title: ntrC mutant high nitrogen vs. wild type high nitrogen_Rep3

city: Columbia

first: William

last: Franck

state: MO

address: 1201 East Rollins St.,        201 Lifes Science Center

department: Division of Plant Sciences

institute: University of Missouri-Columbia

description: Transcriptional profiling of wild type and ntrC mutant strains cultured under high nitrogen conditions.

hyb_protocol: Both cy3 and cy5 labeled cDNAs to be compared were mixed, dried to completion, and then resuspended in 70 ul of preheated hybridization buffer (nuclease free water:formamide:20X SSC:1% SDS = 4:2.5:2.5:1) at 42 C. After adding 0.7 ul salmon sperm DNA (10 mg/ml) to prevent non-specific binding to the array, the mixture was hybridized at 42 C for 16 to 18 h. Hybridized arrays were washed with 1X SSC, 0.2% SDS at 42 C for 6 min, and, subsequently, with 0.1X SSC, 0.2% SDS at room temperature for 6 min, and twice with 0.1X SSC at room temperature for 3 min.

scan_protocol: The arrays were scanned using an Axon GenePix 4000B scanner (Molecular Devices Corp., Sunnyvale, CA). Signal intensities were analyzed using GenePix Pro 6.0 software (Molecular Devices Corp., Sunnyvale, CA).

data_processing: Signal intensities were normalized for spot and slide abnormalities using spatial lowess. Lowess adjusted data were subsequently analyzed by mixed effect microarray analysis of variance (MAANOVA) (Kerr et al. 2000). The resulting variety-by-gene interaction (VG) values were combined with the residual noise from each spot to obtain the filtered and adjusted expression values (Kerr et al. 2000; Kerr and Churchill 2001). Both lowess and MAANOVA are part of the R/maanova microarray statistical analysis package (http://www.jax.org/staff/churchill/labsite/). Expression values from two technical replicates in each array were combined and averaged. Significant genes were selected based on a 2.0-cut off threshold with a false discovery rate lower than 5%.

organism: Bradyrhizobium japonicum

source_name: ntrC mutant high nitrogen condition replication 3

label_protocol: 10 ug of total RNA was used for cDNA synthesis with superscript III reverse transcriptase and random hexamers (Invitrogen Corp.). After digesting the remaining RNA by RNase H (Fermentas), cDNA was purified using a Microcon YM-30 column (Millipore) and concentration was determined using a Nanodrop spectrophotometer (NanoDrop Technologies, Wilmington, DE). Four micrograms of cDNA were used for labeling with either cy3 or cy5 (Armersham) and unincorporated dyes were removed using a Qiaquick PCR purification Kit (Qiagen).

growth_protocol: A Bradyrhizobium japonicum USDA 110 ntrC mutant was cultured in minimal medium containing 10mM ammonium and 10mM glutamate as nitrogen sources and harvested for RNA extraction at an OD600 of 0.4-0.6.

extract_protocol: Standard hot-phenol method

treatment_protocol: Cells were cultured in 10mM ammonium and 10mM glutamate as nitrogen sources

value: ntrC mutant

source_name: wild type high nitrogen condition replication 3

growth_protocol: Bradyrhizobium japonicum USDA 110 was cultured in minimal medium containing 10mM ammonium and 10mM glutamate as nitrogen sources and harvested for RNA extraction at an OD600 of 0.4-0.6.

value: wild type


title: wild type high nitrogen vs. ntrC mutant high nitrogen_Rep3

status: Public on Jul 01 2012

type: RNA

middle: L

country: USA

molecule: total RNA

tag: genotype/variation


title: microRNA profile of case NPC351065

city: Guangzhou

first: Jun

last: Ma

address: 651 Dongfeng Road East

country: China

institute: Sun Yat-sen University Cancer Center

hyb_protocol: The labeled RNAs were hybridized to the array with a 1×hybridization solution (5× Denhart’s solution, 0.5% SDS, 5× SSC) in a Hybridization Chamber (Corning Inc, Corning, NY, USA) at 46°C for 12 to 16 hours.

scan_protocol: Scanned in a LuxScanTM -10K Scanner (capitalBio Inc.,Beijing, China).

data_processing: Quantile normalization across multiple arrays, log 2 transformation of expression levels, BRB ArrayTools v.3.8.0 was used.

organism: Homo sapiens

source_name: Nasopharyngeal carcinoma

label_protocol: 2.5 μg of total RNA was employed with 100 nmol/L of pCp-DY647 (Dharmacon, Lafayette, CO, USA) and 15 Units of T4 RNA ligase (USB, Cleveland, Oh, USA) in a total reaction volume of 20 µL at 16°C overnight

extract_protocol: Total RNA was extracted using an acid phenol/chloroform extraction method followed by ethanol precipitation.

tag: survival status  (1-death,0-survival)

tag: gender  (1-male,2-female)

tag: age (years)

tag: stage  (1-stage i,2-stage ii,3-stage iii,4-stage iv)


title: ntrC mutant high nitrogen vs. wild type high nitrogen_Rep2

source_name: ntrC mutant high nitrogen condition replication 2

source_name: wild type high nitrogen condition replication 2

growth_protocol: Bradyrhizobium japonicum USDA110 was cultured in minimal medium containing 10mM ammonium and 10mM glutamate as nitrogen sources and harvested for RNA extraction at an OD600 of 0.4-0.6.


title: gastrointestinal stromal tumor T3 vs blood reference

type: genomic

city: Porto

first: Rune

last: Matthiesen

address: Rua Dr. Roberto Frias s/n

country: Portugal

institute: IPATIMUP

hyb_protocol: Cy3- and Cy5-labeled DNA samples were combined in a total volume of 79 μl and mixed with 6.5 μg Cot-1 DNA (Invitrogen), 25.5 μl of 10× blocking agent (Agilent Technologies), 130 μl of 2× hybridization buffer (Agilent Technologies), and 15.5 μl MilliQ water. The hybridization mixture was heated for 3 min at 95°C and immediately incubated for 30 min at 37°C. After centrifugation for 60 sec at 14,000 rpm, the hybridization mixture was applied to the 2x 105K array slide and placed in an assembly chamber for 24 hr at 65°C and 20 rpm (Agilent Technologies). After hybridization, slides were washed in the following steps; 1 min with wash buffer 1 at room temperature (RT), 5 min with wash buffer 1 at RT with rotation speed (750 rpm), 1 min with wash buffer 2 at 37°C with rotation speed (750 rpm), and finally a 1 min wash step with acetonitrile at RT.

scan_protocol: Images of the arrays were acquired using a microarray scanner G2505B (Agilent technologies) and image analysis was performed using feature extraction software (version 9.1; Agilent Technologies). The Agilent CGH-v4_91 protocol was applied using default settings. Spot intensities were corrected for local background, and only spots with intensities at least twofold above the background signal intensities were included in the analysis.

data_processing:
image analysis was performed using feature extraction software (version 9.1; Agilent Technologies). Spot intensities were corrected for local background, and only spots with intensities at least twofold above the background signal intensities were included in the analysis.
Two samples were excluded based on their noisy profiles and high Median Absolute Deviation value (>0.5). The data from the remaining 47 samples had their background deducted and were normalized by median centering. Inherent wave bias using the Smoothing Waves algorithm was used to correct the profiles [35]. The data was then segmented using the DNACopy algorithm to find fragments of copy number increase or decrease [36]. Copy number states were deduced by using the CGHCall algorithm [37]. 85% tumor tissue was specified as parameter for the calling and for all other parameters default values was used.  The oligonucleotides were mapped according to the human genome build NCBI 36 for the 2 × 105 K array format. Of both Cy3 and Cy5 channels, local background was subtracted from the median intensities. The log2 tumor to normal ratio was calculated for each spot and normalized against the median of the ratios of all autosomes. When two or more neighbouring oligonucleotides showed significant copy number differences from zero, this was considered to be a possible CNA (copy number aberration).

molecule: genomic DNA

source_name: T3 GIST

label_protocol: Labelling was performed using the Enzo Genomic DNA Labeling kit according to the manufacturer's instructions (Enzo Life Sciences). Briefly, 500 ng genomic DNA was combined with a mixture of primers and reaction buffer to a final volume of 39 μl. The DNA was denatured at 99°C for 10 min, and placed on ice. While on ice, 10 μl cyanine 3-dUTP and cyanine 5-dUTP nucleotide mixture was added to the test and reference DNA, respectively, and finally 1 μl Klenow DNA polymerase was added to each sample to extend the primers. After 4 hr incubation at 37°C, 5 μl stop buffer was added to stop the reaction. Label was purified using the QIAquick PCR Purification Kit (Qiagen, Westburg, Leusden, NL).

extract_protocol: Qiagen’s QIAamp DNA Micro kit (Qiagen, Hilden, Germany)

tag: tissue

value: gastrointestinal stromal tumor

source_name: Pooled blood reference

value: normal pooled blood reference


title: gastrointestinal stromal tumor T22 vs blood reference

source_name: T22 GIST


title: STAT3-deficient naïve T cells stimulated for 3 hours with IL-6 3

city: Bethesda

first: Golnaz

last: Vahedi

state: MD

address: 9000 Rockville Pike Bldg 10 Rm 13C101A

department: NIAMS

institute: National Institutes of Health

description: Gene expression data from STAT3KO naïve CD4+ T cells stimulated for 3 hours with IL-6

hyb_protocol: aRNA was hybridized to GeneChip Mouse Genome 430 2.0 Arrays from Affymetrix according the manufacturers protocol.

scan_protocol: Expression values were determined using GeneChip Operating Software (GCOS) v1.1.1 software.

data_processing: The data were analyzed with GeneChip Operating Software (GCOS) v1.1.1. The trimmed mean target intensity of each array was set to 500.

label: biotin

organism: Mus musculus

source_name: primary CD4+ T cells from spleen and lymph nodes

label_protocol: RNA was biotin-labeled using the MessageAmpII-Biotin Enhanced Kit from Ambion

growth_protocol: Control and STAT-deficient naïve CD4+CD44-CD62L+CD25- T cells were isolated and sorted on the flow cytometer. Cells were stimulated with IL-6 (20 ng/ml), IL-27 (20 ng/ml) or no stimulation for 3 hours.

extract_protocol: Total RNA was extracted using the MirVana RNA Isolation kit from Ambion.

treatment_protocol: After 3hours stimulation in vitro, cells were hervasted.

tag: cell type

value: CD4+ T

tag: strain

value: Cd4-Cre_C57BL6-STAT3<tm1Dlv> (STAT3KO)

tag: treatment

value: stimulated for 3 hours with IL-6 (20 ng/ml)


title: STAT3-deficient naïve T cells stimulated for 3 hours with IL-27 1

description: Gene expression data from STAT3KO naïve CD4+ T cells stimulated for 3 hours with IL-27

value: stimulated for 3 hours with IL-27 (20 ng/ml)


title: gastrointestinal stromal tumor T194 vs blood reference

source_name: T194 GIST


title: microRNA profile of case NPC350982


title: ntrC mutant high nitrogen vs. wild type high nitrogen_Rep1

source_name: ntrC mutant high nitrogen condition replication 1

source_name: wild type high nitrogen condition replication 1


title: wild type high nitrogen vs. ntrC mutant high nitrogen_Rep2


title: wild type high nitrogen vs. ntrC mutant high nitrogen_Rep1


title: STAT3-deficient naïve T cells stimulated for 3 hours with IL-6 2


title: gastrointestinal stromal tumor T66 vs blood reference

source_name: T66 GIST


title: gastrointestinal stromal tumor T37 vs blood reference

source_name: T37 GIST


title: Sarcoidosis 47

city: Reno

first: Tong

last: Zhou

state: NV

address: 1664 N Virginia St

institute: University of Nevada School of Medicine

description:
Gene expression data from PBMC total RNA from healthy controls.
Sarcoidosis_47

hyb_protocol: Samples were hybridized with Affymetrix GeneChip Human Exon 1.0 ST Arrays per manufacturer’s instructions.

scan_protocol: Array scanning was performed according to the manufacturer's instruction by the University of Chicago Functional Genomics Facility.

data_processing: The transcript expression data were summarized by RMA using the Affymetrix Power Tools (v.1.12.0) and were later corrected for batch effect using the R COMBAT script.

