title: OvaryTiling_mRNA_rep2

description: Differential mRNA expression of upSET mutan ovaries vs wildtype.

data_processing: Raw signals of corresponding experimental replicates were loess normalized within arrays and quantile normalized between arrays. Enrichment statistics (test versus control signals) were computed using the ‘sam’ algorithm within Bioconductor . Fdr values of the sam statistic were determined using ‘locfdr’ . Region summarization was performed using the HMM algorithm of TileMap . Probes were considered to be bound significantly if the posterior probability of the HMM was greater than 0.9.

source_name: mRNA Tiling for upSET mutant ovary

label_protocol: 3 µg cDNA was directly labeled by Klenow (New England Biolabs) random priming with Cy5 nonamers (upSET mutant fly ovaries) or with Cy3 nonamers (wildtype fly ovaries) per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

growth_protocol: Flies were fattened with yeast and molase media for 2 days

extract_protocol: Flies were fattened for 2-Day old wildtype after eclosion, Ovaries from wildtype and mutant flies were dissected in in CCM3 media and wash twice in PBS. Total RNA was extracted with Trizol and DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen). RNA quality and concentration was determined by analysis with an Agilent 2100 bioanalyzer at the Harvard-Partners Center for Genetics and Genomics (Harvard Medical School, Cambridge, MA USA). 2 micrograms of total RNA was reverse transcribed and treated with RNase H.

value: upSET mutant

value: 2-day old flies

value: ovary

source_name: mRNA Tiling for wildtype mutant ovary

value: wild type


title: OvaryTiling_mRNA_rep1

status: Public on Dec 07 2012

type: RNA

city: Seattle

first: Hector

last: Rincon-Arano

state: Washington

address: 1100 Fairview Ave N

department: Basic Science Division

country: USA

institute: Fred Hutchinson Cancer Research Center

hyb_protocol: The labeled DNA was precipitated with 0.1 volume 5M NaCl and 1 volume isopropanol, and hybridized in 45 ul of buffer containing 20% formamide, 1.2 M betaine, 0.1 ug/ul herring sperm DNA and 10 ug of human COT1 DNA (Invitrogen). Arrays were hybridized in Maui hybridization stations for 16-18 h at 42C, and then washed in 42C 0.2% SDS/0.2x SSC, room temperature 0.2x SSC, and 0.05x SSC. Hybridization buffers and washes were completed using manufacturer's protocols (http://www.nimblegen.com/products/lit/lit.html)

scan_protocol: Arrays were scanned on an Axon 4000B scanner per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

data_processing:
FRaw signals of corresponding experimental replicates were loess normalized within arrays and quantile normalized between arrays. Enrichment statistics (test versus control signals) were computed using the ‘sam’ algorithm within Bioconductor . Fdr values of the sam statistic were determined using ‘locfdr’ . Region summarization was performed using the HMM algorithm of TileMap . Probes were considered to be bound significantly if the posterior probability of the HMM was greater than 0.9 .
value definition (in the nomalized/processed data file):  Log 2 ratio (upSET mutant vs wild type)

molecule: total RNA

organism: Drosophila melanogaster

tag: genotype/variation

tag: age

tag: tissue

label_protocol: 3 µg cDNA was directly labeled by Klenow (New England Biolabs) random priming with Cy5 hexamers (UpSET mutant fly ovaries) or with Cy3 nonamers (wildtype fly ovaries) per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).


title: Rotem Number Rip Chip 1 4-10-09

city: Bethesda

first: Andrei

middle: Nikolai

last: Trostel

state: Maryland

address: 9000 Rockville Pike, Building 37, Room 5138

department: Laboratory of Molecular Biology

institute: National Institutes of Health

hyb_protocol: Tilling array chips on which the complete Escherichia coli MG1655 genome sequence is represented were used (E. coli_Tab520346F; Affymetrix, Santa Clara, CA). The RNA samples were hybridized directly to the oligonucleotide arrays with no prior labelling or cDNA synthesis. The RNA samples were added to the hybridization solution [1x MES (100 mM MES, 1 M NaCl, 20 mM EDTA, 0.01% Tween 20, pH 6.6), 0.1 mg ml-1 herring sperm DNA, 0.5 mg ml-1 BSA and 50 pM of the control Biotinoligonucleotide B2 (GeneChip® Expression Analysis Technical Manual)], heated to 99oC for 5 minutes and then incubated at 45oC for an additional 5 minutes before being placed in the microarray cartridge. Hybridization was carried out at 45oC for 16 hours on a rotary mixer at 60 r.p.m. Following hybridization, the sample solution was removed and the array was washed as recommended in the technical manual (Affymetrix).

scan_protocol: Arrays were scanned on an GeneChip© Scanner 3000 per manufacturer’s protocol.

data_processing:
The program used to generate the bed/bar files is Affymetrix Tiling Analysis Software.
pvalue.bar files also provided
.bar files are generated using Affymetrix Tiling Analysis Software.
The TAS software provides analysis capabilities specifically for the GeneChip Tiling Arrays. TAS analyzes feature intensity data stored in GCOS output .CEL files and produces:
Signal and p-values for each genomic position interrogated.
Computation of genomic intervals based on computed signal and p-values
Computation of summary statistics
Visualizations for assessing the quality of the array data

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM707nnn/GSM707222/suppl/GSM707222_Rotem Number Rip Chip 1 4-10-09 minus_pvalue.bar.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM707nnn/GSM707222/suppl/GSM707222_Rotem Number Rip Chip 1 4-10-09 plus_pvalue.bar.gz

label: biotin

organism: Escherichia coli

source_name: Total input

label_protocol: Hybridization was assayed using antibodies specific to the RNA:DNA hybrid and the Digene HC ExpressArray™ Kit (Digene, Gaithersburg, MD). This antibody is not a commercially available since it was developed for experimental research purposes. 25 ml of an RNA:DNA polyclonal antibody (1.3 mg ml-1) was resuspended in 475 ml of matrix solution, loaded on the array and incubated at 25oC for 20 minutes. After removal of the first antibody stain and 10 wash cycles, the array was incubated with the second antibody stain, containing 0.036 mg ml-1 biotin rabbit anti-goat IgG and 0.4 mg ml-1 rabbit IgG in 1x MES. Then, the RNA:DNA hybrids then were fluorescently labelled by incubating with 10 mg ml-1 streptavidin-phycoerythrin (Molecular Probes, Eugene, OR) and 2 mg ml-1 BSA in 1x MES. Hybridized, washed and stained tilling arrays were scanned using a Genechip Scanner 3000 (Affymetrix).

growth_protocol: Cells of E .coli MG1655 derivative with eight myc tags fused to Hub were grown in M63 medium supplemented with 0.2% glucose, 0.1% casaminoacids and 0.002% vitamin B1 at 37oC to exponential phase (OD600 = 0.4).

extract_protocol: Immunoprecipitation reaction consisted of 20 ml anti-myc antibody, 15 mg of protein-A-sepharose (Amersham Biosciences, Piscataway, NJ) and 400 ml of cell extract. RNA was isolated from immunoprecipitated pellets by RNaeasy kit (Qiagen). The RNA pellet was dissolved in DEPC H2O.

tag: strain


title: 2091 mir22 rep6

city: Austin

first: Vishy

last: Iyer

state: TX

address: 2500 Speedway Dr. MBB 3.212

department: Molecular Biosciences

institute: University of Texas at Austin

hyb_protocol: Hybridizations were performed in humidity chambers (Corning) at 65 degrees C for 16 hours.

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with a GenePix 4000A/4000B fluorescent scanner and image intesnity data were extracted and analyzed with GenePix Pro 4.0/5.0 analysis software.

data_processing: After background correction and removal of flagged values, log base 2 expression ratios were mean centered and linear transformed to obtain the log values given in the data table.

organism: Homo sapiens

source_name: Quiescent human 2091 fibroblasts - Control

label_protocol: Amino allyl Cy3 or Cy5

growth_protocol: 2091 cells were serum starved 48 hours.  Cells were collected 24 hours after transfection

extract_protocol: 24 hours after transfection, cells were harvested with TRIzol and total RNA was extracted according to the manufacturers protocol

treatment_protocol: 2091 cells were transfected with either 100nM miR-22 RNA duplexes or control transfected

tag: cell type

value: Quiescent primary human 2091 fibroblasts

tag: treatment

value: control transfection

source_name: Quiescent human 2091 fibroblasts - miR-22

value: miR-22 transfection


title: AR0757_05 NPC1B

city: Takatsuki

first: Hisato

last: Kondoh

state: Osaka

address: Murasakicho 1-1

country: Japan

institute: Biohistory Research Hall

description: Gene expression in NPC1

hyb_protocol: 0.6 ug of Cy3-labeled cRNA was hybridized a 65°C for 17 hr using Gene Expression Hybridization Kit (Agilent) and washied using Gene Expression Wash Buffers Pack Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565A).

data_processing: The scanned images were analyzed with an Agilent Feature Extraction Software to obtain background subtracted and spatially detrented Processed Signal intensities.

organism: Mus musculus

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng RNA using Low Input Quick Amp Labeling kit, one color (Agilent) with fragmentation at 60°C for 30 min, according to the manufacturer's instruction.

growth_protocol: Epiblast stem cells (EpiSCs) were placed in the epiblastic cell maintenance condition (EpiSC) or in a neural plate developmental condition (Iwafuchi-Doi et al. Dev Biol 352, 354-366, 2011) for one (NPC1) or two (NPC2) days.

extract_protocol: Total RNAs were extracted using TRI Reagent (Sigma-Aldrich) according to the manufacturer's instructions.

value: EpiSCs

tag: culture condition

value: EpiSC under NPC condition 1 day


title: 2091 mir22 rep5


title: Uveal melanoma from enucleation 79 [RPCI]

status: Public on Dec 06 2012

type: genomic

city: Saint Louis

first: Michael

middle: D

last: Onken

state: MO

address: 660 S. Euclid Ave

department: Biochemistry & Molecular Biophysics

institute: Washington University School of Medicine

hyb_protocol: DNA was hybridized to the arrays for 16 hours at 55°C using a GeneTAC hybridization station (Genomic Solutions, Inc.).

scan_protocol: The hybridized aCGH slides were then scanned using a GenePix 4200A Scanner (Molecular Devices) to generate images for both Cy3 (test) and Cy5 (control) channels. Image analysis was performed using the ImaGene (version 6.0.1) software from BioDiscovery, Inc.

data_processing: A loess corrected log2 ratio of the background subtracted test/control was calculated for each clone to compensate for non-linear raw aCGH profiles in each sample.

molecule: genomic DNA

source_name: Uveal melanoma from enucleation 79

label_protocol: 1μg of reference and test sample genomic DNA were individually fluorescently labeled using the BioArray CGH Labeling System following manufacturer's protocol.

extract_protocol: Genomic DNA was prepared using the Wizard Genomic DNA purification kit (Promega).

value: Fresh frozen sample from enucleated eye

tag: disease

value: Primary uveal melanoma tumor

tag: gep class

source_name: Normal Human Male Reference DNA

tag: reference

value: Normal Human Male Reference DNA


title: AR0757_01 EpiSCA

description: Gene expression in EpiSC

source_name: EpiSCA

value: EpiSC under epiblastic condition


title: AR0757_04 EpiSCB

description: Gene expression in EpiSC

source_name: EpiSCB


title: Uveal melanoma from enucleation 78 [RPCI]

source_name: Uveal melanoma from enucleation 78


title: Uveal melanoma from enucleation 89 [RPCI]

source_name: Uveal melanoma from enucleation 89


title: Uveal melanoma from enucleation 77 [RPCI]

source_name: Uveal melanoma from enucleation 77


title: AR0757_02 NPC1A

description: Gene expression in NPC1


title: Uveal melanoma from enucleation 87 [RPCI]

source_name: Uveal melanoma from enucleation 87


title: Uveal melanoma from enucleation 88 [RPCI]

source_name: Uveal melanoma from enucleation 88


title: Uveal melanoma from enucleation 93 [RPCI]

source_name: Uveal melanoma from enucleation 93


title: AR0757_03 NPC2A

description: Gene expression in NPC2

value: EpiSC under NPC condition 2 days


title: Uveal melanoma from enucleation 90 [RPCI]

source_name: Uveal melanoma from enucleation 90


title: Uveal melanoma from enucleation 86 [RPCI]

source_name: Uveal melanoma from enucleation 86


title: Uveal melanoma from enucleation 91 [RPCI]

source_name: Uveal melanoma from enucleation 91


title: 2091 mir22 rep7


title: Uveal melanoma from enucleation 81 [RPCI]

source_name: Uveal melanoma from enucleation 81


title: Uveal melanoma from enucleation 83 [RPCI]

source_name: Uveal melanoma from enucleation 83


title: Uveal melanoma from enucleation 92 [RPCI]

source_name: Uveal melanoma from enucleation 92


title: Uveal melanoma from enucleation 80 [RPCI]

