title: Germline stem cells (GSC_1) sample_1

source_name: Germline stem cells (GSCs) established from testes of OG2 mice

growth_protocol: The culture medium for GSCs consisted of StemPro-34 SFM (Invitrogen) supplemented with StemPro supplement (Invitrogen), 1 × N2 supplement (Invitrogen), 6 mg/ml D-(+)-glucose (Invitrogen), 30 microgram/ml pyruvic acids (Invitrogen), 1 microliter/ml DL-lactic acids (Invitrogen), 5 mg/ml bovine albumin (Invitrogen), 2 mM L-glutamine (Invitrogen), 50 mM 2-mercaptoethanol (Invitrogen), minimal essential medium (MEM) vitamin solution (Invitrogen), MEM nonessential amino acid solution (Invitrogen), 30 ng/ml beta-estradiol (Sigma), 20 ng/ml mouse epidermal growth factor (EGF) (Invitrogen), 10 ng/ml human basic fibroblast growth factor (bFGF) (Tebu-bio), 10 ng/ml human glial cell line-derived neurotrophic factor (GDNF), and 103 U/ml ESGRO (murine leukemia inhibitory factor) (Chemicon). The cells were maintained at 37°C in an atmosphere of 5% CO2 in air.

treatment_protocol:
Testicular cells were obtained from the testes of Oct4-GFP transgenic mice (B6;CBA-Tg[Pou5f1-EGFP]2Mnn/J; The Jackson Laboratory), subsequently referred to as OG2. The testes were decapsulated, minced using fine scissors and treated by 2-step enzymatic digestion. Briefly, minced testis tissue was placed in Digestion solution I, which contained collagenase type IV (1 mg/ml) (Sigma) and DNAse (0.5 mg/ml) (Sigma), in a 37°C water bath. After separation of interstitial cells by gravity for 10 minutes, testicular tubules were washed with DMEM/F12 (Invitrogen) and treated with Digestion solution II, which contained collagenase IV (1 mg/ml), DNAse (0.5 mg/ml), and hyaluronidase (0.5 mg/ml) (Sigma) at 37°C for 10 minutes.
The digested tubules were additionally pipetted to obtain a single cell suspension, followed by washing with DMEM/F12 supplemented with 15% FCS and filtering through a 45 mm nylon mesh. Cell numbers were assessed using a Thomas chamber. The suspension of testicular cells in germline stem cell (GSC) culture medium was plated onto gelatine-coated culture dishes (2 × 105 cells/3.8 cm2). Within 7 to 10 days in culture, GSC colonies were observed under the microscope. GSC colonies were detached by gentle pipetting and replated onto mitomycin C-inactivated mouse embryonic fibroblasts (MEFs). The cells were maintained on MEFs and passaged every 4 to 7 days at a dilution of 1:2 to 1:3.

value: Oct4-GFP transgenic mice (B6;CBA-Tg[Pou5f1-EGFP]2Mnn/J) referred to as OG2 mice. Tissue:testes.


title: Germline stem cells (GSC_2) sample_2

status: Public on Jul 15 2009

type: RNA

city: Aachen

first: Martin

last: Zenke

state: NRW

address: Universitatsklinikum Aachen, RWTH

department: Cell Biology

country: Germany

institute: Institute for Biomedical Engineering

description: BioConductor software package (Gentleman, R. C., Carey, V. J., Bates, D. M. et al. Bioconductor: Open software development for computational biology and bioinformatics. Genome Biol. 2004; 5: R80) (www.bioconductor.org).

hyb_protocol: Affymetrix arrays were prehybridized with 200 ml MES hybridization buffer for 10 minutes at 45˚C with rotation (60 U/min) in an Affymetrix Hybridization Oven 640. After removing the prehybridization solution, 10 microgram of labeled cRNA in 200 ml MES hybridization buffer were applied to the array leaving a small air bubble. Arrays were incubated overnight at 45˚C with rotation (60U/min) in the hybridization chamber.

scan_protocol: Arrays were scanned using Affymetrix GeneChip Scanner 3000.

data_processing: CEL files were processed using the BioConductor software package (www.bioconductor.org). Normalization was done employing RMA (Irizarry et al., Biostatistics 4, 249-264, 2003). Hierarchical clustering of samples was done with the functions “pdis”, “linkage” and “cluster” of the Statistical toolbox of Matlab®. Scatter plots were performed using in-house developed functions in Matlab®.

label: biotin

molecule: total RNA

organism: Mus musculus

label_protocol: Probe preparation was with 1 microgram RNA using the Affymetrix One-Cycle Target Labeling Kit according to the manufacturer's instructions. Labeled RNA was fragmented by heating to 95°C for 35 minutes in 200 mM TRIS (pH 8.1), 500 mM KOAc, 150 mM MgOAc buffer.

extract_protocol: Total RNA was extracted using RNeasy Midi kit (Qiagen, Hilden, Germany) with DNAse digestion using the maufacturer's buffers and protocols. RNA quality was assessed by Agilent 2100 Bioanalyzer System.

tag: Strain


title: Mouse embryonic fibroblasts (MEF_2) sample_2

source_name: Mouse embryonic fibroblasts (MEFs)

treatment_protocol: Mouse embryonic fibroblast were prepared from C3H mice at day E12.5 and cultured under standard conditions.

value: C3H mice


title: Mouse embryonic fibroblasts (MEF_1) sample_1


title: Germline stem cells (GSC_3) sample_3


title: Germline pluripotent stem cells (gPSC_1) sample_1

source_name: Germline pluripotent stem cells (gPS cells, gPSCs) derived from germline stem cells (GSCs) by in-vitro culture

growth_protocol: To expand the gPS cells, the gPS cells colonies were enzymatically dissociated into single cells and cultured under ESC culture conditions at 37°C in an atmosphere of 5% CO2 in air.

treatment_protocol: To obtain embryonic stem cell (ESC)-like cells, approximately 1,000 GSCs were plated per well in 24-well plates containing mouse embryonic fibroblast MEFs. Cultures were maintained in GSC culture medium without subculturing. Within 3 to 4 weeks, colonies with high green fluorescent protein (GFP) intensity and a morphology distinct from typical GSC colonies appeared; the GFP-positive colonies were round-shaped, while GSC colonies appear irregular. To expand the ESC-like cells, colonies were isolated mechanically, dissociated by trypsinisation, and plated onto MEFs in ESC medium.

value: Oct4-GFP transgenic mice (B6;CBA-Tg[Pou5f1-EGFP]2Mnn/J) referred to as OG2 mice.


title: small airways, non-smoker 085

status: Public on Jul 13 2009

city: New York

first: Yael

last: Strulovici-Barel

state: NY

address: 1300 York Avenue

department: Department of Genetic Medicine

country: USA

institute: Weill Cornell Medical College

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

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

organism: Homo sapiens

source_name: airway epithelial cells obtained by bronchoscopy and brushing

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

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

tag: age

tag: sex

value: F

tag: ethnic group

value: white

tag: smoking status

value: non-smoker


title: small airways, non-smoker 076

value: M

value: hispanic


title: small airways, smoker 141

value: smoker, 13 pack-years


title: small airways, smoker 167

value: black

value: smoker, 43 pack-years


title: small airways, non-smoker 080

value: asian


title: OE-Fe-rep2

status: Public on Jul 07 2009

city: Taipei

first: Wolfgang

last: Schmidt

address: No. 128, Sec 2, Academia Rd, Nankang

department: Institute of Plant and Microbial Biology

country: Taiwan

institute: Academia Sinica

description: gene expression data from transgenic arabidopsis roots under iron deficiency medium

hyb_protocol: Ten microgram labeled samples were hybridized to the ATH1 Genome Array at 45℃ for 16.5 h. Washing and staining involved Fluidics Station-450 and the ATH1 Genome.

scan_protocol: Array was scanned with the Affymetrix GeneChip Scanner 7G.

data_processing: The results were quantified and analyzed by use of MicroArray Suite 5.0 software (Affymetrix Inc.)

label: Biotin

organism: Arabidopsis thaliana

source_name: Arabidopsis OE in iron minus medium

label_protocol: Ten microgram of total RNA was used for cDNA synthesis, labeled by in vitro transcription, followed by fragmentation according to the manufacturer's suggestion (GeneChip Expression Analysis Technical Manual rev5, Affymetrix).

growth_protocol: 10-day old seedlings were transferred to ES (+Fe) and ES without addition of FeEDTA (–Fe) medium, respectively. Tissues were harvested and immediately frozen in liquid nitrogen 3 days after the transfer.

extract_protocol: Total RNA was extracted using the Qiagen RNeasy mini kit.

tag: strain

tag: genome/variation

value: CsUBC13 overexpression

tag: environmental factor

value: Iron (Fe) deficiency

tag: tissue

value: root


title: Col-Fe-rep3

description: gene expression data from arabidopsis roots under iron deficiency medium

source_name: Arabidopsis Col-0 in iron minus medium

value: wild type


title: small airways, smoker 161

value: smoker, 5 pack-years


title: OE-Fe-rep1


title: Spleen_IFNAR_CD8_alphaminus denritic cells_rep1

city: Munich

first: Jacek

last: Puchałka

address: Lindwurmstrasse 2a

department: University Children's Hospital

institute: Munich University Hospital

description:
Strain: C57BL/6
Gender: Female
Age: 10 weeks
Tissue: spleen

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: Data were normalized with quantile normalization. The expression values were computed using GC-RMA algorithm. All computations were performed with appropriate functions from the Affy package of the Bioconductor suite.

source_name: C57BL/6 IFNAR ko spleen CD8 alpha minus dendritic cells

label_protocol: standard Affymetrix procedures

extract_protocol: ethanol extraction followed by Qiagen RNeasy total RNA cleanup protocol

value: C57BL/6 IFNAR ko

tag: Gender

value: Female

tag: Age

value: 10 weeks

tag: Tissue

value: spleen


title: Col-Fe-rep2


title: OE-es-rep2

description: gene expression data from transgenic arabidopsis roots under iron efficiency medium

source_name: Arabidopsis OE in iron plus medium


title: small airways, smoker 129

value: smoker, 11 pack-years


title: OE-es-rep3


title: Col-es-rep3

description: gene expression data from arabidopsis roots under iron efficiency medium

source_name: Arabidopsis Col-0 in iron plus medium


title: OE-es-rep1


title: small airways, smoker 125

value: F

value: smoker, 19 pack-years


title: OE-Fe-rep3


title: Spleen_IFNbeta_CD8_alphaminus denritic cells_rep2

source_name: C57BL/6 IFNbeta ko spleen CD8 alpha minus dendritic cells

value: C57BL/6 IFNbeta ko


title: Spleen_IFNbeta_CD8_alphaplus denritic cells_rep2

source_name: C57BL/6 IFNbeta ko spleen CD8 alpha plus dendritic cells


title: Col-es-rep2


title: Spleen_IFNbeta_CD8_alphaplus denritic cells_rep1


title: Col-es-rep1


title: small airways, non-smoker 072

value: non-smoker


title: small airways, non-smoker 046

value: M

value: white


title: Spleen_IFNAR_CD8_alphaminus denritic cells_rep2


title: Col-Fe-rep1


title: Spleen_IFNAR_CD8_alphaplus denritic cells_rep1

source_name: C57BL/6 IFNAR ko spleen CD8 alpha plus dendritic cells


title: Spleen_IFNbeta_CD8_alphaminus denritic cells_rep1


title: small airways, non-smoker 055


title: Wnt1/C2mE_1

status: Public on Jul 02 2009

city: Tsukuba

first: Hiraku

last: Itadani

address: Okubo 3

country: Japan

institute: Banyu Tsukuba Research Institute

description: Gene expression data from glandular stomach of K19-Wnt1/C2mE mouse

hyb_protocol: Labeled cRNAs were hybed according to the standard Affymetrix protocol.

scan_protocol: GeneChip arrays were scanned using the GeneChip Scanner 3000.

data_processing: The data were analyzed with Resolver software.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

extract_protocol: Total RNA was extracted by TRIzol according to the manufacturer's instructions.

