title: S_coelicolor_WL6268_19hr_replicate_1

source_name: S. coelicolor RNA R5- medium 19hr


title: S_coelicolor_WL6268_19hr_replicate_2

status: Public on Oct 25 2010

type: mixed

city: Minneapolis

first: Marlene

last: Castro-Melchor

state: MN

address: 421 Washington Ave SE

department: Department of Chemical Engineering and Materials Science

country: USA

institute: University of Minnesota

hyb_protocol: The labeled cDNA and gDNA were then mixed and co-hybridized to microarray slides in the presence of 50% formamide. After 16 hours incubation at 50°C, slides were washed and scanned.

scan_protocol: Arrays were scanned using ScanArray5000 (Perkin Elmer, Wellesley, MA). Images were analyzed using GenePix (Axon Instruments, Union City, CA) to obtain raw intensity data for each spot. The median fluorescence intensity from each spot was used for all subsequent analysis.

data_processing: A quantile normalization method was employed to normalize these log2 ratios from each hybridization (S Mehra, W Lian, KP Jayapal, SP Charaniya, DH Sherman, WS Hu: A framework to analyze multiple time series data: a case study with Streptomyces coelicolor. J Ind Microbiol Biotechnol 2006, 33:159-72). The resulting log2 ratios were not only used to compare transcript levels of the same mRNA species in different biological samples, but also used as an estimate of the relative abundance of each mRNA species.

molecule: total RNA

organism: Streptomyces coelicolor

label_protocol: The cDNA was then incubated with Alexa 647 (Invitrogen, Carlsbad, CA) for labeling as per manufacturer's instructions.

growth_protocol: S. coelicolor A3(2) strain WL6268 was maintained on R5 solid agar (Kieser, T., M. J. Bibb, M. J. Buttner, K. F. Chater, and D. A. Hopwood. 2000. Practical Streptomyces Genetics. The John Innes Foundation, Norwich, UK) for high density spores. For liquid culture, spores were pre-germinated in 2xYT medium (Kieser, T., M. J. Bibb, M. J. Buttner, K. F. Chater, and D. A. Hopwood. 2000. Practical Streptomyces Genetics. The John Innes Foundation, Norwich, UK) and inoculated into R5- liquid medium (Huang, J., C. J. Lih, K. H. Pan, and S. N. Cohen. 2001. Global analysis of growth phase responsive gene expression and regulation of antibiotic biosynthetic pathways in Streptomyces coelicolor using DNA microarrays. Genes Dev 15:3183-92) at a density of ~10exp7 spores/ml. Baffled 2L flasks containing stainless steel coils with 350 ml working volume were used for liquid cultures. Cultures were incubated at 30°C in an orbital shaker at 300 rpm. For measuring cell growth, samples were collected at regular intervals and mixed with one-eighth volume of 2.5 M HCl and then subjected to sonication to break mycelial pellets (Brana, A. F., S. Wolfe, and A. L. Demain. 1986. Relationship between nitrogen assimilation and cephalosporin synthesis in Streptomyces clavuligerus. Arch Microbiol 146:46-51). Absorbance of the resulting solution at 450 nm was then taken as a measure of growth. Proper dilution was made to ensure an OD450 measurement below 1, which is in the linear range of detection.

extract_protocol: Immediately after culture samples were collected, one-fifth volume of an ice-cold stop solution (5% phenol in ethanol) (Bernstein, J. A., A. B. Khodursky, P. H. Lin, S. Lin-Chao, and S. N. Cohen. 2002. Global analysis of mRNA decay and abundance in Escherichia coli at single-gene resolution using two-color fluorescent DNA microarrays. Proc Natl Acad Sci U S A 99:9697-702) was added to the sample volume to prevent RNA degradation. The sample was quickly centrifuged at 4°C and the supernatant was discarded. The remaining sample was then stored at -80°C. To isolate RNA, the frozen pellets were transferred to a mortar and pestle and ground to fine powder in the presence of liquid nitrogen. RLT solution from RNeasy Mini Kit (Qiagen Inc., Valencia, CA) was added before the ground pellets thawed. The remaining steps for RNA isolation were carried out as per manufacturer’s instructions. RNA integrity was determined by gel electrophoresis while its quantity and purity were estimated by UV absorbance at OD260 and OD260/OD280, respectively. Total RNA was reverse transcribed to cDNA by SuperscriptII (Invitrogen, Carlsbad, CA) with random hexamers (IDT, Coralville, IA) incorporating aminoallyl-dUTP (Ambion, Austin, TX).

tag: strain

tag: time

tag: replicate

molecule: genomic DNA

source_name: S. coelicolor genomic DNA

label_protocol: The DNA was labeled with Label IT® Cy3 Labeling Kit (Mirus Bio Corp., Madison, WI) according to suppliers instructions.

growth_protocol: Spores for S. coelicolor M145 were generated on Mannitol-Soy flour or R5 agar Cultures for genomic DNA preparation were performed in YEME medium with 0.5% glycine supplement at 30°C until early stationary phase (refer to T Kieser, MJ Bibb, MJ Buttner, KF Chater, DA Hopwood: Practical Streptomyces Genetics: The John Innes Foundation, Norwich, UK; 2000).

extract_protocol: Genomic DNA (gDNA) extraction was carried out using Kirby mix procedure as described elsewhere (T Kieser, MJ Bibb, MJ Buttner, KF Chater, DA Hopwood: Practical Streptomyces Genetics: The John Innes Foundation, Norwich, UK; 2000). About 500 µl of 20 µg/µl gDNA was sonicated briefly for 30-40 sec for shearing them to ~500 bp average size (confirmed by gel electrophoresis).


title: S_coelicolor_WL6268_16hr_replicate_2

source_name: S. coelicolor RNA R5- medium 16hr


title: S_coelicolor_WL6268_25hr_replicate_1

source_name: S. coelicolor RNA R5- medium 25hr


title: E30 HS 1hr rec 3hr vs. NS rep1

type: RNA

city: Mississauga

first: Zak

last: Razak

state: Ontario

address: 3359 Mississauga Rd

country: Canada

institute: Canadian Drosophila Microarray Centre

hyb_protocol: differently labeled samples, heat shocked and non heat shocked of the same genotype, were pooled and cohybridized to the 14K long oligo array from the Canadian Drosophila Microarray Centre (www.flyarrays.com) according to previously described methods (Neal, 2002)

scan_protocol: Images of the hybridized microarrays were obtained using a ScanArray 4000 scanner (Perkin-Elmer) and were quantified using QuantArray 3.0 software (Perkin-Elmer)

data_processing: Data were normalized using lowest sub-grid normalization (Yang, 2002) and Genetraffic Duo (Stratagene /Agilent) analysis software.

organism: Drosophila melanogaster

source_name: Drosophila melanogaster, E30 Heat Shocked at 37 degrees C for 1hr, 3 hrs recovery

label_protocol: Total RNA samples were labeled using the ‘indirect’ method (Semotok 2008)

growth_protocol: Strains used in these studies were maintained on standard yeast-agar media in a 25°C incubator, and include Oregon-R, tubulin (tub)-GAL4 (Bloomington No. 5138), nanos (nos)-GAL4 (Bloomington No. 4442), mwh1 (Bloomington No. 549), Hsp70- (also referred to as Df(3R)Hsp70A, Df(3R)Hsp70B) (Bloomington No. 8841), Hsp70B- (also referred to as Df(3R)Hsp70B) (Bloomington No. 8843), and hsf4 (Bloomington No. 5489).

extract_protocol: total RNA was extracted with TRIzol reagent according to the manufacture's protocol. RNA quality was evaluated using spectrophotometry and integrity was confirmed using gel electrophoresis of glyoxal-denatured samples.  Samples were cleaned using MEGAclear kit (Ambion AM1908).

tag: treatment

value: heat shocked at 37 degrees C for 1hr, 3 hrs recovery

source_name: Drosophila melanogaster, E30 flies

value: non-shocked


title: UAS-Mnn-1 HS 1hr rec 3hr vs. NS rep3

source_name: Drosophila melanogaster, nos-GAL4 Heat Shocked at 37 degrees C for 1hr, 3 hrs recovery

source_name: Drosophila melanogaster, nos-GAL4 flies


title: S_coelicolor_WL6268_12hr

source_name: S. coelicolor RNA R5- medium 12hr


title: nos-GAL4 HS 1hr rec 3hr vs. NS rep1


title: S_coelicolor_YSK3654_37hr_replicate_2

source_name: S. coelicolor RNA R5- medium 37hr

growth_protocol: S. coelicolor A3(2) strain YSK3654 was maintained on R5 solid agar (Kieser, T., M. J. Bibb, M. J. Buttner, K. F. Chater, and D. A. Hopwood. 2000. Practical Streptomyces Genetics. The John Innes Foundation, Norwich, UK) for high density spores. For liquid culture, spores were pre-germinated in 2xYT medium (Kieser, T., M. J. Bibb, M. J. Buttner, K. F. Chater, and D. A. Hopwood. 2000. Practical Streptomyces Genetics. The John Innes Foundation, Norwich, UK) and inoculated into R5- liquid medium (Huang, J., C. J. Lih, K. H. Pan, and S. N. Cohen. 2001. Global analysis of growth phase responsive gene expression and regulation of antibiotic biosynthetic pathways in Streptomyces coelicolor using DNA microarrays. Genes Dev 15:3183-92) at a density of ~10exp7 spores/ml. Baffled 2L flasks containing stainless steel coils with 350 ml working volume were used for liquid cultures. Cultures were incubated at 30°C in an orbital shaker at 300 rpm. For measuring cell growth, samples were collected at regular intervals and mixed with one-eighth volume of 2.5 M HCl and then subjected to sonication to break mycelial pellets (Brana, A. F., S. Wolfe, and A. L. Demain. 1986. Relationship between nitrogen assimilation and cephalosporin synthesis in Streptomyces clavuligerus. Arch Microbiol 146:46-51). Absorbance of the resulting solution at 450 nm was then taken as a measure of growth. Proper dilution was made to ensure an OD450 measurement below 1, which is in the linear range of detection.


title: S_coelicolor_WL6268_16hr_replicate_1


title: E30 HS 1hr rec 3hr vs. NS rep2


title: E30 HS 1hr rec 3hr vs. NS rep3

source_name: Drosophila melanogaster, UAS-Mnn-1 Heat Shocked at 37 degrees C for 1hr, 3 hrs recovery

source_name: Drosophila melanogaster, UAS-Mnn-1 flies


title: UAS-Mnn-1-RNAi HS 1hr vs NS rep1

source_name: Drosophila melanogaster, UAS-Mnn-1-RNAi Heat Shocked at 37 degrees C for 1hr

value: heat shocked at 37 degrees C for 1hr

source_name: Drosophila melanogaster, UAS-Mnn-1-RNAi flies


title: UAS-Mnn-1 HS 1hr rec 3hr vs. NS rep1


title: UAS-Mnn-1 HS 1hr rec 0hr vs. NS rep2

source_name: Drosophila melanogaster, UAS-Mnn-1 Heat Shocked at 37 degrees C for 1hr


title: UAS-Mnn-1 HS 1hr rec 3hr vs. NS rep2


title: UAS-Mnn-1-RNAi HS 1hr vs NS rep2


title: UAS-Mnn-1-RNAi HS 1hr vs NS rep3

source_name: Drosophila melanogaster, E30 Heat Shocked at 37 degrees C for 1hr


title: nos-GAL4 HS 1 hr rec 0hr vs. NS rep3


title: UAS-Mnn-1 HS 1hr rec 0hr vs. NS rep3


title: UAS-Mnn-1 HS 1hr rec 0hr vs. NS rep1


title: S_coelicolor_YSK3654_37hr_replicate_1


title: S_coelicolor_YSK3654_35hr_replicate_2

source_name: S. coelicolor RNA R5- medium 35hr


title: S_coelicolor_YSK3654_25hr_replicate_1


title: S_coelicolor_YSK3654_31hr_replicate_1

source_name: S. coelicolor RNA R5- medium 31hr


title: S_coelicolor_YSK3654_19hr_replicate_2

source_name: S. coelicolor RNA R5- medium 19hr

source_name: S. coelicolor genomic DNA


title: S_coelicolor_YSK3654_25hr_replicate_2

source_name: S. coelicolor RNA R5- medium 25hr


title: S_coelicolor_YSK3654_22hr_replicate_1

source_name: S. coelicolor RNA R5- medium 22hr


title: S_coelicolor_YSK3654_22hr_replicate_2


title: E30 HS 1hr rec 0hr vs. NS rep3

source_name: Drosophila melanogaster, nos-GAL4 Heat Shocked at 37 degrees C for 1hr


title: nos-GAL4 HS 1 hr rec 0hr vs. NS rep1


title: E30 HS 1hr rec 0hr vs. NS rep1

source_name: Drosophila melanogaster, E30 flies


title: nos-GAL4 HS 1 hr rec 0hr vs. NS rep2

source_name: Drosophila melanogaster, nos-GAL4 flies


title: S_coelicolor_YSK3654_19hr_replicate_1


title: S_coelicolor_YSK3654_31hr_replicate_2


title: S_coelicolor_YSK3654_35hr_replicate_1


title: S_coelicolor_YSK3654_13hr_replicate_2

source_name: S. coelicolor RNA R5- medium 13hr


title: S_coelicolor_YSK3654_16hr_replicate_1

source_name: S. coelicolor RNA R5- medium 16hr


title: S_coelicolor_YSK3654_16hr_replicate_2


title: nos-GAL4 HS 10min vs NS rep2

source_name: Drosophila melanogaster, nos-GAL4 Heat Shocked at 37 degrees C for 10 min

