title: shCD271, 1

status: Public on Nov 19 2013

city: Berlin

first: Christian

last: Regenbrecht

address: Chariteplatz 1

department: Tumor stem cells

institute: Charité University Medicine Berlin, Germany

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing:
Illumina raw data of BeadChip HumanHT-12V4 platform were summarized via the BeadStudio without normalization and background correction. Follow-up processing was done via the R/Bioconductor environment employing packages lumi, limma and q-value. Data were normalized with quantile normalization.
Genes were termed significantly differentially expressed when the average detection p-value of at least one case was < 0.05  the ratio was outside the interval [0.75,1.33], one of the p-values from limma test, Student's t-test, Welch test and Wilcoxon test was < 0.05. At least one of the q-values corresponding to one of these tests < 0.05.

source_name: melanoma cells_shCD271

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

growth_protocol: Cells were grown in Tumor-growth medium Quantum 263 in absence of serum supplemented with penecilin and streptomycin. Transfected cells were stably selected in presence of puromycine, 10 µg/ml.

extract_protocol: RNA isolation from frozen cell pellets was performed with the RNeasy Mini Kit (Qiagen,Germany), following the manufacturers protocol. Reverse transcription of 500 ng - 2.5 μg RNA was performed with SuperScript VILO cDNA synthesis kit (Invitrogen, Germany) and diluted to a final volume of 50 μl , followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser. RIN-values were in a range of 9.6 - 10.0

treatment_protocol: Cells were expandet under in vitro conditions

value: patient-derived malignant melanoma cells

tag: transfected with

value: CD271-targeting shRNA


title: EPN_848_1

status: Public on Aug 30 2013

type: RNA

city: Aurora

first: Lindsey

middle: M.

last: Hoffman

state: Colorado

address: 12800 East 19th Avenue

department: Pediatric Neuro-Oncology

country: USA

institute: University of Colorado Denver

description:
included_in_corresponding_manuscript:yes
Gene expression data from surgical tumor sample of ependymoma

hyb_protocol: Following fragmentation, 11.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

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

data_processing: Microarray .CEL file data was background corrected and normalized using the gcRMA algorithm, resulting in log 2 expression values. The Affymetrix HG-U133 plus 2 microarray contains 54,675 probe sets including multiple probe sets for the same gene. In order to reduce error associated with multiple testing we used only a single probe set for each gene that possessed the highest gcRMA expression level across all our samples. This filtered list of the best expressed probe sets contained 17,664 genes.

label: biotin

molecule: total RNA

organism: Homo sapiens

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

extract_protocol:
Tumor samples were snap frozen in liquid nitrogen or transferred to RNAlater immediately after surgical removal as part of patient care. All samples were collected with appropriate IRB approval (COM-IRB#95-500 and 09-0906 )
RNeasy (Qiagen) extraction of total RNA was performed according to the manufacturer's instructions.

tag: group

value: Primary

tag: tissue

value: brain tumor (ependymoma)


title: EPN_870_1


title: shRNA Control, 3

country: Germany

source_name: melanoma cells_shRNA control

tag: cell type

value: shRNA control plasmid


title: shRNA Control, 1


title: shCD271, 2


title: EPN_909_1


title: EPN_816_2

value: Recurrent


title: EPN_821_1


title: shCD271, 3


title: EPN_816_1


title: untransfected 2

source_name: melanoma cells_untransfected

value: none (mock control)


title: untransfected 1


title: shRNA Control, 2


title: EPN_770_1


title: EPN_758_1


title: EPN_790_1


title: EPN_930_1


title: EPN_781_1


title: EPN_534_1


title: EPN_727_1


title: EPN_459_1


title: EPN_321_1


title: PA-882

status: Public on Aug 25 2013

first: Andrew

middle: M

last: Donson

state: CO

department: Pediatrics

institute: CU Anschutz Medical Campus

description:
Gene expression data from surgical tumor sample of pilocytic astrocytoma
[collection protocol] Tumor samples were snap frozen in liquid nitrogen or transferred to RNAlater immediately after surgical removal as part of patient care. All samples were collected with appropriate IRB approval (COM-IRB#95-500 and 09-0906 )

data_processing: Microarray .CEL file data was background corrected and normalized using the gcRMA algorithm, resulting in log 2 expression values. The Affymetrix HG-U133 plus 2 microarray contains 54,675 probe sets including multiple probe sets for the same gene. In order to reduce error associated with multiple testing we used only a single probe set for each gene that possessed the highest gcRMA expression level across all our samples. This filtered list of the best expressed probe sets contained 21,050 genes.

source_name: brain tumor (pilocytic astrocytoma)

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

tag: disease state

value: brain tumor

value: pilocytic astrocytoma


title: EPN_318_1


title: PA-855


title: EPN_319_1


title: NORMAL-514-Parietal

description:
Gene expression data from surgical tumor sample of normal brain
[collection protocol] Tumor samples were snap frozen in liquid nitrogen or transferred to RNAlater immediately after surgical removal as part of patient care. All samples were collected with appropriate IRB approval (COM-IRB#95-500 and 09-0906 )

source_name: normal brain (parietal lobe of cerebral cortex)

value: normal

value: parietal lobe of cerebral cortex


title: NORMAL-514-Thal

source_name: normal brain (thalamus)

value: thalamus


title: NORMAL-605-Occipital

source_name: normal brain (occipital lobe of cerebral cortex)

value: occipital lobe of cerebral cortex


title: PA-879


title: PA-748


title: untransfected 3


title: EPN-306

description:
Gene expression data from surgical tumor sample of ependymoma
[collection protocol] Tumor samples were snap frozen in liquid nitrogen or transferred to RNAlater immediately after surgical removal as part of patient care. All samples were collected with appropriate IRB approval (COM-IRB#95-500 and 09-0906 )

source_name: brain tumor (ependymoma)

value: ependymoma


title: GBM-668

description:
Gene expression data from surgical tumor sample of glioblastoma
[collection protocol] Tumor samples were snap frozen in liquid nitrogen or transferred to RNAlater immediately after surgical removal as part of patient care. All samples were collected with appropriate IRB approval (COM-IRB#95-500 and 09-0906 )

source_name: brain tumor (glioblastoma)

value: glioblastoma


title: EPN-881


title: NORMAL-514-Medulla

source_name: normal brain (medulla)

value: medulla


title: EPN-218


title: NORMAL-605-Parietal


title: PA-784


title: NORMAL-514-Midbrain

source_name: normal brain (midbrain)

value: midbrain


title: NORMAL-514-Occipital


title: Blood_OJcontrol_T2_S56

status: Public on Jul 25 2013

city: Oklahoma City

first: Dennis

last: Burian

state: OK

address: 6500 S. MacArthur Blvd., AAM610

department: Aviation Medicine

institute: Federal Aviation Administration

hyb_protocol: Arrays were hybridized for 18 hours at 45 deg C at 60 rpm in a GeneChip Hybridization Oven model 640 (Affymetric, Inc.). Fluidics protocol FS450_0004 was used with the GeneChip Fluidics Station model 450 to wash the arrays.

scan_protocol: Scanning done on a GeneChip Laser Scanner model 3000 with system running GCOS version 1.4.

data_processing: GCOS report derived with TGT Value set at 500. The ethanol data was imported as CEL files into S+ArrayAnalyzer™ (version 2.1.1). Tools available in ArrayAnalyzer were used to assess data quality at the chip level. Background subtraction and summarization was done with RMA [Irizarry, 2003] and GCRMA, and the summarized data was quantile normalized [Bolstad, 2003].  RMA summarized data was filtered for log2 (RMA expression) >6 in at least six chips; GCRMA summarized data was filtered for log2 (GCRMA expression) >5.  Each list was further filtered for a fold change in at least one pairwise comparison greater than 1.25. The Local Pooled Error (LPE T-test) [Jain, 2003] was used for differential expression testing across all possible pairwise timepoint comparisons. The False Discovery Rate (FDR) was controlled by implementation of the Benjamini and Hochberg correction [Benjamini, 1995]. Statistically significant genes (p<0.05) from the ten pairwise timepoint comparisons from both the RMA and GCRMA summarized data were combined into one list. A second list of significant genes was generated using the application, EDGE (Storey, 2007). RMA summarized data filtered for expression as above was used for input. The resulting list, ranked by Q-value, was filtered for a fold change in at least one pairwise comparison greater than 1.25.

source_name: whole blood, OJ time 2

label_protocol: For the OJcontrol samples 50 ng total RNA was both reverse transcribed and amplified using the Ovation RNA amplification System V2 (Nugen Technologies). Microarray template material was fragmented and biotin labeled using the FL-Ovation cDNA Biotin Module V2 (Nugen Technologies, Inc.). For the alcohol experimental samples 50 ng total RNA was reverse transcribed and amplified using the 3' IVT one-cycle kit (Affymetrix), fragmented and biotin labeled using the GeneChip IVT labeling kit (Affymetrix).

extract_protocol: Total RNA was extracted using the protocol provided with the Paxgene tubeswith the optional on-column DNase treatment

treatment_protocol: Blood was pulled directly into Paxgene tubes

tag: gender

value: male

value: whole blood

tag: intervention

value: OJ time 2


title: Blood_OJcontrol_T4_S56

source_name: whole blood, OJ time 4

value: OJ time 4


title: EPN-242


title: US 175

status: Public on Aug 01 2014

city: Milano

first: Elena

last: Landoni

address: Via Vanzetti 5

country: Italy

institute: Fondazione IRCCS Istituto Nazionale dei Tumori

description: miRNA profile of archival plasma sample

hyb_protocol: Hybridization for 20 h at 55 °C on SurePrint G3 Human v16 miRNA 8x60K microarrays (G4870A) designed on miRBase 16.0 from Agilent Technologies. The arrays were washed in Agilent GE Wash Buffers, following the manufacturer’s instructions

scan_protocol: All slides were immediately scanned at 2 mm resolution using an Agilent DNA microarray scanner

data_processing: The resulting images were analyzed using Agilent’s Feature Extraction software v10.7. In the employed platform, each miRNA is targeted by one to 4 different probes and each probe is spotted 10 to 40 times on the array. Then, the total gene signal for each miRNA was obtained by summing the probe signals derived using the Agilent Feature Extraction software. Using this software, each probe is defined detected if its value is greater than 3 times its standard error, and each miRNA is defined as detected if at least one of the probes is detected. Summarized data were log2 transformed

source_name: plasma

label_protocol: 2.5 µl of total RNA was dephosphorylated at 37°C for 30 min with calf intestinal phosphatase and denatured using 100% DMSO at 100°C for  5 min, labeled with pCp-Cy3 using T4 ligase by incubation at 16°C for 1 hour

growth_protocol: Plasma samples used in this study belong to the human plasma collection of the Fenretinide Breast Cancer Prevention Trial and RNA was extracted from 350 µl of sample.