tag: genotype

value: female

value: glandular stomach


title: Wnt1/C2mE_5


title: Nog_1

description: Gene expression data from glandular stomach of K19-Nog mouse


title: C2mE_1

description: Gene expression data from glandular stomach of K19-C2mE mouse


title: Nog/C2mE_3

description: Gene expression data from glandular stomach of K19-Nog/C2mE mouse


title: Wnt1/C2mE_2


title: Nog/C2mE_1


title: Wnt1/C2mE_4


title: C2mE_2


title: Nog_2


title: Nog/C2mE_2


title: Musa_DNA_ATH1

status: Public on Jul 04 2009

type: genomic

city: Loughborough

last: Nottingham Arabidopsis Stock Centre (NASC)

address: Sutton Bonington Campus

department: School of Biosciences, University of Nottingham

country: United Kingdom

description: Musa DNA hybridized onto Arabidopsis array.

hyb_protocol: Genomic DNA hybridisation was carried out essentially as described by Hammond et al. In brief, labeled gDNA was hybridised to the Arabidopsis ATH1 Genome Array for 16 h at 45oC, using standard Affymetrix hybridisation protocols. This was then followed by the Affymetrix eukaryotic wash protocol that included antibody staining. The GeneChip Genome Arrays were then hybridised with 0.5 ug of target Musa genomic DNA. GeneChip arrays were stained with Streptavidin-Phycoerythrin solution as described by the Affymetrix GeneChip Expression Analysis Technical Manual (http://www.affymetrix.com). Only one genomic DNA hybridisation was performed, as replicate genomic DNA hybridisations all challenge the GeneChip arrays with the whole genome.

scan_protocol: Scanning done with G2500A GeneArray scanner as described in the Affymetrix GeneChip Expression Analysis Technical Manual.

data_processing: From these results a genomic DNA cell intensity file (.cel file) was generated using the Microarray Analysis Suite software (MAS, v5.0, Affymetrix). This .cel file contains the hybridisation intensities between Musa genomic DNA fragments and all the A. thaliana GeneChip oligonucleotide probes. Probes showing a suitably strong cross-hybridisation signal were selected from the .cel file, using a .cel file parser script (Xspecies v 1.1, available with instructions at http://affymetrix.arabidopsis.info/xspecies/) written in the Perl programming language (http://www.perl.com). This Perl script creates a probe mask (.cdf) file, which is compatible with a range of microarray analysis software packages and provides the template for the generation of a signal across the probeset when analyzing the test (Musa) transcriptome (i.e. the RNA .cel files). Specifically it allows information to be extracted from the RNA .cel files for only those probe-pairs whose perfect-match (PM) probe genomic DNA hybridisation intensity value is above a user-defined hybridisation intensity threshold (CDF value). In practice the optimal genomic DNA CDF is determined systematically and empirically using probe masks created with CDF values of between 50 and 1000. A probeset is retained for analysis when it is represented by at least one PM probe-pair per probeset. Therefore one 25 bp probe, identical in sequence to a Musa genomic DNA fragment is the minimum requirement for inclusion of that probeset in the subsequent transcriptome analysis of the target Musa RNA.

molecule: genomic DNA

organism: Musa sp.

source_name: Musa DNA

label_protocol: Musa genomic DNA was labeled using the Bioprime DNA hybridisation System (Invitrogen).

growth_protocol: Plants were grown at a density of 24 plants per table under a standardised light/dark regime of 12/12 h at 26/23oC respectively with a light intensity of around 10,000 lux (300 watts/m2) and a relative humidity of 75%. At the onset of the experiment, all plants were hand-watered until water drained freely from the base of the pots. The control plants were then watered once a day by flooding the tables with a fertigation solution and allowing the pots to stand for 30 min. Water-deficit (drought) conditions were imposed by withholding water supply for in total up to five weeks. Leaf samples consisted of a 5-8 cm wide strip (~3g fresh weight) removed from one side of the middle of the second, fully expanded leaf down from the top of the plant. Samples were snap frozen in liquid nitrogen and stored at -80oC until analysis. All sampling took place between 14:00 and 17:00 pm.

extract_protocol: Genomic DNA (gDNA) was isolated from young leaves which had been kept in the dark for 48 h to deplete starch and polysaccharide levels using a modified CTAB method essentially as according to Michiels et al. Contaminating RNA was removed by addition of 2.5 ul of a 10 ug/ml stock solution of RNase and incubation at 37oC for 30 min. To check the quality and quantity of DNA, 1 ul samples of isolated DNA were run on a 1% agarose gel in TAE buffer (0.04 M Tris-acetate; 1 mM EDTA, pH 8) as outlined by Sambrook et al. After staining of the gel with ethidium bromide for 15 min, DNA concentrations were visually estimated by comparison to different amounts of lambda-DNA run at the same time. genomic DNA quality was determined spectrophotometrically using the AU absorbance ratios at 260/280 nm. Samples with a 260/280 ratio of 1.9-2.0 were considered 'pure'.

value: leaf

tag: cultivar

value: 'Cachac'


title: C2mE_3


title: Wnt1/C2mE_3


title: Wnt1_5

description: Gene expression data from glandular stomach of K19-Wnt1 mouse


title: Wnt1_1


title: WT_1

description: Gene expression data from glandular stomach of wild-type mouse

source_name: wild-type

value: wild-type


title: Wnt1_6


title: Wnt1_2


title: WT_2


title: WT_3


title: Wnt1_4


title: Lec1

city: Durham

first: Jason

middle: R

last: Rock

state: NC

address: 353 Nanaline Duke, Research Drive

institute: Duke University Medical Center

hyb_protocol: Standard Affymetrix protocol

scan_protocol: GCOS

data_processing: RMA

source_name: lectin+, GFP- #1

label_protocol: Nugen

growth_protocol: Enzymatic digestion and manual dissection were used to obtain a single cell suspension from KRT5-GFP hemizygous mice.

extract_protocol: QIAGEN RNEasy micro kit

treatment_protocol: FACS based on GFP and binding of GSI-A3B isolectin yielded three populations of tracheal epithelium.

value: tracheal epithelium

value: KRT5-GFP transgenic

tag: cell line

value: KRT5-GFP-, lectin+ BCs


title: Gfp2

source_name: lectin+, GFP+ #2

value: KRT5-GFP+, lectin+ BCs


title: Lec3

source_name: lectin+, GFP- #3


title: Gfp1

source_name: lectin+, GFP+ #1


title: Gfp3

source_name: lectin+, GFP+ #3


title: Neg3

source_name: lectin-,GFP- #3

value: KRT5-GFP-, lectin- columnar epithelium


title: Lec2

source_name: lectin+, GFP- #2


title: Neg2

source_name: lectin-,GFP- #2


title: Neg1

source_name: lectin-,GFP- #1


title: Mouse_Iso_20w_Rep2

status: Public on Jul 01 2009

city: Chicago

first: Suzanne

middle: Daniela

last: Conzen

state: IL

address: 5841 S. Maryland Ave, SBRI J301, MC 2115

department: Medicine

institute: The University of Chicago

description: Total mammary gland RNA used

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on Affymetrix mouse genome  genechip. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Gene expression microarray data were normalized using the Robust Multiarray Average (RMA) algorithm  as implemented in the affy package in Bioconductor (http://bioconductor.org).  Differences in gene expression between isolated and group-housed animals’ glands were assessed using Significance Analysis of Microarrays (SAM).  In SAM, each gene “i” is assigned a score di that is proportional to the difference in expression between the two groups relative to the standard deviation, and is similar to the t-statistic. Genes with scores exceeding adjustable cut-offs are called significant.  These cut-off points are determined by selecting a threshold parameter “Δ” so that the corresponding false discovery rate (FDR) is at the desired level (e.g. 5%).  In addition, fold changes greater than 1.25 were required for a gene to be considered significantly up- or downregulated. The SAM p-values were determined based on permutations, and analyses were done using an R package samr (http://cran.r-project.org).

source_name: SV40TAg mammary gland-isolated

label_protocol: Biotinylated cRNA were prepared according to the  standard Affymetrix protocol from 6 micrograms total  mammary gland RNA

growth_protocol: Female FVB/N mice homozygous for the SV40 large Tag gene driven by a fragment [C3(1)] of the rat prostatic steroid binding protein gene promoter were provided by the National Cancer Institute through the Mouse Models of Cancer Consortium. Female mice were weaned at 21 days and then transferred to a special social environment animal laboratory, the Institute of Mind and Biology, at the University of Chicago.

extract_protocol: Frozen mammary glands were thawed on ice, homogenized, and total RNA isolated (RNeasy Mini Kit, Qiagen).  RNA quality was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies), and concentration and 260/280 ratios (>1.8 for each sample was considered acceptable) were determined using an ND-1000 spectrophotometer (NanoDrop).

treatment_protocol: Female SV40 Tag offspring were weaned from their mothers at three weeks of age and placed with their female siblings.  Based on results from the open-field behavior test at 3.5 weeks (innate vigilance), balanced behavioral cohorts of female mice were divided into either socially isolated (single-housed) or group-housed environments. Details regarding separation of animals into housing environments are given below.  Isolated cages measured 11 x 6.5 x 5 inches, and group-housed cages measured 15 x 9 x 9 inches.  A 12hr light:dark cycle was maintained with lights out from 1100:2300, so that mice were active during investigators’ measurements and their sleep cycle was not interrupted. Vaginal cytology was assessed daily in both groups to identify the length and periodicity of the estrous cycle.  Of critical importance, all mice were sacrificed precisely six hours into the dark cycle and during the estrus phase of the reproductive cycle to minimize experimental variability and maximize interindividual reproducibility of gene expression.

value: SV40TAg mammary gland

value: 20 weeks

tag: housing

value: Isolated


title: Mouse_Group_20w_Rep3

description: Total mammary gland RNA used

source_name: SV40TAg mammary gland-grouped

value: Grouped


title: Mouse_Iso_15w_Rep1

description: Total mammary gland RNA used

value: 15 weeks

tag: gender


title: Mouse_Iso_20w_Rep4

description: Total mammary gland RNA used


title: Mouse_Iso_15w_Rep3

description: Total mammary gland RNA used


title: Mouse_Group_15w_Rep1

description: Total mammary gland RNA used


title: Mouse_Group_15w_Rep4

description: Total mammary gland RNA used


title: Mouse_Iso_15w_Rep2

description: Total mammary gland RNA used


title: Mouse_Iso_20w_Rep3

description: Total mammary gland RNA used


title: Mouse_Group_20w_Rep1

description: Total mammary gland RNA used


title: Mouse_Group_20w_Rep4

description: Total mammary gland RNA used


title: Mouse_Group_15w_Rep3

description: Total mammary gland RNA used


title: AcP+AcPb expressing_IL1 stim_rep3

city: Seattle

first: Chris

middle: B

last: Russell

state: WA

address: 1201 Amgen Ct W

department: Molecular Sciences

institute: Amgen

scan_protocol: GeneChip Scanner 3000

data_processing: Rosetta Resolver with Reporters

source_name: cortical neurons, IL1 stim, 4 hrs

label_protocol: Eberwine

growth_protocol: Serum-free neuronal growth medium (2% B-27 supplement + 1% Pen-Strep-Glutamine in Neurobasal Medium (Invitrogen Corp))

extract_protocol: Qiagen RNeasy

treatment_protocol: IL-1b (diluted in medium) added directly to cells to afinal concentration of 10ng/ml

value: embryonic cortical neurons


title: AcP+AcPb expressing_IL1 stim_rep1


title: AcPb expressing_IL1 stim_rep3


title: AcP+AcPb expressing_control_rep3

source_name: cortical neurons, control stim, 4 hrs


title: AcPb expressing_IL1 stim_rep1


title: AcP+AcPb expressing_IL1 stim_rep2


title: AcP+AcPb expressing_control_rep1


title: AcP+AcPb expressing_control_rep2


title: AcPb expressing_IL1 stim_rep2


title: AcPb expressing_control_rep3


title: AcP expressing_IL1 stim_rep2


title: Mouse_Group_15w_Rep2

description: Total mammary gland RNA used


title: AcPb expressing_control_rep1


title: AcP expressing_control_rep3


title: CD25 expressing_IL1 stim_rep1


title: AcPb expressing_control_rep2


title: CD25 expressing_IL1 stim_rep2


title: AcP expressing_control_rep2


title: CD25 expressing_control_rep1


title: AcP expressing_IL1 stim_rep1


title: AcP expressing_control_rep1


title: Mouse_Group_20w_Rep2

description: Total mammary gland RNA used


title: Mouse_Iso_20w_Rep1

description: Total mammary gland RNA used


title: CD25 expressing_control_rep2


title: CD25 expressing_control_rep3


title: Mouse_Iso_15w_Rep4

description: Total mammary gland RNA used


title: HZI1448

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

institute: HCI - Helmholtz Centre for Infection Research

description: CD8 T cells

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at conditions recommended by the manufacturer. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GCS 3000.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 150.