source_name: Uveal melanoma from enucleation 80


title: Uveal melanoma from enucleation 82 [RPCI]

source_name: Uveal melanoma from enucleation 82


title: 2091 mir22 rep8

source_name: Quiescent human 2091 fibroblasts - Control

source_name: Quiescent human 2091 fibroblasts - miR-22


title: Uveal melanoma from enucleation 76 [RPCI]

source_name: Uveal melanoma from enucleation 76

source_name: Normal Human Male Reference DNA


title: Uveal melanoma from enucleation 74 [RPCI]

source_name: Uveal melanoma from enucleation 74


title: Uveal melanoma from enucleation 72 [RPCI]

source_name: Uveal melanoma from enucleation 72


title: Uveal melanoma from enucleation 66 [RPCI]

source_name: Uveal melanoma from enucleation 66


title: Uveal melanoma from enucleation 70 [RPCI]

source_name: Uveal melanoma from enucleation 70


title: Uveal melanoma from enucleation 71 [RPCI]

source_name: Uveal melanoma from enucleation 71


title: Uveal melanoma from enucleation 64 [RPCI]

source_name: Uveal melanoma from enucleation 64


title: Uveal melanoma from enucleation 57 [RPCI]

source_name: Uveal melanoma from enucleation 57


title: Uveal melanoma from enucleation 53 [RPCI]

source_name: Uveal melanoma from enucleation 53


title: Uveal melanoma from enucleation 65 [RPCI]

source_name: Uveal melanoma from enucleation 65


title: Uveal melanoma from enucleation 38 [RPCI]

source_name: Uveal melanoma from enucleation 38


title: Uveal melanoma from enucleation 31 [RPCI]

source_name: Uveal melanoma from enucleation 31


title: INPUT_I vs MeDIP_I

city: Lyon

first: François

last: ROUDIER

address: 46 Allée d'Italie

department: Biologie

country: France

institute: Ecole Normale Supérieure de Lyon

description: DNA methylation profiling

hyb_protocol: Co-hybridization was performed using the NimbleGen 3x720K array design and following manufacturer’s instructions

scan_protocol: Data acquisition was performed according to Roche Nimblegen instructions.

data_processing: Hybridization data were normalized using an ANOVA model to remove technical biases.

organism: Arabidopsis thaliana

label_protocol: Cy3 and Cy5 labeling were performed using the Nimblegen Dual color DNA labeling kit (Roche NimbleGen) according to manufacturer’s instructions, amplification=yes, DNA recovered after MeDIP and directly from input chromatin was amplified using the Sigma GenomePlex Complete Whole Genome Amplification (WGA) Kit following instructions of the manufacturer.

growth_protocol: Primary root of 7 day-old plants grown in 0.5X MS agar plates; 1% sucrose, 16 hours photoperiod.

extract_protocol: DNA was extracted using the Qiagen MaxiPrep kit (Qiagen) and sonicated using a Diagenode Bioruptor. Immunoprecipitation was done on 1.5µg of DNA (IP fraction) and 150ng serves as INPUT DNA. First, IP fraction was denaturated by incubating 10 minutes at 95°C and 2 minutes on ice in 600µl of buffer 1 (10 mM Tris HCl pH 7.5, 500 mM NaCl, 1 mM EDTA). Immunoprecipitation was performed by adding 5µg of 5mC antibody (Diagenode, cat n° MAb-006-500) to denatured IP fraction and incubating overnight at 4°C with gentle agitation. Forty microliters of washed M280 Dynabeads (Invitrogen) were added to the IP fraction and incubated at 4°C for 4 hr with gentle agitation. Supernatant was collected in a new tube (Supernatant fraction). Three hundred microliters of buffer 1 were added to IP tube and incubated 10 min at room temperature with gentle agitation. This first wash was added to Supernatant fraction. Then IP fraction was washed three times by gentle mixing for 10 min at room temperature with 600 ml of buffer 1. To elute, IP fraction was incubated 1 hour at 42°C with 300µl of buffer 2 (30mM Tris HCl pH: 8.0) and 7µl of Proteinase K (NEB, 20µg/µl). DNA from the Supernatant an IP fractions was recovered by phenol-chloroform extraction and ethanol precipitation.

treatment_protocol: no treatment

tag: ecotype

value: 7 days

value: primary root

tag: antibody

tag: vendor

value: Diagenode

tag: catalog#

label_protocol: Cy3 and Cy5 labeling were performed using the Nimblegen Dual color DNA labeling kit (Roche NimbleGen) according to manufacturer’s instructions, amplification=yes, DNA recovered after MeDIP and directly from input DNA was amplified using the Sigma GenomePlex Complete Whole Genome Amplification (WGA) Kit following instructions of the manufacturer.

value: none (input)


title: INPUT_II vs MeDIP_II

description: DNA methylation profiling

data_processing: Hybridization data were normalized using an ANOVA model to remove technical biases. Data were averaged on the dye-swap to remove tile-specific dye biases. Normalized data were analysed under stringent criteria using Parsimonious Higher-Order Hidden Markov Models (www.jstacs.de/index.php/PHHMM). Adjacent tiles are joined into domains by requiring a minimal run of 400 bp and allowing a maximal gap of 200 bp.


title: MeDIP_II vs INPUT_II

description: DNA methylation profiling


title: MeDIP_I vs INPUT_I

description: DNA methylation profiling

label_protocol: Cy3 and Cy5 labeling were performed using the Nimblegen Dual color DNA labeling kit (Roche NimbleGen) according to manufacturer’s instructions, amplification=yes, DNA recovered after MeIP and directly from input DNA was amplified using the Sigma GenomePlex Complete Whole Genome Amplification (WGA) Kit following instructions of the manufacturer.


title: Genomic DNA from colon biopsy 55

city: Moscow

first: Vladimir

last: Naumov

address: Malaya Pirogovskaya 1a

department: Molecular Biology

country: Russia

institute: Research Institute of Physico-Chemical Medicine

description: Colon adenocarcinoma.

hyb_protocol: Bisulphite-converted DNA was amplified, fragmented and hybridised to Illumina HumanMethylation450 Beadchips using the standard Illumina protocol.

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

data_processing: GenomeStudio Software v2011.1. Average Beta values were normalized using internal controls.

label: Cy5 and Cy3

source_name: colon biopsy, adenocarcinoma

label_protocol: Standard Illumina protocol.

extract_protocol: Genomic DNA was extracted and purified from frozen samples using Qiagen.

value: colon adenocarcinoma

tag: cancer patient

value: yes

tag: sample name


title: Uveal melanoma from enucleation 85 [RPCI]

source_name: Uveal melanoma from enucleation 85


title: Uveal melanoma from enucleation 94 [RPCI]

source_name: Uveal melanoma from enucleation 94


title: Genomic DNA from colon biopsy 59

description: Colon adenocarcinoma.


title: Genomic DNA from colon biopsy 56

description: Colon adenocarcinoma.


title: Genomic DNA from colon biopsy 53

description: Colon adenocarcinoma.


title: Genomic DNA from colon biopsy 52

description: Colon adenocarcinoma.


title: Genomic DNA from colon biopsy 54

description: Colon adenocarcinoma.


title: Genomic DNA from colon biopsy 57

description: Colon adenocarcinoma.


title: Genomic DNA from colon biopsy 50

description: Colon adenocarcinoma.


title: Genomic DNA from colon biopsy 63

description: Colon adenocarcinoma.


title: Genomic DNA from colon biopsy 60

description: Colon adenocarcinoma.


title: Genomic DNA from colon biopsy 58

description: Colon adenocarcinoma.


title: Genomic DNA from colon biopsy 61

description: Colon adenocarcinoma.


title: Genomic DNA from colon biopsy 62

description: Colon adenocarcinoma.


title: Genomic DNA from colon biopsy 47

description: Colon adenocarcinoma.


title: Genomic DNA from colon biopsy 51

description: Colon adenocarcinoma.


title: Genomic DNA from colon biopsy 49

description: Colon adenocarcinoma.


title: Genomic DNA from colon biopsy 43

description: Colon adenocarcinoma.


title: Genomic DNA from colon biopsy 44

description: Colon adenocarcinoma.


title: Genomic DNA from colon biopsy 42

description: Colon adenocarcinoma.


title: Genomic DNA from colon biopsy 38

description: Normal colon (from cancer patient).

source_name: colon biopsy, from cancer patient, normal

value: normal colon


title: Genomic DNA from colon biopsy 46

description: Colon adenocarcinoma.


title: Genomic DNA from colon biopsy 36

description: Normal colon (from cancer patient).


title: Genomic DNA from colon biopsy 48

description: Colon adenocarcinoma.


title: Genomic DNA from colon biopsy 45

description: Colon adenocarcinoma.


title: Genomic DNA from colon biopsy 39

description: Normal colon (from cancer patient).


title: Genomic DNA from colon biopsy 37

description: Normal colon (from cancer patient).


title: Genomic DNA from colon biopsy 27

description: Normal colon (from cancer patient).


title: Genomic DNA from colon biopsy 33

description: Normal colon (from cancer patient).


title: Genomic DNA from colon biopsy 34

description: Normal colon (from cancer patient).


title: Genomic DNA from colon biopsy 35

description: Normal colon (from cancer patient).


title: Genomic DNA from colon biopsy 40

description: Normal colon (from cancer patient).


title: Genomic DNA from colon biopsy 41

description: Normal colon (from cancer patient).


title: Genomic DNA from colon biopsy 29

description: Normal colon (from cancer patient).


title: Genomic DNA from colon biopsy 19

description: Normal colon (cancer unrelated).

source_name: colon biopsy, normal

value: no


title: Genomic DNA from colon biopsy 23

description: Normal colon (from cancer patient).


title: Genomic DNA from colon biopsy 32

description: Normal colon (from cancer patient).


title: Genomic DNA from colon biopsy 26

description: Normal colon (from cancer patient).


title: Genomic DNA from colon biopsy 22

description: Normal colon (from cancer patient).


title: Genomic DNA from colon biopsy 30

description: Normal colon (from cancer patient).


title: Genomic DNA from colon biopsy 15

description: Normal colon (cancer unrelated).


title: Genomic DNA from colon biopsy 18

description: Normal colon (cancer unrelated).


title: 36hr ttk^twk/ttk^twk ovary, biological rep2

first: Nathaniel

last: Peters

department: Genome Sciences

institute: University of Washington

description: Gene expression data from ttktwk/ttktwk ovaries containing egg chambers undergoing defective DA tube expansion

hyb_protocol: Following fragmentation, 10ug of labeled aRNA was hybridized for 16hr at 45C on GeneChip Drosophila2.0 Arrays. GeneChips were washed and stained in an Affymetrix Fluidics Station FS450.

scan_protocol: GeneChips were scanned using an Affymetrix 3000 7G scanner.

data_processing: The data were analyzed using GeneChip® Operating Software (GCOS) and the Microarray Suite 5.0 (MAS 5.0) algorithm.  Expression Console (Affymetrix) was used for robust multichip analysis (RMA) normalization.  Multi Experiment Viewer (MeV version 10.2) software and significance analysis of microarrays (SAM) analysis identify statisically significant differential gene expression in the ttktwk mutant relative to wild type.

source_name: Drosophila ovaries containing egg chambers undergoing defective DA tube expansion

label_protocol: Biotinylated aRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA (GeneChip® 3’ IVT Express Kit Manual, 2008, Affymetrix).

growth_protocol: Female flies from Canton S (wild type) and ttktwk (twin peaks; mutant) backgrounds were aged for 36 hours at 25C in the presence of wet yeast.

extract_protocol: Total RNA extraction was performed using the RNAqueous Kit (Ambion) according to the manufacturer's instruction.

treatment_protocol: Ovaries were dissected into EBR buffer from 50 female flies within 20 min, and, as they were dissected, washed in clean EBR buffer and transferred into RNALater (Ambion) in a 5mL glass dounce homogenizer.  At the completion of dissection for a given sample, RNALater was removed, lysis buffer from the RNAqueous kit (Ambion) was added, and samples were mechanically homogenized.

value: whole ovary

tag: genotype

value: rosy ttk^twk/ttk^twk

tag: gender

value: female

tag: genetic background

value: Canton S

value: ovaries dissected at 36hr post-eclosion


title: Genomic DNA from colon biopsy 25

description: Normal colon (from cancer patient).

tag: tissue


title: Genomic DNA from colon biopsy 31

description: Normal colon (from cancer patient).


title: Genomic DNA from colon biopsy 16

description: Normal colon (cancer unrelated).


title: Genomic DNA from colon biopsy 14

description: Normal colon (cancer unrelated).


title: 36hr wild type ovary, biological rep2

description: Gene expression data from wild type ovaries containing egg chambers undergoing normal DA tube expansion

source_name: Drosophila ovaries containing egg chambers undergoing normal DA tube expansion

value: wild type

tag: age


title: 36hr wild type ovary, biological rep1


title: 36hr ttk^twk/ttk^twk ovary, biological rep1


title: Genomic DNA from colon biopsy 17

description: Normal colon (cancer unrelated).