extract_protocol: Total RNA was extracted from plasma using the commercial column-based system Qiagen miRNeasy® Mini Kit (Qiagen, Valencia, CA, USA), slightly modified by Exiqon (Vedbaek, Denmark. The eluate was digested using 1 u/µl heparinase I (Sigma-Aldrich, St. Luis, MO, USA), in the presence of an RNase inhibitor, (RNAsin; Promega, Madison, WI, USA) for 1 hour at room temperature, and RNA was stored at −80 °C.

value: plasma

tag: plasmaid

tag: drawing year

tag: age at drawing

tag: time from surgery

tag: hemolysis score (hs)

tag: hs class

value: no hemolysis


title: Blood_OJcontrol_T5_S56

source_name: whole blood, OJ time 5

value: OJ time 5


title: Blood_OJcontrol_T4_S54


title: Blood_OJcontrol_T3_S56

source_name: whole blood, OJ time 3

value: OJ time 3


title: Blood_OJcontrol_T2_S53


title: Blood_OJcontrol_T3_S54


title: Blood_OJcontrol_T4_S53


title: Blood_OJcontrol_T5_S52


title: Blood_OJcontrol_T1_S53

source_name: whole blood, OJ time 1

value: OJ time 1


title: Blood_OJcontrol_T1_S56


title: Blood_OJcontrol_T1_S54


title: Blood_OJcontrol_T3_S52


title: Blood_OJcontrol_T4_S51


title: Blood_OJcontrol_T2_S54


title: Blood_OJcontrol_T1_S52


title: Blood_OJcontrol_T3_S53


title: Blood_OJcontrol_T5_S53


title: Blood_OJcontrol_T2_S51


title: Blood_OJcontrol_T1_S51


title: Blood_alcohol_T3_S8

source_name: whole blood, BAC 0.08%


title: Blood_alcohol_T2_S8

source_name: whole blood, BAC 0.04%rising

value: BAC 0.04%rising


title: Blood_OJcontrol_T5_S51


title: Blood_alcohol_T4_S8

source_name: whole blood, BAC 0.04%declining

value: BAC 0.04%declining


title: Blood_OJcontrol_T4_S52


title: Blood_alcohol_T3_S19


title: Blood_alcohol_T4_S19


title: Blood_alcohol_T1_S8

source_name: whole blood, BAC 0%

value: BAC 0%


title: Blood_OJcontrol_T2_S52


title: Blood_alcohol_T5_S8

source_name: whole blood, BAC 0.02%declining

value: BAC 0.02%declining


title: Blood_alcohol_T5_S19


title: Blood_alcohol_T1_S19


title: Blood_alcohol_T5_S18


title: Blood_alcohol_T3_S18


title: Blood_alcohol_T2_S19


title: Blood_alcohol_T2_S18


title: Blood_OJcontrol_T3_S51


title: Blood_alcohol_T5_S17


title: ∆ackA pta_FMC_rep.5

status: Public on May 11 2013

city: Busan

first: Jeong Nam

last: Kim

address: Biology Building 402, Busandaehang-ro, 63beon-gil 2, Geumjeong-gu

department: Microbiology

country: South Korea

institute: Pusan National University

hyb_protocol: The generated cDNA was coupled to Cy3 or Cy5 dye (Amersham Biosciences) according to manufacturer's protocol.

scan_protocol: The array slides were scanned on a GenePix 4400A Microarray Scanner. Array data acquisition was performed using TM4 Spotfinder v3.2.1 (http://www.tm4.org/spotfinder.html).

data_processing: TM4 MIDAS v2.22 software was used: LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. IA and IB columns in *mev files correspond to 'Cy3' and 'Cy5' data columns, respectively.

organism: Streptococcus mutans UA159

source_name: Wild-Type, grown in FMC media supplemented with 25 mM glucose until 0.4 optical density at 600 nm

label_protocol: 2 µg of total RNA were primed with 2 µl of 50 ng Random Hexamers at 65°C for 5 min, then reversed transcribed at 42°C for overnight in the presence of 400 U SuperScript III Reverse Transcriptase (Invitrogen), 500 µM each dATP, dCTP, dGTP, 200 µM dTTP, 1 mM amino allyl-modified dUTP (Sigma), 0.01 M dithiothreitol (DTT) (Sigma), and 40 U RNaseOut (Invitrogen).

growth_protocol: One condition experiment used, which all strains were grown in defined medum FMC supplemented with 25 mM Glucose.

extract_protocol: Total RNA extracted using RNeasy mini kit (QIAGEN) following manufacturer's instructions

tag: genotype

value: Wild-Type

source_name: ∆ackA pta mutant, grown in FMC media supplemented with 25 mM glucose until 0.4 optical density at 600 nm

value: ∆ackA pta mutant


title: Blood_alcohol_T3_S17


title: ∆ackA pta_FMC_rep.2


title: ∆ackA pta_FMC_rep.4


title: ∆ackA pta_FMC_rep.3


title: ∆ackA pta_FMC_rep.1


title: ∆ackA_FMC_rep.5

source_name: ∆ackA mutant, grown in FMC media supplemented with 25 mM glucose until 0.4 optical density at 600 nm

value: ∆ackA mutant


title: Blood_alcohol_T1_S17


title: ∆ackA_FMC_rep.4


title: ∆ackA_FMC_rep.3


title: ∆ackA_FMC_rep.1


title: Blood_alcohol_T5_S15


title: Blood_alcohol_T3_S13


title: Blood_alcohol_T4_S17


title: Blood_alcohol_T1_S13


title: Blood_alcohol_T3_S15


title: Blood_alcohol_T2_S17


title: Blood_alcohol_T5_S13


title: Blood_alcohol_T1_S18


title: Blood_alcohol_T2_S13


title: Blood_alcohol_T2_S15


title: ∆ackA_FMC_rep.2


title: Blood_alcohol_T4_S15


title: Blood_alcohol_T1_S15


title: Blood_alcohol_T4_S13


title: PNET, ID00776

status: Public on Jan 21 2013

first: Diane

middle: K

last: Birks

department: Neurosurgery

institute: University of Colorado, Denver - Anschutz Medical Campus

hyb_protocol: Standard Affymetrix procedure.

scan_protocol: Standard Affymetrix procedure.

data_processing: Data were background corrected and normalized using gcRMA (as implemented in Bioconductor).

source_name: brain tumor, primitive neuroectodermal tumor

label_protocol: For most samples, five micrograms of total RNA was reverse-transcribed using a T7-(dT) 24 oligomer and Superscript II Reverse Transcriptase (Invitrogen Corp., Carlsbad, CA). Subsequently, biotin-labeled cRNA was generated from the double-stranded cDNA template by in vitro transcription using T7 RNA polymerase and a BioArray High Yield RNA Transcript Labeling Kit (Enzo Diagnostics, Farmingdale, NY). Biotinylated cRNA (20 micrograms) was fragmented to an average size of 35 to 200 bases with fragmentation buffer.  For a few samples, limited amount of starting RNA precluded use of this protocol. Instead, RNA was prepared using the Ambion Message Amp Premier RNA Amplification Kit (Applied Biosystems) according to manufacturer's directions, using a starting amount of 400 nanograms of RNA.

growth_protocol: All samples were collected at time of surgery.

extract_protocol: RNA was extracted from each sample using an RNeasy or DNA/RNA AllPrep kit (Qiagen) according to the manufacturer’s directions.

value: primitive neuroectodermal tumor


title: PNET, ID00777


title: ATRT, ID00880

description: brain tumor, atypical teratoid / rhabdoid tumor

hyb_protocol: Standard Affymetrix procedure

scan_protocol: Standard Affymetrix procedure

label_protocol: For most samples, five micrograms of total RNA was reverse-transcribed using a T7-(dT) 24 oligomer and Superscript II Reverse Transcriptase (Invitrogen Corp., Carlsbad, CA). Subsequently, biotin-labeled cRNA was generated from the double-stranded cDNA template by in vitro transcription using T7 RNA polymerase and a BioArray High Yield RNA Transcript Labeling Kit (Enzo Diagnostics, Farmingdale, NY). Biotinylated cRNA (20 micrograms) was fragmented to an average size of 35 to 200 bases with fragmentation buffer. For a few samples, limited amount of starting RNA precluded use of this protocol. Instead, RNA was prepared using the Ambion Message Amp Premier RNA Amplification Kit (Applied Biosystems) according to manufacturer's directions, using a starting amount of 400 nanograms of RNA.

growth_protocol: All samples were collected at time of surgery

extract_protocol: RNA was extracted from each sample using an RNeasy or DNA/RNA AllPrep kit (Qiagen) according to the manufacturer’s directions

value: atypical teratoid / rhabdoid tumor


title: Blood_OJcontrol_T5_S54

value: male

value: whole blood


title: ATRT, ID00818

source_name: brain tumor, atypical teratoid / rhabdoid tumor


title: PNET, ID00536


title: PNET, ID00224


title: PNET, ID00178


title: PNET, ID00760


title: AT/RT, ID00515

source_name: brain tumor, AT/RT


title: PNET, ID00079


title: AT/RT, ID90005


title: AT/RT, ID90004


title: AT/RT, ID00605


title: PNET, ID00599


title: PNET, ID00383


title: GBM, ID00678

source_name: brain tumor, glioblastoma

value: glioblastoma


title: AT/RT, ID00663


title: AT/RT, ID90007


title: AT/RT, ID03161


title: AT/RT, ID00687


title: 1016-00014_LS

status: Public on Jul 26 2012

city: Spring House

first: K

last: Li

state: PA

address: 1400 McKean Road

institute: Janssen R&D

hyb_protocol: Following fragmentation, 11 microg of cRNA were hybridized for 16 hr at 45oC on a GeneChip HG U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: The data was normalized by GCRMA.