source_name: EA_Complicated sarcoidosis_PBMCs

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

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

tag: ethnicity

value: European descent American (EA)

value: peripheral blood mononuclear cells

tag: diagnosis

value: Complicated sarcoidosis


title: microRNA profile of case NPC350779


title: STAT3-deficient naïve T cells stimulated for 3 hours with IL-6 1


title: Sarcoidosis 33

description:
Gene expression data from PBMC total RNA from healthy controls.
Sarcoidosis_33

source_name: EA_Uncomplicated sarcoidosis_PBMCs

value: Uncomplicated sarcoidosis


title: microRNA profile of case NPC350992


title: STAT3-deficient naïve T cells stimulated for 3 hours with medium alone 3

description: Gene expression data from STAT3KO naïve CD4+ T cells stimulated for 3 hours with medium alone


title: Sarcoidosis 41

description:
Gene expression data from PBMC total RNA from healthy controls.
Sarcoidosis_41


title: STAT3-deficient naïve T cells stimulated for 3 hours with medium alone 2


title: Sarcoidosis 21

description:
Gene expression data from PBMC total RNA from healthy controls.
Sarcoidosis_21


title: microRNA profile of case NPC350579


title: STAT3-deficient naïve T cells stimulated for 3 hours with medium alone 1


title: gastrointestinal stromal tumor T83 vs blood reference

source_name: T83 GIST


title: gastrointestinal stromal tumor T58 vs blood reference

source_name: T58 GIST


title: microRNA profile of case NPC350286


title: Sarcoidosis 19

description:
Gene expression data from PBMC total RNA from healthy controls.
Sarcoidosis_19


title: microRNA profile of case NPC350776


title: microRNA profile of case NPC350187


title: gastrointestinal stromal tumor T73 vs blood reference

source_name: T73 GIST


title: STAT1-deficient naïve T cells stimulated for 3 hours with IL-27 3

description: Gene expression data from STAT1KO naïve CD4+ T cells stimulated for 3 hours with IL-27

value: C57BL6-STAT1<tm1Dlv> (STAT1KO)


title: gastrointestinal stromal tumor T27 vs blood reference

source_name: T27 GIST


title: gastrointestinal stromal tumor T60 vs blood reference

source_name: T60 GIST


title: Sarcoidosis 15

description:
Gene expression data from PBMC total RNA from healthy controls.
Sarcoidosis_15


title: microRNA profile of case NPC350080

source_name: Nasopharyngeal carcinoma


title: STAT1-deficient naïve T cells stimulated for 3 hours with IL-27 2


title: Sarcoidosis 16

description:
Gene expression data from PBMC total RNA from healthy controls.
Sarcoidosis_16


title: Sarcoidosis 14

description:
Gene expression data from PBMC total RNA from healthy controls.
Sarcoidosis_14


title: STAT1-deficient naïve T cells stimulated for 3 hours with IL-27 1


title: Sarcoidosis 6

description:
Gene expression data from PBMC total RNA from healthy controls.
Sarcoidosis_6


title: STAT1-deficient naïve T cells stimulated for 3 hours with IL-6 3

description: Gene expression data from STAT1KO naïve CD4+ T cells stimulated for 3 hours with IL-6


title: microRNA profile of case NPC350078


title: Sarcoidosis 10

description:
Gene expression data from PBMC total RNA from healthy controls.
Sarcoidosis_10


title: STAT1-deficient naïve T cells stimulated for 3 hours with IL-6 1


title: gastrointestinal stromal tumor T61 vs blood reference

source_name: T61 GIST


title: STAT1-deficient naïve T cells stimulated for 3 hours with IL-6 2


title: gastrointestinal stromal tumor T55 vs blood reference

source_name: T55 GIST

source_name: Pooled blood reference


title: gastrointestinal stromal tumor T24 vs blood reference

source_name: T24 GIST


title: microRNA profile of case NPC350009


title: gastrointestinal stromal tumor T46 vs blood reference

source_name: T46 GIST


title: Control 64

description:
Gene expression data from PBMC total RNA from healthy controls.
Healthy_control_64

value: Healthy


title: Control 62

description:
Gene expression data from PBMC total RNA from healthy controls.
Healthy_control_62


title: microRNA profile of case NPC349396


title: Control 63

description:
Gene expression data from PBMC total RNA from healthy controls.
Healthy_control_63


title: gastrointestinal stromal tumor T30 vs blood reference

source_name: T30 GIST


title: microRNA profile of case NPC349168


title: microRNA profile of case NPC348968


title: microRNA profile of case NPC349054


title: microRNA profile of case NPC348872


title: Control 61

description:
Gene expression data from PBMC total RNA from healthy controls.
Healthy_control_61


title: STAT1-deficient naïve T cells stimulated for 3 hours with medium alone 2

description: Gene expression data from STAT1KO naïve CD4+ T cells stimulated for 3 hours with medium alone

source_name: primary CD4+ T cells from spleen and lymph nodes


title: Wild type naïve T cells stimulated for 3 hours with IL-27 3

description: Gene expression data from wild type naïve CD4+ T cells stimulated for 3 hours with IL-27


title: gastrointestinal stromal tumor T48 vs blood reference

source_name: T48 GIST


title: microRNA profile of case NPC348729


title: STAT1-deficient naïve T cells stimulated for 3 hours with medium alone 3


title: microRNA profile of case NPC348692


title: gastrointestinal stromal tumor T42 vs blood reference

source_name: T42 GIST


title: gastrointestinal stromal tumor T52 vs blood reference

source_name: T52 GIST


title: Control 57

description:
Gene expression data from PBMC total RNA from healthy controls.
Healthy_control_57


title: Wild type naïve T cells stimulated for 3 hours with IL-27 2


title: STAT1-deficient naïve T cells stimulated for 3 hours with medium alone 1


title: Control 58

description:
Gene expression data from PBMC total RNA from healthy controls.
Healthy_control_58


title: Wild type naïve T cells stimulated for 3 hours with IL-6 2

description: Gene expression data from wild type naïve CD4+ T cells stimulated for 3 hours with IL-6


title: gastrointestinal stromal tumor T21 vs blood reference

source_name: T21 GIST


title: Wild type naïve T cells stimulated for 3 hours with IL-27 1


title: gastrointestinal stromal tumor T26 vs blood reference

source_name: T26 GIST


title: Control 59

description:
Gene expression data from PBMC total RNA from healthy controls.
Healthy_control_59


title: Wild type naïve T cells stimulated for 3 hours with IL-6 3


title: gastrointestinal stromal tumor T19 vs blood reference

source_name: T19 GIST


title: Control 60

description:
Gene expression data from PBMC total RNA from healthy controls.
Healthy_control_60


title: gastrointestinal stromal tumor T31 vs blood reference

source_name: T31 GIST


title: Control 56

description:
Gene expression data from PBMC total RNA from healthy controls.
Healthy_control_56


title: microRNA profile of case NPC348688


title: microRNA profile of case NPC348465


title: microRNA profile of case NPC348480


title: microRNA profile of case NPC348602


title: microRNA profile of case NPC348437


title: microRNA profile of case NPC348349


title: Control 54

description:
Gene expression data from PBMC total RNA from healthy controls.
Healthy_control_54


title: Control 55

description:
Gene expression data from PBMC total RNA from healthy controls.
Healthy_control_55


title: Wild type naïve T cells stimulated for 3 hours with medium alone 3

description: Gene expression data from wild type naïve CD4+ T cells stimulated for 3 hours with medium alone


title: Wild type naïve T cells stimulated for 3 hours with IL-6 1


title: gastrointestinal stromal tumor T14 vs blood reference

source_name: T14 GIST


title: gastrointestinal stromal tumor T20 vs blood reference

source_name: T20 GIST


title: Wild type naïve T cells stimulated for 3 hours with medium alone 2


title: Control 41

description:
Gene expression data from PBMC total RNA from healthy controls.
Healthy_control_41


title: Control 44

description:
Gene expression data from PBMC total RNA from healthy controls.
Healthy_control_44


title: Control 38

description:
Gene expression data from PBMC total RNA from healthy controls.
Healthy_control_38


title: microRNA profile of case NPC348086

source_name: Nasopharyngeal carcinoma


title: gastrointestinal stromal tumor T77 vs blood reference

source_name: T77 GIST


title: gastrointestinal stromal tumor T25 vs blood reference

source_name: T25 GIST


title: Wild type naïve T cells stimulated for 3 hours with medium alone 1


title: microRNA profile of case NPC348278


title: Control 45

description:
Gene expression data from PBMC total RNA from healthy controls.
Healthy_control_45


title: TSA treatment, 24h, rep4

city: Heidelberg

first: Stefan

last: Wolfl

address: Im Neuenheimer Feld 364

department: Institute of Pharmacy and Molecular Biotechnology

country: Germany

institute: Heidelberg University, Heidelberg, Germany

description:
TSA_24h_s4
Gene expression data from TSA-treated sample.

hyb_protocol: Mouse GeneChips Moe_430_2 were hybridized and analyzed in an Affymetrix workstation (fluidic-station and scanner). Primary data were obtained with the Affymetrix Microarray Suite.

scan_protocol: Affymetrix scanner and Microarray Suite Software Package.

data_processing: Primary data analysis was done with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings. Further analysis was done using normalized data, which were normalized using a rank-based normalization algorithm (rank mean). Signal intensity obtained after rank-based normalization (rank mean/quantile) of primary data obtained using dChip (Li C, Wong WH (2001) Model-based analysis of oligonucleotide arrays: expression index computation and outlier detection. Proc Natl Acad Sci USA 98:31–6).

source_name: mouse neurospheres, TSA, 24h

label_protocol: Labeled cRNA was prepared following the basic Affymetrix protocol with minor modifications. In short, double-stranded cDNA was synthesized using a customary oligodT-T7 cDNA synthesis primer (Affymetrix, Santa Clara, CA, USA). The labeled antisense cRNA was generated using T7-RNA-polymerase (Enzo, Farmingdale, NY, USA) and biotin-labeled NTPs (Enzo).  For fragmentation, labeled cRNA was heated to 94° C for 35 min in the presence of 150 mM magnesium (Mg2+).

growth_protocol: Neurosphere (NS) cultures were prepared from E15.5 GE essentially as described (Shaked, M., Weissmuller, K., Svoboda, H., Hortschansky, P., Nishino, N., Wolfl, S., and Tucker, K. L. (2008) PLoS ONE 3, e2668); full protocol described in (Gritti, A., Galli, R., and Vescovi, A. L. (2001) Cultures of stem cells of the central nervous system. in Protocols for Neuronal Cell Culture (Fedoroff, S., and Richardson, A. eds.), 3rd Ed., Humana Press, Totowa, N.J. pp 173 - 197).  Lateral and medial ganglionic eminences (GE) were prepared and GE cells were mechanically dissociated with Pasteur pipette and plated in cell culture flasks with 100,000 cells per milliliter (ml) in NS Medium (F12/DMEM (1:1) with B27 supplement (Invitrogen), penicillin/streptomycin (100U/ml, Invitrogen), human EGF (20ng/ml; Sigma) and human bFGF (10ng/ml; R&D Systems, Wiesbaden, Germany). NS were incubated in suspension at 37°C, 5% CO2 for 1 week and fed on the 5th day with an equal volume of NS medium. For differentiation, 7 day-old NS were collected into 50-ml tubes and centrifuged for 3 minutes at 100xg. The NS were mechanically dissociated using a fp Pasteur pipette and plated out with 150,000 cells per cm2 in petri dishes (pre-plated with 200 mg/ml polyornithine) in NS medium without EGF and with 1% fetal calf serum (FCS, Invitrogen), a medium that supports the differentiation of both neurons and astrocytes.

extract_protocol: RNA extraction was done at the indicated time points using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions. RNA quality was examined by agarose gel electrophoresis and concentration was determined by UV absorbance.

treatment_protocol: After 2.5 days of incubation, the medium was changed to NS medium without bFGF and EGF but with 1% FCS. The following pharmacological reagents were added in different experiments: 50nM trichostatin A (Sigma, Calbiochem), recombinant BMP2 (10ng/ml) for 6h and 24h, weakly buffered with 1 mM Hepes, reduced FCS (0.1%) and low glucose (1 g/l).

value: neurosphere from embryonic striatum

value: trichostatin A (TSA)

tag: treatment duration


title: gastrointestinal stromal tumor T39 vs blood reference

source_name: T39 GIST

source_name: Pooled blood reference


title: gastrointestinal stromal tumor 9T vs blood reference

source_name: 9T GIST


title: Control 37

description:
Gene expression data from PBMC total RNA from healthy controls.
Healthy_control_37


title: gastrointestinal stromal tumor T51 vs blood reference

source_name: T51 GIST


title: TSA treatment, 24h, rep2

description:
TSA_24h_s2
Gene expression data from TSA-treated sample.


title: Control 52

description:
Gene expression data from PBMC total RNA from healthy controls.
Healthy_control_52


title: TSA treatment, 24h, rep3

description:
TSA_24h_s3
Gene expression data from TSA-treated sample.


title: gastrointestinal stromal tumor T40 vs blood reference

source_name: T40 GIST


title: microRNA profile of case NPC348000


title: microRNA profile of case NPC347968


title: Control 36

description:
Gene expression data from PBMC total RNA from healthy controls.
Healthy_control_36


title: TSA treatment, 6h, rep2

description:
TSA_6h_s2
Gene expression data from TSA-treated sample.

source_name: mouse neurospheres, TSA, 6h


title: gastrointestinal stromal tumor T63 vs blood reference

source_name: T63 GIST


title: microRNA profile of case NPC347764


title: microRNA profile of case NPC347806


title: microRNA profile of case NPC347549


title: TSA treatment, 24h, rep1

description:
TSA_24h_s1
Gene expression data from TSA-treated sample.


title: gastrointestinal stromal tumor T23 vs blood reference

source_name: T23 GIST


title: Control 35

description:
Gene expression data from PBMC total RNA from healthy controls.
Healthy_control_35


title: TSA treatment, 6h, rep1

description:
TSA_6h_s1
Gene expression data from TSA-treated sample.