title: 36hr ttk^twk/ttk^twk ovary, biological rep3


title: Genomic DNA from colon biopsy 13

description: Normal colon (cancer unrelated).


title: Genomic DNA from colon biopsy 24

description: Normal colon (from cancer patient).


title: Genomic DNA from colon biopsy 21

description: Normal colon (from cancer patient).


title: Genomic DNA from colon biopsy 7

description: Normal colon (cancer unrelated).


title: Genomic DNA from colon biopsy 4

description: Normal colon (cancer unrelated).


title: Genomic DNA from colon biopsy 9

description: Normal colon (cancer unrelated).


title: 36hr wild type ovary, biological rep3


title: Bone 2

city: Oslo

first: Leonardo

middle: A.

last: Meza-Zepeda

address: Ullernchausseen 70

department: Dept. of Tumor Biology

country: Norway

institute: The Norwegian Radium Hospital

description: Bone 2 Illumina HumanWG-6 Expression BeadChip version 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data was vst transformed and normalised using quantile normalisation in R

label: Biotin

source_name: Normal bone

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

growth_protocol: The osteosarcoma cells were grown in RPMI1640 (Lonza, Basel, Switzerland) or DMEM (Lonza) supplemented with 10 % foetal calf serum (PAA Laboratories GmbH, Pasching, Austria), GlutaMAX (Invitrogen, California, USA) and penicillin/streptomycin (Lonza), at 37°C with 5 % CO2. All cells were split when reaching 80 % confluency. The osteoblast cells were maintained in medium provided by the manufacturer, split when reaching 80 % confluency, and harvested when enough cells for DNA and RNA isolation were obtained.

extract_protocol: RNA was isolated using the standard TRIzol procedure (Invitrogen), and further purified with an RNeasy mini column (Qiagen GmbH, Hilden, Germany), according to the manufacturers’ instructions.

tag: cell type

value: Normal bone

tag: age (yrs)


title: Genomic DNA from colon biopsy 12

description: Normal colon (cancer unrelated).


title: Genomic DNA from colon biopsy 28

description: Normal colon (from cancer patient).


title: Bone 3

description: Bone 3 Illumina HumanWG-6 Expression BeadChip version 2

value: Not available


title: Genomic DNA from colon biopsy 11

description: Normal colon (cancer unrelated).


title: Genomic DNA from colon biopsy 20

description: Normal colon (from cancer patient).


title: Genomic DNA from colon biopsy 10

description: Normal colon (cancer unrelated).


title: Genomic DNA from colon biopsy 8

description: Normal colon (cancer unrelated).


title: Osteosarcoma cell line ZK-58

description: Osteosarcoma cell line ZK-58 Illumina HumanWG-6 Expression BeadChip version 2

source_name: Osteosarcoma cell line

tag: cell line

value: Osteosarcoma

tag: sample origin

value: male


title: Osteoblast 1

description: Osteoblast 1 Illumina HumanWG-6 Expression BeadChip version 2

source_name: Normal osteoblast

value: Normal osteoblast


title: Osteosarcoma cell line Saos-2

description: Osteosarcoma cell line Saos-2 Illumina HumanWG-6 Expression BeadChip version 2

tag: atcc number


title: Osteosarcoma cell line U-2 OS

description: Osteosarcoma cell line U-2 OS Illumina HumanWG-6 Expression BeadChip version 2

value: U-2 OS


title: Osteosarcoma cell line MHM

description: Osteosarcoma cell line MHM Illumina HumanWG-6 Expression BeadChip version 2

value: MHM

value: Metastasis


title: Osteosarcoma cell line OSA

description: Osteosarcoma cell line OSA  Illumina HumanWG-6 Expression BeadChip version 2

value: OSA


title: Genomic DNA from colon biopsy 6

description: Normal colon (cancer unrelated).

value: normal colon


title: Osteosarcoma cell line OHS

description: Osteosarcoma cell line OHS Illumina HumanWG-6 Expression BeadChip version 2

value: OHS

value: Primary tumour


title: Osteosarcoma cell line MNNG/HOS

description: Osteosarcoma cell line MNNG/HOS Illumina HumanWG-6 Expression BeadChip version 2

value: MNNG/HOS


title: Bone 1

description: Bone 1 Illumina HumanWG-6 Expression BeadChip version 2


title: Osteoblast 2

description: Osteoblast 2 Illumina HumanWG-6 Expression BeadChip version 2


title: Genomic DNA from colon biopsy 5

description: Normal colon (cancer unrelated).

value: no


title: Genomic DNA from colon biopsy 2

description: Normal colon (cancer unrelated).


title: Bone 4

description: Bone 4 Illumina HumanWG-6 Expression BeadChip version 2


title: Genomic DNA from colon biopsy 1

description: Normal colon (cancer unrelated).


title: Alveolar rhabdomyosarcoma cell line Rh41

city: Zurich

first: Beat

middle: W

last: Schafer

address: Steinwiesstrasse 75

country: Switzerland

institute: University Childrens Hospital

description: Gene expression data from alveolar rhabdomyosarcoma cell line Rh41

hyb_protocol: Hybridization solution was prepared according to Affymetrix´ GeneChip Expression Analysis Technical Manual. The final concentration of cRNA is 60 ng/μl.Hybridization was performed for 16-18 hours at 45°C and 60 rpm in a rotating hybridization oven (Hybridization Oven 640, Affymetrix).

scan_protocol: Scanning was performed with the GeneChip Scanner 3000 7G (Affymetrix), which is controlled by Affymetrix´ software GeneChip Operating System (GCOS) v1.4

data_processing: CEL-Files were imported into d-Chip software and expression values and ABS calls were exported

label_protocol: cDNA synthesis and in vitro-transcription was done with Ambion´s Message Amp II 96 Kit (Cat. No. 1819) according to the manufacturers’ instructions, starting with 1 μg of total RNA.

growth_protocol: Cell lines were grown under standard growth conditions in DME supplemented with 10% fetal bovine serum, 2mM L-glutamine and 100 U/ml penicillin/streptomycin for 2 days

extract_protocol: RNA was isolated using the RNeays Kit from Qiagen according to the instructions from the manufacturer

treatment_protocol: No treatment was applied

value: Alveolar rhabdomyosarcoma


title: Alveolar rhabdomyosarcoma cell line CW9019

description: Gene expression data from alveolar rhabdomyosarcoma cell line CW9019


title: Alveolar rhabdomyosarcoma cell line Rh18

description: Gene expression data from alveolar rhabdomyosarcoma cell line Rh18


title: Osteosarcoma cell line MG-63

description: Osteosarcoma cell line MG-63  Illumina HumanWG-6 Expression BeadChip version 2


title: Osteosarcoma cell line KPD

description: Osteosarcoma cell line KPD Illumina HumanWG-6 Expression BeadChip version 2

value: KPD


title: Alveolar rhabdomyosarcoma cell line Rh4

description: Gene expression data from alveolar rhabdomyosarcoma cell line Rh4

source_name: Alveolar rhabdomyosarcoma cell line Rh4


title: Genomic DNA from colon biopsy 3

description: Normal colon (cancer unrelated).


title: Osteosarcoma cell line IOR/OS10

description: Osteosarcoma cell line IOR/OS10 Illumina HumanWG-6 Expression BeadChip version 2

value: female


title: Osteosarcoma cell line IOR/SARG

description: Osteosarcoma cell line IOR/SARG Illumina HumanWG-6 Expression BeadChip version 2

value: IOR/SARG


title: Osteosarcoma cell line IOR/OS18

description: Osteosarcoma cell line IOR/OS18 Illumina HumanWG-6 Expression BeadChip version 2


title: Osteosarcoma cell line IOR/MOS

description: Osteosarcoma cell line IOR/MOS Illumina HumanWG-6 Expression BeadChip version 2

value: IOR/MOS


title: Alveolar rhabdomyosarcoma cell line RMS13

description: Gene expression data from alveolar rhabdomyosarcoma cell line RMS13


title: Osteosarcoma cell line IOR/OS15

description: Osteosarcoma cell line IOR/OS15 Illumina HumanWG-6 Expression BeadChip version 2

value: Osteosarcoma


title: Alveolar rhabdomyosarcoma cell line Rh30

description: Gene expression data from alveolar rhabdomyosarcoma cell line Rh30


title: Osteosarcoma cell line HOS

description: Osteosarcoma cell line HOS Illumina HumanWG-6 Expression BeadChip version 2

value: HOS

value: Not available


title: Alveolar rhabdomyosarcoma cell line Rh10

description: Gene expression data from alveolar rhabdomyosarcoma cell line Rh10


title: Osteosarcoma cell line IOR/OS9

description: Osteosarcoma cell line IOR/OS9 Illumina HumanWG-6 Expression BeadChip version 2

value: male


title: Osteosarcoma cell line HAL

description: Osteosarcoma cell line HAL Illumina HumanWG-6 Expression BeadChip version 2

value: HAL

value: Bone marrow


title: Osteosarcoma cell line IOR/OS14

description: Osteosarcoma cell line IOR/OS14 Illumina HumanWG-6 Expression BeadChip version 2


title: Alveolar rhabdomyosarcoma cell line Rh3

description: Gene expression data from alveolar rhabdomyosarcoma cell line Rh3

source_name: Alveolar rhabdomyosarcoma cell line Rh3


title: Osteosarcoma cell line 143B

description: Osteosarcoma cell line 143B Illumina HumanWG-6 Expression BeadChip version 2


title: Cell line SLM2, mutant status WT, condition Control 2

city: Charlottesville

first: Stephen

last: Turner

state: VA

address: 1670 Discovery Drive

institute: Signature Science, LLC

hyb_protocol: The gene array was performed using Illumina 3’IVT human HT-12 BeadChip arrays by Gene Analysis (Durham, NC).

data_processing: Quantile normalized and log2-transformed

source_name: RNA from Cell line SLM2, mutant status WT, condition Control

growth_protocol: SLM2, VMM39, and DM331 cells were plated and incubated overnight before being treated, in duplicate, with inhibitors or vehicle control in phenol red-free RPMI Medium 1640 without fetal bovine serum for 8 hours at 37°C. Cells were placed on ice and rinsed with cold 1x PBS.

extract_protocol: Cells were collected and RNA was isolated using the Qiashredder (Qiagen, Valencia, CA) and RNeasy Mini Kit (Qiagen, Valencia, CA).

tag: mutation

value: WT

tag: treatment

value: Control


title: Cell line SLM2, mutant status WT, condition Treated with Diclofenac 2

scan_protocol: The gene array was performed using Illumina 3’IVT human HT-12 BeadChip arrays by Gene Analysis (Durham, NC).

source_name: RNA from Cell line SLM2, mutant status WT, condition Treated with Diclofenac

value: Treated with Diclofenac


title: Cell line SLM2, mutant status WT, condition Treated with Sorafenib 2

source_name: RNA from Cell line SLM2, mutant status WT, condition Treated with Sorafenib

label_protocol: The gene array was performed using Illumina 3’IVT human HT-12 BeadChip arrays by Gene Analysis (Durham, NC).

value: Treated with Sorafenib


title: Cell line SLM2, mutant status WT, condition Treated with Sorafenib+Diclofenac 1

source_name: RNA from Cell line SLM2, mutant status WT, condition Treated with Sorafenib+Diclofenac

value: Treated with Sorafenib+Diclofenac


title: Cell line SLM2, mutant status WT, condition Treated with Sorafenib+Diclofenac 2


title: haploid_male_11d_SB_colony_Q7_329

city: Lausanne

first: Mingkwan

last: Nipitwattanaphon

address: Biophore Building, UNIL-Sorge

department: Department of Ecology and Evolution

institute: University of Lausanne

description: RNA from the whole body of an individual ant of specific genotype and age

hyb_protocol: Hybridization buffer (3x SSC, 0.18% SDS, 200 ng/μl yeast tRNA, 200 ng/µl polyA DNA; final concentration) was added to samples; samples were denatured, applied to microarrays, and hybridized overnight at 64°C. After hybridization, slides were washed sequential.

scan_protocol: Scanner: Agilent Technologies microarray scanner. Image quantification GenePix 5.1

data_processing: printTipLoess normalization and between-array normalization with limma (Bioconductor)

organism: Solenopsis invicta

source_name: Reference RNA batch 2006

label_protocol: Total RNA was amplified using the Ambion Message Amp II kit. Amplified RNA plus Alien spike control RNAs (Stratagene) were labeled using the indirect aa-dUTP labeling method. Reverse transcription primers: random 9mers.

extract_protocol: Total RNA was extracted using Qiagen RNeasy Kit following manufacturer's instructions. For adult males, we extracted RNA using standard Trizol protocol.