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

extract_protocol: RNeasy

tag: cell type

value: CD8 T cells

tag: genetic modification

value: TCR -> CD8 spezifisch für HA (CL4 TCR)

value: MLN


title: HZI1575

description: CD8 T cells

source_name: Villin-HA + CL4-TCR

value: TCR -> CD8 spezifisch für HA


title: AcP expressing_IL1 stim_rep3


title: CD25 expressing_IL1 stim_rep3


title: HZI1449

description: CD8 T cells


title: NALT_infected_24h_90-226_rep1

city: Pearl River

first: Ellen

last: Murphy

address: 401 N. Middletown Road

department: Vaccines

institute: Wyeth Research

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

scan_protocol: GeneChips were scanned using the Affymetrix Genechip Scanner 3000

data_processing: Normalization and data filtering was performed by Genesis (GeneLogic, Gaithersburg, MD) using the Affymetrix MAS5 algorithm and the trimmed mean. Data visualization, filtering, and statistical analyses were done by GeneSpring version 7.2 (Agilent Technologies, Carmel, IN).  Genes were excluded if they were flagged “Absent” by GCOS in all samples and were included if they had a normalized mean intensity value > 75 (50% of the chip sensitivity value) in at least one group at 24 h post infection. Using these criteria, only 32% (14,472) of the 45,100 probe sets were considered “detectable”.  The data are presented as the ratio of the mean gene intensity in S. pyogenes-infected mice relative to the mean of time-matched, sham-infected mice.   Genes were defined as differentially transcribed if the average expression level changed at least two-fold compared with those in sham-infected NALTs and were statistically significant by Welch’s t-test, with a p-value < 0.05 and Benjamini and Hochberg multiple testing correction (GeneSpring).

source_name: NALT infected with wild type 90-226, biological rep1

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

growth_protocol: Mice were housed in Biosafety Level 2 facilities after infection with S. pyogenes

extract_protocol: Total RNA was purified using the Qiagen RNeasy kit (Qiagen Inc., Valencia, CA) and on-column DNase digestion.  RNA quality was verified using the Agilent Bioanalyzer and a RNA Nano chip (Agilent Techonologies, Santa Clara, CA) and quantified by Nanodrop spectrophotometer (Nanodrop Technologies, Wilmington, DE).  Good quality RNA had A260/A280 ratios > 1.8.

treatment_protocol: Mice were intranasally infected with exponential phase Streptococcus pyogenes (2-4 x 10^8 CFU per 15 microliters PBS) or 15 ul PBS for 24h (Sham mice)

tag: Strain

value: C57BL/6, Gender:female, Age:6-10 weeks

value: nasal-associated lymphoid tissue (NALT)


title: NALT_sham_24h_rep2

source_name: Sham NALT (PBS), biological replicate 2


title: NALT_infected_24h_90-226_rep3

source_name: NALT infected with wild type 90-226, biological rep3


title: NALT_infected_24h_90-226att_rep4

source_name: NALT infected with 90-226att, 24h, biological rep4


title: NALT_sham_24h_rep3

source_name: Sham NALT (PBS), biological replicate 3


title: NALT_infected_24h_90-226_rep4

source_name: NALT infected with wild type 90-226, biological rep4


title: NALT_infected_24h_90-226_rep2

source_name: NALT infected with wild type 90-226, biological rep2


title: NALT_sham_24h_rep4

source_name: Sham NALT (PBS), biological replicate 4


title: NALT_infected_24h_90-226att_rep3

source_name: NALT infected with 90-226att, 24h, biological rep3


title: NALT_sham_24h_rep1

source_name: Sham NALT (PBS), biological replicate 1


title: NALT_infected_24h_90-226att_rep1

source_name: NALT infected with 90-226att, 24h, biological rep1


title: NALT_infected_24h_90-226att_rep2

source_name: NALT infected with 90-226att, 24h, biological rep2


title: NALT_infected_24h_90-226-dM_rep3

source_name: NALT infected with 90-226 deltaM, 24h, biological rep3


title: NALT_infected_24h_90-226-dM_rep4

source_name: NALT infected with 90-226 deltaM, 24h, biological rep4


title: NALT_infected_24h_90-226-dM_rep1

source_name: NALT infected with 90-226 deltaM, 24h, biological rep1


title: LL7

status: Public on Jun 30 2009

city: Los Angeles

first: Delphine

middle: J

last: Lee

state: CA

address: 10833 Le Conte Ave.

institute: UCLA

molecule: polyA RNA

source_name: lepromatous leprosy

extract_protocol: Standard Affymetrix protocol by UCLA DNA microarray core facility (GTC method)

value: skin lesion


title: LL6

hyb_protocol: Standard Affymetrix protocol by UCLA DNA microarray core facility


title: NALT_infected_24h_90-226-dM_rep2

source_name: NALT infected with 90-226 deltaM, 24h, biological rep2


title: ENL4

scan_protocol: Standard Affymetrix protocol by UCLA DNA microarray core facility

source_name: erythema nodosum leprosum


title: LL5

data_processing: Standard Affymetrix protocol by UCLA DNA microarray core facility


title: ENL3

label_protocol: Standard Affymetrix protocol by UCLA DNA microarray core facility


title: ENL5


title: LL4


title: ENL6


title: LL1


title: LL3


title: ENL2


title: LL2


title: ENL1


title: Tumor Tum_Ph3_rep2

city: Granada

first: Mª Esther

last: Farez-Vidal

address: Avda Dr. Oloriz s/n

country: Spain

institute: Hospital Universitario San Cecilio

description: Tumor paired  15

hyb_protocol: Samples were hybridised to Affymetrix HGU133Plus2.0 genechip using Affymetrix standard hybridization protocol using 15ug of biotinylated cRNA (Affymetrix Expression analysis technical manual). GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: The chips were scanned using an Affymetrix  Genechip Scanner 3000

data_processing: Feature intensity values from scanned arrays were normalised and reduced to expression summaries using the Robust Multichip Average (RMA), following the three steps: background correction, quantile normalization and log2-transformation.

source_name: Human Breast

label_protocol: Affymetrix IVT Labeling kit

extract_protocol: Trizol Reagent Protocol + RNeasy mini kit (Qiagen)

tag: t

tag: n

tag: histology

value: cli

tag: grade

tag: receptor

value: NEG

tag: tumor (t) vs healthy (s)

value: T

tag: phenotypes


title: Tumor Tum_Ph4_rep2

description: Tumor paired  16

value: cdi

value: II

value: POS


title: Tumor Tum_Ph2_rep14

description: Tumor paired  3

value: III


title: Tumor Tum_Ph4_rep1

description: Tumor paired  19


title: Tumor Tum_Ph3_rep1

description: Tumor paired  9


title: Tumor Tum_Ph2_rep11

description: Tumor paired  14


title: MSCs Exposed to Keratinocyte Conditioned Medium_2

city: New Brunswick

first: Pravin

last: Mishra

state: NJ

address: 195 Little Albany St.

department: Pharmacology

institute: UMDNJ

description: cDNA synthesis, Hybridization and scanning was  performed at  RWJMS/UMDNJ microarray Facility.

hyb_protocol: Hybridization ◊ Thaw components of the Eukaryotic Hybridization Control Kit. ◊ Heat 20X Eukaryotic Hybridization Control to 65°C for 5 minutes to denature cRNA controls. ◊ Equilibrate desired probe array to room temperature. ◊ In a new, sterile RNase-free 1.5mL microfuge tube, add the following components: 20µl fragmented cRNA 5µl Control Oligonucleotide B2 (3nM) 15µl 20X Eukaryotic Hybridization Controls 3µl Herring Sperm DNA (10mg/mL) 3µl Acetylated BSA (50mg/mL) 150µl 2X Hybridization Buffer 104µl RNase-free water         Total hybridization volume is 300µl ◊ Heat hybridization cocktail to 95°C for 5 minutes, followed by heating at 45°C for 5 minutes. ◊ In a new, sterile RNase-free 1.5mL microfuge tube, combine a volume of 2X Hybridization Buffer with an equal volume of RNase-free water (make 1X Hybridization Buffer). ◊ Wet the probe array by filling it with 250µl of 1X Hybridization Buffer and incubate in Hybridization Oven 640 set at 45°C for 10 minutes with rotation setting at 60rpm. ◊ Centrifuge hybridization cocktail for 5 minutes at max. speed to spin down any insoluble material. ◊ Remove 1X Hybridization Buffer from probe array and fill with 250µl of hybridization cocktail, taking care not to pipette any insoluble material. ◊ Place probe array in Hybridization Oven 640, heated to 45°C and with rotation setting at 60rpm for 16 hours.  Day #3 Washing, Staining, and Scanning ◊ For each array, in a new, sterile RNase-free 1.5mL microfuge tube, combine the following: 600.0µl of 2X MES Stain Buffer 48.0µl Acetylated BSA (50mg/mL) 12.0µl Streptavidin Phycoerythrin (SAPE) (1mg/mL) 540.0µl water, Molecular Biology Grade         Total volume is 1200µl. ◊ Divide into two aliquots of 600µl each to be used for stains 1 and 3. ◊ For each array, in a new, sterile RNase-free 1.5mL microfuge tube, combine the following: 300.0µl 2X MES Stain Buffer 24.0µl Acetylated BSA (50mg/mL) 6.0µl Norma Goat IgG (10mg/mL) 3.6µl Biotinylated antibody (0.5mg/mL) 266.4µl water, Molecular Biology Grade         Total volume is 600µl. ◊ After 16 hours of hybridization, remove 250µl of sample (in hybridization cocktail) and put back into eppendorf, containing fragmented cRNA sample. ◊ Fill the array with 250µl of Non-Stringent Wash Buffer (Wash A) ◊ Now ready for Fluidics Station, followed by scanning.

scan_protocol: Scanned using affymetrix GeneChip Scanner 3000 7G.

source_name: MSCs Exposed to Keratinocyte Condition Medium for 30 days

label_protocol:
cDNA Synthesis
◊ Starting amount of high-purity, total RNA is 5µg.  Total cDNA synthesis volume is 20µl.  Reaction components total 10µl.  Volume of RNA sample will vary based upon measured concentration.  Water is added to reach a final reaction volume of 20µl.
◊ In a sterile, 1.5mL microcentrifuge tube, combine the following:
5.0µg high-purity total RNA
2.0µl T7-oligo(dT) primer, 50µM
RNase-free water (variable)
◊ Incubate at 70°C for 10 minutes.
◊ Quickly spin and put on ice.
◊ Add the following components:
4µl 5X First strand cDNA buffer
2µl 0.1M DTT
1µl 10mM dNTP mix
◊ Mix well and incubate at 42°C for 2 minutes.
◊ Add 1.0µl SuperScript II RT (200U/µL).
◊ Mix well and gently spin down in centrifuge.
◊ Incubate at 42°C for 1 hour.
◊ Place First Strand reactions on ice for 2 minutes and centrifuge briefly to bring down condensation on sides of the tube.
◊ To the First Strand synthesis tube, add the following:
91µl DEPC-treated water
30µl 5X Second Strand Reaction Buffer
3µl 10mM dNTP mix
1µl E. coli DNA ligase (10U/µl)
4µl E. coli DNA Polymerase I (10U/µl)
1µl E. coli RNase H
        Final volume is 150µl.
◊ Gently tap the tube to mix.
◊ Briefly spin down to remove condensation.
◊ Incubate at 16°C for 2 hours in a cooling water bath.
◊ Add 2µl T4 DNA Polymerase (10U).
◊ Return to 16°C water bath for 5 minutes.
◊ Add 10µl 0.5M EDTA.
◊ Proceed with cDNA clean up or store crude cDNA overnight at -20°C.
Cleanup of Double-Stranded cDNA
◊ Using the GeneChip Sample Cleanup Module, add 600µl cDNA Binding Buffer to the sample.
◊ Mix for 3 seconds and check that the color of the mixture is yellow.
◊ Add 500µl of the sample to a cDNA Cleanup Spin Column sitting in a 2mL Collection Tube and centrifuge for 1 minute at 10,000rpm.
◊ Discard flow-through.
◊ Reload the column with the remaining sample (~262uL) and centrifuge as above.
◊ Discard flow-through and Collection Tube.
◊ Transfer spin column to a new 2mL Collection Tube.
◊ Pipet 750µl cDNA Wash Buffer onto spin column and centrifuge for 1 minute at 10,000rpm.
◊ Discard flow-through.
◊ Open the cap of the spin column and centrifuge for 5 minutes at max. speed.
◊ Discard flow-through and Collection Tube.
◊ Transfer spin column into a 1.5mL Collection Tube.
◊ Pipet 14µl of cDNA Elution Buffer directly onto spin column membrane.
◊ Incubate for 1 minute at room temperature.
◊ Centrifuge for 1 minute at max. speed to elute. (average volume of eluate is about 12µl).
◊ Proceed with IVT labeling.
Synthesis of Biotin-Labeled cRNA
◊ Thaw components of the ENZO BioArray RNA Transcript Labeling Kit and purified cDNA mixture from the previous day.
◊ In a new, sterile, 1.5mL RNase-free microfuge tube, add the following components:
10µl purified cDNA
12µl RNase-free water
4µl 10X HY Reaction Buffer (vial#1)
4µl 10X Biotin-Labeled Ribonucleotides (vial#2)
4µl 10X DTT (vial#3)
4µl 10X RNase Inhibitor Mix (vial#4)
2µl 20X T7 RNA Polymerase (vial#5)
        Total reaction volume is 40µl
◊ Gently mix and spin down.
◊ Incubate in a 37°C water bath for 4 hours.