source_name: skin biopsy, LS

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

extract_protocol: Total RNA was isolated with Qiagen's RNeasy mini kit according to the manufacturer’s instructions.

treatment_protocol: For each patient, one 4-mm skin punch biopsy was collected from a lesion located on the trunk or extremities, with approximately 0.5 mm or more of induration and approximately 5 mm from the edge of the plaque, and another from a macroscopically normal non-lesion on a similar body area to the biopsy plaque (i.e. arm, arm or leg, leg).  Biopsies were kept frozen at -80oC until RNA preparation.

tag: subject

value: moderate-to-severe psoriasis

value: skin

tag: biopsy type

value: psoriasis lesion (LS)


title: 2012-00023_NL

source_name: skin biopsy, NL

value: non-lesion (NL)


title: 1025-00005_NL


title: 2016-00020_LS


title: 1006-00005_NL


title: 2012-00008_NL


title: 2016-00026_NL


title: 1016-00011_LS


title: 1022-00017_NL


title: 1022-00024_LS


title: 1022-00024_NL


title: 2012-00008_LS


title: 2016-00009_LS


title: 2016-00001_NL


title: 1025-00005_LS


title: 1022-00017_LS


title: 1022-00021_NL


title: 1016-00011_NL


title: 2016-00026_LS


title: 2016-00009_NL


title: 2015-00007_LS


title: 2012-00023_LS


title: 1006-00005_LS


title: 2016-00035_LS


title: 2015-00007_NL


title: 1022-00021_LS


title: 2016-00020_NL


title: 2016-00035_NL


title: 2016-00001_LS


title: 1016-00014_NL


title: 2016-00019_LS


title: 1016-00017_LS


title: 1012-00003_LS


title: 2016-00019_NL


title: 1012-00004_NL


title: 1019-00015_LS


title: 1019-00015_NL


title: 2012-00031_NL


title: 1012-00005_LS


title: 1022-00004_LS


title: 1012-00005_NL


title: 1019-00016_LS


title: 1012-00003_NL


title: 1006-00002_NL


title: 1019-00008_LS


title: 2012-00036_LS


title: 2016-00008_LS


title: 1019-00010_NL


title: 1006-00002_LS


title: 2012-00036_NL


title: 1016-00017_NL


title: 1012-00004_LS


title: 1019-00008_NL


title: 2016-00008_NL


title: 2012-00031_LS


title: 1022-00002_LS


title: 1022-00004_NL


title: 1022-00025_LS


title: 1022-00025_NL


title: 1019-00016_NL


title: 2015-00005_LS


title: 1022-00027_LS


title: 2015-00005_NL


title: 2015-00001_LS


title: 2015-00001_NL


title: 1016-00001_NL


title: 1022-00020_LS


title: 1022-00009_LS


title: 2012-00042_LS


title: 1016-00001_LS


title: 1006-00004_NL


title: 2016-00025_NL


title: 1022-00016_LS


title: 1025-00002_NL


title: 1022-00001_NL


title: 1022-00002_NL


title: 2016-00025_LS


title: 1019-00003_NL


title: 1019-00003_LS


title: 1006-00004_LS


title: 1022-00020_NL


title: 1016-00008_LS


title: 1016-00008_NL


title: 1022-00016_NL


title: 1022-00001_LS


title: 2016-00006_LS


title: 1025-00002_LS


title: 2012-00042_NL


title: 1022-00009_NL


title: 1012-00007_LS


title: 1012-00007_NL


title: 2016-00006_NL


title: 1012-00001_LS


title: 1016-00003_LS


title: 1019-00007_NL


title: 1016-00003_NL


title: 1022-00012_NL


title: 1012-00001_NL


title: 1019-00009_LS


title: 2015-00002_NL


title: 1019-00009_NL


title: 1022-00003_LS


title: 1022-00003_NL


title: 2015-00002_LS


title: 1019-00007_LS


title: 2012-00019_NL


title: 1022-00005_NL


title: 2012-00038_LS


title: 1012-00008_LS


title: 2012-00038_NL


title: 2015-00014_NL


title: 1022-00012_LS


title: 2015-00012_LS


title: 2012-00019_LS


title: 1025-00008_LS


title: 2015-00014_LS


title: 1012-00008_NL


title: 2015-00012_NL


title: 2016-00018_LS


title: 1019-00010_LS


title: 1025-00008_NL


title: 2016-00018_NL


title: 1022-00005_LS


title: 1012-00002_LS


title: 1019-00013_LS


title: TM73

status: Public on Mar 09 2012

city: Milan

first: Loris

last: De Cecco

address: via Venezian 1

institute: IRCSS Istituto Nazionale Tumori

hyb_protocol: Fluorescently labelled cDNA PCR products were hybridized to the Illumina Sentrix BeadChip according to the protocols provided by the manufacturer.

data_processing: Array data export processing and analysis was performed using Illumina BeadStudio v3.1.3 (Gene Expression Module v3.3.8). The data were normalised using quantile normalisation.

source_name: ovarian cancer

label_protocol: Biotinylated cDNA were prepared from 500 ng total RNA using the high-throughput Gene expression profiling, the DASL Assay (cDNA-mediated annealing, selection, extension and ligation)

extract_protocol: Total RNA for test set was isolated by polling and processing four scalpel-scraped 20mm slices using the RecoverAll Total Nucleic Acid Isolation kit (Ambion) according to the supplied protocol. Quantity was assessed using a NanoDrop ND-100 Spectrophotometer

tag: age

tag: histotype

value: serous

tag: Stage

value: IV

tag: grading

tag: debulking

value: mRD

tag: therapy code

value: P

tag: end point

value: late

tag: ttr code

tag: ttr (months)

tag: os code

tag: overall survival (months)


title: TM78

value: III


title: TM74

value: endometrioid

value: PT


title: TM85

value: undifferentiated

value: GRD


title: TM83

value: early


title: TM77


title: TM71


title: TM80


title: TM81


title: TM84


title: TM69

value: NED


title: TM68


title: TM75


title: TM72


title: TM82


title: TM66


title: 1019-00001_NL

tag: disease state

tag: tissue


title: TM70


title: 1019-00001_LS


title: TM79


title: TM65


title: 1022-00027_NL


title: TM61


title: TM63


title: TM67


title: TM64


title: TM59


title: TM56


title: TM57


title: TM58


title: TM51

label_protocol: Biotinylated cDNA were prepared from 750 ng total RNA using the high-throughput Gene expression profiling, the DASL Assay (cDNA-mediated annealing, selection, extension and ligation)

extract_protocol: For total RNA extraction, approximately 100 mg of frozen tissue was homogenized using a bench-top homogenizer (MM200, Retsch, Germany) in 1 mL of TRIzol Reagent (Invitrogen). Subsequent miRNA extraction was performed using the miRNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions.


title: TM55


title: TM52


title: TM53

description: Progression during treatment.


title: TM49


title: TM50


title: TM62


title: TM42


title: TM43

value: clear cells


title: TM45

description: Progression during treatment.


title: TM46


title: TM47


title: TM48


title: TM44


title: TM40


title: TM37


title: TM39


title: TM41


title: TM38


title: TM54


title: TM36

value: mixed


title: 1012-00002_NL

value: moderate-to-severe psoriasis

value: skin


title: TM60


title: TM35


title: TM31

description: Progression during treatment.


title: TM32

value: endo


title: TM33

value: serous


title: TM30


title: TM28


title: TM21

value: IV


title: TM19


title: TM24


title: TM23


title: TM20


title: TM25


title: TM26


title: TM22

value: mRD


title: TM29


title: TM18


title: TM17

value: mullerian

value: P


title: TM16

description: Progression during treatment.

value: III


title: TM14

value: late


title: TM12

value: PT


title: TM13


title: TM10

value: undifferentiated


title: TM11

value: GRD


title: TM27

value: early


title: TM15


title: TM08


title: TM07

description: Progression during treatment.


title: TM34

value: NED


title: TM09


title: TM05


title: TM06


title: TM03


title: TM01


title: 1019-00013_NL

value: non-lesion (NL)


title: TM04

description: Progression during treatment.


title: TM02


title: Cervical tumor biopsy, P-360

status: Public on Jul 19 2011

city: Oslo

first: Heidi

last: Lyng

address: Montebello

department: Department of Radiation Biology

country: Norway

institute: Oslo University Hospital

description:
P-360
Validation cohort

data_processing: The data were normalised using quantile normalisation in BeadStudio 3.1.3.0

source_name: Cervical tumor

label_protocol: Biotinylated cRNA were prepared according to the standard Illumina protocol

growth_protocol: 1-4 tumor samples wer collected from each patient at the time of diagnosis

extract_protocol: RNA was extracted with Trizol reagent, followed by double precipitation with isopropanol and final precipitation with 5M lithium chloride. RNA from different biopsies of the same tumor was pooled. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: The samples were immediately snap-frozen in liquid nitrogen and stored at -80 C until used for analysis. Biopsies with more than 50% tumor cells in HE stained sections from the central part of the specimen were used further.