value: whole organism

tag: batch

value: year 2006

tag: sample type

value: Amplified total RNA isolated en masse from hundreds of adult workers collected from the foraging area of 30 colonies (eight and seven of each social form from Georgia and Louisiana, respectively)

source_name: 11-day-old haploid male heterozygote SB

tag: caste

value: haploid male

value: SB


title: Cell line SLM2, mutant status WT, condition Treated with Diclofenac 1


title: Cell line SLM2, mutant status WT, condition Treated with Sorafenib 1


title: haploid_male_11d_SB_colony_Q5_115


title: Cell line DM331, mutant status Braf, condition Treated with Sorafenib+Diclofenac 2

source_name: RNA from Cell line DM331, mutant status Braf, condition Treated with Sorafenib+Diclofenac

value: Braf


title: Cell line DM331, mutant status Braf, condition Treated with Sorafenib 2

source_name: RNA from Cell line DM331, mutant status Braf, condition Treated with Sorafenib


title: Cell line SLM2, mutant status WT, condition Control 1


title: Cell line DM331, mutant status Braf, condition Control 1

source_name: RNA from Cell line DM331, mutant status Braf, condition Control


title: Cell line DM331, mutant status Braf, condition Control 2


title: Cell line DM331, mutant status Braf, condition Treated with Diclofenac 2

source_name: RNA from Cell line DM331, mutant status Braf, condition Treated with Diclofenac


title: haploid_male_11d_SB_colony_Q2_346_H


title: Cell line VMM39, mutant status Ras, condition Treated with Sorafenib 2

source_name: RNA from Cell line VMM39, mutant status Ras, condition Treated with Sorafenib

value: Ras


title: Cell line DM331, mutant status Braf, condition Treated with Sorafenib+Diclofenac 1


title: haploid_male_11d_Sb_colony_Q5_115

source_name: 11-day-old haploid male homozygote Sb

value: Sb


title: haploid_male_11d_SB_colony_Q1_346


title: Cell line VMM39, mutant status Ras, condition Treated with Sorafenib+Diclofenac 2

source_name: RNA from Cell line VMM39, mutant status Ras, condition Treated with Sorafenib+Diclofenac


title: Cell line DM331, mutant status Braf, condition Treated with Diclofenac 1


title: haploid_male_11d_Sb_colony_Q3_350_H


title: haploid_male_11d_Sb_colony_Q7_329


title: Cell line DM331, mutant status Braf, condition Treated with Sorafenib 1


title: Cell line VMM39, mutant status Ras, condition Treated with Sorafenib+Diclofenac 1


title: Bone 3 [methylation]

description: Bone 3 Illumina HumanMethylation27 BeadChip

hyb_protocol: Standard Ilumina hyb protocol

scan_protocol: Standard Ilumina scan protocol

data_processing: Data extraction and initial quality control of the bead summary raw data were performed using BeadStudio v3.1.0.0 and the Methylation module v1.9, both provided by Illumina.

label: Biotin and dinitrophenyl

source_name: Normal BONE3

label_protocol: Standard Ilumina label protocol

growth_protocol: The osteosarcoma cells were grown in RPMI1640 (Lonza, Basel, Switzerland) or DMEM (Lonza) supplemented with 10 % foetal calf serum (PAA Laboratories GmbH, Pasching,  Austria), GlutaMAX (Invitrogen, California, USA) and penicillin/streptomycin (Lonza), at 37°C with 5 % CO2. All cells were split when reaching 80 % confluency. The osteoblast cells were maintained in medium provided by the manufacturer, split when reaching 80 % confluency, and harvested when enough cells for DNA and RNA isolation were obtained.   The cells were grown in RPMI1640 (Lonza, Basel, Switzerland) or DMEM (Lonza) supplemented with 10 % foetal calf serum (PAA Laboratories GmbH, Pasching,  Austria), GlutaMAX (Invitrogen, California, USA) and penicillin/streptomycin (Lonza), at 37°C with 5 % CO2. All cells were split when reaching 80 % confluency.   The cells were grown in RPMI1640 (Lonza, Basel, Switzerland) or DMEM (Lonza) supplemented with 10 % foetal calf serum (PAA Laboratories GmbH, Pasching,  Austria), GlutaMAX (Invitrogen, California, USA) and penicillin/streptomycin (Lonza), at 37°C with 5 % CO2. All cells were split when reaching 80 % confluency.   The cells were grown in RPMI1640 (Lonza, Basel, Switzerland) or DMEM (Lonza) supplemented with 10 % foetal calf serum (PAA Laboratories GmbH, Pasching,  Austria), GlutaMAX (Invitrogen, California, USA) and penicillin/streptomycin (Lonza), at 37°C with 5 % CO2. All cells were split when reaching 80 % confluency.

extract_protocol: DNA was isolated using the Wizard Genomic DNA Purification Kit (Promega, Madison, USA).

value: Normal bone

value: Not available


title: Cell line VMM39, mutant status Ras, condition Control 2

source_name: RNA from Cell line VMM39, mutant status Ras, condition Control


title: diploid_male_11d_heterozygote_SBSb_colony_Q4_356

source_name: 11-day-old diploid male heterozygote SB/Sb

value: diploid male

value: SB/Sb


title: Osteoblast 1 [methylation]

description: Osteoblast 1 Illumina HumanMethylation27 BeadChip

source_name: Normal osteoblast 1

value: Normal osteoblast

value: male


title: Bone 4 [methylation]

description: Bone 4 Illumina HumanMethylation27 BeadChip

source_name: Normal BONE4


title: haploid_male_11d_Sb_colony_Q2_346_H


title: haploid_male_11d_Sb_colony_Q1_346


title: Osteoblast 2 [methylation]

description: Osteoblast 2 Illumina HumanMethylation27 BeadChip

source_name: Normal osteoblast 2


title: Bone 2 [methylation]

description: Bone 2 Illumina HumanMethylation27 BeadChip

source_name: Normal BONE2

value: female


title: Osteosarcoma cell line ZK-58 [methylation]

description: Osteosarcoma cell line ZK-58  Illumina HumanMethylation27 BeadChip

source_name: Osteosarcoma cell line ZK-58

value: Osteosarcoma


title: Cell line VMM39, mutant status Ras, condition Treated with Sorafenib 1

value: Treated with Sorafenib


title: Osteosarcoma cell line Saos-2 [methylation]

description: Osteosarcoma cell line Saos-2  Illumina HumanMethylation27 BeadChip

source_name: Osteosarcoma cell line Saos-2


title: Cell line VMM39, mutant status Ras, condition Treated with Diclofenac 1

source_name: RNA from Cell line VMM39, mutant status Ras, condition Treated with Diclofenac

value: Treated with Diclofenac


title: haploid_male_11d_SB_colony_Q3_350_H

source_name: Reference RNA batch 2006

value: whole organism

value: year 2006

source_name: 11-day-old haploid male heterozygote SB


title: diploid_male_11d_heterozygote_SBSb_colony_Q2_383

value: Amplified total RNA isolated en masse from hundreds of adult workers collected from the foraging area of 30 colonies (eight and seven of each social form from Georgia and Louisiana, respectively)


title: diploid_male_11d_heterozygote_SBSb_colony_Q2_346


title: diploid_male_11d_heterozygote_SBSb_colony_Q2_350


title: Osteosarcoma cell line OSA [methylation]

description: Osteosarcoma cell line OSA  Illumina HumanMethylation27 BeadChip

source_name: Osteosarcoma cell line OSA

value: OSA


title: diploid_male_11d_homozygote_SBSB_colony_Q2_383

source_name: 11-day-old diploid male homozygote SB/SB

value: SB/SB


title: Control_Solventogenic

city: Wooster

first: Yan

last: Zhang

state: OH

address: 1680 Madison Avenue

department: Animal Sciences

institute: The Ohio State University

hyb_protocol: Ten micrograms of each fluor-labeled cRNA was hybridized separately to one array, and hybridization was performed for 20 h at 45°C in a hybridization buffer containing 6x SSPE (20X SSPE stock: 3M NaCl, 20mM EDTA, 118.2mM NaH2PO4 and 81.8mM Na2HPO4), 10% de-ionized formamide, 0.01 mg/ml acetylated BSA, 0.01% Tween-20, and 1% control oligos (provided by Mycroarray Inc). After hybridization, the slide was washed with fresh 6x SSPE buffer (24°C) and transferred to fresh 0.5x SSPE buffer prior to drying. The slide was dried immediately by centrifugation at 2000g for 3 min.

scan_protocol: The slide was scanned using an Axon 4000B Scanner set at 5μm per pixel resolution and 100% laser power. The scanned images were extracted and analyzed using version 6.1.0.4 GenePix Pro Software (Molecular Devices, Sunnyvale, CA). For signal extraction, circular feature indicators (35μm diameter) were centered over each spot and the median feature pixel intensity was extracted. Data images were extracted from the center of the spot area (35µm in diameter) where the sequence fidelity is exceptional instead of the larger indicator feature spot diameter area (~60 µm).

data_processing: To minimize error due to differences in sample behavior from array to array, a scale factor was created to normalize signal across all arrays. A scale factor (SF) for each array was calculated as follows: SF = μ (median pixel signal)control/μ (median pixel signal) treatment. Trimmed mean was used to generate the final signal value for the 5 identical probe replicates which identified differential expression pattern of each gene on the array. The trimmed mean was calculated by discarding the maximum and minimum adjusted signal within each set of 5 probe replicates, followed by averaging the adjusted signal values of the remaining three probes. Relative expression levels (gene expression ratio) for each gene was calculated by dividing the signal intensity of the array from the furfural-challenged C. beijerinckii 8052 culture by the intensity of the unchallenged control culture. To facilitate a fair comparison of up- and down-regulated genes, fold change was calculated: for genes with an expression ratio ≥1, the fold change is same as the expression ratio, whereas genes whose expression ratio is <1 has a fold change that equals the reciprocal of expression ratio multiplied by -1 (Babu, 2004). To make data distribution symmetrical, the gene expression ratio was used to calculate log2 transformation ratio as described previously (Quackenbush, 2002).

label: Alexa Fluor 555

organism: Clostridium beijerinckii NCIMB 8052

source_name: solventogenic clostridia, untreated

label_protocol: To enhance hybridization, 10 ug of total RNA was converted to enriched mRNA using the MICROBExpress™ Bacterial mRNA Enrichment Kit (Life Technologies, Grand Island, NY) following the manufacturer's protocol. About 200ng of enriched mRNA was converted to complementary RNA (cRNA) using the MessageAmp™ II-Bacteria RNA Amplification Kit (Life Technologies, Grand Island, NY) following the manufacturer's protocol. Alexa Fluor 555 (Life Technologies, Grand Island, NY) was coupled to cRNA following the manufacturer's instructions. Removal of unincorporated dye was conducted using RNeasy Mini Columns (Qiagen Inc., Valencia, CA) following the manufacturer's protocol. About 30-50 μl eluate containing ~40 μg labeled cRNA was generated. The resulting dye-coupled cRNA was made up to 60 μl with 2 μl 150 mM ZnSO4 and elution buffer to bring the final concentration of ZnSO4 to 5 mM followed by incubation (fragmentation) at 75°C for 10 min.

growth_protocol: Stocks of Clostridium beijerinckii 8052 spores were stored in sterile, double-distilled water at 4°C. To revive C. beijerinckii 8052 spores, 200 μl were heat-shocked for 10 min at 75°C followed by cooling on ice. The heat-shocked spores were inoculated into 10-ml anoxic pre-sterilized tryptone-glucose-yeast extract (TGY) medium and incubated in an anaerobic chamber (Coy Laboratory Products Inc., Ann Arbor, Michigan) with a modified atmosphere of 82% N2, 15% CO2, and 3% H2 for 12 to 14 h at 35 ±1°C until active growth (OD600 nm λ attained 0.9-1.1) was attained. Eight milliliters of actively growing culture was subsequently transferred into 92 mL of anoxic TGY medium. The culture was  grown anaerobically at 35°C ±1°C for 4 to 5 h, during which it reached an optical density (OD600 nm λ) of 0.9 - 1.1. This was used as the pre-culture.