growth_protocol: cells were cultured under standard cell culture protocols i.e. 37° C ,5%co2.

extract_protocol: Cells were harvested following exposure to KCM or KGM and RNA was isolated using RNeasy mini kit (Qiagen Sciences, MD).

treatment_protocol:
Unprocessed bone marrow (36×106 cells/ml) was purchased from Lonza (Walkersville, Md). A Ficoll gradient was used for isolation of hMSCs and to eliminate unwanted cell types from bone marrow. Cells were then plated in T75 cm2 tissue culture flasks with Mesencult media containing hMSC stimulatory supplements and fetal bovine serum (FBS) for hMSCs
 Normal human epithelial primary keratinocyte cell line (NHEK;C-12001) derived from foreskin(~500,000 cells) was obtained from Promocell GmbH (Germany)  and cultured in  Keratinocyte Growth medium (KGM;C-20011). Conditioned medium (CM) from these human keratinocytes was harvested following overnight culture, centrifuged at 3000 rpm for 5 min and supernatant passed through Millipore sterile 50 ml filtration system with 0.45 μm PVDF membrane. hMSCs were exposed to fresh keratinocyte conditioned media (KCM) repeatedly for 30 days with freshly harvested KCM being added every third day.

tag: Human Mesenchymal Stem Cells Isolated from unprocessed bone marrow were exposed to human epithelial primary keratinocyte cell Conditioned medium for 30 days.


title: Tumor Tum_Ph2_rep10

description: Tumor paired  17


title: Tumor Tum_Ph2_rep15

description: Tumor paired  2


title: Tumor Tum_Ph3_rep3

description: Tumor paired  13


title: Tumor Tum_Ph3_rep4

description: Tumor paired  1


title: Tumor Tum_Ph2_rep7

description: Tumor paired  20


title: Tumor Tum_Ph2_rep5

description: Tumor paired  24


title: Tumor Tum_Ph2_rep13

description: Tumor paired  5


title: Tumor Tum_Ph2_rep6

description: Tumor paired  22


title: MSCs Exposed to Keratinocyte Growth Medium_2

source_name: MSCs Exposed to Keratinocyte Growth Medium for 30 days

treatment_protocol:
Unprocessed bone marrow (36×106 cells/ml) was purchased from Lonza (Walkersville, Md). A Ficoll gradient was used for isolation of hMSCs and to eliminate unwanted cell types from bone marrow. Cells were then plated in T75 cm2 tissue culture flasks with Mesencult media containing hMSC stimulatory supplements and fetal bovine serum (FBS) for hMSCs
 Keratinocyte Growth Media was obtained from Promocell GmbH (Germany). hMSCs were exposed to fresh keratinocyte Growth Media (KGM) repeatedly for 30 days ,added every third day.

tag: Human Mesenchymal Stem Cells Isolated from unprocessed bone marrow were exposed to keratinocyte growth medium for 30 days.


title: Tumor Tum_Ph2_rep12

description: Tumor paired  7

value: I


title: MSCs Exposed to Keratinocyte Conditioned Medium_3


title: MSCs Exposed to Keratinocyte Growth Medium_1


title: Tumor Tum_Ph2_rep8

description: Tumor paired  12

value: cdi/cli


title: MSCs Exposed to Keratinocyte Growth Medium_3


title: Tumor Tum_Ph2_rep9

description: not paired


title: Tumor Tum_Ph1_rep10

description: Tumor paired  4


title: Tumor Tum_Ph2_rep2

description: not paired


title: Tumor Tum_Ph2_rep3

description: Tumor paired  26


title: Tumor Tum_Ph1_rep9

description: Tumor paired  6


title: Tumor Tum_Ph2_rep4

description: Tumor paired  25


title: Tumor Tum_Ph2_rep1

description: not paired


title: Tumor Tum_Ph1_rep4

description: Tumor paired  8


title: Tumor Tum_Ph1_rep6

description: Tumor paired  21


title: Control Con_rep25

description: Control paired  3

value: S


title: Tumor Tum_Ph1_rep8

description: Tumor paired  10


title: Control Con_rep19

description: Control paired  12


title: Tumor Tum_Ph1_rep5

description: Tumor paired  18


title: Control Con_rep23

description: Control paired  5


title: T3-treated, v-erbA-transfected AML12 (24h)

city: Jackson

first: Tereza

last: Ventura-Holman

state: MS

address: 2500 North State St.

institute: University of Mississippi Medical Center

description: v-erbA-transfected AML12 cells exposed to 10nM T3 for 3h

hyb_protocol: following Affymetrix GeneChip Expression Analysis Manual

data_processing: Expression data were analyzed by the software DNA-Chip Analyzer (dCHIP) available at www.dchip.org

extract_protocol: total RNA was extracted with Trizol and processed using the RNeasy kit

treatment_protocol: v-erbA transfected AML12 hepatocytes were exposed to 10 nM thyroid hormone (T3) for 24h

value: v-erbA-transfected cultured hepatocytes


title: T3-treated, v-erbA-transfected AML12 (3h)

scan_protocol: following Affymetrix GeneChip Expression Analysis Manual

treatment_protocol: v-erbA transfected AML12 hepatocytes were exposed to 10 nM thyroid hormone (T3) for 3h


title: AML12+T3 (3h)

description: AML12 cells exposed to 10nM T3 for 3h

label_protocol: following Affymetrix GeneChip Expression Analysis Manual

treatment_protocol: AML12 hepatocytes were exposed to 10 nM thyroid hormone (T3) for 3h

value: cultured hepatocytes


title: AML12+T3 (24h)

description: AML12 cells exposed to 10nM T3 for 24h

treatment_protocol: AML12 hepatocytes were exposed to 10 nM thyroid hormone (T3) for 24h


title: Tumor Tum_Ph1_rep2

description: not paired


title: Control Con_rep26

description: Control paired  2


title: MSCs Exposed to Keratinocyte Conditioned Medium_1

source_name: MSCs  Exposed to Keratinocyte Condition Medium for 30 days

tag: Human Mesenchymal Stem Cells Isolated from unprocessed bone marrow were exposed to  human epithelial primary keratinocyte cell Conditioned medium for 30 days.


title: Tumor Tum_Ph1_rep7

description: Tumor paired  11


title: Control Con_rep22

description: Control paired  6


title: Control Con_rep20

description: Control paired  11


title: Control Con_rep21

description: Control paired  7


title: Control Con_rep18

description: Control paired  14


title: Control Con_rep27

description: Control paired  1


title: Tumor Tum_Ph1_rep1

description: not paired


title: Control Con_rep24

description: Control paired  4


title: Control Con_rep16

description: Control paired  16


title: Tumor Tum_Ph1_rep3

description: Tumor paired  23


title: Control Con_rep15

description: Control paired  17


title: Control Con_rep17

description: Control paired  15


title: Control Con_rep14

description: Control paired  18


title: Control Con_rep13

description: Control paired  20


title: Control Con_rep6

description: Control paired  9


title: Control Con_rep9

description: Control paired  19


title: Control Con_rep10

description: Control paired  13


title: Control Con_rep12

description: not paired


title: Control Con_rep4

description: Control paired  23


title: Control Con_rep11

description: Control paired  10


title: Control Con_rep8

description: Control paired  21


title: Control Con_rep5

description: Control paired  22


title: Control Con_rep2

description: Control paired  25


title: Control Con_rep7

description: Control paired  8


title: Control Con_rep1

description: Control paired  26


title: Control Con_rep3

description: Control paired  24


title: GFP-CD133+ Cells (Gate R2) Mouse #5

status: Public on Jun 26 2009

city: Cambridge

first: Ryan

last: Driskell

state: Cambridgeshire

address: Tennis Court Rd.

department: Department of Genetics

institute: University of Cambridge

description: This is the GFP-CD133+ population (zigzag dermal papillae) from mouse #5.

hyb_protocol: The hybridization cocktail was prepared using the NugEN Cocktail PICR v1.0 protocol .  The hybridization cocktail protocol is derived from the NuGEN FL-Ovation cDNA Biotin Module v2 user guide (FLBv2 User Guide)

scan_protocol: The Affymetrix GeneChip scanner 3000 running GCOS software located the PICR.

data_processing: RMA Normalization was used.

source_name: GFP-CD133+ populations (R2) mouse #5

label_protocol: The RNA was amplified using the WT-Ovation Pico target prep v 1.0 protocol which was derived from the NuGE WT-Ovation Pico RNA Amplification system (WTO Pico UserGuide) and the NugEN FL-Ovation cDNA Biotin Module

extract_protocol: The isolation protocol used was from an Invitrogen Purelink micro-midi Total RNA isolation Kit.

tag: cell population

value: GFP-CD133+ (R2) Mouse #5


title: GFP-CD133- (Gate R1) Mouse #4

description: This is the GFP-CD133 population (No dermal papilla population) from mouse #4.

source_name: GFP-CD133- populations (R1) mouse #4

value: GFP-CD133- (R1) mouse #4


title: GFP+CD133+ Cells (Gate R3) mouse #5

description: This is the GFP+CD133+ population (guard/awl/auchene dermal papillae) from mouse #5.

source_name: GFP+CD133+ populations (R3) mouse #5

value: GFP+CD133+ (R3) Mouse #5


title: Mammary gland, LPS-treated, biological rep2

city: Nishigo

first: Mayumi

last: Sugimoto

institute: National Livstock Breeding Center

description: Gene expression data from OCUBM cells treated with LPS.

hyb_protocol: Following fragmentation, 15 microg of cRNA were hybridized for 16 hr at 45C on GeneChip Human Expression Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray Scanner 3000.

data_processing: The data were analyzed with GeneChip Operating Software Ver 1.2.1.001 (GCOS) using Affymetrix default analysis settings.

source_name: OCUBM

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5microg total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).

growth_protocol: DMEM with 10%FBS

extract_protocol: RNeasy Mini kit (QIAGEN) extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Cells were treated with Lipofectamine2000 (Invitrogen) and LPS (SIGMA).

tag: obtained from RIKEN CELL BANK


title: Mammary gland, IGF1R-overexpressed, biological rep1

description: Gene expression data from OCUBM cells transfected with IGF1R.

treatment_protocol: Cells were treated with Lipofectamine2000 (Invitrogen).


title: Mammary gland, control, biological repl 1

description: Gene expression data from OCUBM cells treated without expression vectors.


title: GFP+CD133+ (Gate R3) Mouse #4

description: This is the GFP+CD133+ population (guard/awl/auchene dermal papillae) from mouse #4.

source_name: GFP+CD133+ populations (R3) mouse #4

value: GFP+CD133+ (R3) mouse #4


title: GFP-CD133- (Gate R1) Mouse #5

description: This is the GFP-CD133- (No dermal papillae) from mouse #5.

source_name: GFP-CD133- populations (R1) mouse #5

value: GFP-CD133- (R1) Mouse #5


title: GFP-CD133+ Cell Populations (R2)

description: This is the GFP-CD133+ population (zigzag dermal papillae) from mouse #2.

source_name: GFP-CD133+ populations (R2) mouse #2

value: GFP-CD133+ (R2) mouse #2


title: Mammary gland, IGF1R-overexpressed, biological rep2


title: GFP+CD133+ Cell Population (Gate R3) #2

description: This is the CD133+GFP+ population (guard/awl/auchene dermal papillae) from mouse #2.

source_name: GFP+CD133+ populations (R3) mouse #2

value: GFP+CD133+ (R3) mouse #2


title: Mammary gland, LPS-treated, biological rep1


title: Mammary gland, 12G FEZL-overexpressed, biological rep1

description: Gene expression data from OCUBM cells transfected with 12G FEZL.


title: Mammary gland, 12G FEZL-overexpressed, biological rep2


title: GFP-CD133+ (Gate R2) Mouse #4

description: This is the GFP-CD133+ population (zigzag dermal papillae) from mouse #4.

source_name: GFP-CD133+ populations (R2) mouse #4

value: GFP-CD133+ (R2) mouse #4


title: Mammary gland, control, biological repl 2


title: 9906_P9B01

status: Public on Jun 25 2009

city: Albuquerque

first: Maurice

state: NM

address: 9501 Camino de Salud

department: UNM Cancer Center

institute: UNM Health Sciences Center

description: Diagnostic sample, cryopreserved leukemic blood or bone marrow. See sample charateristics for details.

hyb_protocol: cRNA was fragmented and hybridized overnight to Affymetrix U133 Plus 2.0 Genechips.

