CCRFCCEM cells were allowed to grow with no further treatments

tag: cell line

value: CCRF-CEM (ALL)

tag: origin

value: was initially obtained from peripheral blood

tag: gender and age

value: 2 year old Caucasian female

tag: diagnosis

value: It was diagnosed as lymphosarcoma which progressed later on to acute leukemia (Foley, Lazarus et al. 1965)

value: The child has undergone irradiation therapy and chemotherapy prior to obtaining the cell line. Although remission was achieved at various stages, the disease progressed rapidly (Foley, Lazarus et al. 1965).

source_name: TE671 human rhabdomyosarcoma cell line

growth_protocol: Both cell lines were seeded at time -24h and left overnight to grow. After 24h (time: 0h) sample was taken from both cell lines in order to perform measurements and every 24h thereafter. TE-671 cells were grown in DMEM (Gibco) medium supplemented with 2 mM L-Glutamine, 10% FBS and 100 U/ml Streptomycin/Penicillin. Cells were allowed to grow to ~80% confluence for TE-671. Cells were harvested at confluence using 0.1% trypsin only for TE-671 and centrifugation at 1000 rpm for 10 min. Supernatant was discarded and cells were washed with pre-warmed 1x PBS, re-centrifuged at 1000 rpm for 10 min and pellet was kept for further processing.

treatment_protocol: TE671 cells were allowed to grow with no further treatments

value: The TE-671 cell line was initially reported to have been obtained from a cerebellar medulloblastoma, before irradiation therapy.

value: a six-year old Caucasian female.

value: initially, cerebellar medulloblastoma, later on it was found to be rhabdomyosarcoma.


title: Human Rectal Adenoma Replicate 3

description: Biological replicate 3 of 8.Human Rectal Adenoma Biopsy Tissue


title: Prostate tumor 81

status: Public on Dec 19 2011

city: Stanford

first: Stephanie

last: Huang

state: CA

address: 269 Campus Drive, CCSR 3240

department: Pathology

institute: Stanford University

description: PC 237T

hyb_protocol: Oligo aCGH hybridization buffer (Agilent) were added along with 50ug Human Cot-1 DNA and 100ug Yeast tRNA, denatured by boiling for 2 mins, incubated at 37C for 30mins, and applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers.

scan_protocol: Scanned on an Agilent G2505C scanner.

data_processing: Agilent Feature Extraction (v.9.5.3) was used to quantify and normalize the data.

source_name: Prostate cancer tissue

label_protocol: 1.5ug of genomic DNA was digested with DpnII for 1.5 hrs at 37C, then labeled with C5 (test) or Cy3 (reference) using the BioPrime array CGH Genomic Labeling Module

extract_protocol: DNA was extracted using the Qiagen Allprep DNA/RNA minikit

tag: pre-psa

tag: tumor stage

tag: gleason grade

tag: psa recurrence-free survival event

tag: psa recurrence-free survival months

tag: Stage

source_name: normal male reference DNA (pooled from eight donor leukocyte preps)

value: reference DNA


title: DSS + MTA rep1

tag: treatment

value: Dextran Sulfate Sodium + Methylthioadenosine

tag: strain

tag: gender


title: Prostate tumor 77

tag: sample type


title: Prostate tumor 76

description: PC 538T


title: Prostate tumor 83

description: PC 352T


title: Prostate tumor 79


title: Prostate tumor 80


title: Prostate tumor 85

description: PC 482T


title: Prostate tumor 84

description: PC 283T


title: Prostate tumor 72

description: PC 599T


title: Prostate tumor 75

description: PC 88T


title: Prostate tumor 74

description: PC 498T


title: Prostate tumor 78


title: Prostate tumor 86


title: Prostate tumor 71

description: PC 626T


title: Prostate tumor 82

description: PC 490T


title: Prostate tumor 67

description: PC 430T


title: Prostate tumor 73

description: PC 619T


title: Prostate tumor 69

description: PC 473T


title: CCRFCEM vs. TE671 Exp1


title: Prostate tumor 66

description: PC 453T


title: Prostate tumor 64

description: PC 480T


title: control 3 (saline-treated at P4 and 7)