extract_protocol: Aliquots of C. beijerinckii 8052 samples were placed on ice immediately after taken from bottles. C. beijerinckii 8052 pellets were obtained by centrifugation at 5000 g for 10 min at 4°C prior to suspension in a solution containing a 2:1 ratio of RNAprotect cell reagent to phosphate-buffered saline (PBS) (Qiagen Inc., Valencia, CA) to stabilize the RNA. The suspension was incubated at room temperature for 5 min, centrifuged to obtain cell pellets, and stored at -80 °C overnight as described previously (Servinsky et al., 2010). The total cellular RNA was purified from 2 mL C. beijerinckii 8052 culture. Briefly, C. beijerinckii 8052 cell pellets from 2 mL culture aliquots were thawed on ice and resuspended in 750 μL RLT buffer™ (Qiagen Inc., Valencia, CA) supplemented with 1% (v/v) β-mercaptoethanol (β- ME).For complete lysis of C. beijerinckii 8052, a 2 mL microcentrifuge tube was half filled with 0.1 mm diameter zirconia/silica beads (Biospec, Bartlesville, OK) followed by the addition of 750 μL RLT buffer™ supplemented with 1% (v/v) β-ME and chilling on ice. C. beijerinckii 8052 suspension (750 μL) was added to the pre-chilled tube with beads and agitated in a TissueLyser LT (Qiagen Inc., Valencia, CA) for 8 min at a setting of 50Hz to break C. beijerinckii 8052 cells. Total RNA was purified from homogenized cells using an RNeasy mini kit (Qiagen Inc., Valencia, CA) according to the manufacturer's instructions. RNA quality was analyzed using a Nanochip 2100 Bioanalyzer (Agilent Technologies Inc., Wilmington, DE), and RNA concentration was measured by NanoDrop 3300 (Thermo scientific, Wilmington, DE) according to the manufacturer's instructions.

treatment_protocol: Batch ABE fermentation by C. beijerinckii 8052 was performed in 250-ml Pyrex screw-capped media bottles containing anoxic 200 mL P2 medium (glucose 60 g/L and yeast extract 1 g/L) and P2 stock solutions as described previously (Zhang et al., 2012). To evaluate the response of C. beijerinckii 8052 to furfural during the acidogenic and solventogenic phases, 1 L flask containing 600 mL anoxic P2 medium plus P2 stock solutions was inoculated (6% v/v) with C. beijerinckii 8052 pre-culture and incubated anaerobically for 8 h, during which the OD600 attained 0.9 ± 0.05. The culture was then subdivided into aliquots of 100 mL in four 150-ml Pyrex screw-capped media bottles. Subsequently, the bottles were grouped into two pairs to study the effect of furfural stress on C. beijerinckii 8052 during the acidogenic and solventogenic phase. One bottle was challenged with furfural (2 g/L) and the other bottle was left unchallenged. After 3 h growth at 35 °C, C. beijerinckii 8052 samples were collected, during which the original concentration of furfural in the growth medium was reduced to more than half. Like the first pair, the second pair of cultures was incubated anaerobically 24 h, during which the OD600 attained 4.0 ± 0.2. One bottle was challenged with 3 g/L of furfural and the other bottle was unchallenged. Following 3 h post furfural challenge, during which the original concentration of furfural in the growth medium was reduced to more than half, C. beijerinckii 8052 samples were collected for analysis.

tag: strain

value: NCIMB 8052

tag: growth phase

value: solventogenic


title: diploid_male_11d_homozygote_SBSB_colony_Q4_356

tag: genotype


title: Bone 1 [methylation]

description: Bone 1 Illumina HumanMethylation27 BeadChip

source_name: Normal BONE1

value: Normal bone

tag: gender


title: Osteosarcoma cell line OHS [methylation]

description: Osteosarcoma cell line MNNG/HOS  Illumina HumanMethylation27 BeadChip

source_name: Osteosarcoma cell line OHS

value: OHS

value: Primary tumour


title: Osteosarcoma cell line U-2 OS [methylation]

description: Osteosarcoma cell line U-2 OS  Illumina HumanMethylation27 BeadChip

source_name: Osteosarcoma cell line U-2 OS

value: U-2 OS

value: Not available


title: Control_Acidogenic

source_name: acidogenic clostridia, untreated

value: acidogenic


title: Osteosarcoma cell line MHM [methylation]

description: Osteosarcoma cell line MHM  Illumina HumanMethylation27 BeadChip

source_name: Osteosarcoma cell line MHM

value: MHM

value: Metastasis

value: female


title: Osteosarcoma cell line MNNG/HOS [methylation]

source_name: Osteosarcoma cell line MNNG/HOS

value: MNNG/HOS

value: Osteosarcoma


title: Furfural3_Solventogenic

source_name: solventogenic clostridia, furfural treated

value: furfural


title: Furfural2_Acidogenic

source_name: acidogenic clostridia, furfural treated


title: Osteosarcoma cell line MG-63 [methylation]

description: Osteosarcoma cell line MG-63  Illumina HumanMethylation27 BeadChip

source_name: Osteosarcoma cell line MG-63

value: male


title: diploid_male_11d_homozygote_SBSB_colony_Q2_327

value: whole organism

value: year 2006

value: Amplified total RNA isolated en masse from hundreds of adult workers collected from the foraging area of 30 colonies (eight and seven of each social form from Georgia and Louisiana, respectively)

value: diploid male


title: Cell line VMM39, mutant status Ras, condition Treated with Diclofenac 2

value: Ras

value: Treated with Diclofenac


title: diploid_male_11d_homozygote_SBSB_colony_Q2_346

value: SB/SB


title: virgin_queen_11d_heterozygote_SBSb_colony_Pg359

description:
Reanalysis of GSM1031761
RNA from the whole body of an individual ant of specific genotype and age

source_name: 11-day-old queen heterozygote SB/Sb

value: queen

value: SB/Sb


title: Cell line VMM39, mutant status Ras, condition Control 1

source_name: RNA from Cell line VMM39, mutant status Ras, condition Control

value: Control


title: diploid_male_11d_heterozygote_SBSb_colony_Q2_327

source_name: 11-day-old diploid male heterozygote SB/Sb


title: virgin_queen_11d_heterozygote_SBSb_colony_Pg346

description:
Reanalysis of GSM1031762
RNA from the whole body of an individual ant of specific genotype and age

source_name: Reference RNA batch 2006


title: virgin_queen_11d_heterozygote_SBSb_colony_Pg343

description:
Reanalysis of GSM1031756
RNA from the whole body of an individual ant of specific genotype and age


title: Osteosarcoma cell line KPD [methylation]

description: Osteosarcoma cell line KPD  Illumina HumanMethylation27 BeadChip

source_name: Osteosarcoma cell line KPD

value: KPD

value: Primary tumour


title: Osteosarcoma cell line IOR/OS18 [methylation]

description: Osteosarcoma cell line IOR/OS18  Illumina HumanMethylation27 BeadChip

source_name: Osteosarcoma cell line IOR/OS18

value: Metastasis


title: virgin_queen_11d_heterozygote_SBSb_colony_Pg347

description:
Reanalysis of GSM1031758
RNA from the whole body of an individual ant of specific genotype and age


title: Osteosarcoma cell line IOR/OS15 [methylation]

description: Osteosarcoma cell line IOR/OS15  Illumina HumanMethylation27 BeadChip

source_name: Osteosarcoma cell line IOR/OS15

value: female


title: Tgfbr2fspKO_laser captured epithelia (ID=FSP373)

first: Darawalee

last: Wangsa

state: MD

address: 50 South Drive, Bldg 50, Rm 1408

institute: National Cancer Institute

description: Sample 6

hyb_protocol: Hybridization was carried out using Mouse Genome CGH Microarray 44K format from Agilent Technologies (Santa Clara, CA) according to the Agilent Oligonucleotide Array-based CGH for Genomic DNA Analysis, Enzymatic Labeling for Blood Cells or Tissues protocol (Agilent Technologies).  Slides were hybridized in a hybridization oven at 65C for 40 hours.

scan_protocol: Slides were scanned with the DNA microarray scanner with Surescan High-Resolution Technology (Agilent Technologies).

data_processing: Data was processed with Agilent Genomic Workbench Standard Edition 5.0.14.

source_name: Laser captured epithelia from the forestomach of SQUAMOUS CELL CARCINOMA Tgfbr2fspKO mouse (ID=FSP373)

label_protocol: Array-CGH was performed using test DNA from laser captured epithelia and stroma from Tgfbr2fspKO mice, and reference DNA using laser captured epithelia from Tgfbr2flox/flox mice. DNA was labeled with Cy3 (test) or Cy5 (control) fluorescent dyes (PerkinElmer).

growth_protocol: Cre-Tgfbr2flox/flox female and Cre+Tgfbr2flox/wt male mice were kindly provided by Dr. Harold Moses, Vanderbilt Cancer center, Nashville, TN. Mice were bred to yield Tgfbr2fspKO mice. All mice were housed at the National Cancer Institute (NCI) animal facility Animal studies were performed under NCI- IACUC approved protocol.

extract_protocol: The DNA was extracted using a QIAamp DNA micro kit (Qiagen, CA, USA)

treatment_protocol: Laser capture microdissection of Tgfbr2flox/flox (n=3) and Tgfbr2fspKO (n=3) forestomach tissues was performed using an Arcturus XT (Life Technologies, CA, USA). Frozen tissue sections on PEN membrane frame slides (Applied Biosystems) were H&E stained followed by dehydration using the standard protocol to improve visualization of the cells at the microscope. The epithelia and stroma were identified by morphology, captured using a low-power infrared laser pulse, and transferred onto a cap (Capsure™ Macro LCM Caps, Life Technologies).

value: epithelia of the forestomach

tag: genotype/variation

tag: ID

source_name: epithelia from normal forestomach of Tgfbr2flox/flox mice

value: epithelia from normal forestomach


title: virgin_queen_11d_homozygote_SBSB_colony_Pg359

description:
Reanalysis of GSM1031753
RNA from the whole body of an individual ant of specific genotype and age

tag: tissue

source_name: 11-day-old queen homozygote SB/SB

tag: age


title: Osteosarcoma cell line IOR/SARG [methylation]

description: Osteosarcoma cell line IOR/SARG  Illumina HumanMethylation27 BeadChip

source_name: Osteosarcoma cell line IOR/SARG

value: IOR/SARG

tag: cell type

value: Osteosarcoma

value: male

tag: age (yrs)


title: Tgfbr2fspKO_laser captured epithelia (ID=FSP273)

description: Sample 4

source_name: Laser captured epithelia from the forestomach of SQUAMOUS CELL CARCINOMA Tgfbr2fspKO mouse (ID=FSP273)


title: Osteosarcoma cell line IOR/OS14 [methylation]

description: Osteosarcoma cell line IOR/OS14  Illumina HumanMethylation27 BeadChip

source_name: Osteosarcoma cell line IOR/OS14

tag: cell line

tag: sample origin


title: Osteosarcoma cell line IOR/OS10 [methylation]

description: Osteosarcoma cell line IOR/OS10  Illumina HumanMethylation27 BeadChip

source_name: Osteosarcoma cell line IOR/OS10


title: virgin_queen_11d_heterozygote_SBSb_colony_Pg329

description:
Reanalysis of GSM1031757
RNA from the whole body of an individual ant of specific genotype and age

value: whole organism

value: year 2006

value: Amplified total RNA isolated en masse from hundreds of adult workers collected from the foraging area of 30 colonies (eight and seven of each social form from Georgia and Louisiana, respectively)


title: Tgfbr2fspKO_laser captured stroma (ID=FSP270)

description: Sample 1

source_name: Laser captured stroma from the forestomach of SQUAMOUS CELL CARCINOMA Tgfbr2fspKO mouse (ID=FSP270)

value: stroma of the forestomach


title: virgin_queen_11d_homozygote_SBSB_colony_Pg347

description:
Reanalysis of GSM1031750
RNA from the whole body of an individual ant of specific genotype and age

value: SB/SB


title: Tgfbr2fspKO_laser captured stroma (ID=FSP373)

description: Sample 5

source_name: Laser captured stroma from the forestomach of SQUAMOUS CELL CARCINOMA Tgfbr2fspKO mouse (ID=FSP373)


title: Tgfbr2fspKO_laser captured stroma (ID=FSP273)

description: Sample 3

source_name: Laser captured stroma from the forestomach of SQUAMOUS CELL CARCINOMA Tgfbr2fspKO mouse (ID=FSP273)


title: Osteosarcoma cell line HOS [methylation]

description: Osteosarcoma cell line HOS  Illumina HumanMethylation27 BeadChip

source_name: Osteosarcoma cell line HOS

value: HOS

value: Not available

tag: atcc number


title: Tgfbr2fspKO_laser captured epithelia (ID=FSP270)

description: Sample 2

source_name: Laser captured epithelia from the forestomach of SQUAMOUS CELL CARCINOMA Tgfbr2fspKO mouse (ID=FSP270)


title: virgin_queen_11d_homozygote_SBSB_colony_Pg343

description:
Reanalysis of GSM1031748
RNA from the whole body of an individual ant of specific genotype and age

value: queen


title: virgin_queen_11d_homozygote_SBSB_colony_Pg346

description:
Reanalysis of GSM1031754
RNA from the whole body of an individual ant of specific genotype and age


title: virgin_queen_11d_homozygote_SBSB_colony_Pg329

description:
Reanalysis of GSM1031749
RNA from the whole body of an individual ant of specific genotype and age


title: Osteosarcoma cell lineI OR/MOS [methylation]

description: Osteosarcoma cell lineI OR/MOS Illumina HumanMethylation27 BeadChip

source_name: Osteosarcoma cell lineI OR/MOS

value: IOR/MOS


title: Osteosarcoma cell line IOR/OS9 [methylation]

description: Osteosarcoma cell line IOR/OS9  Illumina HumanMethylation27 BeadChip

source_name: Osteosarcoma cell line IOR/OS9


title: Osteosarcoma cell line 143B [methylation]

description: Osteosarcoma cell line 143B  Illumina HumanMethylation27 BeadChip

source_name: Osteosarcoma cell line 143B


title: Osteosarcoma cell line HAL [methylation]

description: Osteosarcoma cell line HAL  Illumina HumanMethylation27 BeadChip

source_name: Osteosarcoma cell line HAL

value: HAL

value: Bone marrow


title: haploid_male_1d_Sb_colony_Q2_346_H

description: RNA from the whole body of an individual ant of specific genotype and age

source_name: Reference RNA batch 2006

source_name: 1-day-old haploid male homozygote Sb

value: haploid male

value: Sb


title: Cultured GRK2-K220R-expressing HEK cell clone-rep2

first: Ursula

last: Quitterer

address: Winterthurerstrasse 190

department: Molecular Pharmacology

institute: ETH Zurich

description:
HEK-K220R-2
Cultured GRK2-K220R-expressing HEK cell clone
Gene expression data of cultured GRK2-K220R-expressing HEK cell clone

hyb_protocol: For hybridization, 15 µg of fragmented cRNA were incubated with the chip (Affymetrix Human genome U133 Plus 2.0 Array) in 200 µl of the hybrization solution in a Hybridization Oven 640 (Affymetrix) for 16 h at 45 °C. GeneChips were then washed and stained using the Affymetrix Fluidics Station 450 according to the GeneChip Expression Analysis Technical Manual (Rev. 5).