value: heat shocked at 37 degrees C for 10 min


title: nos-GAL4 HS 10min vs NS rep1


title: nos-GAL4 HS 10min vs NS rep3

source_name: Drosophila melanogaster, E30 Heat Shocked at 37 degrees C for 10 min


title: E30 HS 1hr rec 0hr vs. NS rep2


title: UAS-Mnn-1 HS 10min vs NS rep3


title: S_coelicolor_YSK3654_13hr_replicate_1


title: cervical cancer sample 06_I_3

type: genomic

city: Pieve Emanuele

first: Charlotte

middle: K Y

last: Ng

state: MI

address: Via Rita Montalcini 4

department: Biomedical Sciences

country: Italy

institute: Humanitas University

hyb_protocol: according to manufacturer's protocol, performed by Oxford Gene Technologies (OGT)

scan_protocol: Arrays were scanned using the Agilent G2505C scanner using feature extraction software version 10.5.1.1

data_processing: R & Bioconductor, snapCGH, DNAcopy and CGHcall packages

organism: Homo sapiens

source_name: cervical cancer sample 06_I_3

extract_protocol: genomic DNA isolated using Qiagen Dneasy kit

tag: sample type

value: tissue

tag: tissue origin

value: cervix

value: Pre-treatment

tag: patient number

tag: tumour region

value: 3 (of tumour divided into 4 smaller pieces)

source_name: female reference (promega)

value: blood

value: normal reference


title: S_coelicolor_YSK3654_10hr_replicate_1

source_name: S. coelicolor RNA R5- medium 10hr


title: cervical cancer sample 01_I_4

source_name: cervical cancer sample 01_I_4

label_protocol: according to manufacturer's protocol, performed by Oxford Gene Technologies (OGT)

value: 4 (of tumour divided into 4 smaller pieces)


title: cervical cancer sample 14_I_1

source_name: cervical cancer sample 14_I_1

value: 1 (of tumour divided into 4 smaller pieces)


title: S_coelicolor_YSK3654_10hr_replicate_2


title: cervical cancer sample 09_III_1

source_name: cervical cancer sample 09_III_1

value: Post-treatment


title: UAS-Mnn-1 HS 10min vs NS rep1

source_name: Drosophila melanogaster, UAS-Mnn-1 Heat Shocked at 37 degrees C for 10 min

source_name: Drosophila melanogaster, UAS-Mnn-1 flies


title: cervical cancer sample 14_I_3

source_name: cervical cancer sample 14_I_3


title: UAS-Mnn-1 HS 10min vs NS rep2


title: HO15.19, Rapamycin, Rep2

city: Providence

first: Jennifer

middle: Ann

last: Sanders

state: RI

address: 593 Eddy Street

department: Pediatric Endocrinology

institute: Rhode Island Hospital

description: Derived from TGR-1 cells. c-myc was inactivated by homologous recombination

hyb_protocol: cRNA (750ng) was hybridized at 58°C for 16 hours on a RatRef-12 Expression BeadChips.  BeadChips were washed and stained as outlined in the Illumina protocol.

scan_protocol: BeadChips were scanned using the Illumina Iscan.

data_processing: Scanned files were quantile normalized using BeadStudio software (Illumina).  The data was further analyzed using Partek software, version 6.3 (Partek).  For gene expression comparisons, genes with detection p-values >0.01 from BeadStudio or fold-change less than 1.2 were excluded from further analyses.  A two-sample t-test using a p-value cut-off of 0.05 with multiple test correction (Benjamini and Hochberg false discovery rate) was applied for each gene to determine if the gene was differentially expressed in the pairwise comparison.  Triplicate control and rapamycin samples from each cell line were used in these comparisons.

label: Biotin

organism: Rattus norvegicus

source_name: HO15.19 cells, 50nM Rapamycin

label_protocol: Biotinylated cRNA was prepared from 500ng of total RNA using the TotalPrep RNA Amplification kit (Applied Biosystems) according to the manufacturer's directions.

growth_protocol: Cells were cultured in DMEM medium containing high glucose, sodium pyruvate, Glutamax, 10% bovine calf serum and 1% penicillin/streptomycin.  Cells were grown at 37°C with 5.0% carbon dioxide.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.  Total RNA was further purified using the RNeasy kit (Qiagen). RNA quality was evaluated using the Agilent Bioanalyzer.

treatment_protocol: 7.5X10^5 TGR-1 cells and 8.5X10^5 HO15.19 cells were plated on 100mm plates and allowed to attach overnight.  Cells were treated with DMSO vehicle or 50nM rapamycin for 24 hours.

tag: cell type

tag: genotype

value: c-Myc-/-

tag: doubling time


title: Oregon-R HS 10min vs NS rep3


title: Oregon-R HS 10min vs NS rep2

source_name: Drosophila melanogaster, Oregon-R Heat Shocked at 37 degrees C for 10 min

value: Oregon-R

source_name: Drosophila melanogaster, Oregon-R flies


title: HO15.19, Control, Rep 3

source_name: HO15.19 cells, Vehicle Control


title: UAS-Mnn-1-RNAi HS 10min vs NS rep3


title: HO15.19, Control, Rep 1


title: HO15.19, Rapamycin, Rep1


title: HO15.19, Rapamycin, Rep3


title: TGR-1, Rapamycin, Rep 2

description: hrpt- subclone of immortalized embryonic rat fibroblast cell line Rat-1

source_name: TGR-1 cells, 50nM Rapamycin

value: c-Myc+/+


title: HO15.19, Control, Rep 2


title: TGR-1, Rapamycin, Rep 1


title: TGR-1, Rapamycin, Rep 3


title: cervical cancer sample 13_III_2

source_name: cervical cancer sample 13_III_2

value: 2 (of tumour divided into 4 smaller pieces)


title: cervical cancer sample 09_I_3

source_name: cervical cancer sample 09_I_3


title: cervical cancer sample 13_I_4

source_name: cervical cancer sample 13_I_4


title: Liver, Dor, 2008 (D8)

city: Haifa

first: Moshe

last: Tom

department: Marine Biology and Biotechnology

country: Israel

institute: Israel Oceanographic and Limnological Research

description:
D8

Combined hybridization results from 10 fish: Fish 81, 82, 85, 89, 90, 91, 92, 93, 95, 96.
Dye-swaps were performed for each fish.

The reference RNA is an equalized pool of the RNAs from all 10 fish comprising sample D7.

hyb_protocol: Microarray slides were hybridized according to Yudkovski, Y., Shechter, A., Chalifa-Caspi, V., Auslander, M., Ophir, R., Dauphin-Villemant, C., Waterman, M., Sagi, A., Tom M., 2007. Hepatopancreatic multi-transcript expression patterns in the crayfish Cherax quadricarinatus during the molt cycle. Insect Mol. Biol. 16, 661–674 (PMID 18092996).

scan_protocol: The slides were scanned by an Axon 4000B laser scanner in two wavelengths, corresponding to the Cy3 and Cy5 emissions. The TIF imaged dual fluorescence was quantified by the GenePix Pro 6.1 software (Axon), which provided also the weight index of the quality for each hybridized spot.

data_processing:
Data analysis was conducted under the R/BioConductor environment (R version 2.10.1; Smyth, G.K. (2005). Limma: linear models for microarray data. In: Bioinformatics and Computational Biology Solutions using R and Bioconductor. R. Gentleman, V. Carey, S. Dudoit, R. Irizarry, W. Huber (eds), Springer, New York, pages 397--420). Calculation and statistical analysis of log2 expression ratios (VALUE column of the sample data table) of each unique spot across a binary comparison was carried out using the LIMMA (version 3.2.1.) package (Linear Models for Microarray data Analysis; Smyth, 2004). GenePix Pro 6.1 quantified image files were imported into LIMMA, spots with quality flags < -49 were marked as unreliable, and the Cy5 and Cy3 intensities within each slide were normalized using global Loess method. No background correction was applied. Only spots with fluorescent value > 800 (out of 65536) in at least one of the dyes were included in the analysis. LIMMA calculated for each spot on an individual slide an M-value [M=log2(Cy5)/Cy3); Cy5/Cy3 are the normalized emission intensities of the spot] and an emission intensity A-value [A=(log2(Cy5)*Cy3))/2]. Subsequently, LIMMA fitted a linear model to the expression data followed by Empirical Bayes smoothing. Inter-duplicate correlation method was used at the linear modeling step. The LIMMA summary statistics of each unique spot included an estimated average M-value across each binary comparison associated to the statistical p-value. P-value is the statistical probability examining the null hypothesis that M value of a specific gene equals zero, namely that no differential expression takes place in comparison to the reference RNA. P is derived from a moderated t-statistic after multiple testing correction according to Benjamini Y, Hochberg Y. (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J Royal Stat Soc Ser B; 57:289–300.

Probability definition: The statistical probability for rejecting the null hypothesis that VALUE=0 even if true. The null hypothesis is accepted when the probability is greater than an commonly agreed threshold.

organism: Lithognathus mormyrus

source_name: Reference RNA

label_protocol: Messenger RNA was labeled by the fluorescent dyes Cy3 and Cy5 according to Yudkovski, Y., Shechter, A., Chalifa-Caspi, V., Auslander, M., Ophir, R., Dauphin-Villemant, C., Waterman, M., Sagi, A., Tom M., 2007. Hepatopancreatic multi-transcript expression patterns in the crayfish Cherax quadricarinatus during the molt cycle. Insect Mol. Biol. 16, 661–674 (PMID 18092996).

growth_protocol: Fish were sampled at sea and kept alive for 2-3 hours in 700 liter clean seawater flow-through tanks under an ambient temperature regime before their sacrifice.

extract_protocol: The EZ-RNA II Kit (Biological Industries, Israel) was used for total RNA extraction. The polyTtract kit (Promega) was used for mRNA extraction from total RNA solutions.

treatment_protocol: Fish were not experimentally treated.

value: reference

source_name: Liver, Dor, 2008

tag: location

value: Haifa, Israel

tag: year

tag: tissue

value: liver

tag: reproduction

value: no reproductive activity


title: Liver, Haifa, 2007 (H7)

description:
H7

Combined hybridization results from 10 fish: Fish 36, 37, 40, 41, 43, 44, 45, 46, 47, 49.
Dye-swaps were performed for each fish.

The reference RNA is an equalized pool of the RNAs from all 10 fish comprising sample D7.

source_name: Liver, Haifa, 2007

value: Dor, Israel


title: Liver, Haifa, 2008 (H8)

description:
H8

Combined hybridization results from 10 fish: Fish 52, 55, 56, 58, 60, 62, 64, 68, 69,71.
Dye-swaps were performed for each fish.

The reference RNA is an equalized pool of the RNAs from all 10 fish comprising sample D7.

source_name: Liver, Haifa, 2008


title: Liver, Dor, 2007 (D7)

description:
D7

Combined hybridization results from 10 fish: Fish 7, 9, 11, 12, 13, 14, 17, 18, 23, 25.
Dye-swaps were performed for each fish.

The reference RNA is an equalized pool of the RNAs from all 10 fish comprising sample D7.

source_name: Liver, Dor, 2007


title: cervical cancer sample 13_I_3

source_name: cervical cancer sample 13_I_3

value: tissue

value: cervix

source_name: female reference (promega)


title: cervical cancer sample 13_I_2

source_name: cervical cancer sample 13_I_2

value: Pre-treatment


title: UAS-Mnn-1-RNAi HS 10min vs NS rep2

source_name: Drosophila melanogaster, UAS-Mnn-1-RNAi Heat Shocked at 37 degrees C for 10 min

value: heat shocked at 37 degrees C for 10 min

source_name: Drosophila melanogaster, UAS-Mnn-1-RNAi flies

value: non-shocked


title: cervical cancer sample 09_I_1

source_name: cervical cancer sample 09_I_1

value: blood

value: normal reference


title: A2Cy3B2Cy5-3

status: Public on Oct 23 2010

type: other

city: Buffalo

first: Qianqian

last: Zhu

state: NY

address: 701 Ellicott St.

department: Biochemistry

institute: State University of New York at Buffalo

description:
PCR-amplified Drosophila cDNAs spiked in at defined fold changes
We mixed the clones with designated amounts to generate samples corresponding to two conditions. So the two conditions A and B are not real biological conditions. They correspond to how we mix the clones together.

hyb_protocol: Labeled A samples were hybridized with B samples labeled with reverse dye by following Two-Color Microarray-Based Gene Expression Analysis (Quick Amp Labeling) Protocol

scan_protocol: Images were quantified using Agilent Feature Extraction Software (version 9.5.3.1).

data_processing:
24 different routes were evaluated for detecting differentially expressed genes
Agilentprobe.fcvalue.txt contains the designated fold change values of Agilent probes. They are not processed from arrays. In this spike-in experiment, we mixed the clones with known relative amount. Therefore the fold change values were known beforehand.