tag: cohort (gse36562 study)

value: Validation cohort

tag: hypoxia score

value: Low

value: cervical tumor

tag: figo stage

tag: histology

value: Squamous cell carcinoma

tag: cohort

tag: cohort (gse38964 study)

tag: 3p status

value: Not determined


title: Cervical tumor biopsy, P-363

description:
P-363
Validation cohort


title: Cervical tumor biopsy, P-343

description:
P-343
Validation cohort

value: High


title: Cervical tumor biopsy, P-347

description:
P-347
Validation cohort


title: Cervical tumor biopsy, P-351

description:
P-351
Validation cohort


title: TM76

tag: age

tag: histotype

value: serous

tag: Stage

tag: grading


title: Cervical tumor biopsy, P-333

description:
P-333
Validation cohort


title: Cervical tumor biopsy, P-332

description:
P-332
Validation cohort


title: Cervical tumor biopsy, P-371

description:
P-371
Validation cohort


title: Cervical tumor biopsy, P-390

description:
P-390
Validation cohort


title: Cervical tumor biopsy, P-368

description:
P-368
Validation cohort


title: Cervical tumor biopsy, P-387

description:
P-387
Validation cohort


title: Cervical tumor biopsy, P-350

description:
P-350
Validation cohort


title: Cervical tumor biopsy, P-355

description:
P-355
Validation cohort


title: Cervical tumor biopsy, P-391

description:
P-391
Validation cohort


title: Cervical tumor biopsy, P-392

description:
P-392
Validation cohort


title: Cervical tumor biopsy, P-340

description:
P-340
Validation cohort


title: Cervical tumor biopsy, P-376

description:
P-376
Validation cohort


title: Cervical tumor biopsy, P-352

description:
P-352
Validation cohort


title: Cervical tumor biopsy, P-374

description:
P-374
Validation cohort


title: Cervical tumor biopsy, P-303

description:
P-303
Validation cohort


title: Cervical tumor biopsy, P-325

description:
P-325
Validation cohort


title: Cervical tumor biopsy, P-361

description:
P-361
Validation cohort


title: Cervical tumor biopsy, P-349

description:
P-349
Validation cohort


title: Cervical tumor biopsy, P-389

description:
P-389
Validation cohort


title: Cervical tumor biopsy, P-326

description:
P-326
Validation cohort


title: Cervical tumor biopsy, P-346

description:
P-346
Validation cohort


title: Cervical tumor biopsy, P-384

description:
P-384
Validation cohort


title: Cervical tumor biopsy, P-372

description:
P-372
Validation cohort


title: Cervical tumor biopsy, P-331

description:
P-331
Validation cohort


title: Cervical tumor biopsy, P-244

description:
Basic cohort
P-244

value: basic cohort

tag: lymph node status (gse38433 study)


title: Cervical tumor biopsy, P-240

description:
Basic cohort
P-240


title: Cervical tumor biopsy, P-284

description:
Basic cohort
P-284


title: Cervical tumor biopsy, P-288

description:
Basic cohort
P-288


title: Cervical tumor biopsy, P-302

description:
Basic cohort
P-302


title: Cervical tumor biopsy, P-227

description:
P-227
Validation cohort


title: Cervical tumor biopsy, P-294

description:
Basic cohort
P-294


title: Cervical tumor biopsy, P-290

description:
Basic cohort
P-290


title: Cervical tumor biopsy, P-283

description:
Basic cohort
P-283


title: Cervical tumor biopsy, P-279

description:
Basic cohort
P-279


title: Cervical tumor biopsy, P-231

description:
Basic cohort
P-231


title: Cervical tumor biopsy, P-281

description:
Basic cohort
P-281


title: Cervical tumor biopsy, P-228

description:
Basic cohort
P-228


title: Cervical tumor biopsy, P-235

description:
Basic cohort
P-235


title: Cervical tumor biopsy, P-278

description:
Basic cohort
P-278


title: Cervical tumor biopsy, P-239

description:
Basic cohort
P-239


title: Cervical tumor biopsy, P-272

description:
Basic cohort
P-272


title: Cervical tumor biopsy, P-258

description:
Basic cohort
P-258


title: Cervical tumor biopsy, P-236

description:
Basic cohort
P-236


title: Cervical tumor biopsy, P-215

description:
Basic cohort
P-215

hyb_protocol: The samples were hybridized to the arrays at 58oC overnight, using the standard Illumina hybridization protocol.

scan_protocol: Scanning was performed with an Illumina BeadArray reader, using the standard Illumina scanning protocol.

data_processing: The data were normalized using quantile normalization in J-Express.

source_name: Cervical tumor, 2B

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

growth_protocol: 1-4 tumor samples were collected from each patient at the time of diagnosis.

extract_protocol: RNA was extracted with Trizol reagent, followed by double precipitation with isopropanol and final precipitation with 5M lithium chloride. RNA from different biopsies of the same tumor was pooled. Quality control was performed with the Agilent Bioanalyzer.

treatment_protocol: The samples were immediately snap-frozen in liquid nitrogen and stored at -80oC until used for analysis. Biopsies with more than 50% tumor cells in HE stained sections from the central part of the specimen were used further.

value: Integrative cohort

value: Loss


title: Cervical tumor biopsy, P-174

description:
Basic cohort
P-174

source_name: Cervical tumor, 1B2


title: Cervical tumor biopsy, P-149

description:
Basic cohort
P-149

source_name: Cervical tumor, 4A

value: No loss


title: Cervical tumor biopsy, P-151

description:
Basic cohort
P-151

source_name: Cervical tumor, 3B


title: Cervical tumor biopsy, P-144

description:
P-144
Validation cohort


title: Cervical tumor biopsy, P-214

description:
Basic cohort
P-214


title: Cervical tumor biopsy, P-213

description:
Basic cohort
P-213


title: Cervical tumor biopsy, P-190

description:
Basic cohort
P-190


title: Cervical tumor biopsy, P-184

description:
Basic cohort
P-184


title: Cervical tumor biopsy, P-125

description:
Basic cohort
P-125


title: Cervical tumor biopsy, P-142

description:
Basic cohort
P-142


title: 6755

status: Public on Jul 19 2010

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

description: Cells: HeLa-Tet-Off (Clontech) stabily transfected with Flag-NIPP1m (point mutant with a disrupted PP1-docking motif, cell line m n°1)

hyb_protocol: 28 pmol Cy3 incorporated dye was fragmented and resuspended in hybridization buffer HI-RPM (Agilent Technologies). The arrays were hybridized in microarray hybridization chambers (Agilent Technologies) overnight at 65ºC, rpm=10 for 17 hours.

scan_protocol: After washing the slides were scanned with a DNA microarray scanner (Agilent Technologies) and images were processed with the Feature Extraction Software (Agilent Technologies).

data_processing: We use the Agilent processed signal values (i.e., feature gProcessedSignal) from Agilent Feature Extraction software and compute log2-intensities.  We remove Agilent control probes, as well as probes with signals below background on all arrays (absent spots). To decide whether a signal is significantly above background, we use the feature gIsPosAndSignif, also provided by the Agilent software. In case of multiple probes for the same Agilent ID, log2-intensities are averaged.

label_protocol: 1µg of sample was spiked with a set of 10 positive control transcripts (Agilent Technologies), converted to double stranded cDNA in a reverse transcription reaction, amplified and labeled with Cy3 in an in vitro transcription reaction according to the manufacturer's protocol (Agilent Technologies).

extract_protocol: HTO_parental was cultured in Dulbecco's modified Eagle's medium (DMEM) supplemented with 10% FCS and 250 µg/ml geneticin, HTO_NIPP1wt and HTO_NIPP1m were cultured in Dulbecco's modified Eagle's medium (DMEM) supplemented with 10% FCS and 250 µg/ml geneticin, 200 µg/ml hygromycin and 50 ng/ml doxycyclin.  HTO_NIPP1wt and HTO_NIPP1m were cultured for 72 hours without doxycycline after which total RNA was isolated from all three cell lines using the Genelute Mammalian Total RNA Miniprep kit.

tag: cell line

value: HeLa-Tet-Off (Clontech) stably transfected with Flag-NIPP1m (point mutant with a disrupted PP1-docking motif, m n°1)


title: 6683

description: Cells: HeLa-Tet-Off (Clontech) stabily transfected with Flag-NIPP1 (cell line wt n°2)

source_name: HTO_NIPP1wt_cell line wt n°2_rep4

value: HeLa-Tet-Off (Clontech) stably transfected with Flag-NIPP1 (wt n°2)


title: Cervical tumor biopsy, P-188

description:
Basic cohort
P-188


title: 6679

description: Cells: HeLa-Tet-Off (Clontech) stabily transfected with Flag-NIPP1(cell line wt n°2)

source_name: HTO_NIPP1wt_cell line wt n°2_rep3


title: Cervical tumor biopsy, P-014

description:
Basic cohort
P-014


title: 6068

description: Cells: HeLa-Tet-Off (Clontech) stabily transfected with Flag-NIPP1 (cell line wt n°1)

source_name: HTO_NIPP1wt_cell line wt n°1_rep1

value: HeLa-Tet-Off (Clontech) stably transfected with Flag-NIPP1 (wt n°1)


title: 6070


title: Cervical tumor biopsy, P-148

description:
Basic cohort
P-148


title: 6681


title: 6074


title: 6072

description: Cells: HeLa-Tet-Off (Clontech) stabily transfected with Flag-NIPP1  (cell line wt n°1)

source_name: HTO_NIPP1wt_cell line wt n°1_rep2


title: Cervical tumor biopsy, P-120

description:
Basic cohort
P-120


title: Cervical tumor biopsy, P-083

description:
Basic cohort
P-083


title: Cervical tumor biopsy, P-042

description:
Basic cohort
P-042


title: Cervical tumor biopsy, P-024

description:
Basic cohort
P-024

value: DCE-MRI cohort


title: Cervical tumor biopsy, P-028

description:
Basic cohort
P-028


title: Cervical tumor biopsy, P-004

description:
Basic cohort
P-004


title: Cervical tumor biopsy, P-115

description:
Basic cohort
P-115


title: Cervical tumor biopsy, P-062

description:
Basic cohort
P-062


title: Buccal Cell Smoker 28 replicate B

status: Public on Mar 01 2010

hyb_protocol: Arrays were hybridized for 18 hours at 45 deg C at 60 rpm in a GeneChip Hybridization Oven model 640 (Affymetric, Inc.).  Fluidics protocol FS450_0004 was used with the GeneChip Fluidics Station model 450 to wash the arrays.