value: control


title: Prostate tumor 70

description: PC 604T


title: Prostate tumor 68

description: PC 457T


title: Prostate tumor 60

description: PC 228T


title: Prostate tumor 63

description: PC 252T


title: Prostate tumor 59

description: PC 455T


title: Prostate tumor 62


title: Prostate tumor 61

description: PC 501T


title: Prostate tumor 65


title: Prostate tumor 56

description: PC 398T


title: Prostate tumor 52

description: PC 185T


title: Prostate tumor 57

description: PC 370T


title: Prostate tumor 55

description: PC 366T


title: Prostate tumor 47

description: PC 485T


title: Prostate tumor 43

description: PC 474T


title: Prostate tumor 40

description: PC 45T


title: Prostate tumor 53

description: PC 452T


title: Prostate tumor 51

description: PC 470T


title: Sample-1051-Before

city: buffalo

first: Dan

address: Elm & Carlton Streets

institute: RPCI

hyb_protocol: Labeled RNA were hybridized on Human v2 MicroRNA Expression BeadChips (Cat. no. MI-102–1024; Illumina) according to the manufacturer's recommendations (Illumina MicroRNA Expression Profiling Assay Guide).

scan_protocol: Illumina BeadArray Reader with standard scanning protocol.

data_processing: The data were normalized using quantile normalization with the lumi package in R.

source_name: Serum, baseline

label_protocol: Two hundred ng of total RNA from each sample were labeled according to the manufacturer's recommendations (Illumina MicroRNA Expression Profiling Assay Guide).

extract_protocol: Total RNA, including miRNA from plasma, was isolated using the miRNeasy kit (Qiagen) with minor modifications. The quality and quantity of the RNA was evaluated by 260/280 ratio using NanoDrop spectrophotometry (NanoDrop ND-1000 Technologies Inc.) and the Agilent 2100 Bioanalyzer (Agilent Technologies).

value: female

tag: disease state

value: healthy

value: serum

tag: diet intervention stage

value: before

tag: individual


title: Sample-1051-After

source_name: Serum, post-intervention

tag: tissue

value: after


title: Prostate tumor 44

description: PC 248T


title: Prostate tumor 49

description: PC 15T


title: Prostate tumor 41

description: PC 646T


title: Prostate tumor 42

description: PC 537T


title: Prostate tumor 54

description: PC 184T


title: Prostate tumor 45


title: Prostate tumor 35

description: PC 367T


title: Sample-1045-After


title: Prostate tumor 39

description: PC 265T


title: Prostate tumor 46

description: PC 274T


title: Prostate tumor 58

description: PC 477T


title: Prostate tumor 50

description: PC 242T


title: Prostate tumor 31

description: PC 85T


title: Prostate tumor 36

description: PC 97T


title: Prostate tumor 34

description: PC 86T


title: Prostate tumor 32

description: PC 623T


title: Prostate tumor 38

description: PC 540T


title: Sample-1045-Before


title: Prostate tumor 30

description: PC 362T


title: Prostate tumor 27

description: PC 348T


title: Sample-1041-Before


title: Sample-1041-After


title: Sample-1033-After


title: Sample-1039-After


title: Sample-1039-Before


title: Prostate tumor 28

description: PC 575T


title: Sample-1032-After


title: Sample-1032-Before


title: Prostate tumor 24

description: PC 84T


title: Prostate tumor 23

description: PC 405T


title: Prostate tumor 22

description: PC 629T


title: Sample-1031-After


title: Prostate tumor 25

description: PC 21T


title: Sample-1031-Before


title: Prostate tumor 37

description: PC 375T


title: Prostate tumor 20

description: PC 645T


title: Prostate tumor 29

description: PC 19T


title: Prostate tumor 26

description: PC 167T


title: Prostate tumor 18

description: PC 159T


title: Prostate tumor 21

description: PC 579T


title: Prostate tumor 33

description: PC 188T


title: Prostate tumor 17

description: PC 47T


title: Prostate tumor 16

description: PC 551T


title: Sample-1033-Before


title: Sample-1027-After


title: Sample-1027-Before


title: Sample-1021-After


title: Sample-1017-After


title: Sample-1021-Before


title: Prostate tumor 19

description: PC 99T


title: Sample-1017-Before


title: Sample-1012-After


title: Prostate tumor 11

description: PC 634T


title: Sample-1007-After


title: Sample-1012-Before


title: Prostate tumor 13

description: PC 563T


title: Prostate tumor 12

description: PC 616T


title: Prostate tumor 8

description: PC 45T

scan_protocol: Scanned on an Agilent G2505C scanner

data_processing: Agilent Feature Extraction (v.9.5.3)