title: Control 33

description:
Gene expression data from PBMC total RNA from healthy controls.
Healthy_control_33


title: Primary Breast Tumor no brain metastasis 99B/04

city: Indianapolis

first: Sunil

last: Badve

state: IN

address: 350 West 11th street

department: Pathology

institute: Indiana University

hyb_protocol: standard Illumina protocol

scan_protocol: standard Illumina protocol

data_processing: standard Illumina protocol

source_name: Primary Breast Tumor

label_protocol: standard Illumina protocol

extract_protocol: Trizol

tag: sentrix barcode

value: primary breast cancer tumor

tag: set

value: TRAINING

tag: date of birth

tag: menopausal status (1=pre, 2=post)

tag: type of cancer histology

tag: lobulare

tag: date of primary tumor diagnosis

tag: grading

tag: err

tag: pgr

tag: her2 ihc

tag: her2 fish

tag: induction chemotherapy (0=no, 1=yes)

tag: induction hormonal therapy with ta (0=no, 1=yes)

tag: induction hormonal therapy with ar (0=no, 1=yes)

tag: adjuvant chemotherapy (0=no, 1=yes)

tag: adjuvant hormonal therapy with tamox (0=no, 1=yes)

tag: adjuvant hormonal therapy with ia (0=no, 1=yes)

tag: adjuvant rtg therapy  (0=no, 1=yes)

tag: trastuzumab therapy (0=no, 1=yes)

tag: brain metasteses  (0=no, 1=yes)

tag: overall survival  (0=no, 1=yes)

tag: date of death


title: Control 24

description:
Gene expression data from PBMC total RNA from healthy controls.
Healthy_control_24

tag: ethnicity

tag: cell type

tag: diagnosis


title: gastrointestinal stromal tumor T36 vs blood reference

source_name: T36 GIST

tag: tissue


title: Primary Breast Tumor no brain metastasis 9930B/02

tag: sentrix barcode

tag: set

tag: date of birth

tag: menopausal status (1=pre, 2=post)

tag: type of cancer histology

tag: lobulare

tag: date of primary tumor diagnosis

tag: grading

tag: err

tag: pgr

tag: her2 ihc


title: Control 30

description:
Gene expression data from PBMC total RNA from healthy controls.
Healthy_control_30


title: gastrointestinal stromal tumor T10 vs blood reference

source_name: GIST T10


title: microRNA profile of case NPC347638

tag: survival status  (1-death,0-survival)

tag: gender  (1-male,2-female)

tag: age (years)

tag: stage  (1-stage i,2-stage ii,3-stage iii,4-stage iv)


title: microRNA profile of case NPC347804


title: BMP2 treatment, 6h, rep2

description:
BMP2_6h_s2
Gene expression data from BMP2-treated sample.

source_name: mouse neurospheres, BMP2, 6h

tag: treatment

value: bone morphogenetic protein 2 (BMP2)

tag: treatment duration


title: Control 21

description:
Gene expression data from PBMC total RNA from healthy controls.
Healthy_control_21

tag: ethnicity

tag: cell type

tag: diagnosis


title: BMP2 treatment, 24h, rep2

description:
BMP2_24h_s2
Gene expression data from BMP2-treated sample.

source_name: mouse neurospheres, BMP2, 24h

tag: tissue


title: Primary Breast Tumor no brain metastasis 981217-32Du

tag: sentrix barcode

tag: set

tag: date of birth

tag: menopausal status (1=pre, 2=post)

tag: type of cancer histology

tag: her2 fish

tag: induction chemotherapy (0=no, 1=yes)

tag: induction hormonal therapy with ta (0=no, 1=yes)

tag: induction hormonal therapy with ar (0=no, 1=yes)

tag: adjuvant chemotherapy (0=no, 1=yes)

tag: adjuvant hormonal therapy with tamox (0=no, 1=yes)

tag: adjuvant hormonal therapy with ia (0=no, 1=yes)

tag: adjuvant rtg therapy  (0=no, 1=yes)

tag: trastuzumab therapy (0=no, 1=yes)

tag: brain metasteses  (0=no, 1=yes)

tag: overall survival  (0=no, 1=yes)

tag: date of death


title: Control, 24h, rep5

description:
Cont_24h_s5
Gene expression data from control sample.

source_name: mouse neurospheres, control, 24h

tag: tissue

tag: treatment

value: control

tag: treatment duration


title: gastrointestinal stromal tumor T81 vs blood reference

source_name: T81 GIST

value: gastrointestinal stromal tumor

value: normal pooled blood reference


title: microRNA profile of case NPC347500

source_name: Nasopharyngeal carcinoma

tag: survival status  (1-death,0-survival)

tag: gender  (1-male,2-female)

tag: age (years)

tag: stage  (1-stage i,2-stage ii,3-stage iii,4-stage iv)


title: Control 23

description:
Gene expression data from PBMC total RNA from healthy controls.
Healthy_control_23

tag: ethnicity

tag: cell type

tag: diagnosis


title: BMP2 treatment, 6h, rep1

description:
BMP2_6h_s1
Gene expression data from BMP2-treated sample.


title: Control, 24h, rep4

description:
Cont_24h_s4
Gene expression data from control sample.


title: microRNA profile of case NPC347504


title: microRNA profile of case NPC347443


title: Primary Breast Tumor brain metastasis 9579/99

tag: sentrix barcode

tag: set

tag: date of birth

tag: menopausal status (1=pre, 2=post)

tag: type of cancer histology

tag: lobulare

tag: date of primary tumor diagnosis

tag: grading

tag: err

tag: pgr

tag: her2 ihc

tag: her2 fish

tag: induction chemotherapy (0=no, 1=yes)

tag: induction hormonal therapy with ta (0=no, 1=yes)

tag: induction hormonal therapy with ar (0=no, 1=yes)

tag: adjuvant chemotherapy (0=no, 1=yes)

tag: adjuvant hormonal therapy with tamox (0=no, 1=yes)

tag: date brain met diagnosis


title: Primary Breast Tumor no brain metastasis 8646/02

tag: sentrix barcode

tag: tissue

tag: set

tag: adjuvant hormonal therapy with ia (0=no, 1=yes)

tag: adjuvant rtg therapy  (0=no, 1=yes)

tag: trastuzumab therapy (0=no, 1=yes)

tag: brain metasteses  (0=no, 1=yes)

tag: overall survival  (0=no, 1=yes)

tag: date of death


title: Primary Breast Tumor no brain metastasis 9560A/4

tag: date of birth

tag: menopausal status (1=pre, 2=post)

tag: type of cancer histology

tag: lobulare

tag: date of primary tumor diagnosis

tag: grading

tag: err

tag: pgr

tag: her2 ihc


title: microRNA profile of case NPC347507

tag: survival status  (1-death,0-survival)

tag: gender  (1-male,2-female)

tag: age (years)

tag: stage  (1-stage i,2-stage ii,3-stage iii,4-stage iv)


title: Control 14

description:
Gene expression data from PBMC total RNA from healthy controls.
Healthy_control_14

tag: ethnicity

tag: cell type

tag: diagnosis


title: Control 20

description:
Gene expression data from PBMC total RNA from healthy controls.
Healthy_control_20


title: Sarcoidosis 48

description:
Gene expression data from PBMC total RNA from healthy controls.
Sarcoidosis_48

source_name: AA_Complicated sarcoidosis_PBMCs

value: African descent American (AA)


title: Sarcoidosis 45

description:
Gene expression data from PBMC total RNA from healthy controls.
Sarcoidosis_45


title: Sarcoidosis 49

description:
Gene expression data from PBMC total RNA from healthy controls.
Sarcoidosis_49


title: Control, 24h, rep2

description:
Cont_24h_s2
Gene expression data from control sample.

tag: tissue

tag: treatment

tag: treatment duration


title: Control, 24h, rep1

description:
Cont_24h_s1
Gene expression data from control sample.


title: BMP2 treatment, 24h, rep1

description:
BMP2_24h_s1
Gene expression data from BMP2-treated sample.


title: Control, 24h, rep3

description:
Cont_24h_s3
Gene expression data from control sample.


title: microRNA profile of case NPC347420


title: Primary Breast Tumor no brain metastasis 7775E

tag: sentrix barcode

tag: set

value: INTERNAL TEST

tag: date of birth

tag: menopausal status (1=pre, 2=post)

tag: type of cancer histology

tag: her2 fish

tag: induction chemotherapy (0=no, 1=yes)

tag: induction hormonal therapy with ta (0=no, 1=yes)

tag: induction hormonal therapy with ar (0=no, 1=yes)

tag: adjuvant chemotherapy (0=no, 1=yes)

tag: adjuvant hormonal therapy with tamox (0=no, 1=yes)

tag: adjuvant hormonal therapy with ia (0=no, 1=yes)

tag: adjuvant rtg therapy  (0=no, 1=yes)

tag: trastuzumab therapy (0=no, 1=yes)

tag: brain metasteses  (0=no, 1=yes)

tag: overall survival  (0=no, 1=yes)

tag: date of death


title: Primary Breast Tumor brain metastasis 5525-27

tag: sentrix barcode

tag: tissue

tag: lobulare

tag: date of primary tumor diagnosis

tag: grading

tag: err

tag: pgr

tag: her2 ihc

tag: date brain met diagnosis

tag: date of last information


title: microRNA profile of case NPC347230

tag: survival status  (1-death,0-survival)

tag: gender  (1-male,2-female)

tag: age (years)

tag: stage  (1-stage i,2-stage ii,3-stage iii,4-stage iv)


title: Control, 24h, rep6

description:
Cont_24h_s6
Gene expression data from control sample.

tag: treatment

tag: treatment duration


title: Control 17

description:
Gene expression data from PBMC total RNA from healthy controls.
Healthy_control_17

tag: ethnicity

tag: cell type

tag: diagnosis


title: microRNA profile of case NPC346808


title: microRNA profile of case NPC347362


title: wild type, not treated

city: London

first: David

middle: E

last: Carter

state: ON

address: 1151 Richmond Street North

department: London Regional Genomics Centre

country: Canada

institute: Robarts Research Institute

description: Gene expression data from WT embryonic fibroblasts

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 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 7G.

data_processing: The data were analyzed with GeneSpring GX using the RMA normalization method.

source_name: wild type, not treated, embryonic fibroblast

label_protocol: Biotinylated cRNA were prepared according to the two-cycle Affymetrix protocol from 100 ng total RNA (Expression Analysis Technical Manual, 2005-2009, Affymetrix).

growth_protocol: Mouse embryonic fibroblasts taken from FAK (focal adhesion kinase) +/+ and FAK -/- mice were grown in DMEM media containing 10% FBS, 2mM L-glutamine and antibiotics (100U/mL penicillin and 100 µg/mL streptomycin). Cells were grown at 37°C, 5%CO2 and used at passage 5.

treatment_protocol: wild type and knock out cells at 50% confluence were starved for 24h in serum-free medium, then treated with or without endothelin-1 for 24h.

value: embryonic fibroblast

value: untreated

tag: genotype

value: FAK +/+


title: Primary Breast Tumor brain metastasis 6376/00

tag: sentrix barcode

tag: tissue

tag: set

tag: date of birth

tag: menopausal status (1=pre, 2=post)

tag: type of cancer histology

tag: lobulare

tag: date of primary tumor diagnosis

tag: her2 fish

tag: induction chemotherapy (0=no, 1=yes)

tag: induction hormonal therapy with ta (0=no, 1=yes)

tag: induction hormonal therapy with ar (0=no, 1=yes)

tag: adjuvant chemotherapy (0=no, 1=yes)

tag: adjuvant hormonal therapy with tamox (0=no, 1=yes)

tag: adjuvant hormonal therapy with ia (0=no, 1=yes)

tag: adjuvant rtg therapy  (0=no, 1=yes)

tag: trastuzumab therapy (0=no, 1=yes)

tag: brain metasteses  (0=no, 1=yes)

tag: overall survival  (0=no, 1=yes)

tag: date of death


title: Control, 6h, rep2

description:
Cont_6h_s2
Gene expression data from control sample.

source_name: mouse neurospheres, control, 6h

tag: tissue

tag: treatment

tag: treatment duration


title: Primary Breast Tumor no brain metastasis 49705/03

tag: sentrix barcode

tag: set

tag: date of birth

tag: menopausal status (1=pre, 2=post)

tag: type of cancer histology

tag: lobulare

tag: grading

tag: err

tag: pgr

tag: her2 ihc

tag: date of last information


title: microRNA profile of case NPC347239

tag: survival status  (1-death,0-survival)

tag: gender  (1-male,2-female)

tag: age (years)

tag: stage  (1-stage i,2-stage ii,3-stage iii,4-stage iv)


title: Primary Breast Tumor brain metastasis 5271B/05

tag: tissue

tag: date of primary tumor diagnosis

tag: her2 fish

tag: induction chemotherapy (0=no, 1=yes)

tag: induction hormonal therapy with ta (0=no, 1=yes)

tag: induction hormonal therapy with ar (0=no, 1=yes)

tag: adjuvant chemotherapy (0=no, 1=yes)

tag: adjuvant hormonal therapy with tamox (0=no, 1=yes)

tag: adjuvant hormonal therapy with ia (0=no, 1=yes)

tag: adjuvant rtg therapy  (0=no, 1=yes)

tag: trastuzumab therapy (0=no, 1=yes)

tag: brain metasteses  (0=no, 1=yes)

tag: date brain met diagnosis

tag: overall survival  (0=no, 1=yes)

tag: date of death


title: Primary Breast Tumor brain metastasis 7247/03

tag: sentrix barcode

tag: set

tag: date of birth

tag: menopausal status (1=pre, 2=post)

tag: type of cancer histology

tag: lobulare

tag: grading

tag: err

tag: pgr

tag: her2 ihc


title: Control, 6h, rep1

description:
Cont_6h_s1
Gene expression data from control sample.