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

data_processing: The data were analyzed using Microarray Suite version 5.0 (MAS 5.0) in the Affymetrix Gene Chip Operating Software Version 1.4. Probe masking was used; see the supplementary file 9906_TT207_Affymetrix_probe_mask.msk. Otherwise all Affymetrix default parameter settings were used. Global scaling as the normalization method, with the default target intensity of 500, was used.

label_protocol: Biotinylated cRNA was generated from total RNA using the Affymetrix labeling protocol.

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

tag: age in days at diagnosis

tag: congenital abnormality

value: Female

tag: race

value: White

tag: WBC, 1000/microliter

tag: MLL

value: Negative

tag: CNS status

value: No CNS disease

tag: testicular involvement

tag: trisomy 4 and 10

tag: tissue type

value: bone marrow

tag: blast count, % of sample, -1=unavailable

tag: sample viability, % of sample, -1=unavailable

tag: amplification set

tag: hybridization set

tag: training or test set

value: test set


title: 9906_P9E02

source_name: Diagnostic sample, cryopreserved leukemic blood or bone marrow. See sample charateristics for details.

value: Unknown

tag: gender

value: Male

value: training set


title: 9906_P9D01

value: Positive


title: 9906_P9C01

value: Black or African American


title: 9906_P9E01


title: Mammary gland, control, biological rep1


title: 9906_P9A01


title: 9906_P9F01

value: Hispanic or Latino

value: > 5 CSF WBC/ul with blasts on cytospin and/or eye involvement, cranial nerve  involvement, parenchymal brain involvement


title: 9906_PAA02


title: 9906_P9B02

value: peripheral blood


title: 9906_P8H01


title: 9906_P8E02


title: 9906_P9A02


title: 9906_P9C02


title: 9906_P8F01

value: Asian


title: 9906_P8C03


title: 9906_P8F02


title: GFP-CD133- Cell population (Gate R1)

description: This is the negative sort population without dermal papilla isolated from gate R1 in the sort.

source_name: GFP-CD133- populations (R1) mouse #2

tag: cell population

value: GFP-CD133- (R1) mouse #2


title: 9906_P9G01


title: 9906_P8D01


title: 9906_P8D03

value: < 5 CSF (cerebrospinal fluid) WBC/ul with blasts on cytospin


title: 9906_P8B02


title: 9906_P7G04

value: Female


title: 9906_P8C01


title: 9906_P8A01

value: White


title: 9906_P8A02

value: Negative


title: 9906_P8D02

value: No CNS disease


title: 9906_P7E03

value: bone marrow


title: 9906_P8B01

value: American Indian or Alaska native


title: 9906_P8E01

value: test set


title: 9906_P7C01


title: 9906_P4G01

value: Unknown


title: 9906_P4C03

value: training set


title: 9906_P4E01

value: Male


title: 9906_P4A03


title: 9906_P4E02

value: Positive


title: 9906_P4E03

value: Hispanic or Latino


title: 9906_P4B03

value: Black or African American

value: > 5 CSF WBC/ul with blasts on cytospin and/or eye involvement, cranial nerve  involvement, parenchymal brain involvement


title: 9906_P4A01


title: 9906_P3H02


title: 9906_P3G07


title: 9906_P3G10


title: 9906_P4D03

value: Native Hawaiian or other Pacific Islander


title: 9906_P3H11


title: 9906_P4A02


title: 9906_P3G11

value: peripheral blood


title: 9906_P3H10


title: 9906_P3H04


title: 9906_P3H08


title: 9906_P3F11


title: 9906_P3F08


title: 9906_P3H05

value: Downs

value: < 5 CSF (cerebrospinal fluid) WBC/ul with blasts on cytospin


title: 9906_P3G05


title: 9906_P3G01

value: White


title: 9906_P3G08

value: Female

value: Other

value: Negative


title: 9906_P3G02

value: bone marrow


title: 9906_P3F07

value: No CNS disease

value: test set


title: 9906_P3F06

value: training set


title: 9906_P3F10

value: Male


title: 9906_P3F04


title: 9906_P3F01

value: Unknown


title: 9906_P3E11

value: Positive


title: 9906_P3F02

value: American Indian or Alaska native


title: 9906_P3E03


title: 9906_P3E04


title: 9906_P3E10

value: > 5 CSF WBC/ul with blasts on cytospin and/or eye involvement, cranial nerve  involvement, parenchymal brain involvement


title: 9906_P3E12


title: 9906_P3F03

value: Black or African American


title: 9906_P3F05


title: 9906_P3D03

value: Hispanic or Latino


title: 9906_P3D08

value: Asian


title: 9906_P3D11


title: 9906_P3E08


title: 9906_P3D04


title: 9906_P3D01


title: 9906_P3E01


title: 9906_P3C01


title: 9906_P3C11

value: < 5 CSF (cerebrospinal fluid) WBC/ul with blasts on cytospin

value: peripheral blood


title: 9906_P3C05

value: Female


title: 9906_P3B11

value: White


title: 9906_P3B10

value: Negative


title: 9906_P3E07

value: bone marrow


title: 9906_P3B07


title: 9906_P3C03


title: 9906_P3C07


title: 9906_P3C02

value: No CNS disease


title: 9906_P3B08

value: test set


title: 9906_P3A09


title: 9906_P3B09

value: Other

value: training set


title: 9906_P3A08

value: Male


title: 9906_P3B03

value: Unknown


title: 9906_P3A12

value: Positive


title: 9906_P3A10


title: 9906_P3A05


title: 9906_P2H10


title: 9906_P3B04


title: 9906_P3A01


title: 9906_P3B05


title: 9906_P7H04


title: 9906_P2H11

value: American Indian or Alaska native


title: 9906_P3B01


title: 9906_P3A04


title: 9906_P3A07


title: 9906_P2H08


title: 9906_P2F10


title: 9906_P2H05


title: 9906_P2G05


title: 9906_P2H02


title: 9906_P2F08


title: 9906_P2F07


title: 9906_P2F06

value: Downs


title: 9906_P2F04

value: Hispanic or Latino


title: 9906_P2F03


title: 9906_P2G07


title: 9906_P2E07


title: 9906_P2F01


title: 9906_P2E02


title: 9906_P2E05


title: 9906_P2F02


title: 9906_P2G08


title: 9906_P2E11

value: Black or African American


title: 9906_P2D10


title: 9906_P2E08

value: < 5 CSF (cerebrospinal fluid) WBC/ul with blasts on cytospin


title: 9906_P2E12


title: 9906_P2D03


title: 9906_P2D11

value: > 5 CSF WBC/ul with blasts on cytospin and/or eye involvement, cranial nerve  involvement, parenchymal brain involvement

value: peripheral blood


title: 9906_P2E03

value: Female

value: White


title: 9906_P2E09

value: Negative

value: bone marrow


title: 9906_P2C07

value: test set


title: 9906_P2C04

value: Asian

value: No CNS disease


title: 9906_P2C12

value: Male

value: training set


title: 9906_P2C09

value: Unknown

value: Positive


title: 9906_P2B12


title: 9906_P2D04


title: 9906_P2D09


title: 9906_P2B03


title: 9906_P2B01


title: 9906_P2E01


title: 9906_P2C03


title: 9906_P2B04


title: 9906_P2C01


title: 9906_P2B05

value: unknown


title: 9906_P2A10


title: 9906_P2C08


title: 9906_P2A11


title: 9906_P2D12

value: Hispanic or Latino


title: 9906_P2D01


title: 9906_P2D07


title: 9906_P2B06


title: 9906_P2A05


title: 9906_P2B09

value: Downs


title: 9906_P1H10


title: 9906_P2A01

value: < 5 CSF (cerebrospinal fluid) WBC/ul with blasts on cytospin


title: 9906_P2A09


title: 9906_P2A04


title: 9906_P2A03

value: Other

value: > 5 CSF WBC/ul with blasts on cytospin and/or eye involvement, cranial nerve  involvement, parenchymal brain involvement


title: 9906_P1H05

value: Female

value: peripheral blood


title: 9906_P1G07

value: White

value: Negative


title: 9906_P2A06


title: 9906_P1F08

value: bone marrow


title: 9906_P1G11

value: test set


title: 9906_P1G02


title: 9906_P1H07

value: No CNS disease


title: 9906_P1F09

value: Male


title: 9906_P1E08

value: training set


title: 9906_P1F02

value: Unknown


title: 9906_P1F06

value: Positive


title: 30DayPhenobarb189, biological rep3

first: William

last: Ward

address: 109 TW Alexander Dr

department: NHEERL

institute: United States EPA

description: Gene expression data from male CD-1 mouse livers

hyb_protocol: For each array, 15 lg of amplified biotin-cRNAs were fragmented and hybridized to the array for 16 h at 45 C in a rotating hybridization oven using the Affymetrix eukaryotic target hybridization controls and protocol. Hybridized probe sets on the array were stained with streptavidin/phycoerythrin using a double-antibody staining procedure and washed using the EukGE-WS2v5 protocol of the Affymetrix fluidics station FS450 for antibody amplification.

scan_protocol: Arrays were scanned with an Affymetrix scanner 3000.

data_processing: The raw signal intensities from each scan (.celfiles) were imported into the gene expression analysis software Rosetta Resolver version 7.1 (Rosetta Inpharmatics, Kirkland, WA). The scans were converted into profiles within this software and the data were normalized using Rosetta error model (Weng et al., 2006).

label_protocol: Total RNA (4 ug) for each sample was amplified and labeled by the Enzo BioArray RNA Amplification and Biotin labeling System (Enzo Life Sciences, Farmingdale, NY).

growth_protocol: Not applicable

extract_protocol: Sample preparation, processing and hybridization to the Affymetrix mouse 430_2 arrays were performed at Expression Analysis (Durham, NC) as described in the GeneChip Expression Analysis Manual (Affymetrix, Santa Clara, CA).  The frozen mouse liver tissues were ground in Tri Reagent (Molecular Research Center, Cincinnati, OH) with an IKA Ultra-Turrax T 25 basic tissue grinder (IKA Works, Wilmington, NC). The total RNA pellet was resuspended in 100 ll of water and purified by an RNeasy kit from Qiagen (Valencia, CA). Purified total RNA was eluted in water and its concentration was measured by a NanoDrop ND-1000 spectrometer (Nano-Drop, Wilmington, DE). The quality of RNA was assessed by an Agilent Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Briefly, male CD-1 mice received propiconazole (2500 ppm), tridimefon (1800 ppm), or phenobarbital (850 ppm) in the feed or, control feed for periods of 4 and 30 days. This resulted in an average daily intake of 349.6 ± 46.7 of propiconazole, 257.1 ± 33.5  of tridimefon or 97.2 ± 5.9 mg/kg/day of phenobarbital.