molecule: other

source_name: spiked-in Drosophila cDNAs

label_protocol: PCR products were in vitro transcribed and labeled with either Cy3 or Cy5 dye based on Two-Color Microarray-Based Gene Expression Analysis (Quick Amp Labeling) Protocol

extract_protocol: PCR products from cDNA clones

tag: condition


title: TGR-1, Control, Rep 1

source_name: TGR-1 cells, Vehicle control


title: A1Cy3B1Cy5-3


title: E30 HS 10min vs NS  rep1

source_name: Drosophila melanogaster, E30 Heat Shocked at 37 degrees C for 10 min

source_name: Drosophila melanogaster, E30 flies


title: TGR-1, Control, Rep 2


title: E30 HS 10min vs NS  rep3


title: Oregon-R HS 10min vs NS rep1

source_name: Drosophila melanogaster, Oregon-R Heat Shocked at 37 degrees C for 10 min

source_name: Drosophila melanogaster, Oregon-R flies


title: E30 HS 10min vs NS  rep2


title: TGR-1, Control, Rep 3


title: A1Cy5B1Cy3-3


title: UAS-Mnn-1-RNAi HS 10min vs NS rep1


title: A2Cy3B2Cy5-2


title: A1Cy5B1Cy3-2


title: A2Cy5B2Cy3-1


title: cervical cancer sample 02_II_4

source_name: cervical cancer sample 02_II_4

value: During treatment

value: 4 (of tumour divided into 4 smaller pieces)


title: A2Cy5B2Cy3-2


title: A2Cy3B2Cy5-1


title: A1Cy3B1Cy5-2


title: A1Cy3B1Cy5-1


title: A1Cy5B1Cy3-1


title: cervical cancer sample 02_I_3

source_name: cervical cancer sample 02_I_3

value: 3 (of tumour divided into 4 smaller pieces)


title: A2Cy5B2Cy3-3


title: cervical cancer sample 02_II_1

source_name: cervical cancer sample 02_II_1

value: 1 (of tumour divided into 4 smaller pieces)


title: cervical cancer sample 02_II_3

source_name: cervical cancer sample 02_II_3


title: cervical cancer sample 02_I_2

source_name: cervical cancer sample 02_I_2

value: 2 (of tumour divided into 4 smaller pieces)


title: cervical cancer sample 02_II_2

source_name: cervical cancer sample 02_II_2


title: cervical cancer sample 02_I_4

source_name: cervical cancer sample 02_I_4

source_name: female reference (promega)


title: VCaP clorgyline 24hr treated

city: Stanford

first: Hongjuan

last: Zhao

state: CA

address: 300 Pasteur Dr

department: Urology

institute: Stanford

description:
Simple annotation: prostate cancer, therapy
Image: http://smd.stanford.edu/MicroArray/gifs/2008-09/81314.gif

hyb_protocol: not provided

scan_protocol: GenePix

data_processing: VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)

source_name: stratagene universal reference RNA

label_protocol: not provided

extract_protocol: not provided

tag: reference

value: stratagene universal reference RNA

source_name: VCaP 24hr treated clorgyline 1 uM RNA

tag: cell line

value: VCaP

value: 24hr treated clorgyline 1 uM RNA


title: MPTP-treated mouse 1 cervical spinal cord regions

city: Seoul

first: Sabina

last: Lim

address: #1 Hoegi-dong Dongdaemoon-gu

country: South Korea

institute: East-West Medical Research Institute, Kyung Hee University

description: Gene expression data from cervical spinal cord regions of MPTP-intoxicated mouse

hyb_protocol: Following labeling, each cDNA was hybridized for 17 hr at 45℃ at 60 rpm on Affymetrix MouseGene 1.0 ST Array. The GeneChips were washed and stained in the Affymetrix Fluidics Station 450_0007.

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

data_processing: The quality control was estimated by confirming the order of the signal intensities of the Poly-A controls and Hybridization controls using Expression Console Software (Affymetrix, USA). The microarray data was analyzed using a GenPlex V3.0 (ISTECH, Korea). The data were analyzed with Robust Multichip Analysis (RMA) quantification method as a probe set summarization algorithm for log transformation with base 2 (log2) and Quantile normalization method as a normalization method in the Preprocessing module of GenPlex V3.0. The mean signal intensities of all genes (35,557 probes (28,853 genes) in a platform) were obtained from 2 chips of each experimental group.

label: biotin

organism: Mus musculus

source_name: MPTP-treated C57BL/6 mouse cervical spinal cord regions

label_protocol: Fragmented and biotinylated cDNA were prepared according to the Affymetrix GeneChip Whole Transcript (WT) Sense Target Labeling Assay manual from 300 ng total RNA (GeneChip Whole Transcript (WT) Sense Target Labeling Assay manual, Affymetrix).

growth_protocol: Six-week old male inbred C57BL/6 mice (20-22 g) were grown up.

extract_protocol: The total RNA in the cervical spinal cord tissues of each group (n=2 per each group) was extracted using an RNeasy Plus Mini kit (QIAGEN, USA) according to the manufacturer’s instruction.

treatment_protocol: While mice in the control group (n=9) were intraperitoneally injected with saline 0.9% (100 µl) once daily for four weeks, the mice in the MPTP group (n=9) were intraperitoneally injected with MPTP-HCl (20 mg/kg of free base) dissolved in saline 0.9% (100 µl) at twenty-four hr intervals for four weeks to produce the sustained chronic model of parkinsonism. Acupuncture was performed by hand two hr after the first MPTP injection and then at forty-eight hr intervals (fourteen total sessions). The acupuncture procedure (acupoint GB34 (Yanglingquan) and acupoint LR3 (Taichong) for acupoints; both sides of the hips for non-acupoints) was performed as previously reported. Mice in the acupoints group were immobilized by hand two hr after MPTP administration. Acupuncture needles were inserted bilaterally to depths of 1 mm at acupoint LR3 and 3 mm at acupoint GB34, and then turned at a rate of two spins per sec for fifteen sec as reported in a previous study. For the non-acupoints group, the needles were inserted to depths of 3 mm at both sides of the hips rather than at the acupoints GB34 and LR3 for the acupoints group, and then the same procedures were performed as with the acupoints.

tag: gender

value: Male

tag: strain

value: Cervical spinal cord tissues

tag: developmental stage

value: Adult

value: MPTP-treated


title: MPTP and nonacupoints acupuncture-treated mouse 2 cervical spinal cord regions

description: Gene expression data from cervical spinal cord regions following nonacupoints-acupuncture-treatment to MPTP-intoxicated mouse

source_name: MPTP and nonacupoints acupuncture-treated mouse cervical spinal cord regions

tag: treatment


title: Control mouse 2 cervical spinal cord regions

description: Gene expression data from normal cervical spinal cord regions

source_name: Control C57BL/6 mouse cervical spinal cord regions

value: Control


title: MPTP and acupoints acupuncture-treated mouse 2 striatal regions

description: Gene expression data from striatal regions following acupoints-acupuncture-treatment to MPTP-intoxicated mouse

source_name: MPTP and acupoints acupuncture-treated mouse striatal regions

extract_protocol: The total RNA in the bilateral striatal tissues of each group (n=2 per each group) was extracted using an RNeasy Plus Mini kit (QIAGEN, USA) according to the manufacturer’s instruction.

value: Striatal tissues

value: MPTP and acupoints acupuncture-treated


title: MPTP and nonacupoints acupuncture-treated mouse 1 cervical spinal cord regions


title: MPTP and acupoints acupuncture-treated mouse 1 striatal regions


title: Control mouse 1 striatal regions

description: Gene expression data from normal striatal regions

source_name: Control C57BL/6 mouse striatal regions


title: CKIalpha KO/p53 KO (1)

city: Jerusalem

first: Gady

last: Cojocaru

address: Kiryat Hadassah

department: Pathology

institute: hadassah medical center

hyb_protocol: RNA was purified from 2 biological replicates in each group using Trizol/Phenol-Chloroform extraction method (Invitrogen). Labeled cRNA was produced and hybridized according to manufacturer's instructions (www.affymetrix.com), at the Center for Genomic Technologies, the Hebrew University. Gene intensities were extracted from CEL files using Affymetrix Expression Console 1.1, using the RMA Sketch method. Raw data was normalized using the median intensities (Irizarry et al., 2003).

source_name: CKI KO/p53 KO

value: enterocyte

value: CKI KO/p53 KO

tag: genetic background


title: Control mouse 1 cervical spinal cord regions


title: MPTP-treated mouse 1 striatal regions

description: Gene expression data from striatal regions of MPTP-intoxicated mouse

source_name: MPTP-treated C57BL/6 mouse striatal regions


title: MPTP and nonacupoints acupuncture-treated mouse 2 striatal regions

description: Gene expression data from striatal regions following nonacupoints-acupuncture-treatment to MPTP-intoxicated mouse

source_name: MPTP and nonacupoints acupuncture-treated mouse striatal regions


title: CKIalpha Het/p21 KO (2)

scan_protocol: RNA was purified from 2 biological replicates in each group using Trizol/Phenol-Chloroform extraction method (Invitrogen). Labeled cRNA was produced and hybridized according to manufacturer's instructions (www.affymetrix.com), at the Center for Genomic Technologies, the Hebrew University. Gene intensities were extracted from CEL files using Affymetrix Expression Console 1.1, using the RMA Sketch method. Raw data was normalized using the median intensities (Irizarry et al., 2003).

source_name: CKI Het/p21 KO

value: CKI heterozygous KO/p21 KO


title: CKIalpha KO/p21 KO (1)

data_processing:
RNA was purified from 2 biological replicates in each group using
Trizol/Phenol-Chloroform extraction method (Invitrogen). Labeled cRNA was
produced and hybridized according to manufacturer's instructions
(www.affymetrix.com), at the Center for Genomic Technologies, the Hebrew
University. Gene intensities were extracted from CEL files using Affymetrix
Expression Console 1.1, using the RMA Sketch method. Raw data was normalized
using the median intensities (Irizarry et al., 2003).

source_name: CKI KO/p21 KO

value: CKI KO/p21 KO


title: MPTP and nonacupoints acupuncture-treated mouse 1 striatal regions


title: MPTP-treated mouse 2 cervical spinal cord regions


title: MPTP-treated mouse 2 striatal regions


title: Control mouse 2 striatal regions


title: MPTP and acupoints acupuncture-treated mouse 2 cervical spinal cord regions

description: Gene expression data from cervical spinal cord regions following acupoints-acupuncture-treatment to MPTP-intoxicated mouse

source_name: MPTP and acupoints acupuncture-treated mouse cervical spinal cord regions


title: MPTP and acupoints acupuncture-treated mouse 1 cervical spinal cord regions


title: CKIalpha KO/p53 KO (2)

label_protocol:
RNA was purified from 2 biological replicates in each group using
Trizol/Phenol-Chloroform extraction method (Invitrogen). Labeled cRNA was
produced and hybridized according to manufacturer's instructions
(www.affymetrix.com), at the Center for Genomic Technologies, the Hebrew
University. Gene intensities were extracted from CEL files using Affymetrix
Expression Console 1.1, using the RMA Sketch method. Raw data was normalized
using the median intensities (Irizarry et al., 2003).


title: CKIalpha Het/p53 KO (2)

source_name: CKI Het/p53 KO

extract_protocol:
RNA was purified from 2 biological replicates in each group using
Trizol/Phenol-Chloroform extraction method (Invitrogen). Labeled cRNA was
produced and hybridized according to manufacturer's instructions
(www.affymetrix.com), at the Center for Genomic Technologies, the Hebrew
University. Gene intensities were extracted from CEL files using Affymetrix
Expression Console 1.1, using the RMA Sketch method. Raw data was normalized
using the median intensities (Irizarry et al., 2003).

value: CKI heterozygous KO/p53 KO


title: CKIalpha Het/p21 KO (1)


title: CKIaplha KO (1)

source_name: CKIaplha KO

value: CKIaplha KO

value: 129/SVJ mouse


title: CKIaplha KO (2)


title: CKIalpha KO/p21 KO (2)


title: CKIalpha Het/p53 KO (1)


title: CKIalpha KO/p53 KO (3)

source_name: CKI KO

value: CKI KO


title: CKIalpha Het (1)

source_name: CKI alpha heterozygote

value: CKI alpha heterozygous KO


title: C023 NNK-exposed Gprc5a knockout mouse lung adenocarcinoma cell replicate 1

city: Houston

first: Humam

last: Kadara

state: TX

address: 2130 W. Holcombe Blvd

institute: University of Texas MD Anderson Cancer Center

hyb_protocol: Fragmented cRNAs were then hybridized to GeneChip® Mouse Genome 430 2.0 arrays (Affymetrix), according to the manufacturer’s instructions.

scan_protocol: The arrays were scanned with a GeneChip® Scanner 3000 from Affymetrix and raw image files were converted to probe set data (*.CEL files), using the Affymetrix GeneChip® Operating Software.

data_processing: robust multi-chip analysis was used for normalization of this sample with other samples and with a statistical test of a p<0.01 of significance of difference across the samples.

source_name: Lung adenocarcinoma cell line derived from lung tumor of NNK-exposed Gprc5a knock-out mouse

label_protocol: Biotin-labeled cRNAs were synthesized by in vitro transcription (IVT) reaction using the ENZO BioArray High Yield RNA transcript labeling kit (Affymetrix, Santa Clara, CA).