tag: tissue

tag: treatment

tag: treatment duration


title: microRNA profile of case NPC346450

tag: survival status  (1-death,0-survival)

tag: gender  (1-male,2-female)

tag: age (years)

tag: stage  (1-stage i,2-stage ii,3-stage iii,4-stage iv)


title: FAK knockout, not treated

description: Gene expression data from knockout embryonic fibroblasts

source_name: knock out, not treated,  embryonic fibroblast

tag: cell type

tag: genotype

value: FAK -/-


title: microRNA profile of case NPC346702


title: Primary Breast Tumor no brain metastasis 46266/03

tag: sentrix barcode

tag: set

tag: date of birth

tag: date of primary tumor diagnosis

tag: her2 fish

tag: induction chemotherapy (0=no, 1=yes)

tag: induction hormonal therapy with ta (0=no, 1=yes)

tag: induction hormonal therapy with ar (0=no, 1=yes)

tag: adjuvant chemotherapy (0=no, 1=yes)

tag: adjuvant hormonal therapy with tamox (0=no, 1=yes)

tag: adjuvant hormonal therapy with ia (0=no, 1=yes)

tag: adjuvant rtg therapy  (0=no, 1=yes)

tag: trastuzumab therapy (0=no, 1=yes)

tag: brain metasteses  (0=no, 1=yes)

tag: overall survival  (0=no, 1=yes)

tag: date of last information


title: Primary Breast Tumor no brain metastasis 4957/03

tag: tissue

tag: menopausal status (1=pre, 2=post)

tag: type of cancer histology

tag: lobulare

tag: grading

tag: err

tag: pgr

tag: her2 ihc

tag: date of death


title: Sarcoidosis 39

description:
Gene expression data from PBMC total RNA from healthy controls.
Sarcoidosis_39

tag: ethnicity

tag: cell type

value: peripheral blood mononuclear cells

tag: diagnosis

value: Complicated sarcoidosis


title: microRNA profile of case NPC346458

tag: survival status  (1-death,0-survival)

tag: gender  (1-male,2-female)

tag: age (years)

tag: stage  (1-stage i,2-stage ii,3-stage iii,4-stage iv)


title: Primary Breast Tumor no brain metastasis 4527/02

tag: sentrix barcode

tag: set

tag: date of birth

tag: date of primary tumor diagnosis

tag: her2 fish

tag: induction chemotherapy (0=no, 1=yes)

tag: induction hormonal therapy with ta (0=no, 1=yes)

tag: induction hormonal therapy with ar (0=no, 1=yes)

tag: adjuvant chemotherapy (0=no, 1=yes)

tag: adjuvant hormonal therapy with tamox (0=no, 1=yes)

tag: adjuvant hormonal therapy with ia (0=no, 1=yes)

tag: adjuvant rtg therapy  (0=no, 1=yes)

tag: trastuzumab therapy (0=no, 1=yes)

tag: brain metasteses  (0=no, 1=yes)

tag: overall survival  (0=no, 1=yes)


title: microRNA profile of case NPC345663

tag: survival status  (1-death,0-survival)

tag: gender  (1-male,2-female)

tag: age (years)


title: Sarcoidosis 34

description:
Gene expression data from PBMC total RNA from healthy controls.
Sarcoidosis_34

tag: ethnicity

tag: cell type

tag: diagnosis


title: Primary Breast Tumor no brain metastasis 4494C/02

tag: sentrix barcode

tag: tissue

tag: set

tag: date of birth

tag: menopausal status (1=pre, 2=post)

tag: type of cancer histology

tag: lobulare

tag: date of primary tumor diagnosis

tag: grading

tag: err

tag: pgr

tag: her2 ihc

tag: her2 fish

tag: date of last information


title: Sarcoidosis 36

description:
Gene expression data from PBMC total RNA from healthy controls.
Sarcoidosis_36

source_name: AA_Uncomplicated sarcoidosis_PBMCs

tag: ethnicity

value: Uncomplicated sarcoidosis


title: microRNA profile of case NPC346036

tag: survival status  (1-death,0-survival)

tag: gender  (1-male,2-female)

tag: age (years)

tag: stage  (1-stage i,2-stage ii,3-stage iii,4-stage iv)


title: Sarcoidosis 42

description:
Gene expression data from PBMC total RNA from healthy controls.
Sarcoidosis_42

tag: cell type

tag: diagnosis


title: Sarcoidosis 35

description:
Gene expression data from PBMC total RNA from healthy controls.
Sarcoidosis_35


title: wild type, endothelin-1 treated

source_name: wild type, endothelin-1 treated, embryonic fibroblast

tag: treatment

tag: genotype


title: Sarcoidosis 40

description:
Gene expression data from PBMC total RNA from healthy controls.
Sarcoidosis_40


title: Sarcoidosis 37

description:
Gene expression data from PBMC total RNA from healthy controls.
Sarcoidosis_37


title: FAK knockout, endothelin-1 treated

source_name: knock out, endothelin-1 treated, embryonic fibroblast


title: microRNA profile of case NPC345070


title: Sarcoidosis 38

description:
Gene expression data from PBMC total RNA from healthy controls.
Sarcoidosis_38


title: Sarcoidosis 24

description:
Gene expression data from PBMC total RNA from healthy controls.
Sarcoidosis_24


title: Primary Breast Tumor no brain metastasis 3830B/05

tag: sentrix barcode

tag: tissue

tag: set

tag: date of birth

tag: menopausal status (1=pre, 2=post)

tag: type of cancer histology

tag: lobulare

tag: induction chemotherapy (0=no, 1=yes)

tag: induction hormonal therapy with ta (0=no, 1=yes)

tag: induction hormonal therapy with ar (0=no, 1=yes)

tag: adjuvant chemotherapy (0=no, 1=yes)

tag: adjuvant hormonal therapy with tamox (0=no, 1=yes)

tag: adjuvant hormonal therapy with ia (0=no, 1=yes)

tag: adjuvant rtg therapy  (0=no, 1=yes)

tag: trastuzumab therapy (0=no, 1=yes)

tag: brain metasteses  (0=no, 1=yes)

tag: overall survival  (0=no, 1=yes)


title: Primary Breast Tumor no brain metastasis 39295/03

tag: sentrix barcode

tag: date of primary tumor diagnosis

tag: grading

tag: err

tag: pgr

tag: her2 ihc

tag: her2 fish

tag: date of last information


title: microRNA profile of case NPC346346

tag: survival status  (1-death,0-survival)

tag: gender  (1-male,2-female)

tag: age (years)

tag: stage  (1-stage i,2-stage ii,3-stage iii,4-stage iv)


title: microRNA profile of case NPC345350


title: Sarcoidosis 32

description:
Gene expression data from PBMC total RNA from healthy controls.
Sarcoidosis_32

tag: ethnicity

tag: cell type

tag: diagnosis


title: Sarcoidosis 23

description:
Gene expression data from PBMC total RNA from healthy controls.
Sarcoidosis_23


title: Sarcoidosis 20

description:
Gene expression data from PBMC total RNA from healthy controls.
Sarcoidosis_20


title: microRNA profile of case NPC344950


title: Primary Breast Tumor no brain metastasis 345190-2

tag: tissue

tag: set

tag: date of birth

tag: menopausal status (1=pre, 2=post)

tag: type of cancer histology

tag: lobulare

tag: induction chemotherapy (0=no, 1=yes)

tag: induction hormonal therapy with ta (0=no, 1=yes)

tag: induction hormonal therapy with ar (0=no, 1=yes)

tag: adjuvant chemotherapy (0=no, 1=yes)

tag: adjuvant hormonal therapy with tamox (0=no, 1=yes)

tag: adjuvant hormonal therapy with ia (0=no, 1=yes)

tag: adjuvant rtg therapy  (0=no, 1=yes)

tag: trastuzumab therapy (0=no, 1=yes)

tag: brain metasteses  (0=no, 1=yes)

tag: date of death


title: Primary Breast Tumor no brain metastasis 341097-9

tag: sentrix barcode

tag: date of primary tumor diagnosis

tag: grading

tag: err

tag: pgr

tag: her2 ihc

tag: her2 fish

tag: overall survival  (0=no, 1=yes)

tag: date of last information


title: microRNA profile of case NPC345099

tag: survival status  (1-death,0-survival)

tag: gender  (1-male,2-female)

tag: age (years)

tag: stage  (1-stage i,2-stage ii,3-stage iii,4-stage iv)


title: microRNA profile of case NPC346303


title: Primary Breast Tumor no brain metastasis 349948-50

tag: tissue

tag: set

tag: date of birth

tag: menopausal status (1=pre, 2=post)

tag: type of cancer histology

tag: lobulare

tag: induction chemotherapy (0=no, 1=yes)

tag: induction hormonal therapy with ta (0=no, 1=yes)

tag: induction hormonal therapy with ar (0=no, 1=yes)

tag: adjuvant chemotherapy (0=no, 1=yes)

tag: adjuvant hormonal therapy with tamox (0=no, 1=yes)

tag: adjuvant hormonal therapy with ia (0=no, 1=yes)

tag: adjuvant rtg therapy  (0=no, 1=yes)


title: Primary Breast Tumor brain metastasis 38044-5

tag: sentrix barcode

tag: date of primary tumor diagnosis

tag: grading

tag: err

tag: pgr

tag: her2 ihc

tag: her2 fish

tag: trastuzumab therapy (0=no, 1=yes)

tag: brain metasteses  (0=no, 1=yes)

tag: date brain met diagnosis

tag: overall survival  (0=no, 1=yes)

tag: date of last information


title: Sarcoidosis 22

description:
Gene expression data from PBMC total RNA from healthy controls.
Sarcoidosis_22

tag: ethnicity

tag: cell type

tag: diagnosis


title: Primary Breast Tumor brain metastasis 333018-20R

tag: tissue

tag: set

tag: date of birth

tag: menopausal status (1=pre, 2=post)

tag: type of cancer histology

tag: lobulare

tag: induction chemotherapy (0=no, 1=yes)

tag: induction hormonal therapy with ta (0=no, 1=yes)

tag: induction hormonal therapy with ar (0=no, 1=yes)

tag: adjuvant chemotherapy (0=no, 1=yes)

tag: adjuvant hormonal therapy with tamox (0=no, 1=yes)

tag: adjuvant hormonal therapy with ia (0=no, 1=yes)


title: microRNA profile of case NPC344457

tag: survival status  (1-death,0-survival)

tag: gender  (1-male,2-female)

tag: age (years)

tag: stage  (1-stage i,2-stage ii,3-stage iii,4-stage iv)


title: microRNA profile of case NPC344643


title: Sarcoidosis 8

description:
Gene expression data from PBMC total RNA from healthy controls.
Sarcoidosis_8

tag: ethnicity

tag: cell type

tag: diagnosis


title: Sarcoidosis 9

description:
Gene expression data from PBMC total RNA from healthy controls.
Sarcoidosis_9


title: Sarcoidosis 7

description:
Gene expression data from PBMC total RNA from healthy controls.
Sarcoidosis_7


title: microRNA profile of case NPC344697


title: Primary Breast Tumor brain metastasis 310982-6*

tag: sentrix barcode

tag: tissue

tag: set

tag: date of birth

tag: date of primary tumor diagnosis

tag: grading

tag: err

tag: pgr

tag: her2 ihc

tag: her2 fish

tag: adjuvant rtg therapy  (0=no, 1=yes)

tag: trastuzumab therapy (0=no, 1=yes)

tag: brain metasteses  (0=no, 1=yes)

tag: date brain met diagnosis

tag: overall survival  (0=no, 1=yes)

tag: date of death


title: microRNA profile of case NPC344447

tag: survival status  (1-death,0-survival)

tag: gender  (1-male,2-female)

tag: age (years)

tag: stage  (1-stage i,2-stage ii,3-stage iii,4-stage iv)


title: Primary Breast Tumor brain metastasis 310982-6

tag: sentrix barcode

tag: tissue

tag: set

tag: date of birth

tag: menopausal status (1=pre, 2=post)

tag: type of cancer histology

tag: lobulare

tag: induction chemotherapy (0=no, 1=yes)

tag: induction hormonal therapy with ta (0=no, 1=yes)

tag: induction hormonal therapy with ar (0=no, 1=yes)

tag: adjuvant chemotherapy (0=no, 1=yes)

tag: adjuvant hormonal therapy with tamox (0=no, 1=yes)

tag: adjuvant hormonal therapy with ia (0=no, 1=yes)


title: microRNA profile of case NPC344425

tag: survival status  (1-death,0-survival)


title: microRNA profile of case NPC344304

tag: gender  (1-male,2-female)


title: Primary Breast Tumor no brain metastasis 30053/04

tag: date of primary tumor diagnosis

tag: grading

tag: err

tag: pgr

tag: her2 ihc

tag: her2 fish

tag: adjuvant rtg therapy  (0=no, 1=yes)

tag: trastuzumab therapy (0=no, 1=yes)

tag: brain metasteses  (0=no, 1=yes)

tag: overall survival  (0=no, 1=yes)

tag: date of last information


title: Primary Breast Tumor brain metastasis 307279-84

tag: sentrix barcode

tag: tissue

tag: set

tag: date of birth

tag: menopausal status (1=pre, 2=post)

tag: type of cancer histology

tag: lobulare

tag: induction chemotherapy (0=no, 1=yes)

tag: induction hormonal therapy with ta (0=no, 1=yes)

tag: induction hormonal therapy with ar (0=no, 1=yes)

tag: date brain met diagnosis

tag: date of death


title: microRNA profile of case NPC344426

tag: survival status  (1-death,0-survival)

tag: gender  (1-male,2-female)

tag: age (years)

tag: stage  (1-stage i,2-stage ii,3-stage iii,4-stage iv)


title: microRNA profile of case NPC344159


title: Primary Breast Tumor brain metastasis 265838-4

tag: date of primary tumor diagnosis

tag: grading

tag: err

tag: pgr

tag: her2 ihc

tag: her2 fish

tag: adjuvant chemotherapy (0=no, 1=yes)

tag: adjuvant hormonal therapy with tamox (0=no, 1=yes)

tag: adjuvant hormonal therapy with ia (0=no, 1=yes)

tag: adjuvant rtg therapy  (0=no, 1=yes)

tag: trastuzumab therapy (0=no, 1=yes)

tag: brain metasteses  (0=no, 1=yes)

tag: overall survival  (0=no, 1=yes)