scan_protocol: Scanning was done on a GeneChip Laser Scanner model 3000 with system running GCOS version 1.4.

data_processing: GCOS (ver 1.4) report derived with TGT Value set at 100.  Bioconductor package AffyQCReport and ProbeLevelModeling was used for quality assessment. Summarized and quantile normalized data was generated using the application at the Automated Microarray Pipeline (http://compbio.dfci.harvard.edu/amp/).  Relative differential gene expression analysis comparing smokers to nonsmokers was performed with SAM, Rank Product Analysis, unsupervised hierarchiacal clustering and T-test using the packages available on the MultiExperiment Viewer, ver 4.3.01 with default settings.

source_name: buccal mucosa cells from swab, from both cheeks of smokers or nonsmokers

label_protocol: 20 ng total RNA was both reverse transcribed and amplified using the Ovation RNA amplificztion System V2 (Nugen Technologies). This template material was fragmented and biotin labeled using the FL-Ovation cDNA Biotin Module V2 (Nugen Technologies, Inc.).

extract_protocol: Total RNA was isolated from buccal samples using the Rneasy Micro Kit with modification as given in Spivack et al. Cancer Res. 2004, 64:6805 and in Kupfer et al submitted.

treatment_protocol: Buccal samples were taken using a sterile cytobrush plus with a 30 second brushing.  Immediately after sampling, each cytobrush was placed in a 2 ml micro-centrifuge containing 1 ml RNAlater.

tag: smoking status

value: smoker

tag: cell type

value: buccal mucosa cells


title: Buccal Cell Smoker 26 replicate A


title: Buccal Cell Smoker 26 replicate B


title: Buccal Cell Non-smoker 23 replicate B

value: non-smoker


title: Buccal Cell Non-smoker 24 replicate B


title: Buccal Cell Smoker 25 replicate B


title: Buccal Cell Smoker 11 replicate A

data_processing: GCOS (ver 1.4) report derived with TGT Value set at 100.  Bioconductor package AffyQCReport and ProbeLevelModeling was used for quality assessment. Summarized and quantile normalized data was generated using the application at the Automated Microarray Pipeline (http://compbio.dfci.harvard.edu/amp/).  Relative differential gene expression analysis comparing smokers to nonsmokers was performed with both SAM, Rank Product Analysis, unsupervised hierarchiacal clustering and T-test were performed using the packages available on the MultiExperiment Viewer, ver 4.3.01 with default settings.

label_protocol: 50 ng total RNA was both reverse transcribed and amplified using the Ovation RNA amplificztion System V2 (Nugen Technologies). This template material was fragmented and biotin labeled using the FL-Ovation cDNA Biotin Module V2 (Nugen Technologies, Inc.).


title: Buccal Cell Smoker 11 replicate B


title: Buccal Cell Non-smoker 24 replicate A


title: Buccal Cell Non-smoker 22 replicate A


title: Buccal Cell Smoker 28 replicate A


title: Buccal Cell Non-smoker 22 replicate B


title: Buccal Cell Smoker 27 replicate A


title: Buccal Cell Non-smoker 21 replicate B


title: Buccal Cell Non-smoker 21 replicate A


title: Buccal Cell Smoker 27 replicate B


title: Buccal Cell Non-smoker 12 replicate B


title: Buccal Cell Non-smoker 12 replicate A


title: alveolar macrophages, COPD 044

status: Public on Aug 10 2009

city: New York

first: Yael

last: Strulovici-Barel

state: NY

address: 1300 York Avenue

department: Department of Genetic Medicine

institute: Weill Cornell Medical College

hyb_protocol: Following fragmentation, 15 microg of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U133 Plus 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

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

source_name: alveolar macrophages obtained from bronchoalveolar lavage

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

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

tag: Sex

value: M

tag: ancestry

value: European

value: COPD, GOLD-I, 35 pack-years


title: alveolar macrophages, COPD 132

value: COPD, GOLD-I, 27 pack-years


title: alveolar macrophages, COPD 136

value: COPD, GOLD-I, 119 pack-years


title: alveolar macrophages, COPD 068

value: COPD, GOLD-II, 60 pack-years


title: alveolar macrophages, COPD 147

value: F

value: Hispanic

value: COPD, GOLD-I, 34.5 pack-years


title: alveolar macrophages, COPD 059

value: African

value: COPD, GOLD-II, 27 pack-years


title: alveolar macrophages, COPD 036

value: COPD, GOLD-I, 48 pack-years


title: alveolar macrophages, COPD 047

value: COPD, GOLD-III, 87 pack-years


title: alveolar macrophages, COPD 089

value: COPD, GOLD-II, 75 pack-years


title: alveolar macrophages, COPD 103

value: COPD, GOLD-I, 23 pack-years


title: alveolar macrophages, COPD 008

value: COPD, GOLD-I, 50 pack-years


title: alveolar macrophages, COPD 119

value: COPD, GOLD-I, 32.5 pack-years


title: Prostate tumor patient 57 (MicroRNA Array)

status: Public on Jul 01 2008

city: Bethesda

first: Robert

middle: Scott

last: Hudson

state: MD

address: National Cancer Institute Room Blgd.37/3044

department: NCI

institute: NIH

description: Race: African American, Smoking Status: Past, Gleason Sum: 7, PT Stage: 2, Extraprostatic Extension: None, Perineural Invasion: No, Seminal vesicle invasion: No, Are Surgical margins involved: All surgical margins are free of tumor, Angio lymphatic invasion:No

hyb_protocol: The chips were hybridized on Tecan HS 4800 hybridization station. Chips were pre-hybridized at 25C for 30 min in the buffer of 6x SSPE/ 30% formamide/ 1x Denhardt's solution. The chips were further hybridized with labeled target in 6x SSPE/ 30% formamide at 25C for 18 hr. Hybridization, post-hybridization washing in 0.75x TNT (Tris, sodium, Tween 20) (see PNAS) at 37C for 40 mins. The chips were stained by streptavidin-alexa647 (1:500) dilution in TNT for 30 mins. Post-staining washing in 1x TNT FOR 40 min. Rinse with water and spin dry.

scan_protocol: Arrays were scanned on the GenePix scanner and analyzed using the GenePix Pro software package.

data_processing: median-centralized normalized

source_name: Adenocarcinoma (NOS) of the prostate

label_protocol: Refer to Liu et al (PNAS 101: 9740-9744 (2004)). 5 ug of total RNA was labeled in reverse transcription at 37C for 90 mins by using biotin-labeled rand-octomer oligo primer. The RT reaction mix was further denatured by using 0.5 N NaOH / 1 mM EDTA at 65C for 15 mins and neutralized by 1 M Tris HCl pH 7.6. Biotin signal was detected with an Alexa 647-Streptavidin conjugate.

extract_protocol: TRIzol

tag: race

value: African American

value: Past

tag: gleason sum

tag: pt stage

tag: extraprostatic extension

tag: perineural invasion

value: No

tag: seminal vesicle invasion

tag: are surgical margins involved

value: All surgical margins are free of tumor

tag: angio lymphatic invasion


title: Prostate tumor patient 53 (MicroRNA Array)

description: Race: Caucasian, Smoking Status: Unknown, Gleason Sum: 7, PT Stage: 2, Extraprostatic Extension: None, Perineural Invasion: Yes, Seminal vesicle invasion: No, Are Surgical margins involved: Tumor focal at margin, Angio lymphatic invasion:No

value: Caucasian

value: Unknown

value: Yes

value: Tumor focal at margin


title: Prostate tumor patient 60 (MicroRNA Array)

description: Race: Caucasian, Smoking Status: Never, Gleason Sum: 7, PT Stage: 2, Extraprostatic Extension: None, Perineural Invasion: Yes, Seminal vesicle invasion: No, Are Surgical margins involved: Tumor focal at margin, Angio lymphatic invasion:No

value: Never


title: Prostate tumor patient 49 (MicroRNA Array)

description: Race: African American, Smoking Status: Unknown, Gleason Sum: 7, PT Stage: 2, Extraprostatic Extension: None, Perineural Invasion: Yes, Seminal vesicle invasion: No, Are Surgical margins involved: Tumor focal at margin, Angio lymphatic invasion:No


title: Prostate tumor patient 56 (MicroRNA Array)

description: Race: African American, Smoking Status: Never, Gleason Sum: 7, PT Stage: 3, Extraprostatic Extension: None, Perineural Invasion: Yes, Seminal vesicle invasion: Yes, Are Surgical margins involved: All surgical margins are free of tumor, Angio lymphatic invasion:No


title: Prostate tumor patient 48 (MicroRNA Array)

description: Race: African American, Smoking Status: Unknown, Gleason Sum: 7, PT Stage: 2, Extraprostatic Extension: None, Perineural Invasion: Yes, Seminal vesicle invasion: No, Are Surgical margins involved: All surgical margins are free of tumor, Angio lymphatic invasion:No


title: Prostate tumor patient 47 (MicroRNA Array)

description: Race: African American, Smoking Status: Past, Gleason Sum: 6, PT Stage: 2, Extraprostatic Extension: None, Perineural Invasion: No, Seminal vesicle invasion: No, Are Surgical margins involved: All surgical margins are free of tumor, Angio lymphatic invasion:No


title: Prostate tumor patient 42 (MicroRNA Array)

description: Race: Caucasian, Smoking Status: Past, Gleason Sum: 7, PT Stage: 2, Extraprostatic Extension: None, Perineural Invasion: Yes, Seminal vesicle invasion: No, Are Surgical margins involved: All surgical margins are free of tumor, Angio lymphatic invasion:No


title: Prostate tumor patient 41 (MicroRNA Array)


title: Prostate tumor patient 59 (MicroRNA Array)

description: Race: African American, Smoking Status: Current, Gleason Sum: 7, PT Stage: 2, Extraprostatic Extension: None, Perineural Invasion: Yes, Seminal vesicle invasion: No, Are Surgical margins involved: All surgical margins are free of tumor, Angio lymphatic invasion:No