extract_protocol: Total RNA was isolated and purified using RNeasy columns (Qiagen, Valencia, CA). The cells were washed twice with ice-cold PBS, lysed with the RLT buffer, incubated with DNase I for RNA isolation according to the manufacturer’s instructions. RNA quality based on the 28S/18S ribosomal RNA ratio (>1.5) was assessed using the RNA 6000 Nano Lab-On-chip and Agilent 2100 Bioanalyzer device (Agilent Technologies, Palo Alto, CA).

value: lung adenocarcinoma cells isolated and cultured from NNK-exposed Gprc5a knockout mouse


title: wild type macrophages, acLDL 24hrs, 2

city: Cleveland

first: Tae Whan

last: Kim

state: OH

address: 9500 Euclid Ave.

institute: Cleveland Clinic

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Expression data normalization and differential expression analysis was handled through the Illumina BeadStudio Gene Expresson module V3.2. The data were first normalized by using the quantile normalization algorithm provided by Illumina Beadstudio and then the differential expression analyses were performed by using Illumina’s custom model.

source_name: bone marrow derived macrophages

label_protocol: A single-round of in vitro transcription (IVT) amplification was carried out using the Illumina RNA Amplification Kit, manufactured by Ambion, Inc., to amplify mRNA and thus to obtain ample amounts of biotinylated cRNA to perform the whole human genome gene expression assay using the mouseRef-8 v2 expression beadchips micro-array (Illumina, San Diego, CA).

growth_protocol: Bone marrow cells were obtained from tibias and femurs by flushing with DMEM, and cultured in L929 cells-conditioned medium for 5 days for differentiation.

extract_protocol: total RNA was isolated from the treated or untreated bone marrow derived macrophages with TRIZOL following the protocol from manufacturer

treatment_protocol: Bone marrow dericed macrophages were treated with acLDL (100ug/ml) for 24 hours

value: female

tag: genotype/variation

value: wild type

value: bone marrow derived macrophages

tag: treatment group

value: acLDL 24hrs


title: cervical cancer sample 13_I_1

source_name: cervical cancer sample 13_I_1

tag: sample type

value: tissue

tag: tissue origin

value: cervix

value: Pre-treatment

tag: patient number

tag: tumour region

value: 1 (of tumour divided into 4 smaller pieces)

source_name: female reference (promega)

value: blood

value: normal reference


title: IRAK4 KI macrophages, acLDL 24hrs, 1

value: IRAK4 KI

tag: cell type


title: CKIalpha Het (2)

value: enterocyte

tag: genotype


title: IRAK4 KI macrophages, acLDL 24hrs, 2


title: IRAK4 KI macrophages, untreated, 1

value: untreated


title: IRAK4 KI macrophages, untreated, 2


title: normal thymus from control mouse_sample_TL20070522_1_2_H4

status: Public on Oct 22 2010

city: Seattle

first: Regine

middle: M

last: Schoenherr

state: WA

address: 1100 Fairview Ave N, LE-360

institute: Fred Hutchinson Cancer Research Center

description:
Dataset Name: Whole thymus array
sample name of age- and cage-matched_mouse: TL20070522_1_2_H3
sample ID: 102506237
sample ID of_age- and cage-matched_mouse: 102506227

hyb_protocol: Biotinylated cRNA (600 ng/ul) was hybridized to GeneChip® Mouse 430 2.0 arrays (Affymetrix, Santa Clara, CA) following the manufacturer’s suggested protocols.

scan_protocol: The arrays were washed and stained using a GeneChip® Fluidics Station and scanned using a GeneChip® Scanner 3000.

data_processing: Two sequential quality control checks were implemented to evaluate whether to include results from each of the GeneChips.  In the first step, recommendations made by Affymetrix were followed.(Zweig, M. H.; Campbell, G. Clin. Chem. 1993, 39, 561-577)  In the second step, we used the affyQCReport and affyPLM software in the Bioconductor package (http://www.bioconductor.org/) to search for poor-quality chips.(Pyeon, D.; et al. Cancer Res. 2007, 67, 4605-4619)  In total, 250 chips from both normal and cancer samples from 5 tissues passed these two steps of quality control evaluation. After passing the quality control checks, the DNA microarray data of each separate tissue type were subjected to a quartile normalization step (using Gene Pattern software version 3.0) where intensities of different arrays (but from the same tissue type) were adjusted to the same scale so that the intensity levels from the different arrays could be compared with one another.  The normalization was performed on log2 transformed data.

source_name: normal whole thymus tissue, at time when breast tumor of matched tumor-bearing mouse had reached 1 cm size

label_protocol: Purified total RNA was normalized to 125ng/ul and reverse transcribed to produce double-stranded cDNA which was amplified, producing biotin-labeled cRNA using the GeneChip HT One-Cycle Target Labeling and Controls Kit (Affymetrix, Santa Clara, CA.)

growth_protocol: All mouse work was performed under IACUC regulations as approved by the Fred Hutchinson Cancer Research Center's animal use committee.  For these studies, a doxycycline-inducible, bitransgenic MMTV-rtTA/TetO-NeuNT (Her2/Neu) mouse model was used.  Corresponding control mice were transgenic for TetO-NeuNT only and were littermates of the bitransgenic mice.  The procedures for animal husbandry and tissue and plasma sample collection were previously reported in Whiteaker J.R., et al., J. Proteome Res. 2007, 10, 3962-3975 and Kelly-Spratt, K.S., et al., J. Proteome Res. 2008, 8, 3613-3618.  Briefly, all mice were fed standard laboratory chow (Harland Teklad, 8664) and acidified water ad libitum and kept on a 12 hour light-dark cycle.

extract_protocol: The tissues from thymus, spleen, liver, blood cells (blood with plasma fraction removed), and breast were homogenized, and total RNA was isolated using a standard Trizol (Invitrogen, Carlsbad, CA) and chloroform extraction protocol.

treatment_protocol: All mice received doxycycline (2 mg/mL + 5% sucrose) in the drinking water starting at 8 weeks of age.  Doxycycline was used to induce tumor development in the bitransgenic mice and breast tumors were allowed to develop to 1.0 cm in diameter after which each tumor-bearing mouse and its corresponding control littermate were euthanized by CO2 inhalation.  Tissue samples were collected when the tumors reached ~1 cm size and the samples were snap-frozen in liquid nitrogen.

value: FVB

value: control mice transgenic for TetO-NeuNT only and littermates of the bitransgenic mice

tag: tissue


title: wild type macrophages, acLDL 24hrs, 1


title: normal thymus from tumor-bearing mouse_sample_TL20070522_1_2_H1

description:
Dataset Name: Whole thymus array
sample name of age- and cage-matched_mouse: TL20070522_1_2_H2
sample ID: 031706215
sample ID of_age- and cage-matched_mouse: 031706205

source_name: normal whole thymus tissue, at time when breast tumor had reached 1 cm size

value: doxycycline-inducible, bitransgenic MMTV-rtTA/TetO-NeuNT (Her2/Neu) mouse model


title: normal thymus from tumor-bearing mouse_sample_TL20070522_1_2_G5

description:
Dataset Name: Whole thymus array
sample name of age- and cage-matched_mouse: TL20070523_1_2_G6
sample ID: 121206226
sample ID of_age- and cage-matched_mouse: 121206236

value: normal whole thymus tissue, at time when breast tumor had reached 1 cm size


title: normal thymus from control mouse_sample_TL20070522_1_2_G2

description:
Dataset Name: Whole thymus array
sample name of age- and cage-matched_mouse: TL20070522_1_2_G1
sample ID: 030306225
sample ID of_age- and cage-matched_mouse: 030306235

value: female

value: normal whole thymus tissue, at time when breast tumor of matched tumor-bearing mouse had reached 1 cm size


title: normal thymus from control mouse_sample_TL20070522_1_2_H2

description:
Dataset Name: Whole thymus array
sample name of age- and cage-matched_mouse: TL20070522_1_2_H1
sample ID: 031706205
sample ID of_age- and cage-matched_mouse: 031706215


title: normal thymus from tumor-bearing mouse_sample_TL20070522_1_2_G1

description:
Dataset Name: Whole thymus array
sample name of age- and cage-matched_mouse: TL20070522_1_2_G2
sample ID: 030306235
sample ID of_age- and cage-matched_mouse: 030306225


title: normal thymus from tumor-bearing mouse_sample_TL20070522_1_2_H5

description:
Dataset Name: Whole thymus array
sample name of age- and cage-matched_mouse: TL20070522_1_2_H6
sample ID: 011107216
sample ID of_age- and cage-matched_mouse: 011107206


title: normal thymus from control mouse_sample_TL20070522_1_2_H6

description:
Dataset Name: Whole thymus array
sample name of age- and cage-matched_mouse: TL20070522_1_2_H5
sample ID: 011107206
sample ID of_age- and cage-matched_mouse: 011107216


title: normal thymus from control mouse_sample_TL20070522_1_2_G4

description:
Dataset Name: Whole thymus array
sample name of age- and cage-matched_mouse: TL20070522_1_2_G3
sample ID: 102506216
sample ID of_age- and cage-matched_mouse: 102506205


title: C025 NNK-exposed Gprc5a knockout mouse lung adenocarcinoma cell replicate 3

value: lung adenocarcinoma cells isolated and cultured from NNK-exposed Gprc5a knockout mouse


title: wild type macrophages, untreated, 1

value: wild type

value: bone marrow derived macrophages


title: C024 NNK-exposed Gprc5a knockout mouse lung adenocarcinoma cell replicate 2


title: normal thymus from tumor-bearing mouse_sample_TL20070522_1_2_G3

description:
Dataset Name: Whole thymus array
sample name of age- and cage-matched_mouse: TL20070522_1_2_G4
sample ID: 102506205
sample ID of_age- and cage-matched_mouse: 102506216


title: normal thymus from control mouse_sample_TL20070522_1_2_F6

description:
Dataset Name: Whole thymus array
sample name of age- and cage-matched_mouse: TL20070522_1_2_F5
sample ID: 120806235
sample ID of_age- and cage-matched_mouse: 120806225


title: normal thymus from tumor-bearing mouse_sample_TL20070522_1_2_H3

description:
Dataset Name: Whole thymus array
sample name of age- and cage-matched_mouse: TL20070522_1_2_H4
sample ID: 102506227
sample ID of_age- and cage-matched_mouse: 102506237


title: normal thymus from tumor-bearing mouse_sample_TL20070522_1_2_F5

description:
Dataset Name: Whole thymus array
sample name of age- and cage-matched_mouse: TL20070522_1_2_F6
sample ID: 120806225
sample ID of_age- and cage-matched_mouse: 120806235


title: normal thymus from control mouse_sample_TL20070523_1_2_G6

description:
Dataset Name: Whole thymus array
sample name of age- and cage-matched_mouse: TL20070522_1_2_G5
sample ID: 121206236
sample ID of_age- and cage-matched_mouse: 121206226


title: wild type macrophages, untreated, 2


title: normal thymus from tumor-bearing mouse_sample_TL20070522_1_2_F3

description:
Dataset Name: Whole thymus array
sample name of age- and cage-matched_mouse: TL20070522_1_2_F4
sample ID: 090706265
sample ID of_age- and cage-matched_mouse: 090706255


title: normal thymus from control mouse_sample_TL20070522_1_2_F4

description:
Dataset Name: Whole thymus array
sample name of age- and cage-matched_mouse: TL20070522_1_2_F3
sample ID: 090706255
sample ID of_age- and cage-matched_mouse: 090706265


title: normal thymus from control mouse_sample_TL20070522_1_2_F2

description:
Dataset Name: Whole thymus array
sample name of age- and cage-matched_mouse: TL20070522_1_2_F1
sample ID: 030306205
sample ID of_age- and cage-matched_mouse: 030306215


title: normal thymus from control mouse_sample_TL20070522_1_2_E2

description:
Dataset Name: Whole thymus array
sample name of age- and cage-matched_mouse: TL20070522_1_2_E1
sample ID: 021706216
sample ID of_age- and cage-matched_mouse: 021706205


title: normal thymus from tumor-bearing mouse_sample_TL20070522_1_2_E3

description:
Dataset Name: Whole thymus array
sample name of age- and cage-matched_mouse: TL20070522_1_2_E4
sample ID: 090706235
sample ID of_age- and cage-matched_mouse: 090706245


title: normal thymus from control mouse_sample_TL20070522_1_2_D4

description:
Dataset Name: Whole thymus array
sample name of age- and cage-matched_mouse: TL20070522_1_2_D3
sample ID: 090706215
sample ID of_age- and cage-matched_mouse: 090706205


title: normal thymus from tumor-bearing mouse_sample_TL20070522_1_2_E1

description:
Dataset Name: Whole thymus array
sample name of age- and cage-matched_mouse: TL20070522_1_2_E2
sample ID: 021706205
sample ID of_age- and cage-matched_mouse: 021706216


title: normal thymus from tumor-bearing mouse_sample_TL20070522_1_2_E5

description:
Dataset Name: Whole thymus array
sample name of age- and cage-matched_mouse: TL20070522_1_2_E6
sample ID: 120806216
sample ID of_age- and cage-matched_mouse: 120806205


title: normal thymus from control mouse_sample_TL20070522_1_2_D6

description:
Dataset Name: Whole thymus array
sample name of age- and cage-matched_mouse: TL20070522_1_2_D5
sample ID: 120106235
sample ID of_age- and cage-matched_mouse: 120106225