tag: date of last information


title: Sarcoidosis 5

description:
Gene expression data from PBMC total RNA from healthy controls.
Sarcoidosis_5

tag: ethnicity

tag: cell type

tag: diagnosis


title: Sarcoidosis 2

description:
Gene expression data from PBMC total RNA from healthy controls.
Sarcoidosis_2


title: Sarcoidosis 1

description:
Gene expression data from PBMC total RNA from healthy controls.
Sarcoidosis_1


title: Primary Breast Tumor brain metastasis 25510/05

tag: sentrix barcode

tag: tissue

tag: set

tag: date of birth

tag: menopausal status (1=pre, 2=post)

tag: type of cancer histology

tag: lobulare

tag: date of primary tumor diagnosis

tag: induction chemotherapy (0=no, 1=yes)

tag: induction hormonal therapy with ta (0=no, 1=yes)

tag: induction hormonal therapy with ar (0=no, 1=yes)

tag: date brain met diagnosis

tag: date of death


title: microRNA profile of case NPC344089

tag: survival status  (1-death,0-survival)

tag: gender  (1-male,2-female)

tag: age (years)

tag: stage  (1-stage i,2-stage ii,3-stage iii,4-stage iv)


title: Primary Breast Tumor no brain metastasis 2379B

tag: sentrix barcode

tag: grading

tag: err

tag: pgr

tag: her2 ihc

tag: her2 fish

tag: adjuvant chemotherapy (0=no, 1=yes)

tag: adjuvant hormonal therapy with tamox (0=no, 1=yes)

tag: adjuvant hormonal therapy with ia (0=no, 1=yes)

tag: adjuvant rtg therapy  (0=no, 1=yes)

tag: trastuzumab therapy (0=no, 1=yes)

tag: brain metasteses  (0=no, 1=yes)

tag: overall survival  (0=no, 1=yes)


title: Primary Breast Tumor no brain metastasis 241708-9

tag: tissue

tag: set

tag: date of birth

tag: menopausal status (1=pre, 2=post)

tag: type of cancer histology

tag: lobulare

tag: date of primary tumor diagnosis

tag: induction chemotherapy (0=no, 1=yes)

tag: induction hormonal therapy with ta (0=no, 1=yes)

tag: induction hormonal therapy with ar (0=no, 1=yes)

tag: date of death


title: Sarcoidosis 4

description:
Gene expression data from PBMC total RNA from healthy controls.
Sarcoidosis_4

tag: ethnicity

tag: cell type

tag: diagnosis


title: Sarcoidosis 3

description:
Gene expression data from PBMC total RNA from healthy controls.
Sarcoidosis_3


title: microRNA profile of case NPC344163

tag: survival status  (1-death,0-survival)

tag: gender  (1-male,2-female)

tag: age (years)

tag: stage  (1-stage i,2-stage ii,3-stage iii,4-stage iv)


title: microRNA profile of case NPC343940


title: microRNA profile of case NPC343945


title: microRNA profile of case NPC343380


title: Primary Breast Tumor no brain metastasis 23036/02

tag: sentrix barcode

tag: tissue

tag: set

tag: grading

tag: err

tag: pgr

tag: her2 ihc

tag: her2 fish

tag: adjuvant chemotherapy (0=no, 1=yes)

tag: adjuvant hormonal therapy with tamox (0=no, 1=yes)

tag: adjuvant hormonal therapy with ia (0=no, 1=yes)

tag: adjuvant rtg therapy  (0=no, 1=yes)

tag: trastuzumab therapy (0=no, 1=yes)

tag: brain metasteses  (0=no, 1=yes)

tag: overall survival  (0=no, 1=yes)

tag: date of last information


title: Primary Breast Tumor brain metastasis 228147-8

tag: date of birth

tag: menopausal status (1=pre, 2=post)

tag: type of cancer histology

tag: lobulare

tag: date of primary tumor diagnosis

tag: induction chemotherapy (0=no, 1=yes)

tag: induction hormonal therapy with ta (0=no, 1=yes)

tag: induction hormonal therapy with ar (0=no, 1=yes)

tag: date brain met diagnosis

tag: date of death


title: Primary Breast Tumor no brain metastasis 22042/04

tag: sentrix barcode

tag: tissue

tag: set

tag: grading

tag: err

tag: pgr

tag: her2 ihc

tag: her2 fish

tag: adjuvant chemotherapy (0=no, 1=yes)

tag: adjuvant hormonal therapy with tamox (0=no, 1=yes)


title: Sarcoidosis 18

description:
Gene expression data from PBMC total RNA from healthy controls.
Sarcoidosis_18

tag: ethnicity

tag: cell type

tag: diagnosis


title: Sarcoidosis 17

description:
Gene expression data from PBMC total RNA from healthy controls.
Sarcoidosis_17


title: Sarcoidosis 13

description:
Gene expression data from PBMC total RNA from healthy controls.
Sarcoidosis_13


title: Sarcoidosis 12

description:
Gene expression data from PBMC total RNA from healthy controls.
Sarcoidosis_12


title: Sarcoidosis 11

description:
Gene expression data from PBMC total RNA from healthy controls.
Sarcoidosis_11


title: microRNA profile of case NPC343078

tag: survival status  (1-death,0-survival)

tag: gender  (1-male,2-female)

tag: age (years)

tag: stage  (1-stage i,2-stage ii,3-stage iii,4-stage iv)


title: Primary Breast Tumor brain metastasis 159008-9

tag: sentrix barcode

tag: date of birth

tag: menopausal status (1=pre, 2=post)

tag: type of cancer histology

tag: lobulare

tag: date of primary tumor diagnosis

tag: induction chemotherapy (0=no, 1=yes)

tag: induction hormonal therapy with ta (0=no, 1=yes)

tag: induction hormonal therapy with ar (0=no, 1=yes)

tag: adjuvant hormonal therapy with ia (0=no, 1=yes)

tag: adjuvant rtg therapy  (0=no, 1=yes)

tag: trastuzumab therapy (0=no, 1=yes)

tag: brain metasteses  (0=no, 1=yes)

tag: date brain met diagnosis

tag: overall survival  (0=no, 1=yes)

tag: date of death


title: Primary Breast Tumor no brain metastasis 16428/01

tag: tissue

tag: set

tag: grading

tag: err

tag: pgr

tag: her2 ihc

tag: her2 fish

tag: adjuvant chemotherapy (0=no, 1=yes)

tag: adjuvant hormonal therapy with tamox (0=no, 1=yes)


title: Control 13

description:
Gene expression data from PBMC total RNA from healthy controls.
Healthy_control_13

tag: ethnicity

tag: cell type

tag: diagnosis

value: Healthy


title: microRNA profile of case NPC343553

tag: survival status  (1-death,0-survival)

tag: gender  (1-male,2-female)

tag: age (years)

tag: stage  (1-stage i,2-stage ii,3-stage iii,4-stage iv)


title: microRNA profile of case NPC343707


title: Primary Breast Tumor no brain metastasis 19682/01

tag: sentrix barcode

tag: date of birth

tag: menopausal status (1=pre, 2=post)

tag: type of cancer histology

tag: lobulare

tag: date of primary tumor diagnosis

tag: induction chemotherapy (0=no, 1=yes)

tag: induction hormonal therapy with ta (0=no, 1=yes)

tag: induction hormonal therapy with ar (0=no, 1=yes)

tag: adjuvant hormonal therapy with ia (0=no, 1=yes)

tag: adjuvant rtg therapy  (0=no, 1=yes)

tag: trastuzumab therapy (0=no, 1=yes)

tag: brain metasteses  (0=no, 1=yes)

tag: overall survival  (0=no, 1=yes)

tag: date of death


title: Primary Breast Tumor no brain metastasis 19212/02

tag: tissue

tag: set

tag: grading

tag: err

tag: pgr

tag: her2 ihc

tag: her2 fish

tag: adjuvant chemotherapy (0=no, 1=yes)

tag: adjuvant hormonal therapy with tamox (0=no, 1=yes)


title: Primary Breast Tumor brain metastasis 17615/99

tag: sentrix barcode

tag: date of birth

tag: menopausal status (1=pre, 2=post)

tag: type of cancer histology

tag: lobulare

tag: date of primary tumor diagnosis

tag: induction chemotherapy (0=no, 1=yes)

tag: induction hormonal therapy with ta (0=no, 1=yes)

tag: date brain met diagnosis


title: Primary Breast Tumor brain metastasis 17021/98

tag: tissue

tag: set

tag: induction hormonal therapy with ar (0=no, 1=yes)

tag: adjuvant hormonal therapy with ia (0=no, 1=yes)

tag: adjuvant rtg therapy  (0=no, 1=yes)

tag: trastuzumab therapy (0=no, 1=yes)

tag: brain metasteses  (0=no, 1=yes)

tag: overall survival  (0=no, 1=yes)

tag: date of death


title: microRNA profile of case NPC343340

tag: survival status  (1-death,0-survival)

tag: gender  (1-male,2-female)

tag: age (years)

tag: stage  (1-stage i,2-stage ii,3-stage iii,4-stage iv)


title: microRNA profile of case NPC342844


title: Primary Breast Tumor brain metastasis 12928-30

tag: sentrix barcode

tag: date of birth

tag: menopausal status (1=pre, 2=post)

tag: type of cancer histology

tag: lobulare

tag: date of primary tumor diagnosis

tag: grading

tag: err

tag: pgr

tag: her2 ihc

tag: her2 fish

tag: adjuvant chemotherapy (0=no, 1=yes)

tag: adjuvant hormonal therapy with tamox (0=no, 1=yes)

tag: date of last information


title: Primary Breast Tumor no brain metastasis 12972/4

tag: tissue

tag: set

tag: induction chemotherapy (0=no, 1=yes)

tag: induction hormonal therapy with ta (0=no, 1=yes)

tag: induction hormonal therapy with ar (0=no, 1=yes)

tag: adjuvant hormonal therapy with ia (0=no, 1=yes)

tag: adjuvant rtg therapy  (0=no, 1=yes)

tag: trastuzumab therapy (0=no, 1=yes)

tag: brain metasteses  (0=no, 1=yes)

tag: overall survival  (0=no, 1=yes)

tag: date of death


title: Control 11

description:
Gene expression data from PBMC total RNA from healthy controls.
Healthy_control_11

tag: ethnicity

tag: cell type

tag: diagnosis


title: Primary Breast Tumor brain metastasis 11015/05

tag: sentrix barcode

tag: date of birth

tag: menopausal status (1=pre, 2=post)

tag: type of cancer histology

tag: lobulare

tag: date of primary tumor diagnosis

tag: grading

tag: err

tag: pgr

tag: her2 ihc

tag: her2 fish

tag: adjuvant chemotherapy (0=no, 1=yes)

tag: date brain met diagnosis


title: Control 18

description:
Gene expression data from PBMC total RNA from healthy controls.
Healthy_control_18


title: Control 19

description:
Gene expression data from PBMC total RNA from healthy controls.
Healthy_control_19


title: microRNA profile of case NPC343337

tag: survival status  (1-death,0-survival)

tag: gender  (1-male,2-female)

tag: age (years)

tag: stage  (1-stage i,2-stage ii,3-stage iii,4-stage iv)


title: microRNA profile of case NPC343311


title: microRNA profile of case NPC342428


title: Primary Breast Tumor brain metastasis 149269-70

tag: sentrix barcode

tag: tissue

tag: set

tag: induction chemotherapy (0=no, 1=yes)

tag: induction hormonal therapy with ta (0=no, 1=yes)

tag: induction hormonal therapy with ar (0=no, 1=yes)

tag: adjuvant hormonal therapy with tamox (0=no, 1=yes)

tag: adjuvant hormonal therapy with ia (0=no, 1=yes)

tag: adjuvant rtg therapy  (0=no, 1=yes)

tag: trastuzumab therapy (0=no, 1=yes)

tag: brain metasteses  (0=no, 1=yes)

tag: overall survival  (0=no, 1=yes)

tag: date of death


title: Primary Breast Tumor no brain metastasis 10680/3

tag: date of birth

tag: menopausal status (1=pre, 2=post)

tag: type of cancer histology

tag: lobulare

tag: date of primary tumor diagnosis

tag: grading

tag: err

tag: pgr

tag: her2 ihc

tag: her2 fish

tag: adjuvant chemotherapy (0=no, 1=yes)


title: microRNA profile of case NPC342303

tag: survival status  (1-death,0-survival)

tag: gender  (1-male,2-female)

tag: age (years)

tag: stage  (1-stage i,2-stage ii,3-stage iii,4-stage iv)


title: Primary Breast Tumor no brain metastasis 896612

tag: sentrix barcode

tag: tissue

tag: set

tag: induction chemotherapy (0=no, 1=yes)

tag: induction hormonal therapy with ta (0=no, 1=yes)

tag: induction hormonal therapy with ar (0=no, 1=yes)

tag: adjuvant hormonal therapy with tamox (0=no, 1=yes)

tag: adjuvant hormonal therapy with ia (0=no, 1=yes)

tag: adjuvant rtg therapy  (0=no, 1=yes)

tag: trastuzumab therapy (0=no, 1=yes)

tag: brain metasteses  (0=no, 1=yes)

tag: overall survival  (0=no, 1=yes)

tag: date of last information


title: Control 15

description:
Gene expression data from PBMC total RNA from healthy controls.
Healthy_control_15

tag: ethnicity

tag: cell type

tag: diagnosis


title: Primary Breast Tumor brain metastasis 913741

tag: date of birth

tag: menopausal status (1=pre, 2=post)

tag: type of cancer histology

tag: lobulare

tag: date of primary tumor diagnosis

tag: grading

tag: err

tag: pgr

tag: her2 ihc

tag: her2 fish

tag: adjuvant chemotherapy (0=no, 1=yes)