tag: tissue

value: liver

tag: strain

tag: age

value: 6 to 8 weeks old


title: 9906_P1G10

tag: age in days at diagnosis

tag: congenital abnormality

tag: race


title: 9906_P1E09

tag: WBC, 1000/microliter

tag: MLL

tag: CNS status


title: 30DayPhenobarb190, biological rep4


title: 9906_P1F05

value: Hispanic or Latino

tag: testicular involvement

tag: trisomy 4 and 10

tag: tissue type


title: 9906_P1E11

tag: blast count, % of sample, -1=unavailable

tag: sample viability, % of sample, -1=unavailable

tag: amplification set


title: 9906_P1H04

tag: gender

tag: hybridization set

tag: training or test set


title: 30DayPhenobarbControl179, biological rep4

tag: tissue

tag: strain


title: 9906_P1G05

tag: age in days at diagnosis

value: Downs


title: 30DayPhenobarbControl181, biological rep5

tag: age


title: 30DayPhenobarb184, biological rep2


title: 9906_P1G03

tag: congenital abnormality

tag: race


title: 30DayPhenobarb182, biological rep1


title: 9906_P1E03

tag: WBC, 1000/microliter

tag: MLL


title: 9906_P1E06

tag: CNS status

tag: testicular involvement


title: 30DayPhenobarb192, biological rep5


title: 30DayPhenobarbControl172, biological rep2


title: 30DayPhenobarbControl177, biological rep3


title: 9906_P1E02

value: < 5 CSF (cerebrospinal fluid) WBC/ul with blasts on cytospin

tag: trisomy 4 and 10

tag: tissue type


title: 30DayTriad, biological rep3


title: 9906_P1D12

tag: blast count, % of sample, -1=unavailable

tag: sample viability, % of sample, -1=unavailable


title: 9906_P1D11

tag: gender

value: > 5 CSF WBC/ul with blasts on cytospin and/or eye involvement, cranial nerve  involvement, parenchymal brain involvement

tag: amplification set


title: 9906_P1D09

tag: hybridization set

tag: training or test set


title: 30DayPropi, biological rep3

tag: tissue

tag: strain


title: 30DayTriad, biological rep2

tag: age


title: 30DayPropi, biological rep2


title: 30DayPhenobarbControl170, biological rep1


title: 30DayConazoleControl, biological rep3


title: 9906_P1D08

tag: age in days at diagnosis

tag: congenital abnormality


title: 30DayConazoleControl, biological rep2


title: 30DayTriad, biological rep1


title: 9906_P1F07

tag: race

tag: WBC, 1000/microliter


title: 30DayPropi, biological rep1


title: 9906_P1D06

tag: MLL

tag: CNS status


title: 9906_P1D07

value: Other

tag: testicular involvement

tag: trisomy 4 and 10


title: 30DayConazoleControl, biological rep1


title: 9906_P1D04

tag: tissue type

tag: blast count, % of sample, -1=unavailable


title: 4DayPhenobarb165, biological rep3


title: 4DayPhenobarb168, biological rep5


title: 9906_P1D05

tag: gender

value: Female

value: peripheral blood

tag: sample viability, % of sample, -1=unavailable


title: 9906_P1D01

value: White

value: Negative

tag: amplification set

tag: hybridization set


title: 9906_P1C11

tag: training or test set

value: test set


title: 9906_P1D02

value: No CNS disease

value: bone marrow


title: 4DayPhenobarb161, biological rep2

tag: tissue

tag: strain


title: 4DayPhenobarbControl154, biological rep5

tag: age


title: 4DayPhenobarb158, biological rep1


title: 9906_P1C05

tag: age in days at diagnosis

tag: congenital abnormality

value: Male

value: training set


title: 9906_P1C02

tag: race

tag: WBC, 1000/microliter

value: Unknown


title: 9906_P1D10

tag: MLL

tag: CNS status


title: 9906_P1B12

tag: testicular involvement

tag: trisomy 4 and 10


title: 9906_P1C01

tag: tissue type

tag: blast count, % of sample, -1=unavailable


title: 4DayTriad, biological rep3

value: liver


title: 9906_P1B09

tag: gender

value: unknown

tag: sample viability, % of sample, -1=unavailable


title: 4DayPhenobarb166, biological rep4

value: 6 to 8 weeks old


title: 4DayPhenobarbControl147, biological rep1


title: 4DayPhenobarbControl148, biological rep2


title: 9906_P1B07

value: Hispanic or Latino

tag: amplification set

tag: hybridization set


title: 9906_P1B05

tag: training or test set


title: 4DayPhenobarbControl153, biological rep4

tag: tissue

tag: strain


title: 9906_P1B03

tag: age in days at diagnosis

value: Positive


title: 4DayPhenobarbControl149, biological rep3

tag: age


title: 4DayTriad, biological rep1


title: 9906_P1A12

tag: congenital abnormality

tag: race


title: 4DayTriad, biological rep2


title: 9906_P1A11

tag: WBC, 1000/microliter

tag: MLL

value: > 5 CSF WBC/ul with blasts on cytospin and/or eye involvement, cranial nerve  involvement, parenchymal brain involvement


title: 9906_P1A10

value: Asian

tag: CNS status

tag: testicular involvement


title: 4DayConazoleControl, biological rep1


title: 4DayPropi, biological rep1


title: 4DayConazoleControl, biological rep3


title: 4DayConazoleControl, biological rep2


title: 9906_P1B02

tag: trisomy 4 and 10

tag: tissue type


title: 4DayPropi, biological rep2


title: 4DayPropi, biological rep3


title: 9906_P1A04

tag: gender

tag: blast count, % of sample, -1=unavailable


title: 9906_P1A09

tag: sample viability, % of sample, -1=unavailable

tag: amplification set


title: 9906_P1A05

tag: hybridization set

tag: training or test set


title: 9906_P1A07


title: 9906_P1A03

value: Black or African American


title: 9906_P1A02

value: Female

value: < 5 CSF (cerebrospinal fluid) WBC/ul with blasts on cytospin

value: peripheral blood


title: SKM-1 control 2

status: Public on Jun 24 2009

city: Berlin

first: Lars

last: Bullinger

address: Augustenburger Platz 1

department: Hematology, Oncology and Tumorimmunology

institute: Charité

description: cell line transduced with a control shRNA

hyb_protocol: Affymetrix standard protocol

scan_protocol: Affymetrix standard protocol

data_processing: GCOS software

source_name: SKM-1 acute myeloid leukemia cells

label_protocol: GeneChip One-Cycle cDNA Synthesis Kit (Affymetrix; manufacturer’s recommendations), amount of RNA labeled: 1µg

extract_protocol: Trizol (manufacturer’s recommendations)

tag: cell line


title: SKM-1 STK33-2077

description: cell line transduced with an shRNA targeting STK33


title: CS-1/ET

city: Boston

first: Zhenfeng

last: Duan

state: MA

address: 100 Fruit St

institute: Massachusetts General Hospital

description: gene expression in ET-743 resistant cell line

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

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: ET-743 resistant cell line

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

growth_protocol: Cell lines were cultured in RPMI 1640 supplemented with 10% fetal bovine serum, 100-units/ml penicillin and 100µg/ml streptomycin

treatment_protocol: CS-1/ER and CS-1/PR cells resistant to ET-743 or PM00104 were derived from the CS-1 parent cell line by continuously exposure to ET-743 or PM00104 with step-by step increase concentration of ET-743 for one year.

tag: tissue

value: Chondrosarcoma


title: NOMO-1 control 1

source_name: NOMO-1 acute myeloid leukemia cells


title: BMDC(-)

city: Tokyo

first: Akihiko

last: Yoshimura

address: 35 Shinanomachi Shinjyuku-ku

department: Microbiology and Immunology

institute: Keio Medical School

description: Gene expression data from untreated mouse BMDC

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Mouse 430 2.0 GeneChip. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

source_name: mouse bone marrow-derived denderitic cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Bone marrow cells were cultured in 10 ng/ml mouse GM-CSF (PeproTech) and the 10-day-cultured BMDCs were used for the experiment.

treatment_protocol: BMDCs were unstimulated or stimulated with LPS (10 ng/ml) alone or with LPS plus cAMP (100 microM) for 3h. LPS (Escherichia coli serotype 055:B5) and 8-Bromoadenosine 3, 5'-cyclic monophosphate sodium salt (8-Br-cAMP) (B7880) were purchased from Sigma. The total RNA of BMDCs was isolated using Trizol (Invitrogen) and biotinylated cRNAs were synthesized using a one-cycle target labeling kit (Affymetrix). Fragmented cRNAs were hybridized to the Mouse 430 2.0 GeneChip (Affymetrix).

tag: cell type

value: dendritic cells

tag: agent


title: BMDC(+LPS+cAMP)

description: Gene expression data from mouse BMDC treated with LPS +cAMP

source_name: mouse bone marrow-derived denderitic cells treated with LPS+cAMP

value: LPS+cAMP


title: BMDC(+LPS)

description: Gene expression data from mouse BMDC treated with LPS

source_name: mouse bone marrow-derived denderitic cells treated with LPS

value: LPS


title: NOMO-1 STK33-2077


title: NOMO-1 control 2


title: SKM-1 STK33-2081


title: CS-1/Zal

description: gene expression in Zalapsis resistant cell line

source_name: Zalapsis resistant cell line


title: SKM-1 control 1


title: CS-1

description: gene expression in parental sensitive cell line

source_name: parental cell line


title: NOMO-1 STK33-2081


title: VeryLowDose_8h_rep3

city: MASON

first: Jay

middle: Patrick

last: Tiesman

state: OH

address: PO BOX 8006

department: Global Biotechnology

institute: Procter & Gamble

description: Cells known to possess both estrogen and progesterone receptors

hyb_protocol: Following fragmentation, cRNA was hybridized for 16 hr at 45C on GeneChip Human U133plus2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 1500.

source_name: Ishikawa Cell Line

label_protocol: Purified RNA was converted to cDNA target using SuperScript Choice system (Invitrogen Corp, Carlsbad, CA) and cDNA was converted to biotinylated cRNA probes using the ENZO BioArray transcript labeling kit (ENZO Life Sciences, Farmingdale, NY).

growth_protocol: Ishikawa cells were maintained and grown (to confluency or at a desired cell density between 500,000 - 1 million cells/mL) in DMEM/F-12 Medium (supplemented with 10% Fetal Bovine Serum + 1X penicillin/streptomycin) in xenoestrogen-free Corning plasticware.

extract_protocol: Total RNA was extracted using TRI-Reagent and protocol provided by supplier (Molecular Research Center, Cincinnati, OH).  Extracted RNA was further purified using Qiagen RNEasy columns and protocol provided by supplier (QIAgen, Valencia, CA).

treatment_protocol: Cells were gently washed in warm PBS and transferred to phenol red-free DMEM/F-12 Medium (supplemented with 10% Charcoal-Stripped Fetal Bovine Serum + 1X penicillin/streptomycin) in Corning Cell Culture Cluster wells overnight and then challenged with 1pM (very low, vL), 100pM (low, L), 10nM (high, H), and 1uM (very high, vH) levels of 17aEE.  Prior to collection, cells were washed in warm PBS, resuspended & briefly incubated in TRI-Reagent, & finally collected (in quintuplicate replicates) at time each specific time point: 8 hours, 24 hours, and 48 hours.

tag: 1 pM 17aEE

tag: 8 Hour Treatment

tag: Cells derived from 39yo parous Japanese female diagnosed with endometrial adenocarcinoma stage 2.