value: Current


title: Prostate tumor patient 45 (MicroRNA Array)

description: Race: Caucasian, Smoking Status: Current, Gleason Sum: 7, PT Stage: 2, Extraprostatic Extension: None, Perineural Invasion: Yes, Seminal vesicle invasion: No, Are Surgical margins involved: All surgical margins are free of tumor, Angio lymphatic invasion:No


title: Prostate tumor patient 51 (MicroRNA Array)

description: Race: African American, Smoking Status: Past, Gleason Sum: 6, PT Stage: 2, Extraprostatic Extension: None, Perineural Invasion: Yes, Seminal vesicle invasion: No, Are Surgical margins involved: All surgical margins are free of tumor, Angio lymphatic invasion:No


title: Prostate tumor patient 58 (MicroRNA Array)

description: Race: African American, Smoking Status: Past, Gleason Sum: 7, PT Stage: 3, Extraprostatic Extension: None, Perineural Invasion: Yes, Seminal vesicle invasion: Yes, Are Surgical margins involved: Tumor focal at margin, Angio lymphatic invasion:Yes


title: Prostate tumor patient 61 (MicroRNA Array)

description: Race: African American, Smoking Status: Past, Gleason Sum: 7, PT Stage: 3, Extraprostatic Extension: Focal, Perineural Invasion: Yes, Seminal vesicle invasion: Yes, Are Surgical margins involved: Tumor focal at margin, Angio lymphatic invasion:No

value: Focal


title: Prostate tumor patient 38 (MicroRNA Array)

description: Race: Caucasian, Smoking Status: Unknown, Gleason Sum: 7, PT Stage: 3, Extraprostatic Extension: Established, Perineural Invasion: Yes, Seminal vesicle invasion: Yes, Are Surgical margins involved: Tumor focal at margin, Angio lymphatic invasion:No

value: Established


title: Prostate tumor patient 39 (MicroRNA Array)

description: Race: Caucasian, Smoking Status: Never, Gleason Sum: 7, PT Stage: 3, Extraprostatic Extension: Focal, Perineural Invasion: Yes, Seminal vesicle invasion: No, Are Surgical margins involved: All surgical margins are free of tumor, Angio lymphatic invasion:No


title: Prostate tumor patient 40 (MicroRNA Array)

description: Race: Caucasian, Smoking Status: Current, Gleason Sum: 7, PT Stage: 3, Extraprostatic Extension: Multifocal, Perineural Invasion: Yes, Seminal vesicle invasion: No, Are Surgical margins involved: Tumor focal at margin, Angio lymphatic invasion:No

value: Multifocal


title: Prostate tumor patient 33 (MicroRNA Array)


title: Prostate tumor patient 34 (MicroRNA Array)

description: Race: African American, Smoking Status: Past, Gleason Sum: 7, PT Stage: 3, Extraprostatic Extension: Multifocal, Perineural Invasion: Yes, Seminal vesicle invasion: No, Are Surgical margins involved: Tumor focal at margin, Angio lymphatic invasion:No


title: Prostate tumor patient 36 (MicroRNA Array)

description: Race: Caucasian, Smoking Status: Unknown, Gleason Sum: 7, PT Stage: 3, Extraprostatic Extension: Focal, Perineural Invasion: Yes, Seminal vesicle invasion: No, Are Surgical margins involved: All surgical margins are free of tumor, Angio lymphatic invasion:No


title: Prostate tumor patient 43 (MicroRNA Array)

description: Race: African American, Smoking Status: Current, Gleason Sum: 8, PT Stage: 3, Extraprostatic Extension: Established, Perineural Invasion: Yes, Seminal vesicle invasion: Yes, Are Surgical margins involved: Tumor focal at margin, Angio lymphatic invasion:No


title: Prostate tumor patient 32 (MicroRNA Array)

description: Race: African American, Smoking Status: Past, Gleason Sum: 9, PT Stage: 3, Extraprostatic Extension: Established, Perineural Invasion: Yes, Seminal vesicle invasion: No, Are Surgical margins involved: Tumor focal at margin, Angio lymphatic invasion:Yes


title: Prostate tumor patient 31 (MicroRNA Array)


title: Prostate tumor patient 37 (MicroRNA Array)

description: Race: African American, Smoking Status: Unknown, Gleason Sum: 7, PT Stage: 3, Extraprostatic Extension: None, Perineural Invasion: Yes, Seminal vesicle invasion: Yes, Are Surgical margins involved: All surgical margins are free of tumor, Angio lymphatic invasion:No


title: Prostate tumor patient 35 (MicroRNA Array)

description: Race: African American, Smoking Status: Unknown, Gleason Sum: 7, PT Stage: 3, Extraprostatic Extension: Multifocal, Perineural Invasion: Yes, Seminal vesicle invasion: No, Are Surgical margins involved: All surgical margins are free of tumor, Angio lymphatic invasion:No


title: Prostate tumor patient 30 (MicroRNA Array)

description: Race: African American, Smoking Status: Unknown, Gleason Sum: 7, PT Stage: 2, Extraprostatic Extension: None, Perineural Invasion: Yes, Seminal vesicle invasion: No, Are Surgical margins involved: All surgical margins are free of tumor, Angio lymphatic invasion:No


title: Prostate tumor patient 27 (MicroRNA Array)

description: Race: African American, Smoking Status: Past, Gleason Sum: 7, PT Stage: 2, Extraprostatic Extension: None, Perineural Invasion: Yes, Seminal vesicle invasion: No, Are Surgical margins involved: All surgical margins are free of tumor, Angio lymphatic invasion:No


title: Prostate tumor patient 29 (MicroRNA Array)

description: Race: African American, Smoking Status: Past, Gleason Sum: 7, PT Stage: 3, Extraprostatic Extension: None, Perineural Invasion: Yes, Seminal vesicle invasion: Yes, Are Surgical margins involved: All surgical margins are free of tumor, Angio lymphatic invasion:No


title: Prostate tumor patient 26 (MicroRNA Array)

description: Race: Caucasian, Smoking Status: Never, Gleason Sum: 6, PT Stage: 2, Extraprostatic Extension: None, Perineural Invasion: Yes, Seminal vesicle invasion: No, Are Surgical margins involved: All surgical margins are free of tumor, Angio lymphatic invasion:No


title: Prostate tumor patient 25 (MicroRNA Array)

description: Race: Caucasian, Smoking Status: Past, Gleason Sum: 6, PT Stage: 2, Extraprostatic Extension: None, Perineural Invasion: No, Seminal vesicle invasion: No, Are Surgical margins involved: All surgical margins are free of tumor, Angio lymphatic invasion:No


title: Prostate tumor patient 22 (MicroRNA Array)

description: Race: African American, Smoking Status: Never, Gleason Sum: 6, PT Stage: 3, Extraprostatic Extension: Focal, Perineural Invasion: Yes, Seminal vesicle invasion: No, Are Surgical margins involved: All surgical margins are free of tumor, Angio lymphatic invasion:No


title: Prostate tumor patient 23 (MicroRNA Array)

description: Race: Caucasian, Smoking Status: Never, Gleason Sum: 7, PT Stage: 2, Extraprostatic Extension: None, Perineural Invasion: Yes, Seminal vesicle invasion: No, Are Surgical margins involved: All surgical margins are free of tumor, Angio lymphatic invasion:No


title: Prostate tumor patient 16 (MicroRNA Array)

description: Race: African American, Smoking Status: Past, Gleason Sum: 7, PT Stage: 2, Extraprostatic Extension: None, Perineural Invasion: No, Seminal vesicle invasion: No, Are Surgical margins involved: All surgical margins are free of tumor, Angio lymphatic invasion:No


title: Prostate tumor patient 46 (MicroRNA Array)

description: Race: Caucasian, Smoking Status: Never, Gleason Sum: 7, PT Stage: 3, Extraprostatic Extension: Established, Perineural Invasion: Yes, Seminal vesicle invasion: No, Are Surgical margins involved: All surgical margins are free of tumor, Angio lymphatic invasion:No


title: Prostate tumor patient 18 (MicroRNA Array)

description: Race: Caucasian, Smoking Status: Unknown, Gleason Sum: 7, PT Stage: 3, Extraprostatic Extension: Focal, Perineural Invasion: Yes, Seminal vesicle invasion: No, Are Surgical margins involved: Tumor focal at margin, Angio lymphatic invasion:No

source_name: hr


title: Prostate tumor patient 21 (MicroRNA Array)

description: Race: African American, Smoking Status: Unknown, Gleason Sum: 7, PT Stage: 3, Extraprostatic Extension: Multifocal, Perineural Invasion: Yes, Seminal vesicle invasion: Yes, Are Surgical margins involved: Tumor focal at margin, Angio lymphatic invasion:No


title: Prostate tumor patient 24 (MicroRNA Array)

description: Race: Caucasian, Smoking Status: Unknown, Gleason Sum: 9, PT Stage: 3, Extraprostatic Extension: Focal, Perineural Invasion: Yes, Seminal vesicle invasion: No, Are Surgical margins involved: Tumor focal at margin, Angio lymphatic invasion:No


title: Prostate tumor patient 14 (MicroRNA Array)

description: Race: African American, Smoking Status: Unknown, Gleason Sum: 6, PT Stage: 2, Extraprostatic Extension: None, Perineural Invasion: No, Seminal vesicle invasion: No, Are Surgical margins involved: Tumor focal at margin, Angio lymphatic invasion:No


title: Prostate tumor patient 20 (MicroRNA Array)

description: Race: African American, Smoking Status: Current, Gleason Sum: 7, PT Stage: 3, Extraprostatic Extension: Focal, Perineural Invasion: Yes, Seminal vesicle invasion: No, Are Surgical margins involved: All surgical margins are free of tumor, Angio lymphatic invasion:No


title: Prostate tumor patient 28 (MicroRNA Array)