tag: date brain met diagnosis

tag: date of death


title: microRNA profile of case NPC342851

tag: survival status  (1-death,0-survival)

tag: gender  (1-male,2-female)

tag: age (years)

tag: stage  (1-stage i,2-stage ii,3-stage iii,4-stage iv)


title: microRNA profile of case NPC342693


title: Control 53

description:
Gene expression data from PBMC total RNA from healthy controls.
Healthy_control_53

tag: ethnicity

tag: cell type

tag: diagnosis


title: microRNA profile of case NPC342636


title: Control 16

description:
Gene expression data from PBMC total RNA from healthy controls.
Healthy_control_16


title: microRNA profile of case NPC341927


title: Control 12

description:
Gene expression data from PBMC total RNA from healthy controls.
Healthy_control_12


title: Primary Breast Tumor brain metastasis 889870

tag: sentrix barcode

tag: tissue

tag: set

tag: date of birth

tag: menopausal status (1=pre, 2=post)

tag: type of cancer histology

tag: lobulare

tag: induction chemotherapy (0=no, 1=yes)

tag: induction hormonal therapy with ta (0=no, 1=yes)

tag: induction hormonal therapy with ar (0=no, 1=yes)

tag: adjuvant hormonal therapy with tamox (0=no, 1=yes)

tag: adjuvant hormonal therapy with ia (0=no, 1=yes)

tag: adjuvant rtg therapy  (0=no, 1=yes)

tag: trastuzumab therapy (0=no, 1=yes)

tag: brain metasteses  (0=no, 1=yes)

tag: overall survival  (0=no, 1=yes)

tag: date of last information


title: Primary Breast Tumor brain metastasis 14409/99

tag: sentrix barcode

tag: date of primary tumor diagnosis

tag: grading

tag: err

tag: pgr

tag: her2 ihc

tag: her2 fish

tag: adjuvant chemotherapy (0=no, 1=yes)

tag: date brain met diagnosis


title: myometrium EP

city: Beijing

first: ligang

last: wang

address: 2 Yuanmingyuan West Road

institute: institute of animal sciense

description: Gene expression data from early pregnant sow myometrium

hyb_protocol: Affymetrix Fluidics Station 450 and Hybridization Oven 640 under standard conditions.

scan_protocol: Image processing was conducted using the Affymetrix GeneArray  3000 scanner.

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. Knock out the smallest and biggst 2%, the average intensity for all the other probes on the array was scaled to 500.

organism: Sus scrofa

source_name: myometrium tissue of early pregnant sow

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

treatment_protocol: The tissues were collected and washed in phosphate-buffered saline (PBS) immediately and then frozen in liquid nitrogen. All samples were stored at -80C until the RNA was extracted.

tag: time point

value: early pregnant

tag: tissue

value: myometrium


title: myometrium LP

description: Gene expression data from late pregnant sow myometrium

source_name: myometrium tissue of late pregnant sow

value: late pregnant


title: Primary Breast Tumor no brain metastasis 884236

source_name: Primary Breast Tumor

value: primary breast cancer tumor

tag: set

value: TRAINING

tag: date of birth

tag: menopausal status (1=pre, 2=post)

tag: type of cancer histology

tag: lobulare

tag: induction chemotherapy (0=no, 1=yes)

tag: induction hormonal therapy with ta (0=no, 1=yes)

tag: induction hormonal therapy with ar (0=no, 1=yes)

tag: adjuvant hormonal therapy with tamox (0=no, 1=yes)

tag: adjuvant hormonal therapy with ia (0=no, 1=yes)


title: microRNA profile of case NPC340747

tag: survival status  (1-death,0-survival)

tag: gender  (1-male,2-female)

tag: age (years)

tag: stage  (1-stage i,2-stage ii,3-stage iii,4-stage iv)


title: myometrium np

description: Gene expression data from none pregnant sow myometrium

source_name: myometrium tissue of none pregnant sow

value: none pregnant


title: microRNA profile of case NPC342494


title: Primary Breast Tumor no brain metastasis 941028

tag: sentrix barcode

tag: date of primary tumor diagnosis

tag: grading

tag: err

tag: pgr

tag: her2 ihc

tag: her2 fish

tag: adjuvant chemotherapy (0=no, 1=yes)

tag: adjuvant rtg therapy  (0=no, 1=yes)

tag: trastuzumab therapy (0=no, 1=yes)

tag: brain metasteses  (0=no, 1=yes)

tag: overall survival  (0=no, 1=yes)

tag: date of last information


title: microRNA profile of case NPC342360

tag: survival status  (1-death,0-survival)


title: ovary EP

description: Gene expression data from early pregnant sow ovary

source_name: ovary tissue of early pregnant sow

tag: time point

tag: tissue

value: ovary


title: Primary Breast Tumor brain metastasis 870607

tag: set

tag: date of birth

tag: menopausal status (1=pre, 2=post)

tag: type of cancer histology

tag: lobulare

tag: induction chemotherapy (0=no, 1=yes)

tag: induction hormonal therapy with ta (0=no, 1=yes)

tag: induction hormonal therapy with ar (0=no, 1=yes)

tag: adjuvant hormonal therapy with tamox (0=no, 1=yes)

tag: adjuvant hormonal therapy with ia (0=no, 1=yes)

tag: date brain met diagnosis

tag: date of death


title: microRNA profile of case NPC339565

tag: gender  (1-male,2-female)

tag: age (years)

tag: stage  (1-stage i,2-stage ii,3-stage iii,4-stage iv)


title: Primary Breast Tumor brain metastasis 891444

tag: sentrix barcode

tag: date of primary tumor diagnosis

tag: grading

tag: err

tag: pgr

tag: her2 ihc

tag: her2 fish

tag: adjuvant chemotherapy (0=no, 1=yes)

tag: adjuvant rtg therapy  (0=no, 1=yes)

tag: trastuzumab therapy (0=no, 1=yes)

tag: brain metasteses  (0=no, 1=yes)

tag: overall survival  (0=no, 1=yes)


title: microRNA profile of case NPC339738

tag: survival status  (1-death,0-survival)


title: microRNA profile of case NPC341471


title: Primary Breast Tumor no brain metastasis 893709

tag: tissue

tag: set

tag: date of birth

tag: menopausal status (1=pre, 2=post)

tag: type of cancer histology

tag: lobulare

tag: induction chemotherapy (0=no, 1=yes)

tag: induction hormonal therapy with ta (0=no, 1=yes)

tag: induction hormonal therapy with ar (0=no, 1=yes)

tag: adjuvant hormonal therapy with tamox (0=no, 1=yes)

tag: adjuvant hormonal therapy with ia (0=no, 1=yes)

tag: date of last information


title: microRNA profile of case NPC339509

tag: gender  (1-male,2-female)

tag: age (years)

tag: stage  (1-stage i,2-stage ii,3-stage iii,4-stage iv)


title: microRNA profile of case NPC340734


title: Primary Breast Tumor no brain metastasis 838590

tag: sentrix barcode

tag: date of primary tumor diagnosis

tag: grading

tag: err

tag: pgr

tag: her2 ihc

tag: her2 fish

tag: adjuvant chemotherapy (0=no, 1=yes)

tag: adjuvant rtg therapy  (0=no, 1=yes)

tag: trastuzumab therapy (0=no, 1=yes)

tag: brain metasteses  (0=no, 1=yes)

tag: overall survival  (0=no, 1=yes)

tag: date of death


title: Primary Breast Tumor brain metastasis 840863

tag: tissue

tag: set

tag: date of birth

tag: menopausal status (1=pre, 2=post)

tag: type of cancer histology

tag: lobulare

tag: induction chemotherapy (0=no, 1=yes)

tag: induction hormonal therapy with ta (0=no, 1=yes)

tag: induction hormonal therapy with ar (0=no, 1=yes)

tag: adjuvant hormonal therapy with tamox (0=no, 1=yes)

tag: adjuvant hormonal therapy with ia (0=no, 1=yes)

tag: date brain met diagnosis

tag: date of last information


title: Primary Breast Tumor no brain metastasis 816067

tag: sentrix barcode

tag: date of primary tumor diagnosis

tag: grading

tag: err

tag: pgr

tag: her2 ihc

tag: her2 fish

tag: adjuvant chemotherapy (0=no, 1=yes)

tag: adjuvant rtg therapy  (0=no, 1=yes)

tag: trastuzumab therapy (0=no, 1=yes)


title: microRNA profile of case NPC339451

tag: survival status  (1-death,0-survival)

tag: gender  (1-male,2-female)

tag: age (years)

tag: stage  (1-stage i,2-stage ii,3-stage iii,4-stage iv)


title: microRNA profile of case NPC339287


title: Primary Breast Tumor no brain metastasis 804564

tag: tissue

tag: set

tag: date of birth

tag: menopausal status (1=pre, 2=post)

tag: type of cancer histology

tag: lobulare

tag: induction chemotherapy (0=no, 1=yes)

tag: induction hormonal therapy with ta (0=no, 1=yes)

tag: induction hormonal therapy with ar (0=no, 1=yes)

tag: adjuvant hormonal therapy with tamox (0=no, 1=yes)

tag: adjuvant hormonal therapy with ia (0=no, 1=yes)

tag: brain metasteses  (0=no, 1=yes)

tag: overall survival  (0=no, 1=yes)


title: microRNA profile of case NPC339435

tag: survival status  (1-death,0-survival)


title: Primary Breast Tumor brain metastasis 796961

tag: sentrix barcode

tag: date of primary tumor diagnosis

tag: grading

tag: err

tag: pgr

tag: her2 ihc

tag: her2 fish

tag: adjuvant chemotherapy (0=no, 1=yes)

tag: adjuvant rtg therapy  (0=no, 1=yes)

tag: trastuzumab therapy (0=no, 1=yes)

tag: date brain met diagnosis

tag: date of death


title: microRNA profile of case NPC339067

tag: gender  (1-male,2-female)

tag: age (years)

tag: stage  (1-stage i,2-stage ii,3-stage iii,4-stage iv)


title: Primary Breast Tumor no brain metastasis 823353

tag: tissue

tag: set

tag: date of birth

tag: menopausal status (1=pre, 2=post)

tag: type of cancer histology

tag: lobulare

tag: induction chemotherapy (0=no, 1=yes)

tag: induction hormonal therapy with ta (0=no, 1=yes)

tag: induction hormonal therapy with ar (0=no, 1=yes)

tag: adjuvant hormonal therapy with tamox (0=no, 1=yes)

tag: adjuvant hormonal therapy with ia (0=no, 1=yes)

tag: brain metasteses  (0=no, 1=yes)

tag: overall survival  (0=no, 1=yes)


title: microRNA profile of case NPC339493

tag: survival status  (1-death,0-survival)


title: Primary Breast Tumor brain metastasis 328913

tag: sentrix barcode

tag: date of primary tumor diagnosis

tag: grading

tag: err

tag: pgr

tag: her2 ihc

tag: her2 fish

tag: adjuvant chemotherapy (0=no, 1=yes)

tag: adjuvant rtg therapy  (0=no, 1=yes)

tag: trastuzumab therapy (0=no, 1=yes)

tag: date brain met diagnosis

tag: date of death


title: Primary Breast Tumor no brain metastasis 353836

tag: tissue

tag: set

tag: date of birth

tag: menopausal status (1=pre, 2=post)

tag: type of cancer histology

tag: lobulare

tag: induction chemotherapy (0=no, 1=yes)

tag: induction hormonal therapy with ta (0=no, 1=yes)

tag: induction hormonal therapy with ar (0=no, 1=yes)

tag: adjuvant hormonal therapy with tamox (0=no, 1=yes)

tag: date of last information


title: ovary LP

description: Gene expression data from late pregnant sow ovary

source_name: ovary tissue of late pregnant sow

tag: time point


title: microRNA profile of case NPC338893

tag: survival status  (1-death,0-survival)

tag: gender  (1-male,2-female)

tag: age (years)

tag: stage  (1-stage i,2-stage ii,3-stage iii,4-stage iv)


title: Primary Breast Tumor brain metastasis 304314

tag: sentrix barcode

tag: date of primary tumor diagnosis

tag: grading

tag: err

tag: pgr

tag: her2 ihc

tag: her2 fish

tag: adjuvant chemotherapy (0=no, 1=yes)

tag: adjuvant hormonal therapy with ia (0=no, 1=yes)

tag: adjuvant rtg therapy  (0=no, 1=yes)

tag: trastuzumab therapy (0=no, 1=yes)

tag: brain metasteses  (0=no, 1=yes)

tag: date brain met diagnosis

tag: overall survival  (0=no, 1=yes)

tag: date of death


title: microRNA profile of case NPC338668

tag: survival status  (1-death,0-survival)

tag: gender  (1-male,2-female)

tag: age (years)


title: ovary np

description: Gene expression data from none pregnant sow ovary

source_name: ovary tissue of none pregnant sow

tag: time point

tag: tissue


title: Primary Breast Tumor brain metastasis 237049

tag: sentrix barcode

tag: set

tag: date of birth

tag: menopausal status (1=pre, 2=post)

tag: type of cancer histology

tag: lobulare

tag: date of primary tumor diagnosis

tag: grading

tag: err

tag: induction chemotherapy (0=no, 1=yes)

tag: induction hormonal therapy with ta (0=no, 1=yes)

tag: induction hormonal therapy with ar (0=no, 1=yes)

tag: adjuvant hormonal therapy with tamox (0=no, 1=yes)


title: Primary Breast Tumor no brain metastasis 236689

tag: pgr

tag: her2 ihc

tag: her2 fish

tag: adjuvant chemotherapy (0=no, 1=yes)

tag: adjuvant hormonal therapy with ia (0=no, 1=yes)

tag: adjuvant rtg therapy  (0=no, 1=yes)

tag: trastuzumab therapy (0=no, 1=yes)

tag: brain metasteses  (0=no, 1=yes)

tag: overall survival  (0=no, 1=yes)

tag: date of last information


title: PAMs_Tongcheng_5dpi_rep1

city: Wuhan

first: Bang

last: Liu

address: Shizishan Road Number 1, Hongshan Area, Wuhan , Hubei Provience, China

institute: Huazhong Agricultural University

hyb_protocol: Five μg fragmented labeled cRNA was hybridized with the GeneChip Porcine Genome Array according to the standard procedures provided by the manufacturer. Chips were washed and stained with a GeneChip Fluidics Station 450 (Affymetrix) using the standard fluidics protocol.