title: VeryLowDose_24h_rep5

tag: 24 Hour Treatment


title: VeryLowDose_24h_rep1


title: VeryLowDose_24h_rep3


title: VeryLowDose_48h_rep2

tag: 48 Hour Treatment


title: VeryLowDose_48h_rep4


title: VeryLowDose_24h_rep4


title: VeryLowDose_8h_rep5


title: VeryLowDose_48h_rep1


title: VeryLowDose_8h_rep4


title: 9906_P1C03

tag: age in days at diagnosis

tag: congenital abnormality

value: Male

tag: race

value: White

tag: WBC, 1000/microliter

tag: MLL

value: Negative

tag: CNS status

value: No CNS disease

tag: testicular involvement

tag: trisomy 4 and 10

value: bone marrow

value: training set


title: VeryHighDose_48h_rep5

tag: 1 uM 17aEE


title: VeryLowDose_48h_rep5


title: VeryLowDose_24h_rep2


title: VeryHighDose_48h_rep4


title: VeryLowDose_48h_rep3


title: VeryLowDose_8h_rep2


title: VeryLowDose_8h_rep1


title: VeryHighDose_48h_rep1


title: VeryHighDose_48h_rep3


title: VeryHighDose_24h_rep4


title: VeryHighDose_24h_rep5


title: VeryHighDose_24h_rep2


title: VeryHighDose_24h_rep1


title: VeryHighDose_24h_rep3


title: VeryHighDose_48h_rep2


title: VeryHighDose_8h_rep5


title: VeryHighDose_8h_rep4


title: LowDose_48h_rep4

tag: 100 pM 17aEE


title: VeryHighDose_8h_rep3


title: VeryHighDose_8h_rep2


title: LowDose_24h_rep4


title: VeryHighDose_8h_rep1


title: LowDose_48h_rep5


title: LowDose_48h_rep2


title: LowDose_24h_rep1


title: LowDose_8h_rep4


title: LowDose_8h_rep5


title: LowDose_24h_rep3


title: LowDose_8h_rep3


title: LowDose_48h_rep3


title: HighDose_48h_rep2

tag: 10 nM 17aEE


title: LowDose_24h_rep2


title: LowDose_48h_rep1


title: LowDose_24h_rep5


title: LowDose_8h_rep2


title: HighDose_48h_rep5


title: HighDose_48h_rep4


title: HighDose_48h_rep3


title: LowDose_8h_rep1


title: HighDose_48h_rep1


title: HighDose_24h_rep5


title: HighDose_24h_rep1


title: HighDose_8h_rep3


title: Control_24h_rep4

tag: Vehicle Control


title: HighDose_8h_rep2


title: HighDose_8h_rep5


title: HighDose_8h_rep4


title: Control_48h_rep1


title: Control_24h_rep5


title: Control_48h_rep5


title: Control_24h_rep3


title: HighDose_24h_rep2


title: HighDose_8h_rep1


title: Control_48h_rep4


title: HighDose_24h_rep4


title: AID+/+ leukemia biological replicate 1

first: Markus

last: Muschen

address: 4650 Sunset Blvd MS 136

department: Hematology Oncology

institute: Childrens Hospital Los Angeles

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

data_processing: The data were analyzed with Partek Genomic Suite using RMA as normalization method with a FDR of less than 0.05.

source_name: AID+/+ leukemia biological replicate 1

extract_protocol: Total RNA was extracted from leukemia cells using Rneasy columns per manufacturers instructions (Qiagen, Valencia, CA)

tag: strain

value: Balb/c

tag: cell type

value: AID+/+ leukemia cells


title: Control_48h_rep2

tag: Cells derived from 39yo parous Japanese female diagnosed with endometrial adenocarcinoma stage 2.


title: Control_24h_rep2

tag: 24 Hour Treatment


title: Control_8h_rep1

tag: 8 Hour Treatment


title: AID+/+ leukemia biological replicate 2

source_name: AID+/+ leukemia biological replicate 2


title: Control_8h_rep2


title: AID-/- leukemia biological replicate 3

source_name: AID-/- leukemia biological replicate 3

value: AID-/- leukemia cells


title: Control_24h_rep1


title: Control_8h_rep5


title: Control_8h_rep4


title: Control_48h_rep3

tag: 48 Hour Treatment


title: AID+/+ leukemia biological replicate 3

source_name: AID+/+ leukemia biological replicate 3


title: Control_8h_rep3


title: HighDose_24h_rep3


title: ovary_Foxl2ko_P0_3

city: Paris

last: Ottolenghi

address: rue des Saint-Peres

country: France

institute: Inserm/Univ.Paris Descartes

description: We studied 43 samples over 15 conditions to cover a wide range of wiltype and pathological states showing highly divergent alterations of cell type composition.

hyb_protocol: 18 hrs at 45 degree, with rotation 60 rpm

scan_protocol: Affymetrix GeneChip Scanner 3000

data_processing: Affymetrix GCOS 1.3

source_name: whole gonad, no annexa; Foxl2-/-

label_protocol: Biotin (FL-Ovation)

extract_protocol: Melt (Ambion) enzymatic extraction and single round of linear RNA amplification with Pico Ovation (Nugen Inc)

tag: C57BL/6 x CD1 x NIHS-BC; Foxl2-/-; female; birth


title: ovary_KitWvWv_P0_3

source_name: whole gonad, no annexa; KitWvWv single ko (Foxl2+/-)

tag: C57BL/6 x CD1 x NIHS-BC; KitWvWv; Foxl2+/-; female; birth


title: ovary_P0_2

source_name: whole gonad, no annexa

tag: C57BL/6 x CD1 x NIHS-BC; Foxl2+/+;female; birth


title: ovary_Foxl2ko_hetE16_1

source_name: whole gonad, no annexa; Foxl2+/- heterozygote

tag: C57BL/6 x CD1 x NIHS-BC; Foxl2+/-;female; 16.5 dpc; Foxl2+/-


title: ovary_Wnt4ko_P0_2

source_name: whole gonad, no annexa; Wnt4-/- single ko (Foxl2+/-)

tag: C57BL/6 x CD1 x 129-Wnt4<tm1Amc>/J; Wnt4-/-;Foxl2+/- female; birth


title: AID-/- leukemia biological replicate 1

source_name: AID-/- leukemia biological replicate 1


title: ovary_KitWvWv_P0_2


title: AID-/- leukemia biological replicate 2

source_name: AID-/- leukemia biological replicate 2


title: ovary_KitWvWv_Foxl2ko_P0_3

source_name: whole gonad, no annexa; KitWvWv Foxl2-/- double ko

tag: C57BL/6 x CD1 x NIHS-BC; KitWvWv; Foxl2-/-; female; birth


title: ovary_Foxl2ko_P0_2


title: ovary_Wnt4ko_E15_2

source_name: whole gonad, no annexa; Wnt4 ko

tag: C57BL/6 x 129-Wnt4<tm1Amc>/J; Wnt4-/-; female; 15.5 dpc


title: ovary_Wnt4ko_E15_1


title: ovary_Foxl2ko_E16_2

tag: C57BL/6 x CD1 x NIHS-BC;  Foxl2-/-; female; 16.5 dpc


title: ovary_Wnt4ko_P0_1


title: ovary_KitWvWv_P0_1


title: ovary_E15_2

source_name: whole gonad, no annexa; Wnt4+/-

tag: C57BL/6 x 129-Wnt4<tm1Amc>/J; Wnt4+/-;female; 15.5 dpc


title: ovary_P0_1


title: ovary_KitWvWv_Foxl2ko_P0_2


title: ovary_Wnt4ko_Foxl2ko_P0_3

source_name: whole gonad, no annexa; Wnt4-/-Foxl2-/- double ko

tag: C57BL/6 x CD1 x 129-Wnt4<tm1Amc>/J; Wnt4-/-;Foxl2-/- female; birth


title: ovary_E15_1


title: ovary_KitWvWv_Foxl2ko_P0_1


title: ovary_Foxl2ko_hetE16_3


title: ovary_Foxl2ko_hetE16_2


title: ovary_Wnt4ko_Foxl2ko_P0_2


title: ovary_Foxl2ko_P0_1


title: ovary_Foxl2ko_E16_3


title: ovary_Foxl2ko_E16_1


title: ovary_Wnt4ko_P0_3


title: ovary_E16_2

tag: C57BL/6 x CD1 x NIHS-BC; Foxl2+/+; female; 16.5 dpc


title: ovary_E16_3


title: ovary_Foxl2ko_E13_3

tag: C57BL/6 x CD1 x NIHS-BC; Foxl2-/-; female; 13.5 dpc


title: ovary_Wnt4ko_Foxl2ko_P0_1


title: ovary_E13_3

source_name: whole gonad, no annexa; Foxl2+/-

tag: C57BL/6 x CD1 x NIHS-BC; Foxl2+/-;female; 13.5 dpc


title: ovary_Foxl2ko_E13_2


title: ovary_Foxl2ko_E13_1


title: ovary_E16_1


title: testis_E13_1

tag: C57BL/6 x CD1 x NIHS-BC; male; 13.5 dpc


title: testis_P0_2

tag: C57BL/6 x CD1 x NIHS-BC; Wnt4-/-; male; birth


title: ovary_E13_1


title: testis_E13_3


title: ovary_E13_2


title: testis_P0_1


title: ovary_P0_3


title: testis_P0_3


title: testis_E13_2


title: Mouse heart, GF Ppara-/- rep 5

status: Public on Jun 23 2009

city: St. Louis

first: Peter

last: Crawford

state: MO

address: 660 S. Euclid Ave.

institute: Washington University School of Medicine

description: Gene expression data from mouse heart

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse 430_2. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GS300

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

source_name: Mouse heart, GF Ppara-/-

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 12 ug total RNA.

growth_protocol: C57Bl/6 mice were born and raised in GF Trexler-style isolators.  Only male mice were used.  At weaning, half of the mice were transferred to a new isolator and received a microbiota transplant (CONV-D), and the other half were weaned but remained in a GF isolator.  Two to three weeks later, treatments were initiated, and hearts were harvested.

extract_protocol: Qiagen RNeasy fibrous tissue mini-prep kit.

treatment_protocol: Wild-type GF and CONV-D mice were sacrificied in the CARB-fed state, after a 24h Fast from the CARB-fed state, or after 30d of swimming exercise training (increased from 5 min, up to 90 min per day, twice per day, CARB-fed mice), and CARB-fed GF and CONV-D Ppara-/- mice

tag: tissue

value: heart

tag: age

value: six to ten week-old

tag: genotype

value: Ppara-/-

tag: gender

value: male


title: Mouse heart, CONV-D Ppara-/- rep 1

description: Gene expression data from mouse heart

source_name: Mouse heart, CONV-D Ppara-/-


title: Mouse heart, GF Ppara-/- rep 3

description: Gene expression data from mouse heart


title: Mouse heart, GF Ppara-/- rep 4

description: Gene expression data from mouse heart


title: Mouse heart, CONV-D Trained, rep 2

description: Gene expression data from mouse heart

source_name: Mouse heart, CONV-D 30d trained

value: wild type (C57Bl/6)


title: Mouse heart, GF Ppara-/- rep 2

description: Gene expression data from mouse heart


title: Mouse heart, CONV-D Trained, rep 5

description: Gene expression data from mouse heart


title: Mouse heart, CONV-D Trained, rep 3

description: Gene expression data from mouse heart


title: Mouse heart, CONV-D Trained, rep 4

description: Gene expression data from mouse heart


title: Mouse heart, CONV-D Ppara-/- rep 3

description: Gene expression data from mouse heart


title: Mouse heart, GF Ppara-/- rep 1

description: Gene expression data from mouse heart


title: Mouse heart, CONV-D Ppara-/- rep 2

description: Gene expression data from mouse heart


title: Mouse heart, CONV-D 24h Fast, rep 3

description: Gene expression data from mouse heart

source_name: Mouse heart, CONV-D 24h Fast


title: Mouse heart, GF Trained, rep 5

description: Gene expression data from mouse heart

source_name: Mouse heart, GF 30d trained


title: Mouse heart, CONV-D 24h Fast, rep 5

description: Gene expression data from mouse heart


title: Mouse heart, GF 24h Fast, rep 4

description: Gene expression data from mouse heart

source_name: Mouse heart, GF 24h Fast


title: Mouse heart, GF Trained, rep 3

description: Gene expression data from mouse heart


title: Mouse heart, GF 24h Fast, rep 3

description: Gene expression data from mouse heart


title: Mouse heart, CONV-D 24h Fast, rep 2

description: Gene expression data from mouse heart


title: Mouse heart, GF 24h Fast, rep 2

description: Gene expression data from mouse heart


title: Mouse heart, GF Trained, rep 2

description: Gene expression data from mouse heart


title: Mouse heart, CONV-D Trained, rep 1

description: Gene expression data from mouse heart


title: Mouse heart, GF Trained, rep 1

description: Gene expression data from mouse heart


title: Mouse heart, CONV-D 24h Fast, rep 4

description: Gene expression data from mouse heart


title: Mouse heart, GF 24h Fast, rep 1

description: Gene expression data from mouse heart


title: Mouse heart, CONV-D CARB-fed, rep 5

description: Gene expression data from mouse heart

source_name: Mouse heart, CONV-D CARB-fed


title: Mouse heart, GF Trained, rep 4

description: Gene expression data from mouse heart


title: Mouse heart, CONV-D 24h Fast, rep 1

description: Gene expression data from mouse heart


title: Mouse heart, CONV-D CARB-fed, rep 3

description: Gene expression data from mouse heart


title: Mouse heart, GF 24h Fast, rep 5

description: Gene expression data from mouse heart


title: Mouse heart, CONV-D CARB-fed, rep 1

description: Gene expression data from mouse heart


title: Mouse heart, CONV-D CARB-fed, rep 2

description: Gene expression data from mouse heart


title: Mouse heart, CONV-D CARB-fed, rep 4

description: Gene expression data from mouse heart


title: Mouse heart, GF CARB-fed, rep 4

description: Gene expression data from mouse heart

source_name: Mouse heart, GF CARB-fed


title: ARG replicate 3

city: Cincinnati

first: Bruce

last: Aronow

institute: Cincinnati Children's Hospital Medical Center

description: heart from beta1-Arg389 transgenic mice at 90 days of age. The alpha-myosin heavy chain promoter was utilized to direct expression of the human beta1-Arg389 cDNAs to cardiac myocytes.