title: normal thymus from control mouse_sample_TL20070522_1_2_E6

description:
Dataset Name: Whole thymus array
sample name of age- and cage-matched_mouse: TL20070522_1_2_E5
sample ID: 120806205
sample ID of_age- and cage-matched_mouse: 120806216


title: normal thymus from tumor-bearing mouse_sample_TL20070522_1_2_D1

description:
Dataset Name: Whole thymus array
sample name of age- and cage-matched_mouse: TL20070522_1_2_D2
sample ID: 012006206
sample ID of_age- and cage-matched_mouse: 012006218


title: normal thymus from tumor-bearing mouse_sample_TL20070522_1_2_F1

description:
Dataset Name: Whole thymus array
sample name of age- and cage-matched_mouse: TL20070522_1_2_F2
sample ID: 030306215
sample ID of_age- and cage-matched_mouse: 030306205


title: normal thymus from control mouse_sample_TL20070522_1_2_C6

description:
Dataset Name: Whole thymus array
sample name of age- and cage-matched_mouse: TL20070522_1_2_C5
sample ID: 120106215
sample ID of_age- and cage-matched_mouse: 120106205


title: normal thymus from control mouse_sample_TL20070522_1_2_D2

description:
Dataset Name: Whole thymus array
sample name of age- and cage-matched_mouse: TL20070522_1_2_D1
sample ID: 012006218
sample ID of_age- and cage-matched_mouse: 012006206


title: normal thymus from tumor-bearing mouse_sample_TL20070522_1_2_D5

description:
Dataset Name: Whole thymus array
sample name of age- and cage-matched_mouse: TL20070522_1_2_D6
sample ID: 120106225
sample ID of_age- and cage-matched_mouse: 120106235


title: normal thymus from control mouse_sample_TL20070522_1_2_E4

description:
Dataset Name: Whole thymus array
sample name of age- and cage-matched_mouse: TL20070522_1_2_E3
sample ID: 090706245
sample ID of_age- and cage-matched_mouse: 090706235


title: normal thymus from tumor-bearing mouse_sample_TL20070522_1_2_C3

description:
Dataset Name: Whole thymus array
sample name of age- and cage-matched_mouse: TL20070522_1_2_C4
sample ID: 082406246
sample ID of_age- and cage-matched_mouse: 082406256


title: normal thymus from tumor-bearing mouse_sample_TL20070522_1_2_C5

description:
Dataset Name: Whole thymus array
sample name of age- and cage-matched_mouse: TL20070522_1_2_C6
sample ID: 120106205
sample ID of_age- and cage-matched_mouse: 120106215


title: normal thymus from control mouse_sample_TL20070522_1_2_C4

description:
Dataset Name: Whole thymus array
sample name of age- and cage-matched_mouse: TL20070522_1_2_C3
sample ID: 082406256
sample ID of_age- and cage-matched_mouse: 082406246


title: normal thymus from control mouse_sample_TL20070522_1_2_C2

description:
Dataset Name: Whole thymus array
sample name of age- and cage-matched_mouse: TL20070522_1_2_C1
sample ID: 011906218
sample ID of_age- and cage-matched_mouse: 011906208


title: normal thymus from tumor-bearing mouse_sample_TL20070522_1_2_C1

description:
Dataset Name: Whole thymus array
sample name of age- and cage-matched_mouse: TL20070522_1_2_C2
sample ID: 011906208
sample ID of_age- and cage-matched_mouse: 011906218


title: normal thymus from tumor-bearing mouse_sample_TL20070522_1_2_D3

description:
Dataset Name: Whole thymus array
sample name of age- and cage-matched_mouse: TL20070522_1_2_D4
sample ID: 090706205
sample ID of_age- and cage-matched_mouse: 090706215


title: normal thymus from tumor-bearing mouse_sample_TL20070522_5_B7

description:
Dataset Name: Whole thymus array
sample name of age- and cage-matched_mouse: TL20070522_5_B8
sample ID: 011107236
sample ID of_age- and cage-matched_mouse: 011107226


title: normal thymus from control mouse_sample_TL20070522_5_B8

description:
Dataset Name: Whole thymus array
sample name of age- and cage-matched_mouse: TL20070522_5_B7
sample ID: 011107226
sample ID of_age- and cage-matched_mouse: 011107236


title: normal thymus from control mouse_sample_TL20070522_1_2_B4

description:
Dataset Name: Whole thymus array
sample name of age- and cage-matched_mouse: TL20070522_1_2_B3
sample ID: 031706245
sample ID of_age- and cage-matched_mouse: 031706255


title: normal thymus from tumor-bearing mouse_sample_TL20070522_1_2_B5

description:
Dataset Name: Whole thymus array
sample name of age- and cage-matched_mouse: TL20070522_1_2_B6
sample ID: 111706225
sample ID of_age- and cage-matched_mouse: 111706235


title: normal thymus from tumor-bearing mouse_sample_TL20070522_1_2_B3

description:
Dataset Name: Whole thymus array
sample name of age- and cage-matched_mouse: TL20070522_1_2_B4
sample ID: 031706255
sample ID of_age- and cage-matched_mouse: 031706245


title: normal thymus from control mouse_sample_TL20070522_1_2_B2

description:
Dataset Name: Whole thymus array
sample name of age- and cage-matched_mouse: TL20070522_1_2_B1
sample ID: 122105223
sample ID of_age- and cage-matched_mouse: 122105207


title: normal thymus from control mouse_sample_TL20070522_1_2_B6

description:
Dataset Name: Whole thymus array
sample name of age- and cage-matched_mouse: TL20070522_1_2_B5
sample ID: 111706235
sample ID of_age- and cage-matched_mouse: 111706225


title: normal thymus from control mouse_sample_TL20070522_1_2_A6

description:
Dataset Name: Whole thymus array
sample name of age- and cage-matched_mouse: TL20070522_1_2_A5
sample ID: 111706215
sample ID of_age- and cage-matched_mouse: 111706205


title: normal thymus from tumor-bearing mouse_sample_TL20070522_1_2_B1

description:
Dataset Name: Whole thymus array
sample name of age- and cage-matched_mouse: TL20070522_1_2_B2
sample ID: 122105207
sample ID of_age- and cage-matched_mouse: 122105223


title: normal blood from control mouse_sample_TL20070522_3_4_H12

description:
Dataset Name: Whole blood array
sample name of age- and cage-matched_mouse: TL20070522_3_4_H11
sample ID: 011107209
sample ID of_age- and cage-matched_mouse: 011107219

source_name: normal whole blood cells (blood with plasma fraction removed), at time when breast tumor of matched tumor-bearing mouse had reached 1 cm size


title: normal thymus from control mouse_sample_TL20070522_1_2_A4

description:
Dataset Name: Whole thymus array
sample name of age- and cage-matched_mouse: TL20070522_1_2_A3
sample ID: 031706235
sample ID of_age- and cage-matched_mouse: 031706225


title: normal thymus from tumor-bearing mouse_sample_TL20070522_1_2_A5

description:
Dataset Name: Whole thymus array
sample name of age- and cage-matched_mouse: TL20070522_1_2_A6
sample ID: 111706205
sample ID of_age- and cage-matched_mouse: 111706215


title: nos-GAL4 HS 1hr rec 3hr vs. NS rep3

source_name: Drosophila melanogaster, nos-GAL4 Heat Shocked at 37 degrees C for 1hr, 3 hrs recovery

value: heat shocked at 37 degrees C for 1hr, 3 hrs recovery

source_name: Drosophila melanogaster, nos-GAL4 flies

value: non-shocked


title: normal thymus from control mouse_sample_TL20070522_1_2_A2

description:
Dataset Name: Whole thymus array
sample name of age- and cage-matched_mouse: TL20070522_1_2_A1
sample ID: 121505207
sample ID of_age- and cage-matched_mouse: 121505220


title: normal blood from tumor-bearing mouse_sample_TL20070522_3_4_H11

description:
Dataset Name: Whole blood array
sample name of age- and cage-matched_mouse: TL20070522_3_4_H12
sample ID: 011107219
sample ID of_age- and cage-matched_mouse: 011107209

source_name: normal whole blood cells (blood with plasma fraction removed), at time when breast tumor had reached 1 cm size


title: normal thymus from tumor-bearing mouse_sample_TL20070522_1_2_A3

description:
Dataset Name: Whole thymus array
sample name of age- and cage-matched_mouse: TL20070522_1_2_A4
sample ID: 031706225
sample ID of_age- and cage-matched_mouse: 031706235


title: normal thymus from tumor-bearing mouse_sample_TL20070522_1_2_A1

description:
Dataset Name: Whole thymus array
sample name of age- and cage-matched_mouse: TL20070522_1_2_A2
sample ID: 121505220
sample ID of_age- and cage-matched_mouse: 121505207


title: normal blood from tumor-bearing mouse_sample_TL20070522_3_4_H7

description:
Dataset Name: Whole blood array
sample name of age- and cage-matched_mouse: TL20070522_3_4_H8
sample ID: 031706219
sample ID of_age- and cage-matched_mouse: 031706209

value: normal whole blood cells (blood with plasma fraction removed), at time when breast tumor had reached 1 cm size


title: normal blood from control mouse_sample_TL20070522_3_4_H10

description:
Dataset Name: Whole blood array
sample name of age- and cage-matched_mouse: TL20070522_3_4_H9
sample ID: 102506240
sample ID of_age- and cage-matched_mouse: 102506243

value: normal whole blood cells (blood with plasma fraction removed), at time when breast tumor of matched tumor-bearing mouse had reached 1 cm size


title: normal blood from control mouse_sample_TL20070522_3_4_G12

description:
Dataset Name: Whole blood array
sample name of age- and cage-matched_mouse: TL20070522_3_4_G11
sample ID: 121206239
sample ID of_age- and cage-matched_mouse: 121206229


title: normal blood from tumor-bearing mouse_sample_TL20070522_3_4_H9

description:
Dataset Name: Whole blood array
sample name of age- and cage-matched_mouse: TL20070522_3_4_H10
sample ID: 102506243
sample ID of_age- and cage-matched_mouse: 102506240


title: normal blood from tumor-bearing mouse_sample_TL20070522_3_4_G9

description:
Dataset Name: Whole blood array
sample name of age- and cage-matched_mouse: TL20070522_3_4_G10
sample ID: 102506208
sample ID of_age- and cage-matched_mouse: 102506219


title: normal blood from control mouse_sample_TL20070522_3_4_F12

description:
Dataset Name: Whole blood array
sample name of age- and cage-matched_mouse: TL20070522_3_4_F11
sample ID: 120806239
sample ID of_age- and cage-matched_mouse: 120806229


title: normal blood from control mouse_sample_TL20070522_3_4_G10

description:
Dataset Name: Whole blood array
sample name of age- and cage-matched_mouse: TL20070522_3_4_G9
sample ID: 102506219
sample ID of_age- and cage-matched_mouse: 102506208


title: normal blood from control mouse_sample_TL20070522_3_4_F10

description:
Dataset Name: Whole blood array
sample name of age- and cage-matched_mouse: TL20070522_3_4_F9
sample ID: 090706259
sample ID of_age- and cage-matched_mouse: 090706269


title: normal blood from tumor-bearing mouse_sample_TL20070522_3_4_F7

description:
Dataset Name: Whole blood array
sample name of age- and cage-matched_mouse: TL20070522_3_4_F8
sample ID: 030306219
sample ID of_age- and cage-matched_mouse: 030306209


title: normal blood from tumor-bearing mouse_sample_TL20070522_3_4_G7

description:
Dataset Name: Whole blood array
sample name of age- and cage-matched_mouse: TL20070522_3_4_G8
sample ID: 030306239
sample ID of_age- and cage-matched_mouse: 030306229


title: normal blood from control mouse_sample_TL20070522_3_4_H8

description:
Dataset Name: Whole blood array
sample name of age- and cage-matched_mouse: TL20070522_3_4_H7
sample ID: 031706209
sample ID of_age- and cage-matched_mouse: 031706219


title: normal blood from tumor-bearing mouse_sample_TL20070522_3_4_F11

description:
Dataset Name: Whole blood array
sample name of age- and cage-matched_mouse: TL20070522_3_4_F12
sample ID: 120806229
sample ID of_age- and cage-matched_mouse: 120806239


title: normal blood from control mouse_sample_TL20070522_3_4_F8

description:
Dataset Name: Whole blood array
sample name of age- and cage-matched_mouse: TL20070522_3_4_F7
sample ID: 030306209
sample ID of_age- and cage-matched_mouse: 030306219


title: normal blood from control mouse_sample_TL20070522_3_4_E12

description:
Dataset Name: Whole blood array
sample name of age- and cage-matched_mouse: TL20070522_3_4_E11
sample ID: 120806209
sample ID of_age- and cage-matched_mouse: 120806219


title: normal blood from tumor-bearing mouse_sample_TL20070522_3_4_F9

description:
Dataset Name: Whole blood array
sample name of age- and cage-matched_mouse: TL20070522_3_4_F10
sample ID: 090706269
sample ID of_age- and cage-matched_mouse: 090706259


title: normal blood from tumor-bearing mouse_sample_TL20070522_3_4_E11

description:
Dataset Name: Whole blood array
sample name of age- and cage-matched_mouse: TL20070522_3_4_E12
sample ID: 120806219
sample ID of_age- and cage-matched_mouse: 120806209