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

data_processing: The signals were processed using Affymetrix GeneChip Operating Software (GCOS; v.1.4; Affymetrix). To compare samples and experiments, the trimmed mean signal of each array was scaled to a target intensity of 200.

source_name: Cultured HEK cell clone with GRK2-K220R expression

label_protocol: Biotinylated cRNA was prepared according to the protocol of the manufacturer (Affymetrix; GeneChip Expression Analysis Technical Manual).

growth_protocol: The study was performed with HEK cell clones stably expressing GRK2 or the kinase-deficient GRK2-K220R mutant. HEK cell clones were either expanded for 4 weeks in vivo in immunodeficient NOD.Scid mice (3 months of age), cultured in vitro, or re-cultured in vitro after expansion in NOD.Scid mice

extract_protocol: Total RNA was isolated from HEK cell clones with the RNeasy Mini kit according to the manufacturer`s instructions (Qiagen).

treatment_protocol: For the microarray study, cell pellets were isolated from three study groups: (i) NOD.Scid mouse-expanded HEK clones expressing either GRK2 or kinase-deficient GRK2-K220R (Scid), (ii) in vitro cultured HEK cell clones expressing GRK2 or GRK2-K220R (HEK), and (iii) in vitro re-cultured HEK cell clones after NOD.Scid mouse expansion (Ex-Scid).

value: HEK cell clones

tag: protocol

value: cultured in vitro


title: haploid_male_1d_SB_colony_Q7_329

tag: batch

source_name: 1-day-old haploid male heterozygote SB

value: SB


title: haploid_male_1d_SB_colony_Q5_115

tag: sample type


title: Re-cultured GRK2-K220R-expressing HEK cell clone after NOD.Scid mouse expansion-rep2

description:
Ex-Scid-K220R-2
Re-cultured GRK2-K220R-expressing HEK cell clone after expansion in NOD.Scid mice
Gene expression data of re-cultured NOD.Scid-mouse-expanded GRK2-K220R-expressing HEK cell clone

value: re-cultured in vitro after expansion in NOD.Scid mice


title: haploid_male_1d_Sb_colony_Q3_350_H

value: whole organism

tag: caste


title: haploid_male_1d_SB_colony_Q2_346_H

value: year 2006


title: Re-cultured GRK2-expressing HEK cell clone after NOD.Scid mouse expansion-rep2

description:
Ex-Scid-GRK-2
Re-cultured GRK2-expressing HEK cell clone after expansion in NOD.Scid mice
Gene expression data of re-cultured NOD.Scid-mouse-expanded GRK2-expressing HEK cell clone


title: haploid_male_1d_Sb_colony_Q7_329

value: Amplified total RNA isolated en masse from hundreds of adult workers collected from the foraging area of 30 colonies (eight and seven of each social form from Georgia and Louisiana, respectively)


title: haploid_male_1d_SB_colony_Q3_350_H


title: Re-cultured GRK2-K220R-expressing HEK cell clone after NOD.Scid mouse expansion-rep1

description:
Ex-Scid-K220R-1
Re-cultured GRK2-K220R-expressing HEK cell clone after expansion in NOD.Scid mice
Gene expression data of re-cultured NOD.Scid-mouse-expanded GRK2-K220R-expressing HEK cell clone


title: diploid_male_1d_heterozygote_SBSb_colony_Q2_383

source_name: 1-day-old diploid male heterozygote SB/Sb

value: diploid male

value: SB/Sb


title: haploid_male_1d_SB_colony_Q1_346


title: NOD.Scid mouse-expanded GRK2-K220R-expressing HEK clone-rep2

description:
Scid-K220R-2
GRK2-K220R-expressing HEK clone expanded for 4 weeks in immunodeficient NOD.Scid mice
Gene expression data of NOD.Scid mouse-expanded GRK2-K220R-expressing HEK clone

source_name: NOD.Scid mouse-expanded HEK clone with GRK2-K220R expression

value: expanded for 4 weeks in NOD.Scid mice


title: Re-cultured GRK2-expressing HEK cell clone after NOD.Scid mouse expansion-rep1

description:
Ex-Scid-GRK-1
Re-cultured GRK2-expressing HEK cell clone after expansion in NOD.Scid mice
Gene expression data of re-cultured NOD.Scid-mouse-expanded GRK2-expressing HEK cell clone


title: Cultured GRK2-expressing HEK cell clone-rep2

description:
HEK-GRK-2
Cultured GRK2-expressing HEK cell clone
Gene expression data of cultured GRK2-expressing HEK cell clone

source_name: Cultured HEK cell clone with GRK2 expression


title: haploid_male_1d_Sb_colony_Q1_346


title: diploid_male_1d_heterozygote_SBSb_colony_Q2_356


title: haploid_male_1d_Sb_colony_Q5_115


title: diploid_male_1d_heterozygote_SBSb_colony_Q4_356


title: diploid_male_1d_heterozygote_SBSb_colony_Q2_350


title: NOD.Scid mouse-expanded GRK2-K220R-expressing HEK clone-rep1

description:
Scid-K220R-1
GRK2-K220R-expressing HEK clone expanded for 4 weeks in immunodeficient NOD.Scid mice
Gene expression data of NOD.Scid mouse-expanded GRK2-K220R-expressing HEK clone


title: Cultured GRK2-K220R-expressing HEK cell clone-rep1

description:
HEK-K220R-1
Cultured GRK2-K220R-expressing HEK cell clone
Gene expression data of cultured GRK2-K220R-expressing HEK cell clone


title: NOD.Scid mouse-expanded GRK2-expressing HEK clone-rep1

description:
Scid-GRK-1
GRK2-expressing HEK clone expanded for 4 weeks in immunodeficient NOD.Scid mice
Gene expression data of NOD.Scid mouse-expanded GRK2-expressing HEK clone

source_name: NOD.Scid mouse-expanded HEK clone with GRK2 expression


title: NOD.Scid mouse-expanded GRK2-expressing HEK clone-rep2

description:
Scid-GRK-2
GRK2-expressing HEK clone expanded for 4 weeks in immunodeficient NOD.Scid mice
Gene expression data of NOD.Scid mouse-expanded GRK2-expressing HEK clone


title: diploid_male_1d_heterozygote_SBSb_colony_Q2_346


title: Post-operation cyanotic normoxic CC14B

city: Bristol

first: Mohamed

middle: T.

last: Ghorbel

address: Level 7, BRI, Marlborough street

department: Bristol Heart Institute

country: United Kingdom

institute: University of Bristol

hyb_protocol: Standard Affymetrix procedures

scan_protocol: Standard Affymetrix procedures

data_processing: RMA normalized using ArrayStar 2.1.

source_name: Right ventricle biopsy

label_protocol: One microgram of total RNA was processed to produce biotinylated cRNA targets using the Affymetrix protocol

extract_protocol: Five to ten milligrams of frozen right ventricle biopsy was homogenized and total RNA extracted using the Qiagen MiniElute protocol (Qiagen, UK).

value: heart Right ventricle biopsy

tag: patient disease status

value: with a diagnosis of cyanotic Tetralogy of Fallot congenital heart disease

tag: intervention

value: corrective surgery using controlled reoxygenation cardiopulmonary bypass


title: Cultured GRK2-expressing HEK cell clone-rep1

description:
HEK-GRK-1
Cultured GRK2-expressing HEK cell clone
Gene expression data of cultured GRK2-expressing HEK cell clone


title: slide-171112

city: Villaviciosa

first: Beatriz

last: Martinez

address: Paseo Río Linares s/n

country: Spain

institute: IPLA-CSIC

description: A dye swap of the wt versus Lcn972R mutant

hyb_protocol: Hybridization (16 h at 45 °C) of labeled cDNA was performed in Ambion Slidehyb #1 hybridization buffer (Ambion Europe) on superamine glass slides (Array-It; SMMBC), containing technical replicates.

scan_protocol: Slides were scanned using the Genepix 4200AL DNA micro array slide scanner.  Quantification of the signal of the spots on slides was done with ArrayPro 4.5.

data_processing: Slide data were processed and normalized using MicroPreP, and CyberT implementation of the Student's t test (ref. van Hijum, S. A., J. Garcia de la Nava, O. Trelles, J. Kok, and O. P. Kuipers. 2003. MicroPreP: a cDNA microarray data pre-processing framework. Appl. Bioinformatics 2:241-244.).

label: Net intensity (tr.mean) {A} {Cy5}

organism: Lactococcus lactis subsp. lactis

source_name: Lactococcus lactis MG1614

label_protocol: Synthesis of cDNA and indirect Cy-3/Cy-5-dCTPs labeling of 15–20 µg of total RNA was performed with the CyScribe Post labeling kit (Amersham Biosciences) according to the supplier's instructions.

growth_protocol: L. lactis strains were incubated in M17 containing 0.5% glucose (GM17) at 30 ºC without shaking

extract_protocol: RNA was isolated from 50 ml of cells grown to midexponential phase of growth (A600 = 0.4). Cells were harvested by centrifugation for 1 min at 10,000 rpm at room temperature. Cell pellets were immediately frozen in liquid nitrogen and stored at –80 °C. Pellets were resuspended in 500 µl of 10 mM Tris-HCl, 1 mM EDTA (T10E1), pH 8.0, after which 50 µl of 10% SDS, 500 µl of phenol/chloroform, 500 mg of glass beads (75–150 µm), and 175 µl of Macaloid suspension (Bentone) were added. Further purification was done using the High Pure RNA isolation (Roche), using the suppliers protocol.

value: Wild type

label: Net intensity (tr.mean) {B} {Cy3}

source_name: Lactococcus lactis D1

value: Lcn972R mutant


title: diploid_male_11d_homozygote_SBSB_colony_Q2_350

source_name: 11-day-old diploid male homozygote SB/SB

tag: genotype

value: SB/SB


title: diploid_male_1d_homozygote_SBSB_colony_Q4_356

source_name: 1-day-old diploid male homozygote SB/SB


title: Post-operation cyanotic normoxic CC4B


title: Post-operation cyanotic hyperoxic CC6B

value: corrective surgery using hyperoxic/standard cardiopulmonary bypass.