description: Race: Caucasian, Smoking Status: Unknown, Gleason Sum: 7, PT Stage: 2, Extraprostatic Extension: None, Perineural Invasion: Yes, Seminal vesicle invasion: No, Are Surgical margins involved: All surgical margins are free of tumor, Angio lymphatic invasion:No


title: Prostate tumor patient 15 (MicroRNA Array)

description: Race: African American, Smoking Status: Past, Gleason Sum: 6, PT Stage: 2, Extraprostatic Extension: None, Perineural Invasion: Yes, Seminal vesicle invasion: No, Are Surgical margins involved: All surgical margins are free of tumor, Angio lymphatic invasion:No


title: Prostate tumor patient 6 (MicroRNA Array)

description: Race: African American, Smoking Status: Never, Gleason Sum: 7, PT Stage: 2, Extraprostatic Extension: None, Perineural Invasion: Yes, Seminal vesicle invasion: No, Are Surgical margins involved: All surgical margins are free of tumor, Angio lymphatic invasion:No


title: Prostate tumor patient 10 (MicroRNA Array)

description: Race: African American, Smoking Status: Never, Gleason Sum: 7, PT Stage: 3, Extraprostatic Extension: Focal, Perineural Invasion: Yes, Seminal vesicle invasion: No, Are Surgical margins involved: Tumor focal at margin, Angio lymphatic invasion:No


title: Prostate tumor patient 17 (MicroRNA Array)

description: Race: Caucasian, Smoking Status: Never, Gleason Sum: 7, PT Stage: 3, Extraprostatic Extension: Focal, Perineural Invasion: Yes, Seminal vesicle invasion: No, Are Surgical margins involved: All surgical margins are free of tumor, Angio lymphatic invasion:No


title: Prostate tumor patient 12 (MicroRNA Array)

description: Race: African American, Smoking Status: Unknown, Gleason Sum: 6, PT Stage: 2, Extraprostatic Extension: None, Perineural Invasion: Yes, Seminal vesicle invasion: No, Are Surgical margins involved: Tumor focal at margin, Angio lymphatic invasion:No


title: Prostate tumor patient 5 (MicroRNA Array)

description: Race: Caucasian, Smoking Status: Never, Gleason Sum: 7, PT Stage: 2, Extraprostatic Extension: None, Perineural Invasion: Yes, Seminal vesicle invasion: No, Are Surgical margins involved: Tumor focal at margin, Angio lymphatic invasion:Yes


title: Prostate tumor patient 11 (MicroRNA Array)

description: Race: African American, Smoking Status: Unknown, Gleason Sum: 7, PT Stage: 3, Extraprostatic Extension: None, Perineural Invasion: Yes, Seminal vesicle invasion: Yes, Are Surgical margins involved: All surgical margins are free of tumor, Angio lymphatic invasion:No


title: Prostate tumor patient 3 (MicroRNA Array)

description: Race: African American, Smoking Status: Past, Gleason Sum: 6, PT Stage: 3, Extraprostatic Extension: Focal, Perineural Invasion: Yes, Seminal vesicle invasion: No, Are Surgical margins involved: Tumor widespread a surgical margins, Angio lymphatic invasion:No

value: Tumor widespread a surgical margins


title: Prostate tumor patient 7 (MicroRNA Array)

description: Race: Caucasian, Smoking Status: Past, Gleason Sum: 7, PT Stage: 2, Extraprostatic Extension: None, Perineural Invasion: Yes, Seminal vesicle invasion: No, Are Surgical margins involved: All surgical margins are free of tumor, Angio lymphatic invasion:No


title: Prostate tumor patient 4 (MicroRNA Array)

description: Race: Caucasian, Smoking Status: Past, Gleason Sum: 7, PT Stage: 2, Extraprostatic Extension: None, Perineural Invasion: Yes, Seminal vesicle invasion: No, Are Surgical margins involved: Tumor focal at margin, Angio lymphatic invasion:No


title: Prostate tumor patient 9 (MicroRNA Array)

description: Race: Caucasian, Smoking Status: Past, Gleason Sum: 6, PT Stage: 3, Extraprostatic Extension: Focal, Perineural Invasion: Yes, Seminal vesicle invasion: No, Are Surgical margins involved: Tumor widespread at margin, Angio lymphatic invasion:No

value: Tumor widespread at margin


title: Prostate tumor patient 8 (MicroRNA Array)

description: Race: Caucasian, Smoking Status: Never, Gleason Sum: 7, PT Stage: 2, Extraprostatic Extension: None, Perineural Invasion: No, Seminal vesicle invasion: No, Are Surgical margins involved: Tumor focal at margin, Angio lymphatic invasion:No


title: Prostate tumor patient 1 (MicroRNA Array)

description: Race: Caucasian, Smoking Status: Past, Gleason Sum: 7, PT Stage: 3, Extraprostatic Extension: Focal, Perineural Invasion: Yes, Seminal vesicle invasion: No, Are Surgical margins involved: Unknown, Angio lymphatic invasion:No


title: Prostate tumor patient 2 (MicroRNA Array)

description: Race: Caucasian, Smoking Status: Unknown, Gleason Sum: 6, PT Stage: 3, Extraprostatic Extension: Focal, Perineural Invasion: Yes, Seminal vesicle invasion: Yes, Are Surgical margins involved: All surgical margins are free of tumor, Angio lymphatic invasion:No


title: Surrounding normal prostate tissue patient 16 (HG-U133A 2.0 Array)

status: Public on Jan 01 2008

description: Race: African American, Smoking Status: Past, Gleason Sum: 7, PT Stage: 2, Extraprostatic Extension: None, Perineural Invasion: No, Seminal vesicle invasion: No, Are Surgical margins involved: All surgical margins are free of tumor, Angio lymphatic invasion: No

hyb_protocol: Standard Affy protocol

scan_protocol: Standard Affy protocol

source_name: Normal prostate

label_protocol: Standard Affy protocol


title: Surrounding normal prostate tissue D (HG-U133A 2.0 Array)

description: Race: Caucasian, Smoking Status: Never, Gleason Sum: 7, PT Stage: 2, Extraprostatic Extension: None, Perineural Invasion: Yes, Seminal vesicle invasion: No, Are Surgical margins involved: All surgical margins are free of tumor, Angio lymphatic invasion: No


title: Surrounding normal prostate tissue patient 45 (HG-U133A 2.0 Array)

description: Race: Caucasian, Smoking Status: Current, Gleason Sum: 7, PT Stage: 2, Extraprostatic Extension: None, Perineural Invasion: Yes, Seminal vesicle invasion: No, Are Surgical margins involved: All surgical margins are free of tumor, Angio lymphatic invasion: No


title: Prostate tumor patient 52 (MicroRNA Array)

description: Race: Caucasian, Smoking Status: Unknown, Gleason Sum: 6, PT Stage: 2, Extraprostatic Extension: None, Perineural Invasion: No, Seminal vesicle invasion: No, Are Surgical margins involved: All surgical margins are free of tumor, Angio lymphatic invasion:No


title: Surrounding normal prostate tissue patient 51 (HG-U133A 2.0 Array)

description: Race: African American, Smoking Status: Past, Gleason Sum: 6, PT Stage: 2, Extraprostatic Extension: None, Perineural Invasion: Yes, Seminal vesicle invasion: No, Are Surgical margins involved: All surgical margins are free of tumor, Angio lymphatic invasion: No


title: Surrounding normal prostate tissue patient 4 (HG-U133A 2.0 Array)

description: Race: Caucasian, Smoking Status: Past, Gleason Sum: 7, PT Stage: 2, Extraprostatic Extension: None, Perineural Invasion: Yes, Seminal vesicle invasion: No, Are Surgical margins involved: Tumor focal at margin, Angio lymphatic invasion: No


title: Surrounding normal prostate tissue patient 46 (HG-U133A 2.0 Array)

description: Race: Caucasian, Smoking Status: Never, Gleason Sum: 7, PT Stage: 3, Extraprostatic Extension: Established, Perineural Invasion: Yes, Seminal vesicle invasion: No, Are Surgical margins involved: All surgical margins are free of tumor, Angio lymphatic invasion: No


title: Surrounding normal prostate tissue patient 21 (HG-U133A 2.0 Array)

description: Race: African American, Smoking Status: Unknown, Gleason Sum: 7, PT Stage: 3, Extraprostatic Extension: Multifocal, Perineural Invasion: Yes, Seminal vesicle invasion: Yes, Are Surgical margins involved: Tumor focal at margin, Angio lymphatic invasion: No


title: Prostate tumor patient 44 (MicroRNA Array)

description: Race: Caucasian, Smoking Status: Unknown, Gleason Sum: 7, PT Stage: 3, Extraprostatic Extension: Focal, Perineural Invasion: Yes, Seminal vesicle invasion: No, Are Surgical margins involved: All surgical margins are free of tumor, Angio lymphatic invasion:No


title: Surrounding normal prostate tissue patient 76 (HG-U133A 2.0 Array)

description: Race: Caucasian, Smoking Status: Past, Gleason Sum: 7, PT Stage: 2, Extraprostatic Extension: None, Perineural Invasion: Yes, Seminal vesicle invasion: No, Are Surgical margins involved: All surgical margins are free of tumor, Angio lymphatic invasion: No


title: Surrounding normal prostate tissue protate cancer patient C (HG-U133A 2.0 Array)


title: Prostate tumor patient 74 (HG-U133A 2.0 Array)

description: Race: Caucasian, Smoking Status: Past, Gleason Sum: 7, PT Stage: 4, Extraprostatic Extension: None, Perineural Invasion: Yes, Seminal vesicle invasion: No, Are Surgical margins involved: All surgical margins are free of tumor, Angio lymphatic invasion: Yes


title: Prostate tumor patient 72 (HG-U133A 2.0 Array)

description: Race: Caucasian, Smoking Status: Never, Gleason Sum: 6, PT Stage: 2, Extraprostatic Extension: None, Perineural Invasion: Yes, Seminal vesicle invasion: No, Are Surgical margins involved: All surgical margins are free of tumor, Angio lymphatic invasion: No


title: Prostate tumor patient 76 (HG-U133A 2.0 Array)