hyb_protocol: Following fragmentation, cRNA were hybridized on the Affymetrix MOE430 plus 2.0 GeneChip array according to the standard Affymetrix protocol.

scan_protocol: GeneChips were scanned using the Affymetrix Genechip Scanner 3000.

data_processing: The data were analyzed with Genespring 7.3.1 (Agilent) using RMA normalization, then normalized to median of the non-transgenic mice.

source_name: heart from beta1-Arg389 transgenic mice

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

extract_protocol:
Trizol (Invitrogen, Carlsbad, CA).
Quality was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies, Inc., Palo Alto, CA).

tag: heart, beta1-Arg389 transgenic mice at 90 days of age


title: Mouse heart, GF CARB-fed, rep 5

description: Gene expression data from mouse heart


title: Mouse heart, GF CARB-fed, rep 1

description: Gene expression data from mouse heart


title: ARG replicate 6


title: ARG replicate 2


title: ARG replicate 1


title: ARG replicate 4


title: GLY replicate 4

description: heart from beta1-Gly389 transgenic mice at 90 days of age. The alpha-myosin heavy chain promoter was utilized to direct expression of the human beta1-Gly389 cDNAs to cardiac myocytes.

source_name: heart from beta1-Gly389 transgenic mice

tag: heart, beta1-Gly389 transgenic mice at 90 days of age


title: Mouse heart, GF CARB-fed, rep 2

description: Gene expression data from mouse heart


title: GLY replicate 6


title: Mouse heart, GF CARB-fed, rep 3

description: Gene expression data from mouse heart


title: ARG replicate 5


title: GLY replicate 3


title: AC5 replicate 6

description: heart from AC5 transgenic mice at 90 days of age. The alpha-myosin heavy chain promoter was utilized to direct expression of the human AC5 cDNAs to cardiac myocytes.

source_name: heart from AC5 transgenic mice

tag: heart, AC5 transgenic mice at 90 days of age


title: GLY replicate 1


title: AC5 replicate 3


title: GLY replicate 2


title: AC5 replicate 1


title: NTG replicate 6

description: heart from non-transgenic mice at 90 days of age

source_name: heart from non-transgenic mice

tag: heart, non-transgenic mice at 90 days of age


title: NTG replicate 3


title: GLY replicate 5


title: AC5 replicate 4


title: NTG replicate 4


title: AC5 replicate 5


title: NTG replicate 1


title: NTG replicate 2


title: AC5 replicate 2


title: NTG replicate 5


title: B6.C3H-Bbaa2Bbaa3 joint uninfected

status: Public on Jun 22 2009

city: Salt Lake City

first: Janis

last: Weis

state: UT

address: 15 North Medical Drive East

department: Pathology

institute: University of Utah

description: gene expression from uninfected ISCLrear ankle joint tissue

hyb_protocol: Hybridization to the Affymetrix GeneChip Mouse Genome 430 2.0 Array was carried out according to Affymetrix directions.

scan_protocol: GeneChips were scanned with the GeneChip Scanner 3000 laser confocal slide scanner

data_processing:
Data were processed using the affy and gcRobust Multiarray Average packages in R
Statistical analysis were performed using significance analysis of microarrays

source_name: uninfected tissue

label_protocol: cDNA was generated from RNA and was labeled with the One-Cycle Target labeling kit (Affymetrix)

growth_protocol: Generation_of_ISCL: ISCL were generated by repeated backcrossing between C3H and C57BL/6 parental mice, using the speed congenic approach and based on QTL linkage analysis for Lyme arthritis severity

extract_protocol: Joint tissue was homogenized in presence of cold acid guanidine and RNA was recovered following cesium chloride centrifugation. RNA was applied to Rneasy kit (Qiagen).

treatment_protocol: Infection_protocol: Mice were infected with 2000 B. burgdorferi of the N40 strain by intradermal injection in the back and controls received BSK medium.  Mice were sacrificed at 1 wk, joint tissue collected and skin removed.

tag: infection

value: no

value: ankle joint

value: B6.C3H-Bbaa2Bbaa3, ISCL

value: 6-7 weeks


title: B6.C3H-Bbaa2Bbaa3 joint infected

description: gene expression from rear ankle joint tissue of CISCL mice infected for 1 wk

source_name: infected tissue

value: yes

value: B6.C3HBbaa2Bbaa3, ISCL


title: BAL_SS5

city: Denver

first: Clifton

last: Hall

state: CO

address: 1400 Jackson Street

institute: National Jewish

description: None Additional

hyb_protocol: Hybridization was performed by incubating 200 uL of each sample to the Affymetrix GeneChip human arrays. The GeneChip Human Genome U133 Plus 2.0 (Affymetrix Inc., Santa Clara, CA) was used. Hybridization was carried at 45 C for 16h using a GeneChip Hybridization Oven 640 (Affymetrix). Following incubation hybridization solutions were removed and arrays were washed and stained with Streptavidin-phycoerythrin using a GeneChip Fluidics Station 400 (Affymetrix). The chips were scanned using the Affymetrix GeneChip Scanner 3000 (Affymetrix). The image data on each individual microarray chip was scaled to 500 target intensity, using the Microarray Suite software (Affymetrix).

data_processing:
The image data on each individual microarray chip was scaled to 500 target intensity, using the Microarray Suite software, MAS 5.0 algorithm (Affymetrix).
Expression analysis parameters:
Alpha1		0.05
Alpha2		0.065
Tau		0.015
Gamma1L	0.002
Gamma1H	0.002
Gamma2L	0.002667
Gamma2H	0.002667
Perturbation 	1.1

source_name: Steroid Sensitive BAL

label_protocol: Total RNA (5 ug) was converted into double-stranded cDNA (ds-cDNA) using the Superscript Choice System (Life Technologies Inc.). An oligo-dT primer containing a T7 RNA polymerase promoter (Genset Corp) was utilized. After the second strand synthesis, the reaction mixture was extracted with phenol-chloroform-isoamyl alcohol, and the ds-cDNA recovered by ethanol precipitation. In vitro transcription was performed to generate biotin-labeled complementary ribonucleic acid (cRNA), using a RNA Transcript Labeling Kit (Enzo, Farmingdale, NY) and 3.3 uL of ds-cDNA template in the presence of a mixture of biotin-labeled ribonucleotides. Biotin-labeled cRNA was purified using an RNeasy affinity column (Qiagen). To ensure optimal hybridization to the oligonucleotide array, the cRNA was fragmented into fragments between 35-200 bases in length by incubating the cRNA at 94 C for 35 minutes in a fragmentation buffer. The samples were then added to a hybridization solution containing 100 mM 2-[N-morpholino] ethanesulfonic acid (MES), 1 M NaCl, and 20 mM ethylenediaminetetraacetic acid (EDTA) in the presence of 0.01% Tween 20. The final concentration of the fragmented cRNA was 0.05 ug/µL. The quality of total RNA and labeled cRNA were assessed with Agilent's Lab-on-a-Chip total RNA nano-biosizing assay (Agilent Technologies, Palo Alto, CA).

extract_protocol: Total RNA was isolated using the Qiagen RNeasy kit using the manufacturer’s recommended protocol.

tag: BAL from 32 year old steroid sensitive asthmatic female


title: BAL_SR4

description: None Additional

scan_protocol: The chips were scanned using the Affymetrix GeneChip Scanner 3000 (Affymetrix).

source_name: Steroid resistant BAL

tag: BAL from 45 year old steroid resistant asthmatic female


title: C3H.B6-Bbaa4 joint uninfected

value: C3H.B6-Bbaa4, ISCL


title: BAL_SS8

description: None additional

source_name: Steroid sensitive BAL

tag: BAL from 38 year old steroid sensitive asthmatic male


title: C3H joint Uninfected

description: gene expression from uninfected C3H rear ankle joint tissue

value: C3H wild type


title: BAL_SR5

description: None additional

source_name: Steriod Resistant BAL

extract_protocol: Total RNA was isolated using the Qiagen RNeasy kit using the manufacturer's recommended protocol.

tag: BAL from 47 year old steroid resistant asthmatic male


title: C3H.B6-Bbaa2Bbaa3 joint infected

value: C3H.B6-Bbaa2Bbaa3, ISCL


title: C3H.B6-Bbaa4 joint infected


title: BAL_SS4

description: None additional

tag: BAL from 37 year old steroid sensitive asthmatic male


title: ESC Stella+ rep2

first: Jason

middle: Allen

last: West

address: One Blackfan Circle Room 7004B

institute: Children's Hospital, Boston

description: no additional info

hyb_protocol: Please seethe Microarray Core Facility website of the Dana-Farber Cancer Institutefor details.

scan_protocol: confocal laser scanner.  Please see theMicroarray Core Facility website of the Dana-Farber Cancer Institute

data_processing: The data were analyzed with MAS 5.0 using Affymetrix default analysis settings. Please see the Microarray Core Facility website of the Dana-Farber Cancer Institutefor more details

source_name: Stella GFP-positve ESCs

label_protocol: Biotin labeled, performed and described at the Microarray Core Facility website of the Dana-Farber Cancer Institute

extract_protocol: Trizol/Qiagen RNAeasy according to the manufacturers protocol.

tag: B6CBA, Adherant culture/MEFs/Pluripotent Conditions


title: D7 EB Stella- rep1

description: no additional info

source_name: StellaGFP-negative cells from Day 7 Ebs (not germ cells)

tag: B6CBA,Suspension culture/EB differentiation media


title: C3H.B6-Bbaa2Bbaa3 joint uninfected


title: D7 EB Stella- rep2

description: no additional info


title: ESC Stella-  rep1

description: no additional info

source_name: Stella GFP-negative ESCs


title: C3H joint infected

description: gene expression from rear ankle joint tissue of C3H mice infected for 1 wk


title: D7 EB Stella+ rep1

description: no additional info

source_name: StellaGFP-positve cells from Day 7 Ebs (in vitro PGCs)


title: ESC Stella-  rep3

description: no additional info


title: BAL_SR7

description: None additional

source_name: Steroid Resistant BAL

tag: BAL from 25 year old steroid resistant asthmatic female


title: D7 EB Stella+ rep2

description: no additional info


title: ESC rep2

description: no additional info

source_name: Stella ESCs (unsorted population)


title: B6.C3H-Bbaa4 joint infected

tag: tissue

value: B6.C3H-Bbaa4, ISCL


title: ESC rep1

description: no additional info


title: D7 EB Stella+ rep3

description: no additional info


title: ESC Stella+ rep1

description: no additional info


title: ESC Stella-  rep2

description: no additional info


title: D7 EB Stella+ rep4

description: no additional info


title: Brain: null RNA control_e1_le1

status: Public on Jun 20 2009

city: Phoenix

first: Winnie

last: Liang

state: AZ

address: 445 N. Fifth Street

institute: Translational Genomics

description: Initial RNA species  without any binding experiment

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: MAS 5

source_name: brain

label_protocol: standard Affymetrix protocol

extract_protocol: none supplied

tag: Null RNA control_e1_le1


title: Brain: deiminated REFP2 bound RNA-sample3 (T3)_le2

description: RNA species eluted from deiminated MA-Brent-1

tag: Deiminated REFP2 bound RNA-sample3 (T3)_le2


title: Brain: control-biorepeat-MA-Brent-1_e1_le1

description: RNA species eluted from  non-deiminated MA-Brent-1