label_protocol: .5ug of genomic DNA was digested with DpnII for 1.5 hrs at 37C, then labeled with C5 (test) or Cy3 (reference) using the BioPrime array CGH Genomic Labeling Module

tag: psa-recurrence free survival outcome

tag: psa-recurrence free survival (months)


title: Prostate tumor 7

description: PC 248T


title: Prostate tumor 14

description: PC 636T


title: Sample-1007-Before


title: Prostate tumor 5

description: PC 166T


title: Prostate tumor 6

description: PC 362T


title: Sample-1005-After


title: Prostate tumor 8

description: PC 627T


title: Prostate tumor 9

description: PC 343T


title: Prostate tumor 4

description: PC 184T


title: Prostate tumor 10

description: PC 491T


title: RWPE1 shRNA #1

hyb_protocol: Agilent HI-RPM Hybridization buffer was added to 1ug each of Cy3 and Cy5 labeled cDNA, boiled, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers

source_name: RWPE-1 cells with CHD1 shRNA #1 knockdown

label_protocol: 10ug of total RNA was reverse transcribed and labeled using the Fairplay III Microarray Labeling kit

growth_protocol: Cells were grown in regular media for OPCN2 and RWPE1.  For LNCaP, cells were grown in phenol-red free RPMI + 10% charcoal treated FBS. The +R1881 samples were stimulated with 1nM R1881.

extract_protocol: RNA was extracted using Qiagen Rneasy Mini kit

treatment_protocol: OPCN2 and RWPE-1 cells were infected with CHD1 shRNA and grown under puromycin selection for 2 weeks.  LNCaP were transfected with CHD1 pool siRNA

tag: cell line

source_name: RWPE-1 cells with non-targeted shRNA knockdown


title: RWPE1 shRNA #2

source_name: RWPE-1 cells with CHD1 shRNA #2 knockdown


title: RWPE1 shRNA #1-2

source_name: RWPE-1 cells with non-targeted shRNA


title: RWPE1 shRNA #2-2


title: Prostate tumor 7

description: PC 593T

tag: pre-psa


title: Prostate tumor 5

description: PC 643T

tag: tumor stage


title: Prostate tumor 6

description: PC 621T

tag: gleason grade


title: Prostate tumor 15

description: PC 594T

tag: psa recurrence-free survival event


title: Sample-1002-Before


title: Sample-1005-Before


title: Sample-1002-After


title: Prostate tumor 2

description: PC 490T


title: OPCN2 shRNA #1-2

source_name: OPCN2 cells with non-targeted shRNA

source_name: OPCN2 cells with CHD1 shRNA #1 knockdown


title: Prostate tumor 3

description: PC 453T


title: OPCN2 shRNA #2-2

source_name: OPCN2 cells with CHD1 shRNA #2 knockdown


title: OPCN2 shRNA #2

source_name: OPCN2 cells with non-targeted shRNA knockdown


title: LNCaP CHD1 +R1881

source_name: LNCaP cells with CHD1 siRNA knockdown +R1881

value: LNCaP

tag: growth condition

value: cells were grown in phenol-red free RPMI with 10% charcoal stripped FBS and were stimulated with 1nM R1881