title: normal blood from control mouse_sample_TL20070522_3_4_E10

description:
Dataset Name: Whole blood array
sample name of age- and cage-matched_mouse: TL20070522_3_4_E9
sample ID: 090706249
sample ID of_age- and cage-matched_mouse: 090706239


title: normal blood from tumor-bearing mouse_sample_TL20070522_3_4_E9

description:
Dataset Name: Whole blood array
sample name of age- and cage-matched_mouse: TL20070522_3_4_E10
sample ID: 090706239
sample ID of_age- and cage-matched_mouse: 090706249


title: normal blood from control mouse_sample_TL20070522_3_4_G8

description:
Dataset Name: Whole blood array
sample name of age- and cage-matched_mouse: TL20070522_3_4_G7
sample ID: 030306229
sample ID of_age- and cage-matched_mouse: 030306239


title: normal blood from control mouse_sample_TL20070522_5_E8

description:
Dataset Name: Whole blood array
sample name of age- and cage-matched_mouse: TL20070522_5_E7
sample ID: 011107229
sample ID of_age- and cage-matched_mouse: 011107239


title: normal blood from tumor-bearing mouse_sample_TL20070522_3_4_G11

description:
Dataset Name: Whole blood array
sample name of age- and cage-matched_mouse: TL20070522_3_4_G12
sample ID: 121206229
sample ID of_age- and cage-matched_mouse: 121206239


title: normal blood from tumor-bearing mouse_sample_TL20070522_3_4_E7_2

description:
Dataset Name: Whole blood array
sample name of age- and cage-matched_mouse: TL20070522_3_4_E8
sample ID: 021706209
sample ID of_age- and cage-matched_mouse: 021706220


title: normal blood from tumor-bearing mouse_sample_TL20070522_3_4_C9

description:
Dataset Name: Whole blood array
sample name of age- and cage-matched_mouse: TL20070522_3_4_C10
sample ID: 082406250
sample ID of_age- and cage-matched_mouse: 082406260


title: normal blood from tumor-bearing mouse_sample_TL20070522_3_4_C7

description:
Dataset Name: Whole blood array
sample name of age- and cage-matched_mouse: TL20070522_3_4_C8
sample ID: 011906210
sample ID of_age- and cage-matched_mouse: 011906220


title: normal blood from control mouse_sample_TL20070522_3_4_B12

description:
Dataset Name: Whole blood array
sample name of age- and cage-matched_mouse: TL20070522_3_4_B11
sample ID: 111706239
sample ID of_age- and cage-matched_mouse: 111706229


title: normal blood from control mouse_sample_TL20070522_3_4_C8

description:
Dataset Name: Whole blood array
sample name of age- and cage-matched_mouse: TL20070522_3_4_C7
sample ID: 011906220
sample ID of_age- and cage-matched_mouse: 011906210


title: normal blood from tumor-bearing mouse_sample_TL20070522_3_4_B9

description:
Dataset Name: Whole blood array
sample name of age- and cage-matched_mouse: TL20070522_3_4_B10
sample ID: 031706259
sample ID of_age- and cage-matched_mouse: 031706249


title: Cut wing discs 24-72h (Biological Replicate2, Dye-swap B)

city: Barcelona

first: Sergi

last: Beltran

address: Baldiri Reixac 10

department: Serveis Cientificotècnics

country: Spain

institute: Universitat de Barcelona

description: The four microarrays hybridized for each pair of conditions were done in biological replicate pairs. Both arrays from each pair were hybridized with the same amplified RNA from sample and common reference (obtained using the Amino-Allyl Messageamp II aRNA Amplification Kit from Ambion, Inc) but with dyes (Cy3 and Cy5 from Amersham, Inc) swapped to take dye-bias into account.

hyb_protocol: Samples were diluted in 2X Hybridization Buffer #5185-5973 (Agilent Technologies) and hybridization was carried out at 60ºC for 18 hours with a G2534A SureHyb Chamber in a G2545A Hybridization Oven (Agilent Technologies).

scan_protocol: GenePix Results (GPR) data files were obtained for each microarray with an Axon 4000B scanner and GenePix Pro 6 (Axon Instruments, Inc).

data_processing: GPR files were analyzed with Limma package from BioConductor (Gentleman et al., 2004; Genome Biol 5, R80; Smyth, 2004; Statistical Applications in Genetics and Molecular Biology 3, Article 3) using the same criteria. Data was background corrected with the "normexp" method and normalized with OLIN (Futschik and Crompton, 2005; Bioinformatics 21, 1724-1726). Quality of spots was assesed by spot size, foreground versus background signals, saturation and coincidence between differently calculated ratio measures and R2 of regression ratio.

source_name: cut wing discs 72 hours after implantation

label_protocol: 1.5ug total RNA was amplified and indirectly labeled with Amino-Allyl Messageamp II aRNA Amplification Kit (Ambion, Inc). Fragmentation was done with RNA Fragmentation Reagents #8740(Ambion, Inc).

growth_protocol: Flies were kept on standard media at 25ºC.

extract_protocol: Total RNA extraction was performed with RNeasy Protect Mini Kit (QIAGEN Inc.). Quality was assessed using the Eukaryote Total RNA Nano Assay on a 2100 Bioanalyzer (Agilent Technologies).

value: w118iso; 2iso; 3iso isogenic line from the DrosDel collection (Ryder et al. 2007)

value: wing imaginal discs and a 90º sector from the posterior (P) compartment, leaving a 3/4 anterior (3/4 A) fragment (Bosch et al. 2005)

value: third instar larvae implanted into recently eclosed Canton S females and kept at 25ºC for 72h (Bosch et al. 2005)

source_name: cut wing discs 24 hours after implantation

value: third instar larvae implanted into recently eclosed Canton S females and kept at 25ºC for 24h (Bosch et al. 2005)


title: Cut wing discs 24-72h (Biological Replicate2, Dye-swap A)


title: normal blood from control mouse_sample_TL20070522_3_4_D12

description:
Dataset Name: Whole blood array
sample name of age- and cage-matched_mouse: TL20070522_3_4_D11
sample ID: 120106239
sample ID of_age- and cage-matched_mouse: 120106229

value: FVB


title: Cut wing discs 24-72h (Biological Replicate1, Dye-swap B)


title: normal blood from tumor-bearing mouse_sample_TL20070522_3_4_A11

description:
Dataset Name: Whole blood array
sample name of age- and cage-matched_mouse: TL20070522_3_4_A12
sample ID: 111706208
sample ID of_age- and cage-matched_mouse: 111706219


title: normal blood from tumor-bearing mouse_sample_TL20070522_3_4_B11

description:
Dataset Name: Whole blood array
sample name of age- and cage-matched_mouse: TL20070522_3_4_B12
sample ID: 111706229
sample ID of_age- and cage-matched_mouse: 111706239


title: normal blood from control mouse_sample_TL20070522_3_4_D8

description:
Dataset Name: Whole blood array
sample name of age- and cage-matched_mouse: TL20070522_3_4_D7
sample ID: 012006220
sample ID of_age- and cage-matched_mouse: 012006209

value: control mice transgenic for TetO-NeuNT only and littermates of the bitransgenic mice


title: normal blood from tumor-bearing mouse_sample_TL20070522_5_E7

description:
Dataset Name: Whole blood array
sample name of age- and cage-matched_mouse: TL20070522_5_E8
sample ID: 011107239
sample ID of_age- and cage-matched_mouse: 011107229

value: doxycycline-inducible, bitransgenic MMTV-rtTA/TetO-NeuNT (Her2/Neu) mouse model


title: Cut wing discs 24-72h (Biological Replicate1, Dye-swap A)


title: Cut wing discs 0-24h (Biological Replicate2, Dye-swap B)

source_name: cut wing discs

value: third instar larvae


title: normal blood from tumor-bearing mouse_sample_TL20070522_3_4_B7

description:
Dataset Name: Whole blood array
sample name of age- and cage-matched_mouse: TL20070522_3_4_B8
sample ID: 122105224
sample ID of_age- and cage-matched_mouse: 122105225

value: female


title: normal blood from tumor-bearing mouse_sample_TL20070522_3_4_D7

description:
Dataset Name: Whole blood array
sample name of age- and cage-matched_mouse: TL20070522_3_4_D8
sample ID: 012006209
sample ID of_age- and cage-matched_mouse: 012006220


title: Cut wing discs 0-24h (Biological Replicate2, Dye-swap A)


title: normal blood from tumor-bearing mouse_sample_TL20070522_3_4_D9

description:
Dataset Name: Whole blood array
sample name of age- and cage-matched_mouse: TL20070522_3_4_D10
sample ID: 090706208
sample ID of_age- and cage-matched_mouse: 090706219


title: normal blood from tumor-bearing mouse_sample_TL20070522_3_4_D11

description:
Dataset Name: Whole blood array
sample name of age- and cage-matched_mouse: TL20070522_3_4_D12
sample ID: 120106229
sample ID of_age- and cage-matched_mouse: 120106239


title: normal blood from control mouse_sample_TL20070522_3_4_B8

description:
Dataset Name: Whole blood array
sample name of age- and cage-matched_mouse: TL20070522_3_4_B7
sample ID: 122105225
sample ID of_age- and cage-matched_mouse: 122105224


title: normal blood from control mouse_sample_TL20070522_3_4_E8

description:
Dataset Name: Whole blood array
sample name of age- and cage-matched_mouse: TL20070522_3_4_E7_2
sample ID: 021706220
sample ID of_age- and cage-matched_mouse: 021706209


title: normal blood from tumor-bearing mouse_sample_TL20070522_3_4_C11

description:
Dataset Name: Whole blood array
sample name of age- and cage-matched_mouse: TL20070522_3_4_C12
sample ID: 120106209
sample ID of_age- and cage-matched_mouse: 120106219


title: normal blood from control mouse_sample_TL20070522_3_4_B10

description:
Dataset Name: Whole blood array
sample name of age- and cage-matched_mouse: TL20070522_3_4_B9
sample ID: 031706249
sample ID of_age- and cage-matched_mouse: 031706259


title: normal blood from control mouse_sample_TL20070522_3_4_C10

description:
Dataset Name: Whole blood array
sample name of age- and cage-matched_mouse: TL20070522_3_4_C9
sample ID: 082406260
sample ID of_age- and cage-matched_mouse: 082406250


title: normal blood from control mouse_sample_TL20070522_3_4_C12

description:
Dataset Name: Whole blood array
sample name of age- and cage-matched_mouse: TL20070522_3_4_C11
sample ID: 120106219
sample ID of_age- and cage-matched_mouse: 120106209


title: normal blood from control mouse_sample_TL20070522_3_4_A12

description:
Dataset Name: Whole blood array
sample name of age- and cage-matched_mouse: TL20070522_3_4_A11
sample ID: 111706219
sample ID of_age- and cage-matched_mouse: 111706208


title: normal spleen from control mouse_sample_TL20070522_1_2_H8

description:
Dataset Name: Whole spleen array
sample name of age- and cage-matched_mouse: TL20070522_1_2_H7
sample ID: 031706204
sample ID of_age- and cage-matched_mouse: 031706214

source_name: normal whole spleen tissue, at time when breast tumor of matched tumor-bearing mouse had reached 1 cm size


title: Non-cut wing discs 0-24h (Biological Replicate1, Dye-swap A)

description: The four microarrays hybridized for each pair of conditions were done in biological replicate pairs. Both arrays from each pair were hybridized with the same amplified RNA from sample and common reference (obtained using the Amino-Allyl Messageamp II aRNA Amplification Kit from Ambion, Inc) but with dyes (Cy3 and Cy5 from Amersham, Inc) swapped to take dye-bias into account.