title: diploid_male_1d_homozygote_SBSB_colony_Q2_356


title: queen_1d_heterozygote_SBSb_colony_Pg347

description:
Re-analysis of GSM1031742
RNA from the whole body of an individual ant of specific genotype and age

source_name: 1-day-old queen heterozygote SB/Sb

value: queen


title: Post-operation cyanotic normoxic CC10B


title: queen_1d_heterozygote_SBSb_colony_Pg346

description:
Re-analysis of GSM1031746
RNA from the whole body of an individual ant of specific genotype and age


title: diploid_male_1d_homozygote_SBSB_colony_Q2_350


title: diploid_male_1d_homozygote_SBSB_colony_Q2_346


title: Post-operation cyanotic normoxic CC9B


title: slide-164942


title: diploid_male_1d_homozygote_SBSB_colony_Q2_383


title: slide-164941

description: wt versus Lcn972R mutant

label: Net intensity (tr.mean) {A} {Cy3}

label: Net intensity (tr.mean) {B} {Cy5}


title: Post-operation cyanotic hyperoxic CC15B

value: corrective surgery using hyperoxic/standard cardiopulmonary bypass


title: Post-operation cyanotic normoxic CC7B


title: slide-171113

description: Biological replicate of wt versus Lcn972R mutant


title: queen_1d_heterozygote_SBSb_colony_Pg359

description:
Re-analysis of GSM1031745
RNA from the whole body of an individual ant of specific genotype and age


title: Post-operation cyanotic hyperoxic CC1B


title: Post-operation cyanotic hyperoxic CC19B


title: Post-operation cyanotic hyperoxic CC3B


title: queen_1d_homozygote_SBSB_colony_Pg343

description:
Re-analysis of GSM1031732
RNA from the whole body of an individual ant of specific genotype and age

source_name: 1-day-old queen homozygote SB/SB


title: Uveal melanoma from enucleation 51 [UCSF]

hyb_protocol: DNA was hybridized to the arrays at 37 °C for over 16-72 h in 50% formamide, 2 x SSC, 10% dextran sulfate, 4% SDS and 500 μg yeast tRNA, pH 7.

scan_protocol: 16 bit 1024x1024 pixel DAPI, Cy3 (test) and Cy5 (control) images using a custom built CCD camera system. “UCSF SPOT” software was used to automatically analyze the spots based on the DAPI images, and to calculate log2ratios of the total integrated Cy3 and Cy5 intensities for each spot.

data_processing: SPROC software was used to reject data based on low reference/DAPI signal intensity and low correlation of the Cy3 and Cy5 intensities with a spot.

source_name: Uveal melanoma from enucleation 51

label_protocol: 1μg of reference and test sample genomic DNA were individually fluorescently labeled using the BioPrime DNA Labeling System following manufacturer's protocol.

value: Fresh frozen sample from enucleated eye

tag: disease

value: Primary uveal melanoma tumor

tag: gep class

source_name: Normal Human Male Reference DNA

tag: reference

value: Normal Human Male Reference DNA


title: queen_1d_homozygote_SBSB_colony_Pg329

description:
Re-analysis of GSM1031733
RNA from the whole body of an individual ant of specific genotype and age

source_name: Reference RNA batch 2006

tag: tissue

value: whole organism

value: year 2006


title: queen_1d_homozygote_SBSB_colony_Pg359

description:
Re-analysis of GSM1031737
RNA from the whole body of an individual ant of specific genotype and age

value: Amplified total RNA isolated en masse from hundreds of adult workers collected from the foraging area of 30 colonies (eight and seven of each social form from Georgia and Louisiana, respectively)

tag: age


title: queen_1d_heterozygote_SBSb_colony_Pg329

description:
Re-analysis of GSM1031741
RNA from the whole body of an individual ant of specific genotype and age

value: SB/Sb


title: queen_1d_homozygote_SBSB_colony_Pg346

description:
Re-analysis of GSM1031738
RNA from the whole body of an individual ant of specific genotype and age


title: queen_1d_heterozygote_SBSb_colony_Pg343

description:
Re-analysis of GSM1031740
RNA from the whole body of an individual ant of specific genotype and age


title: Uveal melanoma from enucleation 60 [UCSF]

source_name: Uveal melanoma from enucleation 60


title: Uveal melanoma from enucleation 55 [UCSF]

source_name: Uveal melanoma from enucleation 55


title: Uveal melanoma from enucleation 49 [UCSF]

source_name: Uveal melanoma from enucleation 49


title: Uveal melanoma from enucleation 63 [UCSF]

source_name: Uveal melanoma from enucleation 63


title: Uveal melanoma from enucleation 46 [UCSF]

source_name: Uveal melanoma from enucleation 46


title: Uveal melanoma from enucleation 48 [UCSF]

source_name: Uveal melanoma from enucleation 48


title: Uveal melanoma from enucleation 61 [UCSF]

source_name: Uveal melanoma from enucleation 61


title: Uveal melanoma from enucleation 54 [UCSF]

source_name: Uveal melanoma from enucleation 54


title: queen_1d_homozygote_SBSB_colony_Pg347

description:
Re-analysis of GSM1031734
RNA from the whole body of an individual ant of specific genotype and age


title: haploid_male_pupa_SB_colony_Q3_350_H

description: RNA from the whole body of an individual ant of specific genotype and age

source_name: haploid male pupa heterozygote SB

value: haploid male

value: SB

value: pupa


title: Uveal melanoma from enucleation 41 [UCSF]

source_name: Uveal melanoma from enucleation 41


title: haploid_male_pupa_Sb_colony_Q7_329

source_name: haploid male pupa homozygote Sb

value: Sb


title: haploid_male_pupa_SB_colony_Q4_97


title: haploid_male_pupa_SB_colony_Q7_329


title: haploid_male_pupa_Sb_colony_Q5_115


title: haploid_male_pupa_SB_colony_Q5_115


title: haploid_male_pupa_Sb_colony_Q4_97


title: Uveal melanoma from enucleation 37 [UCSF]

source_name: Uveal melanoma from enucleation 37


title: Uveal melanoma from enucleation 35 [UCSF]

source_name: Uveal melanoma from enucleation 35


title: Uveal melanoma from enucleation 16 [UCSF]

source_name: Uveal melanoma from enucleation 16


title: Uveal melanoma from enucleation 28 [UCSF]

source_name: Uveal melanoma from enucleation 28


title: Uveal melanoma from enucleation 33 [UCSF]

source_name: Uveal melanoma from enucleation 33

source_name: Normal Human Male Reference DNA


title: Uveal melanoma from enucleation 32 [UCSF]

source_name: Uveal melanoma from enucleation 32


title: Uveal melanoma from enucleation 10 [UCSF]

source_name: Uveal melanoma from enucleation 10


title: Uveal melanoma from enucleation 13 [UCSF]

source_name: Uveal melanoma from enucleation 13


title: diploid_male_pupa_homozygote_SBSB_colony_Q4_356

source_name: Reference RNA batch 2006

source_name: diploid male pupa homozygote SB/SB

value: diploid male


title: haploid_male_pupa_Sb_colony_Q3_350_H


title: diploid_male_pupa_homozygote_SBSB_colony_Q2_346


title: diploid_male_pupa_homozygote_SBSB_colony_Q2_383


title: Uveal melanoma from enucleation 18 [UCSF]

source_name: Uveal melanoma from enucleation 18


title: haploid_male_pupa_Sb_colony_Q2_346_H


title: diploid_male_pupa_heterozygote_SBSb_colony_Q2_346

source_name: diploid male pupa heterozygote SB/Sb


title: diploid_male_pupa_heterozygote_SBSb_colony_Q4_356


title: B6 control heart-rep2

description:
Gene expression data of B6 control heart
B6-2

hyb_protocol: For hybridization, 15 µg of fragmented cRNA were incubated with the chip (Mouse Genome MG430 2.0 Array) in 200 µl of the hybrization solution in a Hybridization Oven 640 (Affymetrix) for 16 h at 45 °C. GeneChips were then washed and stained using the Affymetrix Fluidics Station 450 according to the GeneChip Expression Analysis Technical Manual (Rev. 5).

data_processing: The signals were processed using Affymetrix GeneChip Operating Software (GCOS; v.1.4; Affymetrix). To compare samples and experiments, the trimmed mean signal of each array was scaled to a target intensity of 300.

source_name: B6 control heart

label_protocol: Biotinylated cRNA was prepared according to the protocol of the manufacturer (Affymetrix; GeneChip Expression Analysis Technical Manual;and Invitrogen manual for SuperScript One-Cycle cDNA Kit).

growth_protocol: The study was performed with heart tissue isolated from a transgenic mouse line expressing RKIP under control of the myocardium-specific alpha-MHC promoter. For comparison, a transgenic mouse line with myocardium-specific expression of a GRK-specific peptide inhibitor (GRK-Inh) was used. The third group consisted of B6 control mice.

extract_protocol: Total RNA was isolated from heart tissue with the RNeasy Midi kit according to the manufacturer`s instructions (Qiagen).

treatment_protocol: For the microarray study, hearts were isolated from three study groups: (i) RKIP-transgenic mice, (ii) GRK-Inh-transgenic mice, and (iii) B6 control mice.

tag: strain background

tag: genotype/variation

value: wild type (control)

tag: gender

value: male

value: 2 months

value: heart


title: diploid_male_pupa_heterozygote_SBSb_colony_Q2_350


title: diploid_male_pupa_homozygote_SBSB_colony_Q2_350

value: SB/SB


title: diploid_male_pupa_heterozygote_SBSb_colony_Q2_383


title: diploid_male_pupa_heterozygote_SBSb_colony_Q2_327


title: B6 control heart-rep1

description:
Gene expression data of B6 control heart
B6-1


title: RKIP-transgenic heart-rep2

description:
Gene expression data of RKIP-transgenic heart
RKIP-2

source_name: RKIP-transgenic heart

value: RKIP-transgenic (expressing RKIP under control of the myocardium-specific alpha-MHC promoter)


title: GRK-Inh-transgenic heart-rep1

description:
Gene expression data of GRK-Inh-transgenic heart
GRK-Inh-1

source_name: GRK-Inh-transgenic heart

value: GRK-Inh-transgenic (myocardium-specific expression of a GRK-specific peptide inhibitor)


title: diploid_male_pupa_homozygote_SBSB_colony_Q2_327


title: RKIP-transgenic heart-rep1

description:
Gene expression data of RKIP-transgenic heart
RKIP-1


title: queen_pupa_heterozygote_SBSb_colony_Q3_350_H

source_name: queen pupa heterozygote SB/Sb

value: queen


title: queen_pupa_heterozygote_SBSb_colony_Q5_115

value: whole organism


title: queen_pupa_heterozygote_SBSb_colony_Q2_359

value: year 2006


title: queen_pupa_homozygote_SBSB_colony_Q5_115

value: Amplified total RNA isolated en masse from hundreds of adult workers collected from the foraging area of 30 colonies (eight and seven of each social form from Georgia and Louisiana, respectively)

source_name: queen pupa homozygote SB/SB


title: queen_pupa_heterozygote_SBSb_colony_Q2_346_H

value: SB/Sb


title: queen_pupa_heterozygote_SBSb_colony_Q3_347


title: queen_pupa_homozygote_SBSB_colony_Q3_350_H


title: Mouse ex-iTreg cells, replicate pool 1

city: Milwaukee

first: Martin

last: Hessner

state: WI

address: 8701 Watertown Plank Road

department: Pediatrics

institute: Medical College of Wisconsin

description:
Gene expression interrogating 45101 transcripts
exiTreg 1 erica mouse 10-5-11_(Mouse430_2).CEL

hyb_protocol: Purified total RNA (~50ng) was amplified using the two-cycle cDNA synthesis kit (Affymetrix  900432) and cRNA was synthesized,  labeled,  fragmented and hybridized to the arrays in accordance to standard Affymetrix protocols (Affymetrix,  Santa Clara,  CA)

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: For all the iTregs, nTregs, and ex-iTreg experiments, two sets of arrays were performed, and the results were averaged. The subset of probe sets whose expression increased or decreased by twofold or more relative to Native (not activated) conventional CD4+T cells (GSE14415) as a common standard was identified and used for further analysis. The data was normalized using the RMA algorithm from the Bioconductor suite. Results represent mean fold change values derived from 2 independent arrays for each cell type and FDR<10% by the Rank Product package from Bioconductor.

source_name: ex-iTreg

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: Foxp3EGFP, Foxp3(delta)EGFP on the BALB/c background were generated and screened as described in Haribhai, et.al. (J Immunol 178:2961-2972, 2007). BALB/c Rag1–/– mice and Il10–/– mice were obtained from the Jackson Laboratory.  Il10–/– mice were crossed to Foxp3EGFP mice.  The Animal Resource Committees at the Medical College of Wisconsin approved all animal experiments and moribund mice were sacrificed and analyzed per these protocols.