source_name: LNCaP cells with non-targeted siRNA knockdown +R1881


title: Prostate tumor 2

description: PC 648T

tag: psa recurrence-free survival months

tag: Stage


title: OPCN2 shRNA #1


title: Prostate tumor 4

description: PC 625T


title: Prostate tumor 1

description: PC 555T


title: Prostate tumor 3

description: PC 582T


title: Prostate tumor 1

description: PC 538T


title: Wild type mammary fibroblasts, biological replicate 1

status: Public on Dec 18 2011

city: Columbus

first: Julie

last: Wallace

state: OH

address: 460 W. 12th Ave 840 BRT

institute: OSUCCC

description: Gene expression data from wild type mammary fibroblasts

hyb_protocol: Following fragmentation, 15ug of cRNA was hybridized for 16 hours at 45°C on Affymetrix Mouse Exon 1.0 ST Array GeneChips.  GeneCHips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetric GeneChip Scanner 3000

data_processing: Data were processed using Affymetrix Expression Console software. Robust Multichip Average (RMA) method was used to do background correction, quantile normalization, and expression level summarization.

source_name: wild type mammary fibroblasts

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 1ug total RNA (Expression Analysis Technical Manual, 2005, Affymetrix)

growth_protocol: Fibroblasts and epithelial cells were cultured using a modified protocol for gravity separation.  Endothelial cells were directly isolated from tissue using FACS

treatment_protocol: Fibroblasts and epithelial cells were grown in 10% FBS DMEM in a 37° incubator with 7% CO2

tag: strain

value: FVBN

tag: age

value: 9 weeks

value: Mammary gland

tag: genotype/variation

value: PtenloxP/loxP


title: Pten null mammary fibroblasts, biological replicate 2

description: Gene expression data from Pten null mammary fibroblasts

source_name: Pten null mammary fibroblasts

value: FspCre;PtenloxP/loxP


title: Prostate tumor 48

description: PC 448T

tag: sample type


title: Wild type mammary endothelial cells, biological replicate 1

description: Gene expression data from wild type mammary endothelial cells

source_name: wild type mammary endothelial cells


title: LNCaP CHD1 -R1881

source_name: LNCaP cells with CHD1 siRNA knockdown -R1881

value: cells were grown in the absence of androgen stimulation

source_name: LNCaP cells with non-targeted siRNA knockdown -R1881


title: Wild type mammary endothelial cells from mouse with Pten null fibroblasts, biological replicate 2

description: Gene expression data from mammary endothelial cells from a mouse with Pten null fibroblasts


title: Wild type mammary endothelial cells from mouse with Pten null fibroblasts, biological replicate 1

source_name: mammary endothelial cells from a mouse with Pten null fibroblasts


title: Wild type mammary epithelial cells, biological replicate 1

description: Gene expression data from wild type mammary epithelial cells

source_name: wild type mammary epithelial cells


title: Wild type mammary fibroblasts, biological replicate 2


title: Wild type mammary epithelial cells, biological replicate 2


title: Wild type mammary epithelial cells from mouse with Pten null fibroblasts, biological replicate 2

description: Gene expression data from mammary epithelial cells from a mouse with Pten null fibroblasts


title: Wild type mammary endothelial cells, biological replicate 2


title: Pten null mammary fibroblasts, biological replicate 1


title: Wild type mammary epithelial cells from mouse with Pten null fibroblasts, biological replicate 1

source_name: mammary epithelial cells from a mouse with Pten null fibroblasts


title: 28d_C57_Air_57_blood

city: Morgantown

first: Patti

middle: Christine

last: Zeidler-Erdely

state: WV

address: 1095 Willowdale Road

department: HELD

institute: CDC/NIOSH

description:
4560232062_A
replicate 1

hyb_protocol: 20 hour hybridization period at 58°C

scan_protocol: Illumina BeadStation 500G - BeadArray Reader standard

data_processing: Force positive background correction, variance stabilizing transformation, robust spline normalization

source_name: blood

label_protocol: Illumina TotalPrep RNA Amplification Kit (Applied Biosystems Inc., Foster City, CA, Catalog #AMIL1791)

extract_protocol: Lung RNA isolated from whole lung homogenates using the TRIzol method and cleaned with a Rneasy Mini Kit. Aorta was homogenized with a Qiagen Tissue Lyser and RNA was isolated using the Rneasy fibrous mini kit. Whole blood RNA was isolated using the Mouse RiboPure Blood RNA Isolation Kit and globin RNA was removed using the GLOBINclear kit.