source_name: non-cut wing discs 24 hours after implantation

value: wing imaginal discs

source_name: non-cut wing discs


title: S_coelicolor_WL6268_33hr_replicate_2

source_name: S. coelicolor RNA R5- medium 33hr

tag: time

tag: replicate

source_name: S. coelicolor genomic DNA


title: normal spleen from tumor-bearing mouse_sample_TL20070522_1_2_G11

description:
Dataset Name: Whole spleen array
sample name of age- and cage-matched_mouse: TL20070522_1_2_G12
sample ID: 121206222
sample ID of_age- and cage-matched_mouse: 121206232

source_name: normal whole spleen tissue, at time when breast tumor had reached 1 cm size


title: normal spleen from control mouse_sample_TL20070522_1_2_G12

description:
Dataset Name: Whole spleen array
sample name of age- and cage-matched_mouse: TL20070522_1_2_G11
sample ID: 121206232
sample ID of_age- and cage-matched_mouse: 121206222

value: normal whole spleen tissue, at time when breast tumor of matched tumor-bearing mouse had reached 1 cm size


title: normal spleen from tumor-bearing mouse_sample_TL20070522_1_2_H11

description:
Dataset Name: Whole spleen array
sample name of age- and cage-matched_mouse: TL20070522_1_2_H12
sample ID: 011107212
sample ID of_age- and cage-matched_mouse: 011107202

value: normal whole spleen tissue, at time when breast tumor had reached 1 cm size


title: normal spleen from tumor-bearing mouse_sample_TL20070522_1_2_H9

description:
Dataset Name: Whole spleen array
sample name of age- and cage-matched_mouse: TL20070522_1_2_H10
sample ID: 102506224
sample ID of_age- and cage-matched_mouse: 102506234


title: Non-cut wing discs 0-24h (Biological Replicate2, Dye-swap A)


title: normal spleen from control mouse_sample_TL20070522_1_2_H10

description:
Dataset Name: Whole spleen array
sample name of age- and cage-matched_mouse: TL20070522_1_2_H9
sample ID: 102506234
sample ID of_age- and cage-matched_mouse: 102506224


title: normal blood from control mouse_sample_TL20070522_3_4_A10

description:
Dataset Name: Whole blood array
sample name of age- and cage-matched_mouse: TL20070522_3_4_A9
sample ID: 031706239
sample ID of_age- and cage-matched_mouse: 031706229


title: normal spleen from tumor-bearing mouse_sample_TL20070522_1_2_H7

description:
Dataset Name: Whole spleen array
sample name of age- and cage-matched_mouse: TL20070522_1_2_H8
sample ID: 031706214
sample ID of_age- and cage-matched_mouse: 031706204


title: normal blood from tumor-bearing mouse_sample_TL20070522_3_4_A7

description:
Dataset Name: Whole blood array
sample name of age- and cage-matched_mouse: TL20070522_3_4_A8
sample ID: 121505222
sample ID of_age- and cage-matched_mouse: 121505212


title: normal spleen from control mouse_sample_TL20070522_1_2_G10

description:
Dataset Name: Whole spleen array
sample name of age- and cage-matched_mouse: TL20070522_1_2_G9
sample ID: 102506213
sample ID of_age- and cage-matched_mouse: 102506202


title: normal spleen from tumor-bearing mouse_sample_TL20070522_1_2_G9

description:
Dataset Name: Whole spleen array
sample name of age- and cage-matched_mouse: TL20070522_1_2_G10
sample ID: 102506202
sample ID of_age- and cage-matched_mouse: 102506213


title: Non-cut wing discs 0-24h (Biological Replicate2, Dye-swap B)


title: Non-cut wing discs 0-24h (Biological Replicate1, Dye-swap B)


title: Sohlh1 KO-2

city: Pittsburgh

first: Aleksandar

last: Rajkovic

state: PA

address: 204 Craft Ave. Suite A230

department: Dept. of Obstetrics, Gynecology & Reproductive Sciences

institute: Magee-Womens Research Institute

description: replicate 2

hyb_protocol: Labeled, amplified material was hybridized to the Illumina BeadChip MouseWG-6 2.0 arrays according to the Manufacturer's instructions (Illumina, Inc., San Diego, CA).

scan_protocol: Arrays were scanned with an Illumina Bead array Reader confocal scanner (BeadStation 500GXDW; Illumina, Inc., San Diego, CA) according to the Manufacturer's instructions

data_processing: Array data processing were performed on Illumina BeadStudio software (version 3.2). We normalized gene expression data using Quantile normalization and log2 transformation. To export to a data matrix, Sample Gene Profile option of this software was used.

source_name: ovary

label_protocol: Biotin-labeled cRNA samples for hybridization were prepared according to Illumina's recommended sample labeling procedure: 500 ng of total RNA was used for cDNA synthesis, followed by an amplification/labeling step (in vitro transcription) to synthesize biotin-labeled cRNA using the Illumina. TotalPrep RNA Amplification kit (Ambion Inc., Austin, TX). cRNA concentrations using spectrophotometer (Nanodrop, ND-1000)

extract_protocol: RNA was extracted using RNeasy kit from Qiagen with optional DNase I treatment. Suggested protocol provided from manufacturer was used for RNA extraction.

tag: age

value: newborn

value: ovary

value: Sohlh1 KO


title: Sohlh1 KO-1

description: replicate 1


title: normal blood from control mouse_sample_TL20070522_3_4_D10

description:
Dataset Name: Whole blood array
sample name of age- and cage-matched_mouse: TL20070522_3_4_D9
sample ID: 090706219
sample ID of_age- and cage-matched_mouse: 090706208

tag: gender


title: Sohlh1 KO-3

description: replicate 3

tag: strain


title: normal blood from control mouse_sample_TL20070522_3_4_A8

description:
Dataset Name: Whole blood array
sample name of age- and cage-matched_mouse: TL20070522_3_4_A7
sample ID: 121505212
sample ID of_age- and cage-matched_mouse: 121505222


title: Sohlh2 KO-2

description: replicate 1

value: Sohlh2 KO


title: Sohlh1 KO-4

description: replicate 4


title: normal blood from tumor-bearing mouse_sample_TL20070522_3_4_A9

description:
Dataset Name: Whole blood array
sample name of age- and cage-matched_mouse: TL20070522_3_4_A10
sample ID: 031706229
sample ID of_age- and cage-matched_mouse: 031706239

value: normal whole blood cells (blood with plasma fraction removed), at time when breast tumor had reached 1 cm size


title: Cut wing discs 0-24h (Biological Replicate1, Dye-swap A)

value: w118iso; 2iso; 3iso isogenic line from the DrosDel collection (Ryder et al. 2007)

tag: developmental stage


title: normal spleen from control mouse_sample_TL20070522_1_2_G8

description:
Dataset Name: Whole spleen array
sample name of age- and cage-matched_mouse: TL20070522_1_2_G7
sample ID: 030306224
sample ID of_age- and cage-matched_mouse: 030306234


title: Wildtype-4

description: replicate 4

value: Wildtype


title: normal spleen from tumor-bearing mouse_sample_TL20070522_1_2_G7

description:
Dataset Name: Whole spleen array
sample name of age- and cage-matched_mouse: TL20070522_1_2_G8
sample ID: 030306234
sample ID of_age- and cage-matched_mouse: 030306224


title: normal spleen from control mouse_sample_TL20070522_1_2_F8

description:
Dataset Name: Whole spleen array
sample name of age- and cage-matched_mouse: TL20070522_1_2_F7
sample ID: 030306204
sample ID of_age- and cage-matched_mouse: 030306214


title: Wildtype-1

description: replicate 1


title: Wildtype-2,b

description: replicate 2


title: normal spleen from control mouse_sample_TL20070522_1_2_F10

description:
Dataset Name: Whole spleen array
sample name of age- and cage-matched_mouse: TL20070522_1_2_F9
sample ID: 090706252
sample ID of_age- and cage-matched_mouse: 090706262


title: normal spleen from tumor-bearing mouse_sample_TL20070522_1_2_F7

description:
Dataset Name: Whole spleen array
sample name of age- and cage-matched_mouse: TL20070522_1_2_F8
sample ID: 030306214
sample ID of_age- and cage-matched_mouse: 030306204


title: normal spleen from tumor-bearing mouse_sample_TL20070522_1_2_F9

description:
Dataset Name: Whole spleen array
sample name of age- and cage-matched_mouse: TL20070522_1_2_F10
sample ID: 090706262
sample ID of_age- and cage-matched_mouse: 090706252


title: normal spleen from tumor-bearing mouse_sample_TL20070522_1_2_F11

description:
Dataset Name: Whole spleen array
sample name of age- and cage-matched_mouse: TL20070522_1_2_F12
sample ID: 120806224
sample ID of_age- and cage-matched_mouse: 120806234


title: DKO-3

description: replicate 3

hyb_protocol: Standard Illumina hybridization protocol.The appropriate mass of cRNA is mixed with GEX-HYB hybridization buffer (supplied by Illumina) and nuclease free water as needed to normalize the volume.    Hybridization chambers for each BeadChip are assembled as per manufacturer’s instructions.  Sample mixture is applied to each chamber as appropriate.  BeadChips are hybridized overnight at 55C with rotation.  Following hybridization the BeadChips are washed with manufacturer supplied wash buffer.

scan_protocol: Illumina Bead Array Reader

data_processing: The data were normalised using cubic spline with Illumina’s GenomeStudio application version 3.4.0.

label_protocol: Samples are prepared for Illumina BeadChip® analysis using the Ilumina TotalPrep® RNA amplification kit (Ambion.)

value: Sohlh1/Sohlh2 double KO


title: normal spleen from control mouse_sample_TL20070522_1_2_F12

description:
Dataset Name: Whole spleen array
sample name of age- and cage-matched_mouse: TL20070522_1_2_F11
sample ID: 120806234
sample ID of_age- and cage-matched_mouse: 120806224


title: Wildtype-3,b

description: replicate 3


title: Wildtype-2

description: replicate 1

value: wildtype


title: Sohlh2 KO-4

description: replicate 3


title: DKO-2

description: replicate 2


title: Sohlh2 KO-3

description: replicate 2


title: normal spleen from control mouse_sample_TL20070522_1_2_E12

description:
Dataset Name: Whole spleen array
sample name of age- and cage-matched_mouse: TL20070522_1_2_E11
sample ID: 120806204
sample ID of_age- and cage-matched_mouse: 120806212

value: FVB


title: Wildtype-3

description: replicate 2


title: DKO-5

description: replicate 4


title: normal spleen from tumor-bearing mouse_sample_TL20070522_1_2_E11

description:
Dataset Name: Whole spleen array
sample name of age- and cage-matched_mouse: TL20070522_1_2_E12
sample ID: 120806212
sample ID of_age- and cage-matched_mouse: 120806204


title: normal spleen from control mouse_sample_TL20070522_1_2_E10

description:
Dataset Name: Whole spleen array
sample name of age- and cage-matched_mouse: TL20070522_1_2_E9
sample ID: 090706242
sample ID of_age- and cage-matched_mouse: 090706232

value: control mice transgenic for TetO-NeuNT only and littermates of the bitransgenic mice


title: DKO-1

description: replicate 1


title: normal spleen from control mouse_sample_TL20070522_1_2_E8

description:
Dataset Name: Whole spleen array
sample name of age- and cage-matched_mouse: TL20070522_1_2_E7
sample ID: 021706215
sample ID of_age- and cage-matched_mouse: 021706204


title: normal spleen from control mouse_sample_TL20070522_1_2_D12

description:
Dataset Name: Whole spleen array
sample name of age- and cage-matched_mouse: TL20070522_1_2_D11
sample ID: 120106232
sample ID of_age- and cage-matched_mouse: 120106222


title: Cut wing discs 0-24h (Biological Replicate1, Dye-swap B)

description: The four microarrays hybridized for each pair of conditions were done in biological replicate pairs. Both arrays from each pair were hybridized with the same amplified RNA from sample and common reference (obtained using the Amino-Allyl Messageamp II aRNA Amplification Kit from Ambion, Inc) but with dyes (Cy3 and Cy5 from Amersham, Inc) swapped to take dye-bias into account.

value: wing imaginal discs and a 90º sector from the posterior (P) compartment, leaving a 3/4 anterior (3/4 A) fragment (Bosch et al. 2005)

value: third instar larvae implanted into recently eclosed Canton S females and kept at 25ºC for 24h (Bosch et al. 2005)


title: normal spleen from tumor-bearing mouse_sample_TL20070522_1_2_D11

description:
Dataset Name: Whole spleen array
sample name of age- and cage-matched_mouse: TL20070522_1_2_D12
sample ID: 120106222
sample ID of_age- and cage-matched_mouse: 120106232

value: female

value: doxycycline-inducible, bitransgenic MMTV-rtTA/TetO-NeuNT (Her2/Neu) mouse model


title: normal spleen from tumor-bearing mouse_sample_TL20070522_1_2_E9

description:
Dataset Name: Whole spleen array
sample name of age- and cage-matched_mouse: TL20070522_1_2_E10
sample ID: 090706232
sample ID of_age- and cage-matched_mouse: 090706242


title: normal spleen from tumor-bearing mouse_sample_TL20070522_1_2_E7

description:
Dataset Name: Whole spleen array
sample name of age- and cage-matched_mouse: TL20070522_1_2_E8
sample ID: 021706204
sample ID of_age- and cage-matched_mouse: 021706215


title: normal spleen from control mouse_sample_TL20070522_1_2_D10

description:
Dataset Name: Whole spleen array
sample name of age- and cage-matched_mouse: TL20070522_1_2_D9
sample ID: 090706212
sample ID of_age- and cage-matched_mouse: 090706204

value: normal whole spleen tissue, at time when breast tumor of matched tumor-bearing mouse had reached 1 cm size


title: normal spleen from control mouse_sample_TL20070522_1_2_C12

description:
Dataset Name: Whole spleen array
sample name of age- and cage-matched_mouse: TL20070522_1_2_C11
sample ID: 120106214
sample ID of_age- and cage-matched_mouse: 120106204


title: normal spleen from control mouse_sample_TL20070522_1_2_H12

description:
Dataset Name: Whole spleen array
sample name of age- and cage-matched_mouse: TL20070522_1_2_H11
sample ID: 011107202
sample ID of_age- and cage-matched_mouse: 011107212


title: normal spleen from tumor-bearing mouse_sample_TL20070522_1_2_D9

description:
Dataset Name: Whole spleen array
sample name of age- and cage-matched_mouse: TL20070522_1_2_D10
sample ID: 090706204
sample ID of_age- and cage-matched_mouse: 090706212

value: normal whole spleen tissue, at time when breast tumor had reached 1 cm size


title: normal spleen from tumor-bearing mouse_sample_TL20070522_1_2_D7

description:
Dataset Name: Whole spleen array
sample name of age- and cage-matched_mouse: TL20070522_1_2_D8
sample ID: 012006202
sample ID of_age- and cage-matched_mouse: 012006214


title: normal spleen from control mouse_sample_TL20070522_1_2_D8

description:
Dataset Name: Whole spleen array
sample name of age- and cage-matched_mouse: TL20070522_1_2_D7
sample ID: 012006214
sample ID of_age- and cage-matched_mouse: 012006202


title: normal spleen from control mouse_sample_TL20070522_1_2_C10

description:
Dataset Name: Whole spleen array
sample name of age- and cage-matched_mouse: TL20070522_1_2_C9
sample ID: 082406253
sample ID of_age- and cage-matched_mouse: 082406243


title: L428-KLF4ER cells control A

city: Ulm

first: Alexey

last: Ushmorov

address: Albert-Einstein-Allee 11

department: Institute of Physiological Chemistry

country: Germany

institute: Ulm University

description: Gene expression data from L428-KLF4ER cells incubated with vehicle only for 24 hours

hyb_protocol: Labeled ssDNA was hybridized to Human Gene 1.0 ST Affymetrix GeneChip arrays (Affymetrix, Santa Clara, CA).