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

data_processing: There are 11 paired perfect match (PM) and mismatch (MM) 25-mer probes in the Affymetrix GeneChip porcine genome array for each probeset representing a gene. The signals from these probe pairs are used to determine whether a given gene is expressed and to measure the gene expression level. The probe-pair (PM-MM) data were used to detect the expression level of genes on the array (present call, marginal call, and absent call) by MAS 5.0 (Wilcoxon signed rank test). Raw data from .CEL files were converted to gene signal files by MAS 5.0 (Ver.2.3.1).The data were normalized between slides  using the quantile normalization method by R software(Ver.2.11.1.).The differentially expressed genes, classified as those with Fold changes≧2, P value≦0.05 and FDR≦0.05, were selected using the SAM software(ver.2.1).

source_name: Pulmonary alveolar macrophages of Tongcheng at 5 dpi of HP-PRRSV infection

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA.

growth_protocol: Five-week-old piglets were raised in pathogen-free facilities. The infected groups were challenged with PRRSV-Wuh2 (3 ml/15 kg, 10-5 TCID50/ml) by intramuscular inoculation, with uninfected groups as control.

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

treatment_protocol: The pulmonary alveolar macrophages were collected by bronchoalveolar lavage with PBS contained 5% FCS, 25% DMEM and 2 mM EDTA.

tag: gender

value: male

tag: breed

value: Tongcheng

tag: cell type

value: Pulmonary alveolar macrophage

tag: age

tag: infection

value: HP-PRRSV

tag: time

value: 5 dpi


title: PAMs_Tongcheng_0dpi_rep2

source_name: Pulmonary alveolar macrophages of Tongcheng at 0 dpi of HP-PRRSV infection

value: uninfected

value: 0 dpi


title: PAMs_Tongcheng_5dpi_rep3


title: microRNA profile of case NPC338653

source_name: Nasopharyngeal carcinoma

tag: survival status  (1-death,0-survival)

tag: gender  (1-male,2-female)

tag: age (years)

tag: stage  (1-stage i,2-stage ii,3-stage iii,4-stage iv)


title: PAMs_Tongcheng_5dpi_rep2


title: PAMs_Tongcheng_0dpi_rep1


title: PAMs_Tongcheng_0dpi_rep3


title: NEUROB-4-2

city: Majadahonda

first: Javier

last: Garcia-Castro

state: Madrid

address: Ctra. Majadahonda-Pozuelo km 2,2

department: Centro Nacional de Microbiología

country: Spain

institute: Instituto de Salud Carlos III

description: Gene expression of MSCs from NB patient

hyb_protocol: 1.65 μg Cy3-labeled fragmented cRNA in hybridization buffer was hybridized overnight (17 hours, 65°C) to Agilent Whole Human Genome Oligo Microarrays 4×44K using Agilent’s recommended hybridization chamber and oven.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent’s Microarray Scanner System (Agilent Technologies).

data_processing: The Agilent Feature Extraction Software (FES) was used to read out and process the microarray image files.

source_name: MSCs from NB patient 4

label_protocol: To produce Cy3-labeled cRNA, the RNA samples were amplified and labelled using the Agilent Low RNA Input Linear Amp Kit (Agilent Technologies) following the manufacturer’s protocol.

growth_protocol: Bone marrow-derived MSCs were obtained by adherence to plastic.  Mononucleated cells were obtained after centrifugation using a Ficoll-Paque gradient. Cells were cultured at 37°C with 5% CO2 in DMEM (Lonza) supplemented with 10% Fetal Bovine Serum

extract_protocol: MSCs were stabilized in PrepProtect™ (Miltenyi Biotec) and total RNA was isolated using standard RNA extraction protocols (NucleoSpin® RNA II, Macherey-Nagel).

tag: diagnosis

value: neuroblastoma

value: mesenchymal stem cells

tag: replicate

value: replicate 2


title: NEUROB-4-1

description: Gene expression of MSCs from NB patient

value: replicate 1


title: NEUROB-4-3

description: Gene expression of MSCs from NB patient

value: replicate 3


title: NEUROB-3-3

description: Gene expression of MSCs from NB patient

source_name: MSCs from NB patient 3


title: NEUROB-3-1

description: Gene expression of MSCs from NB patient


title: Primary Breast Tumor no brain metastasis 236344

tag: sentrix barcode

tag: tissue

tag: set

tag: date of birth

tag: menopausal status (1=pre, 2=post)

tag: type of cancer histology

tag: lobulare

tag: date of primary tumor diagnosis

tag: grading

tag: err

tag: pgr

tag: her2 ihc

tag: her2 fish

tag: induction chemotherapy (0=no, 1=yes)

tag: induction hormonal therapy with ta (0=no, 1=yes)

tag: induction hormonal therapy with ar (0=no, 1=yes)

tag: adjuvant chemotherapy (0=no, 1=yes)

tag: adjuvant hormonal therapy with tamox (0=no, 1=yes)

tag: adjuvant hormonal therapy with ia (0=no, 1=yes)

tag: adjuvant rtg therapy  (0=no, 1=yes)


title: microRNA profile of case NPC338646

tag: survival status  (1-death,0-survival)

tag: gender  (1-male,2-female)

tag: age (years)

tag: stage  (1-stage i,2-stage ii,3-stage iii,4-stage iv)


title: microRNA profile of case NPC338520


title: microRNA profile of case NPC338469


title: microRNA profile of case NPC338438


title: Primary Breast Tumor brain metastasis 225212

tag: sentrix barcode

tag: tissue

tag: set

tag: date of birth

tag: menopausal status (1=pre, 2=post)

tag: type of cancer histology

tag: lobulare

tag: date of primary tumor diagnosis

tag: trastuzumab therapy (0=no, 1=yes)

tag: brain metasteses  (0=no, 1=yes)

tag: date brain met diagnosis

tag: overall survival  (0=no, 1=yes)

tag: date of last information


title: Primary Breast Tumor no brain metastasis 226434

value: INTERNAL TEST

tag: grading

tag: err

tag: pgr

tag: her2 ihc

tag: her2 fish

tag: induction chemotherapy (0=no, 1=yes)

tag: induction hormonal therapy with ta (0=no, 1=yes)

tag: induction hormonal therapy with ar (0=no, 1=yes)

tag: adjuvant chemotherapy (0=no, 1=yes)

tag: adjuvant hormonal therapy with tamox (0=no, 1=yes)

tag: adjuvant hormonal therapy with ia (0=no, 1=yes)

tag: adjuvant rtg therapy  (0=no, 1=yes)

tag: date of death


title: microRNA profile of case NPC338263

tag: survival status  (1-death,0-survival)

tag: gender  (1-male,2-female)

tag: age (years)

tag: stage  (1-stage i,2-stage ii,3-stage iii,4-stage iv)


title: microRNA profile of case NPC338096


title: Primary Breast Tumor brain metastasis 224920

tag: sentrix barcode

tag: tissue

value: primary breast cancer tumor

tag: set

tag: date of birth

tag: menopausal status (1=pre, 2=post)

tag: type of cancer histology

tag: lobulare

tag: date of primary tumor diagnosis

tag: grading

tag: trastuzumab therapy (0=no, 1=yes)

tag: brain metasteses  (0=no, 1=yes)

tag: date brain met diagnosis

tag: overall survival  (0=no, 1=yes)

tag: date of last information


title: NEUROB-2-3

description: Gene expression of MSCs from NB patient

source_name: MSCs from NB patient 2

tag: diagnosis

tag: cell type

tag: replicate


title: NEUROB-3-2

description: Gene expression of MSCs from NB patient


title: NEUROB-2-1

description: Gene expression of MSCs from NB patient


title: NEUROB-2-2

description: Gene expression of MSCs from NB patient


title: microRNA profile of case NPC337973

tag: survival status  (1-death,0-survival)

tag: gender  (1-male,2-female)

tag: age (years)

tag: stage  (1-stage i,2-stage ii,3-stage iii,4-stage iv)


title: NEUROB-1-2

description: Gene expression of MSCs from NB patient

source_name: MSCs from NB patient 1


title: Primary Breast Tumor brain metastasis 219643

tag: sentrix barcode

tag: tissue

tag: set

tag: date of birth

tag: menopausal status (1=pre, 2=post)

tag: err

tag: pgr

tag: her2 ihc

tag: her2 fish

tag: induction chemotherapy (0=no, 1=yes)

tag: induction hormonal therapy with ta (0=no, 1=yes)

tag: induction hormonal therapy with ar (0=no, 1=yes)

tag: adjuvant chemotherapy (0=no, 1=yes)

tag: adjuvant hormonal therapy with tamox (0=no, 1=yes)

tag: adjuvant hormonal therapy with ia (0=no, 1=yes)

tag: adjuvant rtg therapy  (0=no, 1=yes)

tag: date of death


title: NEUROB-1-3

description: Gene expression of MSCs from NB patient

tag: diagnosis

tag: cell type

tag: replicate


title: Primary Breast Tumor no brain metastasis 215849

tag: sentrix barcode

tag: tissue

tag: set

tag: date of birth

tag: type of cancer histology

tag: lobulare

tag: date of primary tumor diagnosis

tag: grading

tag: trastuzumab therapy (0=no, 1=yes)

tag: brain metasteses  (0=no, 1=yes)

tag: overall survival  (0=no, 1=yes)

tag: date of last information


title: CONTROL-4-3

description: Gene expression of MSCs from healthy donor

source_name: MSCs from healthy donor 4

value: healthy donor


title: Primary Breast Tumor brain metastasis 231441

value: TRAINING

tag: menopausal status (1=pre, 2=post)

tag: err

tag: pgr

tag: her2 ihc

tag: her2 fish

tag: induction chemotherapy (0=no, 1=yes)

tag: induction hormonal therapy with ta (0=no, 1=yes)

tag: induction hormonal therapy with ar (0=no, 1=yes)

tag: adjuvant chemotherapy (0=no, 1=yes)

tag: adjuvant hormonal therapy with tamox (0=no, 1=yes)

tag: adjuvant hormonal therapy with ia (0=no, 1=yes)

tag: adjuvant rtg therapy  (0=no, 1=yes)

tag: date brain met diagnosis


title: NEUROB-1-1

description: Gene expression of MSCs from NB patient

tag: diagnosis

tag: cell type

tag: replicate


title: microRNA profile of case NPC335303

tag: survival status  (1-death,0-survival)

tag: gender  (1-male,2-female)

tag: age (years)

tag: stage  (1-stage i,2-stage ii,3-stage iii,4-stage iv)


title: microRNA profile of case NPC337239


title: Primary Breast Tumor no brain metastasis 207094

tag: sentrix barcode

tag: tissue

tag: set

tag: date of birth

tag: menopausal status (1=pre, 2=post)

tag: type of cancer histology

tag: lobulare

tag: date of primary tumor diagnosis

tag: grading

tag: err

tag: pgr

tag: her2 ihc

tag: trastuzumab therapy (0=no, 1=yes)

tag: brain metasteses  (0=no, 1=yes)

tag: overall survival  (0=no, 1=yes)

tag: date of death


title: microRNA profile of case NPC334398

tag: survival status  (1-death,0-survival)

tag: gender  (1-male,2-female)

tag: age (years)

tag: stage  (1-stage i,2-stage ii,3-stage iii,4-stage iv)


title: CONTROL-4-2

tag: diagnosis

tag: cell type

tag: replicate


title: Primary Breast Tumor brain metastasis 218192

tag: sentrix barcode

tag: tissue

tag: set

tag: date of birth

tag: menopausal status (1=pre, 2=post)

tag: type of cancer histology

tag: lobulare

tag: her2 fish

tag: induction chemotherapy (0=no, 1=yes)

tag: induction hormonal therapy with ta (0=no, 1=yes)

tag: induction hormonal therapy with ar (0=no, 1=yes)

tag: adjuvant chemotherapy (0=no, 1=yes)

tag: adjuvant hormonal therapy with tamox (0=no, 1=yes)

tag: adjuvant hormonal therapy with ia (0=no, 1=yes)

tag: adjuvant rtg therapy  (0=no, 1=yes)

tag: date brain met diagnosis


title: microRNA profile of case NPC333898

tag: survival status  (1-death,0-survival)

tag: gender  (1-male,2-female)

tag: age (years)

tag: stage  (1-stage i,2-stage ii,3-stage iii,4-stage iv)


title: Primary Breast Tumor brain metastasis 194617

tag: sentrix barcode

tag: tissue

tag: set

tag: date of birth

tag: date of primary tumor diagnosis

tag: grading

tag: err

tag: pgr

tag: her2 ihc

tag: trastuzumab therapy (0=no, 1=yes)

tag: brain metasteses  (0=no, 1=yes)

tag: overall survival  (0=no, 1=yes)

tag: date of death


title: microRNA profile of case NPC332502

tag: survival status  (1-death,0-survival)


title: microRNA profile of case NPC337794

tag: gender  (1-male,2-female)


title: Primary Breast Tumor no brain metastasis 190877

tag: menopausal status (1=pre, 2=post)

tag: type of cancer histology

tag: lobulare

tag: her2 fish

tag: induction chemotherapy (0=no, 1=yes)

tag: induction hormonal therapy with ta (0=no, 1=yes)

tag: induction hormonal therapy with ar (0=no, 1=yes)

tag: adjuvant chemotherapy (0=no, 1=yes)

tag: adjuvant hormonal therapy with tamox (0=no, 1=yes)

tag: adjuvant hormonal therapy with ia (0=no, 1=yes)

tag: adjuvant rtg therapy  (0=no, 1=yes)


title: Primary Breast Tumor no brain metastasis 171821

tag: sentrix barcode

tag: tissue

tag: set

tag: date of birth

tag: date of primary tumor diagnosis

tag: grading

tag: err

tag: pgr

tag: her2 ihc

tag: trastuzumab therapy (0=no, 1=yes)


title: microRNA profile of case NPC330874

tag: survival status  (1-death,0-survival)

tag: gender  (1-male,2-female)

tag: age (years)

tag: stage  (1-stage i,2-stage ii,3-stage iii,4-stage iv)


title: Steer ID# 412 High fat diet, visceral fat

city: Edmonton

first: Josue

middle: Moura

last: Romao

state: Alberta

address: 116 St. and 85 Ave.