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

treatment_protocol: Pooled splenocytes and mesenteric lymph node cells were stained with anti-CD4-Pacific blue and sorted on the basis of antibody and EGFP fluorescence.  Cultured iTreg cells were sorted on the basis of EGFP fluorescence.  All sorting was done on a FACSAria (Becton-Dickenson). The average purity and viability of the sorted CD4+ populations was 98.96+/–0.14% and 84.31+/–0.68% respectively (n=120). For the treatment experiments, 1 ml of a cell suspension in PBS was injected into the peritoneal cavity of colitis mice that had lost 2.5+/– 5.7% of their initial body weight.

tag: strain

value: BALB/c

tag: treatment

value: WT nTreg + WT iTreg

tag: cell type (sorted)

value: ex-iTreg


title: queen_pupa_homozygote_SBSB_colony_Q2_359

tag: batch

value: pupa


title: Uveal melanoma from enucleation 56 [UCSF]

source_name: Uveal melanoma from enucleation 56

value: Fresh frozen sample from enucleated eye

value: Primary uveal melanoma tumor

value: Normal Human Male Reference DNA


title: GRK-Inh-transgenic heart-rep2

description:
Gene expression data of GRK-Inh-transgenic heart
GRK-Inh-2

value: male

value: 2 months


title: queen_pupa_homozygote_SBSB_colony_Q3_347

tag: sample type

value: SB/SB


title: Mouse stable invitro iTreg cells, replicate pool 2

description:
Gene expression interrogating 45101 transcripts
iTreg 2 erica mouse 10-5-11_(Mouse430_2).CEL

source_name: iTreg

value: iTreg


title: Mouse ex-iTreg cells, replicate pool 2

description:
Gene expression interrogating 45101 transcripts
exiTreg 2 erica mouse 10-5-11_(Mouse430_2).CEL


title: haploid_male_pupa_SB_colony_Q2_346_H

source_name: haploid male pupa heterozygote SB

tag: caste

value: haploid male

value: SB


title: Mouse invivo nTreg cells, replicate pool 2

description:
Gene expression interrogating 45101 transcripts
nTreg 2 erica mouse 10-5-11_(Mouse430_2).CEL

source_name: nTreg

value: nTreg


title: queen_pupa_homozygote_SBSB_colony_Q2_346_H

value: whole organism

value: year 2006

value: queen


title: Knockout-cultured keratinocytes from litter C

first: Bradley

middle: A

last: Carlson

address: 9000 Rockville Pike

description: Biological replicate 3 of 3.

hyb_protocol: Hybridization was done according to the manufacturer’s instructions.

scan_protocol: Arrays were scanned on the GeneChip Scanner 3000 (Affymetrix) and image analysis was performed using GCOS 1.3 (Affymetrix).

data_processing: For data processing, data files (in txt format) and cel files were imported into the microarray database (mAdb) and analyzed by software tools provided by the National Cancer Institute, Center for Cancer Research in collaboration with the National Institutes of Health, Center for Information Technology, Bioinformatics and Molecular Analysis Section. All Absent calls were excluded.

source_name: primary keratinocytes derived from skin

label_protocol: GeneChip® IVT Labeling Kit according to manufacturers instructions

growth_protocol: Primary keratinocytes were isolated from newborn mice and cultured, with all media, both for preparation and culture of primary keratinocytes containing 100 nM sodium selenite.

extract_protocol: Total RNA was extracted using Trizol (Invitrogen) following manufacturer's instructions

tag: genetic background

tag: cell type

value: primary keratinocytes derived from skin

value: Gpx4 KO

value: newborn mice


title: Mouse stable invitro iTreg cells, replicate pool 1

description:
Gene expression interrogating 45101 transcripts
iTreg 1 erica mouse 10-5-11_(Mouse430_2).CEL

value: BALB/c

value: WT nTreg + WT iTreg


title: Knockout-cultured keratinocytes from litter B

description: Biological replicate 2 of 3.

tag: genotype


title: Mouse invivo nTreg cells, replicate pool 1

description:
Gene expression interrogating 45101 transcripts
nTreg 1 erica mouse 10-5-11_(Mouse430_2).CEL


title: Control-cultured keratinocytes from litter C

description: Biological replicate 3 of 3.

value: control


title: Knockout-cultured keratinocytes from litter A

description: Biological replicate 1 of 3.


title: Control-cultured keratinocytes from litter B

description: Biological replicate 2 of 3.


title: IL-1Rko_4hr-rep1

status: Public on Dec 05 2012

city: Los Angeles

first: Lloyd

last: Miller

state: CA

address: 52-121 Center for Health Sciences, 10833 Le Conte Avenue

department: Medicine, Orthopaedic Surgery

institute: UCLA

hyb_protocol: 12.5 ug of aRNA was used for target hybridization for 16 hours at 45 degrees C on GeneChip Mouse 430 2.0 arrays, using the GeneChip Hybridization, Wash, and Stain Kit.  Arrays were washed and scanned in the Affymetrix Fluidics Station 400.

scan_protocol: Arrays were scanned using the Affymetrix Scanner 3000 7g

data_processing: CEL files were normalized and compiled in DCHIP (site).  Batch correction was performed according to the data of sample collection (2 batches).  Data were normalized using  the invarient-set method. Model-based expression values were calcualated based on perfect match/mismatch probe difference and smoothing was done using the running median method.  All samples had percent present calls > 40%.

source_name: IL-1R knock-out mouse 4 hrs after Staph aureus infection

label_protocol: Biotinylated aRNA were prepared according to the standard GeneChip 3' IVT Express Kit User Manual from 250ng of total RNA.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. RNA was futher processed using RNeasy Mini kit (Qiagen) according to the manufacturer's instructionsl

treatment_protocol: Skin punch biopsy (8 mm) specimens from uninfected or lesional skin were taken at 4 hrs after S. aureus intradermal inoculation from wt and IL 1R-deficient mice and snap-frozen in Trizol solution.

value: Lesional skin biopsies

value: IL-1R knock-out


title: IL-1Rko_4hr-rep2


title: Control-cultured keratinocytes from litter A

description: Biological replicate 1 of 3.


title: IL-1Rko_0hr-rep3

source_name: IL-1R knock-out mouse without Staph aureus infection


title: IL-1Rko_0hr-rep1


title: IL-1Rko_4hr-rep3


title: IL-1Rko_0hr-rep2


title: WT_4hr-rep1

source_name: Wild-type mouse 4 hrs after Staph aureus infection

value: wild type


title: WT_4hr-rep2


title: WT_0hr-rep2

source_name: Wild-type mouse without Staph aureus infection


title: WT_4hr-rep3


title: WT_0hr-rep1


title: OVX+E2+Ralox

city: Quebec

first: Ezequiel

middle: L

last: Calvo

state: Quebec

address: 2705 Boul. Laurier

department: Molecular Endocrinilogy

country: Canada

institute: CRCHUL

description: Raw data file: R136-03FX9A05C1.CEL

hyb_protocol: Fragmented cRNA (15 ug) was incubated with 1x hybridization buffer (0.1 mg/ml herring sperm DNA, 0.5 mg/ml acetylated BSA, 5 nM control oligonucleotide B2) and 1x eukaryotic hybridization control solution (1.5 pM BioB, 5 pM BioC, 25 pm BioD, and 100 pM cre), for 16h at 45°C with constant rotation (60 rpm). Microarrays were processed using an Affymetrix GeneChip Fluidic Station 400 (protocol EukGE-WS2Av4). Staining was performed with streptavidin-conjugated phycoerythrin (SAPE) followed by amplification with a biotinylated anti-streptavidin antibody and by a second round of SAPE solution.

scan_protocol: GeneChips were scanned using an Agilent GeneArray Scanner (Agilent Technologies).

data_processing: RMA

source_name: Mammary gland of OVX mice, treated with estradiol plus raloxifen

label_protocol: Total mRNA (20 ug) was converted to cDNA by incubation with 400 U SuperScript II reverse transcriptase (Invitrogen) using a T7- oligo-(dt)24 primer [5‑GGCCAGTGAATTGTAATACGACTCACTATAGGGAGGCGG-(dt)24-3_] 1‑first‑strand buffer (50 mM Tris‑HCl pH 8.3, 75 mM KCl, 3 mM MgCl2, 10 mM DTT) and 0.5 mM dNTPs at 42°C for 1h. Second-strand synthesis was performed using 40 U DNA polymerase I (Invitrogen), 10 U Escherichia coli DNA ligase (Invitrogen), 2 U RNase H (Invitrogen), reaction buffer [18.8 mM Tris‑HCl pH 8.3, 90.6 mM KCl, 4.6 mM MgCl2, 3.8 mM DTT, 0.15 mM NAD, 10 mM (NH4)2SO4] and 0.2 mM dNTPs at 16°C for 2 h. cDNAs were blunt-ended with 10 U of T4 DNA polymerase (Invitrogen) incubated 5 min at 16°C. cDNA was extracted with phenol-chloroform using phase lock gels (Brinkman, Mississauga, Ontario, Canada), ethanol precipitated, and resuspended in 10 µl of DEPC-treated H2O. cDNA was in vitro transcribed using a T7 BioArray High Yield RNA Transcript Labeling Kit (Enzo Diagnostics, Farmingdale, NY) to produce biotinylated cRNA. The mixture (20 µl final volume) was incubated at 37°C for 5h, with gentle mixing every 30 min. Labeled cRNA was purified with an RNeasy Mini Kit (Qiagen, Valencia, CA) according to the manufacturer’s protocol. Purified cRNA was fragmented to 30–200 mer using a fragmentation buffer (100 mM potassium acetate, 30 mM magnesium acetate, 40 mM Tris-acetate pH 8.1), for 20 min at 94°C.

growth_protocol: Eleven to twelve week-old female C57BL6 mice obtained from Harlan Sprague Dawley (Indianapolis, IN) were allowed to acclimatate for 1 week after their arrival. Animals weighing between 17 to 23 g (average of 20g) were randomized according to their body weights and were assigned to experimental groups of 8 animals each. Ovariectomy was performed under isoflurane-induced anesthesia 7 days prior to treatment.

extract_protocol: Mammary glands from all mice of the same group were collected, rapidly trimmed, snap-frozen in liquid nitrogen and stored at -80°C until mRNA extraction. Total mRNA was isolated with TRIzol (Invitrogen, Burlington, Ontario) following the manufacturer’s protocol.

treatment_protocol: EM-652.HCl (acolbifene), tamoxifen citrate, raloxifene or ICI 182780 (fulvestrant), were administered to ovariectomized (OVX) mice or to OVX mice simultaneously treated with 17b-estradiol (E2; 0.05 mg/mouse; single sc injection). Mice from the OVX control group received an injection of the vehicle alone. All animals were sacrificed 3h after treatment.

value: estradiol plus raloxifen

value: Mammary gland


title: OVX+E2+TAM

description: Raw data file: R136-03FX8A05C1.CEL

source_name: Mammary gland of OVX mice, treated with estradiol plus tamoxifen

value: estradiol plus tamoxifen


title: WT_0hr-rep3


title: OVX+ICI

description: Raw data file: R136-03FX4A05C1.CEL

source_name: Mammary gland of OVX mice, treated with fulvestrant

value: fulvestrant


title: OVX+E2+EM-rep2

description: Raw data file: R137-03FX5A05C1-R2.CEL

source_name: Mammary gland of OVX mice, treated with estradiol plus acolbifene

value: estradiol plus acolbifene


title: OVX+E2+EM-rep1

description: Raw data file: R137-03FX5A05C1-R1.CEL


title: OVX+TAM

description: Raw data file: R136-03F15A05C1.CEL

source_name: Mammary gland of OVX mice, treated with tamoxifen

value: tamoxifen


title: OVX+Ralox

description: Raw data file: R136-03FX5A05C1.CEL

source_name: Mammary gland of OVX mice, treated with raloxifen

value: raloxifen


title: Osteosarcoma cell line ZK-58 [copy number]

description: Osteosarcoma cell line ZK-58 Affymetrix SNP 6

hyb_protocol: Standard Affymetrix hyb protocol

scan_protocol: Standard Affymetrix scan protocol

data_processing: Quality control was performed using the Genotyping Console v3.0.1 software (Affymetrix), applying the contrast quality control (CQC) algorithm with a minimal call rate of > 86 %. DNA copy number analysis was performed using the Nexus software (BioDiscovery, California, USA), with the SNPRank segmentation algorithm using default settings (threshold of 0.6 for high copy gain, 0.2 for gain, -0.2 for loss and -1.0 for homozygous loss).

source_name: Osteosarcoma cell line ZK-58

label_protocol: Standard Affymetrix label protocol

tag: cell line

value: Osteosarcoma

tag: sample origin

value: Not available

value: male

tag: age (yrs)


title: OVX+EM-rep1

description: Raw data file: R137-03F12A05C1-R1.CEL

source_name: Mammary gland of OVX mice, treated with acolbifene

value: acolbifene

tag: tissue


title: Osteosarcoma cell line Saos-2 [copy number]

description: Osteosarcoma cell line Saos-2 Affymetrix SNP 6

source_name: Osteosarcoma cell line Saos-2

value: female

tag: atcc number


title: Osteosarcoma cell line U-2 OS [copy number]

description: Osteosarcoma cell line U-2 OS Affymetrix SNP 6

source_name: Osteosarcoma cell line U-2 OS

value: U-2 OS


title: OVX+EM-rep2

description: Raw data file: R137-03F12A05C1-R2.CEL


title: OVX-rep2

description: Raw data file: R137-03F02D05C2-R2.CEL

source_name: Mammary gland of OVX mice, treated with vehicle

value: vehicle


title: OVX+E2-rep2

description: Raw data file: R137-03F04A05C1.CEL

source_name: Mammary gland of OVX mice, treated with estradiol

value: estradiol


title: OVX+E2-rep1

description: Raw data file: R136-03F04A05C1.CEL