scan_protocol: The chips were scanned with a Affymetrix GeneChip Scanner 3000 according to the Affimetrix protocol.

data_processing: The microarray data were processed using GeneSifter software (http://www.geospiza.com) using RMA normalization protocol.

source_name: L428-KLF4ER (L428 cells stably transfected by KLF4ER fusion gene) cells

label_protocol: The total RNAs were amplified and labeled following the Whole Transcript (WT) Sense Target Labeling Assay (http://www.affymetrix.com).

growth_protocol: KM-H2 and L428 cHL cells were grown in completete RPMI1640 medium at 37 ºC, 5% CO2

extract_protocol: Total RNA was isolated with RNeasy mini kit (QIAGEN)

treatment_protocol: KM-H2-KLF4ER and L428-KLF4ER cells were incubated with 200 µM 4-OHT or with relevant amount of the vehicle (ethanol). The experiment was done twice. After 24 h of incubation total RNA was isolated with RNeasy mini kit (QIAGEN).

value: B cell lymphoma cell line

tag: cell line

value: control


title: KM-H2-KLF4ER cells treated by 4-OHT B

description: Gene expression data from KM-H2-KLF4ER cells incubated with 4-OHT for 24 hours

source_name: KM-H2-KLF4ER (KM-H2 cells stably transfected by KLF4ER fusion gene) cells

value: 4-OHT for 24 hours


title: L428-KLF4ER cells control B

value: stably transfected by KLF4ER fusion gene


title: KM-H2-KLF4ER cells treated by 4-OHT A


title: normal spleen from tumor-bearing mouse_sample_TL20070522_1_2_C9

description:
Dataset Name: Whole spleen array
sample name of age- and cage-matched_mouse: TL20070522_1_2_C10
sample ID: 082406243
sample ID of_age- and cage-matched_mouse: 082406253


title: normal spleen from control mouse_sample_TL20070522_5_C8

description:
Dataset Name: Whole spleen array
sample name of age- and cage-matched_mouse: TL20070522_5_C7
sample ID: 011107222
sample ID of_age- and cage-matched_mouse: 011107232


title: KM-H2-KLF4ER cells control B

description: Gene expression data from KM-H2-KLF4ER cells incubated with vehicle only for 24 hours


title: L428-KLF4ER cells treated by 4-OHT B

description: Gene expression data from L428-KLF4ER cells incubated with 4-OHT for 24 hours


title: normal spleen from tumor-bearing mouse_sample_TL20070522_5_C7

description:
Dataset Name: Whole spleen array
sample name of age- and cage-matched_mouse: TL20070522_5_C8
sample ID: 011107232
sample ID of_age- and cage-matched_mouse: 011107222


title: normal spleen from control mouse_sample_TL20070522_1_2_C8

description:
Dataset Name: Whole spleen array
sample name of age- and cage-matched_mouse: TL20070522_1_2_C7
sample ID: 011906110
sample ID of_age- and cage-matched_mouse: 011906100


title: normal spleen from tumor-bearing mouse_sample_TL20070522_1_2_C11

description:
Dataset Name: Whole spleen array
sample name of age- and cage-matched_mouse: TL20070522_1_2_C12
sample ID: 120106204
sample ID of_age- and cage-matched_mouse: 120106214


title: normal spleen from tumor-bearing mouse_sample_TL20070522_1_2_C7

description:
Dataset Name: Whole spleen array
sample name of age- and cage-matched_mouse: TL20070522_1_2_C8
sample ID: 011906100
sample ID of_age- and cage-matched_mouse: 011906110


title: L428-KLF4ER cells treated by 4-OHT A


title: normal spleen from control mouse_sample_TL20070522_1_2_B12

description:
Dataset Name: Whole spleen array
sample name of age- and cage-matched_mouse: TL20070522_1_2_B11
sample ID: 111706232
sample ID of_age- and cage-matched_mouse: 111706224


title: IQ 250 µM  sample 4 [12999C]

city: Maastricht

first: Kevin

last: Hochstenbach

address: Universiteitssingel 50

department: Health Risk Analysis and Toxicology

country: Netherlands

institute: Maastricht University

hyb_protocol: Hybridization according to Agilent instructions.

scan_protocol: Slides were scanned on a GenePix® 4000B Microarray Scanner (Molecular Devices, Sunnyvale, USA). Cy3 and Cy5 were excited at wavelengths of 532 and 635 nm, respectively. Laser power was set to 100%. The photo multiplier tube gain was set to a saturation tolerance of 0.02% to minimize background and saturated spots. Photomultiplier gain was set to 587 (Cy3) and 705 (Cy5) for replicates 1 and 2, and 628 (Cy3) and 560 (Cy5) for replicates 3 and 4, based on automatic establishment of ideal scan settings. The images obtained (resolution 5 micron, 16 bit tiff image) were processed with Imagene 8.0.1 software (Biodiscovery, El Segundo, USA) to measure mean signal intensities for spots and local backgrounds followed by a quality control in Microsoft Excel.

data_processing: Data preparations were performed in GeneSight software (BioDiscovery) and included in chronological order: background subtraction, omission of bad spots (controls and irregularly shaped spots), LOWESS normalization, log (base=2) transformations, calculation of difference of test compound versus respective vehicle control.

source_name: control for 60_IQ_100%

label_protocol: The Two-Color Microarray-Based Gene Expression Analysis kit from Agilent Technologies (Amstelveen, The Netherlands) was used to generate Cyanine (Cy) labelled cRNA according to the manufacturer’s protocol.

growth_protocol: Isolated PBMC were resuspended in tissue culture medium RPMI 1640 supplemented with L-glutamine, 10% heat inactivated foetal calf serum (FCS) (Gibco, Paisley, UK) and 100 U/ml penicillin G and 0.1 mg/ml streptomycin (PAA Laboratories GmbH, Pasching, Austria) to a final concentration of 2,4*106  cells/ml.

extract_protocol: RNA was isolated from TRIzol® suspended cells according to the manufacturer’s protocol with minor modifications, followed by a clean up, using an RNeasy Mini Kit (Qiagen, Venlo, The Netherlands) with DNase treatment.

treatment_protocol: For analysis of whole genome gene expression by microarray PBMC from five independent donors per compound were exposed for 20 hours to three concentrations, i.e. the 100% and two serial ten-fold dilutions (10% and 1%), and a DMSO or PBS vehicle control. All exposures were performed in the presence of freshly prepared S9-mix.

tag: agent

value: vehicle control

value: Human PBMC

tag: tox class

value: GTX

value: IQ

tag: concentration


title: normal spleen from tumor-bearing mouse_sample_TL20070522_1_2_B11

description:
Dataset Name: Whole spleen array
sample name of age- and cage-matched_mouse: TL20070522_1_2_B12
sample ID: 111706224
sample ID of_age- and cage-matched_mouse: 111706232


title: IQ 25 µM  sample 5 [12999B]

source_name: control for 91_IQ_10%


title: IQ 250 µM  sample 3 [12999A]

source_name: control for 91_IQ_100%


title: KM-H2-KLF4ER cells control A

tag: genotype/variation

tag: treatment group


title: IQ 250 µM  sample 2 [12998C]

source_name: control for 90_IQ_100%


title: normal spleen from control mouse_sample_TL20070522_1_2_B10

description:
Dataset Name: Whole spleen array
sample name of age- and cage-matched_mouse: TL20070522_1_2_B9
sample ID: 031706244
sample ID of_age- and cage-matched_mouse: 031706254


title: IQ 250 µM  sample 1 [12998A]

source_name: control for 89_IQ_100%


title: normal spleen from tumor-bearing mouse_sample_TL20070522_1_2_B9

description:
Dataset Name: Whole spleen array
sample name of age- and cage-matched_mouse: TL20070522_1_2_B10
sample ID: 031706254
sample ID of_age- and cage-matched_mouse: 031706244


title: IQ 25 µM  sample 4 [12998D]

source_name: control for 90_IQ_10%


title: normal spleen from control mouse_sample_TL20070522_1_2_B8

description:
Dataset Name: Whole spleen array
sample name of age- and cage-matched_mouse: TL20070522_1_2_B7
sample ID: 122105219
sample ID of_age- and cage-matched_mouse: 122105203


title: normal spleen from tumor-bearing mouse_sample_TL20070522_1_2_B7

description:
Dataset Name: Whole spleen array
sample name of age- and cage-matched_mouse: TL20070522_1_2_B8
sample ID: 122105203
sample ID of_age- and cage-matched_mouse: 122105219


title: normal spleen from control mouse_sample_TL20070522_1_2_A12

description:
Dataset Name: Whole spleen array
sample name of age- and cage-matched_mouse: TL20070522_1_2_A11
sample ID: 111706212
sample ID of_age- and cage-matched_mouse: 111706204


title: IQ 25 µM  sample 3 [12998B]

source_name: control for 89_IQ_10%


title: normal spleen from control mouse_sample_TL20070522_1_2_A10

description:
Dataset Name: Whole spleen array
sample name of age- and cage-matched_mouse: TL20070522_1_2_A9
sample ID: 031706234
sample ID of_age- and cage-matched_mouse: 031706224


title: normal spleen from tumor-bearing mouse_sample_TL20070522_1_2_A9

description:
Dataset Name: Whole spleen array
sample name of age- and cage-matched_mouse: TL20070522_1_2_A10
sample ID: 031706224
sample ID of_age- and cage-matched_mouse: 031706234


title: normal liver from control mouse_sample_TL20070522_3_4_H6

description:
Dataset Name: Whole liver array
sample name of age- and cage-matched_mouse: TL20070522_3_4_H5
sample ID: 011107203
sample ID of_age- and cage-matched_mouse: 011107213

source_name: normal whole liver tissue, at time when breast tumor of matched tumor-bearing mouse had reached 1 cm size


title: IQ 25 µM  sample 1 [12999D]

source_name: control for 60_IQ_10%


title: normal spleen from tumor-bearing mouse_sample_TL20070522_1_2_A11

description:
Dataset Name: Whole spleen array
sample name of age- and cage-matched_mouse: TL20070522_1_2_A12
sample ID: 111706204
sample ID of_age- and cage-matched_mouse: 111706212


title: BaP 100 µM sample 4 [12988C]

source_name: control for 42_BaP_100%

value: BaP


title: normal liver from tumor-bearing mouse_sample_TL20070522_3_4_H5

description:
Dataset Name: Whole liver array
sample name of age- and cage-matched_mouse: TL20070522_3_4_H6
sample ID: 011107213
sample ID of_age- and cage-matched_mouse: 011107203

source_name: normal whole liver tissue, at time when breast tumor had reached 1 cm size

value: FVB


title: BaP 100 µM sample 1 [12987A]

source_name: control for 39_BaP_100%


title: normal spleen from tumor-bearing mouse_sample_TL20070522_1_2_A7

description:
Dataset Name: Whole spleen array
sample name of age- and cage-matched_mouse: TL20070522_1_2_A8
sample ID: 121505215
sample ID of_age- and cage-matched_mouse: 121505203


title: BaP 100 µM sample 5 [12989A]

source_name: control for 43_BaP_100%


title: BaP 100 µM sample 3 [12988A]

source_name: control for 41_BaP_100%


title: BaP 10 µM sample 5 [12989B]

source_name: control for 43_BaP_10%


title: IQ 25 µM  sample 2 [13000B]

source_name: control for 61_IQ_10%


title: BaP 10 µM sample 2 [12987D]

source_name: control for 40_BaP_10%


title: normal spleen from control mouse_sample_TL20070522_1_2_A8

description:
Dataset Name: Whole spleen array
sample name of age- and cage-matched_mouse: TL20070522_1_2_A7
sample ID: 121505203
sample ID of_age- and cage-matched_mouse: 121505215

source_name: normal whole spleen tissue, at time when breast tumor of matched tumor-bearing mouse had reached 1 cm size

value: control mice transgenic for TetO-NeuNT only and littermates of the bitransgenic mice


title: normal liver from control mouse_sample_TL20070522_3_4_H4

description:
Dataset Name: Whole liver array
sample name of age- and cage-matched_mouse: TL20070522_3_4_H3
sample ID: 102506235
sample ID of_age- and cage-matched_mouse: 102506225

value: normal whole liver tissue, at time when breast tumor of matched tumor-bearing mouse had reached 1 cm size