department: AFNS

institute: University of Alberta

description:
Sample name: 412KF
Raw data file:
253020810005_201012091619_S01_miRNA_107_Sep09_2_4.txt

hyb_protocol: The labeled RNA was hybridized with array slides with hybridization buffer and 10X GE blocking agent, and were incubated at 55ºC for ~20 hours. Finally, the arrays were washed with GE wash buffers.

scan_protocol: The arrays were scanned at 5 μM resolution on an Agilent G2565CA High Resolution Scanner (Agilent Technologies). Data was processed through Agilent’s Feature Extraction software version 10.7.3.1  using the protocol miRNA_107_Sep09

data_processing: The data was normalized to the 75th percentile using GeneSpring GX 11.5 (Agilent Technologies)

organism: Bos taurus

source_name: Visceral fat (perirenal fat), High fat diet

label_protocol: Total RNA (100 ng/sample) was firstly labeled with the AGILENT miRNA Complete Labeling and Hyb Kit (Version 2.1) by dephosphorylation with Calf Intestinal Phosphatase followed by denaturing and ligation with Cyanine3-pCp to the 3’ end.

extract_protocol: Total RNA extraction was performed by homogenizing the fat tissue samples with TRIZOL® (TRI reagent, Invitrogen, Carlsbad, CA, USA) following the manufactures instructions for samples with high fat content.

tag: diet

value: High fat diet

value: Visceral fat


title: Primary Breast Tumor brain metastasis 220234

tag: menopausal status (1=pre, 2=post)

tag: type of cancer histology

tag: lobulare

tag: her2 fish

tag: induction chemotherapy (0=no, 1=yes)

tag: induction hormonal therapy with ta (0=no, 1=yes)

tag: induction hormonal therapy with ar (0=no, 1=yes)

tag: adjuvant chemotherapy (0=no, 1=yes)

tag: adjuvant hormonal therapy with tamox (0=no, 1=yes)

tag: adjuvant hormonal therapy with ia (0=no, 1=yes)

tag: brain metasteses  (0=no, 1=yes)

tag: date brain met diagnosis

tag: overall survival  (0=no, 1=yes)

tag: date of last information


title: microRNA profile of case NPC332475

tag: survival status  (1-death,0-survival)

tag: gender  (1-male,2-female)

tag: age (years)


title: CONTROL-4-1

tag: diagnosis

tag: cell type

tag: replicate


title: Primary Breast Tumor no brain metastasis 52000

tag: sentrix barcode

tag: tissue

tag: set

tag: date of birth

tag: menopausal status (1=pre, 2=post)

tag: type of cancer histology

tag: lobulare

tag: date of primary tumor diagnosis

tag: grading

tag: err

tag: pgr

tag: her2 ihc

tag: her2 fish

tag: adjuvant rtg therapy  (0=no, 1=yes)

tag: trastuzumab therapy (0=no, 1=yes)


title: Steer ID# 411 High fat diet, visceral fat

description:
Sample name: 411KF
Raw data file:
253020810005_201012091619_S01_miRNA_107_Sep09_2_3.txt

tag: diet


title: Steer ID# 303 High fat diet, visceral fat

description:
Sample name: 303KF
Raw data file:
253020810005_201012091619_S01_miRNA_107_Sep09_2_2.txt


title: microRNA profile of case NPC329998

tag: survival status  (1-death,0-survival)

tag: gender  (1-male,2-female)

tag: age (years)

tag: stage  (1-stage i,2-stage ii,3-stage iii,4-stage iv)


title: microRNA profile of case NPC329727


title: Steer ID# 302 High fat diet, visceral fat

description:
Sample name: 302KF
Raw data file:
253020810005_201012091619_S01_miRNA_107_Sep09_2_1.txt

tag: tissue


title: CONTROL-3-3

source_name: MSCs from healthy donor 3

tag: diagnosis

tag: cell type

tag: replicate


title: microRNA profile of case NPC330355


title: microRNA profile of case NPC328958


title: Steer ID# 204 High fat diet, visceral fat

description:
Sample name: 204KF
Raw data file:
253020810005_201012091619_S01_miRNA_107_Sep09_1_4.txt


title: CONTROL-3-2


title: CONTROL-2-1

source_name: MSCs from healthy donor 2


title: Steer ID# 109 High fat diet, visceral fat

description:
Sample name: 109KF
Raw data file:
253020810005_201012091619_S01_miRNA_107_Sep09_1_2.txt


title: Primary Breast Tumor brain metastasis 27069

tag: sentrix barcode

tag: set

tag: date of birth

tag: menopausal status (1=pre, 2=post)

tag: type of cancer histology

tag: lobulare

tag: date of primary tumor diagnosis

tag: induction chemotherapy (0=no, 1=yes)

tag: induction hormonal therapy with ta (0=no, 1=yes)

tag: induction hormonal therapy with ar (0=no, 1=yes)

tag: adjuvant chemotherapy (0=no, 1=yes)

tag: adjuvant hormonal therapy with tamox (0=no, 1=yes)

tag: adjuvant hormonal therapy with ia (0=no, 1=yes)

tag: brain metasteses  (0=no, 1=yes)

tag: date brain met diagnosis

tag: overall survival  (0=no, 1=yes)

tag: date of death


title: Primary Breast Tumor brain metastasis 25979

tag: sentrix barcode

tag: tissue

tag: grading

tag: err

tag: pgr

tag: her2 ihc

tag: her2 fish

tag: adjuvant rtg therapy  (0=no, 1=yes)

tag: trastuzumab therapy (0=no, 1=yes)


title: Primary Breast Tumor brain metastasis 18407

tag: set

tag: date of birth

tag: menopausal status (1=pre, 2=post)

tag: type of cancer histology

tag: lobulare

tag: date of primary tumor diagnosis

tag: induction chemotherapy (0=no, 1=yes)

tag: induction hormonal therapy with ta (0=no, 1=yes)

tag: induction hormonal therapy with ar (0=no, 1=yes)

tag: date of last information


title: Steer ID# 103 High fat diet, visceral fat

description:
Sample name: 103KF
Raw data file:
253020810005_201012091619_S01_miRNA_107_Sep09_1_1.txt

tag: diet

tag: tissue


title: CONTROL-2-2

tag: diagnosis

tag: cell type

tag: replicate


title: Steer ID# 202 High fat diet, visceral fat

description:
Sample name: 202KF
Raw data file:
253020810005_201012091619_S01_miRNA_107_Sep09_1_3.txt


title: CONTROL-2-3


title: microRNA profile of case NPC328647

tag: survival status  (1-death,0-survival)

tag: gender  (1-male,2-female)

tag: age (years)

tag: stage  (1-stage i,2-stage ii,3-stage iii,4-stage iv)


title: Primary Breast Tumor brain metastasis 26319

tag: sentrix barcode

tag: set

tag: date of birth

tag: menopausal status (1=pre, 2=post)

tag: grading

tag: err

tag: pgr

tag: her2 ihc

tag: her2 fish

tag: adjuvant chemotherapy (0=no, 1=yes)

tag: adjuvant hormonal therapy with tamox (0=no, 1=yes)

tag: adjuvant hormonal therapy with ia (0=no, 1=yes)

tag: adjuvant rtg therapy  (0=no, 1=yes)

tag: trastuzumab therapy (0=no, 1=yes)

tag: brain metasteses  (0=no, 1=yes)

tag: date brain met diagnosis

tag: overall survival  (0=no, 1=yes)

tag: date of death


title: Primary Breast Tumor brain metastasis 47834

tag: sentrix barcode

tag: tissue

tag: set

tag: type of cancer histology

tag: lobulare

tag: date of primary tumor diagnosis

tag: induction chemotherapy (0=no, 1=yes)

tag: induction hormonal therapy with ta (0=no, 1=yes)

tag: induction hormonal therapy with ar (0=no, 1=yes)

tag: date of last information


title: Primary Breast Tumor no brain metastasis 10058

tag: date of birth

tag: menopausal status (1=pre, 2=post)

tag: grading

tag: err

tag: pgr

tag: her2 ihc

tag: her2 fish

tag: adjuvant chemotherapy (0=no, 1=yes)

tag: adjuvant hormonal therapy with tamox (0=no, 1=yes)

tag: adjuvant hormonal therapy with ia (0=no, 1=yes)


title: microRNA profile of case NPC328887

tag: survival status  (1-death,0-survival)

tag: gender  (1-male,2-female)

tag: age (years)

tag: stage  (1-stage i,2-stage ii,3-stage iii,4-stage iv)


title: Primary Breast Tumor no brain metastasis 42224

tag: sentrix barcode

tag: tissue

tag: set

tag: type of cancer histology

tag: lobulare

tag: date of primary tumor diagnosis

tag: induction chemotherapy (0=no, 1=yes)

tag: induction hormonal therapy with ta (0=no, 1=yes)

tag: adjuvant rtg therapy  (0=no, 1=yes)

tag: trastuzumab therapy (0=no, 1=yes)

tag: brain metasteses  (0=no, 1=yes)

tag: overall survival  (0=no, 1=yes)

tag: date of death


title: CONTROL-1-2

source_name: MSCs from healthy donor 1

tag: diagnosis

tag: cell type

tag: replicate


title: CONTROL-3-1


title: CONTROL-1-3


title: CONTROL-1-1


title: Steer ID# 412 High fat diet, subcutaneous fat

description:
Sample name: 412BF
Raw data file:
253020810004_201012091611_S01_miRNA_107_Sep09_2_4.txt

source_name: Subcutaneous fat (backfat), High fat diet

tag: diet

value: Subcutaneous fat


title: microRNA profile of case NPC328504

tag: survival status  (1-death,0-survival)

tag: gender  (1-male,2-female)

tag: age (years)

tag: stage  (1-stage i,2-stage ii,3-stage iii,4-stage iv)


title: microRNA profile of case NPC327288


title: Steer ID# 411 High fat diet, subcutaneous fat

description:
Sample name: 411BF
Raw data file:
253020810004_201012091611_S01_miRNA_107_Sep09_2_3.txt

tag: tissue


title: microRNA profile of case NPC327006


title: microRNA profile of case NPC326862


title: microRNA profile of case NPC326973


title: microRNA profile of case NPC326976


title: microRNA profile of case NPC326721


title: Steer ID# 204 High fat diet, subcutaneous fat

description:
Sample name: 204BF
Raw data file:
253020810004_201012091611_S01_miRNA_107_Sep09_1_4.txt


title: UTI T2 biological rep3 [GU-21.CEL]

city: Gold Coast

first: Glen

middle: C

last: Ulett

state: QLD

address: Parklands Drive

department: School of Medical Science

country: Australia

institute: Griffith University

description:
GU-21.CEL
amplified into double-stranded cDNA with random hexamers tagged with a T7 promoter sequence

hyb_protocol: Hybridization was performed according to the manufacturers’ instructions

scan_protocol: GeneChips were scanned using the Affymetrix 3000 7G scanner

data_processing:
Raw microarray data were normalized using quantile normalization and summarized using RMA as implemented in the affy package in Bioconductor. Differentially expressed genes were identified by analyzing the data using the MAANOVA package (Wu et al., 2003) (http://www.bioconductor.org/packages/bioc/1.8/html/maanova.html)
RMA signal intensity; significant changes in gene expression identified using a shrinkage based t test together with permutation.  A false discovery rate (FDR) of 0.05 was used to generate the significant gene list

source_name: Bladder, 24h Infection

label_protocol: RNA that passed Bioanalyzer analysis was quantified and 100 ng used for cDNA synthesis. RNA-derived biotinylated sense-strand DNA was applied to the whole transcript Gene 1.0 ST Mouse Microarray and hybridization was performed according to the manufacturers’ instructions in an Affymetrix Fluidics Station 400.

growth_protocol: O/N LB culture of UPEC CFT073 at 37C was collected and concentrated into PBS by centrifugation and washes in PBS

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

treatment_protocol: Mice were catheterized using a sterile Teflon catheter and 40 microlitres of PBS containing 10^9 CFU was instilled transurethrally into the bladder. Whole bladders collected at 24h following infection

tag: Sex

value: female

tag: strain

tag: age

value: 10 wk


title: UTI T2 biological rep5 [GU-25.CEL]

description:
GU-25.CEL
amplified into double-stranded cDNA with random hexamers tagged with a T7 promoter sequence