treatment_protocol: Mice were exposed to either air or gas metal arc-stainless steel welding fume for 10 days (3 hours/day) at 40 mg/m3

tag: exposure

value: Air

tag: recovery time


title: 4hr_C57_GSS_62_blood

description:
4560232069_F
replicate 2

value: GMA-SS


title: 28d_C57_Air_58_blood

description:
4560232062_B
replicate 2


title: 28d_C57_Air_60_blood

description:
4560232062_D
replicate 4


title: 28d_C57_GSS_77_blood

description:
4560232062_E
replicate 1


title: 28d_C57_GSS_79_blood

description:
4560232062_G
replicate 3


title: 4hr_C57_GSS_63_blood

description:
4560232069_G
replicate 3


title: 4hr_C57_GSS_61_blood

description:
4560232069_E
replicate 1


title: 4hr_C57_Air_45_blood

description:
4560232069_D
replicate 4


title: 28d_C57_GSS_80_blood

description:
4560232062_H
replicate 4


title: 28d_C57_Air_59_blood

description:
4560232062_C
replicate 3


title: 4hr_C57_Air_43_blood

description:
4560232069_C
replicate 3


title: malignant mesothelioma, Y-MESO-27

city: Nagoya

first: Futoshi

last: Ishiguro

address: 1-1 Kanokoden, Chikusa-ku

department: Molecular Oncology

country: Japan

institute: Aichi Cancer Center Research Institute

description: Biological replicate 17 of 20. malignant mesothlioma cell lines, harvested after several passages.

hyb_protocol: Scanned on an Agilent G2505B scanner.

scan_protocol: Images were quantified using Agilent Feature Extraction Software (version A.9.5.1.1).

data_processing: Scanned images were analyzed with the Agilent Feature Extraction Program ver. 10.7.

source_name: human malignant mesothlioma

label_protocol: The cRNA from MM cell lines or reference samples were labeled with Cy5-CTP or Cy3-CTP fluorophores, respectively. 825 ng of each labeled cRNA was mixed, and hybridizations were performed on 4×44 K oligonucleotide-based whole human genome microarrays (Agilent Technologies) at 65oC for 17 hours. After hybridization, arrays were washed.

growth_protocol: Cells were seeded on flat-bottomed 24-well plates and grown in RPMI1640 medium with 10% FCS.

extract_protocol: Total RNA was prepared using RNeasy Plus RNA extraction kit (Qiagen K.K.) according to the manufacturer's protocol. By using 150 ng of total RNA, cRNA was generated and labeled with the Low Input Quick Amp Labeling Kit (Agilent Technologies) according to the manufacturer’s instructions.

treatment_protocol: After 90 hours, total RNA was extracted following manufacturer's instructions

tag: tissue

value: malignant meshelioma

source_name: normal mesothelial cells

value: normal mesothelial cells


title: malignant mesothelioma, Y-MESO-28

description: Biological replicate 18 of 20. malignant mesothlioma cell lines, harvested after several passages.


title: malignant mesothelioma, Y-MESO-22

description: Biological replicate 14 of 20. malignant mesothlioma cell lines, harvested after several passages.


title: 28d_C57_GSS_78_blood

description:
4560232062_F
replicate 2


title: malignant mesothelioma, Y-MESO-26B

description: Biological replicate 16 of 20. malignant mesothlioma cell lines, harvested after several passages.


title: 4hr_C57_Air_41_blood

description:
4560232069_A
replicate 1


title: 4hr_C57_GSS_103_lung

description:
4320221051_H
replicate 4

source_name: lung


title: malignant mesothelioma, Y-MESO-30

description: Biological replicate 20 of 20. malignant mesothlioma cell lines, harvested after several passages.


title: malignant mesothelioma, Y-MESO-21

description: Biological replicate 13 of 20. malignant mesothlioma cell lines, harvested after several passages.


title: malignant mesothelioma, Y-MESO-29

description: Biological replicate 19 of 20. malignant mesothlioma cell lines, harvested after several passages.


title: malignant mesothelioma, NCI-H2452

description: Biological replicate 9 of 20. malignant mesothlioma cell lines, harvested after several passages.