title: Surrounding normal prostate tissue patient 31 (HG-U133A 2.0 Array)

description: Race: Caucasian, Smoking Status: Unknown, Gleason Sum: 7, PT Stage: 3, Extraprostatic Extension: Focal, Perineural Invasion: Yes, Seminal vesicle invasion: No, Are Surgical margins involved: All surgical margins are free of tumor, Angio lymphatic invasion: No


title: Pooled non-tumor tissue 2 (HG-U133A 2.0 Array)

description: Race: NA, Smoking Status: NA, Gleason Sum: NA, PT Stage: NA, Extraprostatic Extension: NA, Perineural Invasion: NA, Seminal vesicle invasion: NA, Are Surgical margins involved: NA, Angio lymphatic invasion: NA


title: Prostate tumor patient 73 (HG-U133A 2.0 Array)

description: Race: African American, Smoking Status: Current, Gleason Sum: 7, PT Stage: 2, Extraprostatic Extension: None, Perineural Invasion: Yes, Seminal vesicle invasion: No, Are Surgical margins involved: All surgical margins are free of tumor, Angio lymphatic invasion: No


title: Surrounding normal prostate tissue protate cancer patient A (HG-U133A 2.0 Array)

description: Race: African American, Smoking Status: Current, Gleason Sum: NA, PT Stage: NA, Extraprostatic Extension: NA, Perineural Invasion: NA, Seminal vesicle invasion: NA, Are Surgical margins involved: NA, Angio lymphatic invasion: NA


title: Surrounding normal prostate tissue patient 72 (HG-U133A 2.0 Array)


title: Prostate tumor patient 68 (HG-U133A 2.0 Array)

description: Race: Caucasian, Smoking Status: Past, Gleason Sum: 6, PT Stage: 2, Extraprostatic Extension: None, Perineural Invasion: No, Seminal vesicle invasion: No, Are Surgical margins involved: All surgical margins are free of tumor, Angio lymphatic invasion: No


title: Surrounding normal prostate tissue patient 70 (HG-U133A 2.0 Array)

description: Race: Caucasian, Smoking Status: Never, Gleason Sum: 5, PT Stage: 2, Extraprostatic Extension: NA, Perineural Invasion: NA, Seminal vesicle invasion: NA, Are Surgical margins involved: NA, Angio lymphatic invasion: NA


title: Prostate tumor patient 77 (HG-U133A 2.0 Array)

description: Race: African American, Smoking Status: Current, Gleason Sum: 6, PT Stage: 2, Extraprostatic Extension: None, Perineural Invasion: Yes, Seminal vesicle invasion: No, Are Surgical margins involved: All surgical margins are free of tumor, Angio lymphatic invasion: No


title: Surrounding normal prostate tissue protate cancer patient B (HG-U133A 2.0 Array)

description: Race: African American, Smoking Status: Never, Gleason Sum: 6, PT Stage: 2, Extraprostatic Extension: None, Perineural Invasion: No, Seminal vesicle invasion: No, Are Surgical margins involved: NA, Angio lymphatic invasion: No


title: Pooled non-tumor tissue 1 (HG-U133A 2.0 Array)


title: Surrounding normal prostate tissue patient 68 (HG-U133A 2.0 Array)


title: Prostate tumor patient 66 (HG-U133A 2.0 Array)

description: Race: Caucasian, Smoking Status: Never, Gleason Sum: 7, PT Stage: 2, Extraprostatic Extension: None, Perineural Invasion: Yes, Seminal vesicle invasion: No, Are Surgical margins involved: Tumor focal at margin, Angio lymphatic invasion: No


title: Prostate tumor patient 65 (HG-U133A 2.0 Array)

description: Race: African American, Smoking Status: Never, Gleason Sum: 7, PT Stage: 2, Extraprostatic Extension: None, Perineural Invasion: Yes, Seminal vesicle invasion: No, Are Surgical margins involved: All surgical margins are free of tumor, Angio lymphatic invasion: No


title: Prostate tumor patient 61 (HG-U133A 2.0 Array)

description: Race: African American, Smoking Status: Unknown, Gleason Sum: 7, PT Stage: 3, Extraprostatic Extension: Focal, Perineural Invasion: Yes, Seminal vesicle invasion: Yes, Are Surgical margins involved: Tumor focal at margin, Angio lymphatic invasion: No


title: Prostate tumor patient 63 (HG-U133A 2.0 Array)

description: Race: Caucasian, Smoking Status: Past, Gleason Sum: 6, PT Stage: 3, Extraprostatic Extension: None, Perineural Invasion: No, Seminal vesicle invasion: No, Are Surgical margins involved: Tumor focal at margin, Angio lymphatic invasion: No


title: Surrounding normal prostate tissue patient 63 (HG-U133A 2.0 Array)


title: Surrounding normal prostate tissue patient 65 (HG-U133A 2.0 Array)


title: Prostate tumor patient 60 (HG-U133A 2.0 Array)


title: Prostate tumor patient 59 (HG-U133A 2.0 Array)


title: Surrounding normal prostate tissue patient 11 (HG-U133A 2.0 Array)

description: Race: African American, Smoking Status: Unknown, Gleason Sum: 7, PT Stage: 3, Extraprostatic Extension: None, Perineural Invasion: Yes, Seminal vesicle invasion: Yes, Are Surgical margins involved: All surgical margins are free of tumor, Angio lymphatic invasion: No


title: Prostate tumor patient 57 (HG-U133A 2.0 Array)

description: Race: African American, Smoking Status: Past, Gleason Sum: 7, PT Stage: 2, Extraprostatic Extension: None, Perineural Invasion: No, Seminal vesicle invasion: No, Are Surgical margins involved: All surgical margins are free of tumor, Angio lymphatic invasion: No


title: Prostate tumor patient 58 (HG-U133A 2.0 Array)

description: Race: African American, Smoking Status: Past, Gleason Sum: 7, PT Stage: 3, Extraprostatic Extension: None, Perineural Invasion: Yes, Seminal vesicle invasion: Yes, Are Surgical margins involved: Tumor focal at margin, Angio lymphatic invasion: Yes


title: Prostate tumor patient 52 (HG-U133A 2.0 Array)

description: Race: Caucasian, Smoking Status: Unknown, Gleason Sum: 6, PT Stage: 2, Extraprostatic Extension: None, Perineural Invasion: No, Seminal vesicle invasion: No, Are Surgical margins involved: All surgical margins are free of tumor, Angio lymphatic invasion: No


title: Prostate tumor patient 51 (HG-U133A 2.0 Array)

description: Race: African American, Smoking Status: Past, Gleason Sum: 6, PT Stage: 2, Extraprostatic Extension: None, Perineural Invasion: Yes, Seminal vesicle invasion: No, Are Surgical margins involved: All surgical margins are free of tumor, Angio lymphatic invasion: No


title: Prostate tumor patient 53 (HG-U133A 2.0 Array)

description: Race: Caucasian, Smoking Status: Unknown, Gleason Sum: 7, PT Stage: 2, Extraprostatic Extension: None, Perineural Invasion: Yes, Seminal vesicle invasion: No, Are Surgical margins involved: Tumor focal at margin, Angio lymphatic invasion: No


title: Prostate tumor patient 56 (HG-U133A 2.0 Array)

description: Race: African American, Smoking Status: Never, Gleason Sum: 7, PT Stage: 3, Extraprostatic Extension: None, Perineural Invasion: Yes, Seminal vesicle invasion: Yes, Are Surgical margins involved: All surgical margins are free of tumor, Angio lymphatic invasion: No


title: Prostate tumor patient 55 (HG-U133A 2.0 Array)

description: Race: African American, Smoking Status: Past, Gleason Sum: 7, PT Stage: 2, Extraprostatic Extension: None, Perineural Invasion: Yes, Seminal vesicle invasion: No, Are Surgical margins involved: Tumor focal at margin, Angio lymphatic invasion: No


title: Prostate tumor patient 48 (HG-U133A 2.0 Array)

description: Race: African American, Smoking Status: Unknown, Gleason Sum: 7, PT Stage: 2, Extraprostatic Extension: None, Perineural Invasion: Yes, Seminal vesicle invasion: No, Are Surgical margins involved: All surgical margins are free of tumor, Angio lymphatic invasion: No


title: Prostate tumor patient 54 (HG-U133A 2.0 Array)

description: Race: Caucasian, Smoking Status: Unknown, Gleason Sum: 7, PT Stage: 2, Extraprostatic Extension: None, Perineural Invasion: Yes, Seminal vesicle invasion: No, Are Surgical margins involved: All surgical margins are free of tumor, Angio lymphatic invasion: No


title: Prostate tumor patient 49 (HG-U133A 2.0 Array)

description: Race: African American, Smoking Status: Unknown, Gleason Sum: 7, PT Stage: 2, Extraprostatic Extension: None, Perineural Invasion: Yes, Seminal vesicle invasion: No, Are Surgical margins involved: Tumor focal at margin, Angio lymphatic invasion: No


title: Prostate tumor patient 45 (HG-U133A 2.0 Array)

description: Race: Caucasian, Smoking Status: Current, Gleason Sum: 7, PT Stage: 2, Extraprostatic Extension: None, Perineural Invasion: Yes, Seminal vesicle invasion: No, Are Surgical margins involved: All surgical margins are free of tumor, Angio lymphatic invasion: No


title: Prostate tumor patient 46 (HG-U133A 2.0 Array)

description: Race: Caucasian, Smoking Status: Never, Gleason Sum: 7, PT Stage: 3, Extraprostatic Extension: Established, Perineural Invasion: Yes, Seminal vesicle invasion: No, Are Surgical margins involved: All surgical margins are free of tumor, Angio lymphatic invasion: No


title: Prostate tumor patient 47 (HG-U133A 2.0 Array)

description: Race: African American, Smoking Status: Past, Gleason Sum: 6, PT Stage: 2, Extraprostatic Extension: None, Perineural Invasion: No, Seminal vesicle invasion: No, Are Surgical margins involved: All surgical margins are free of tumor, Angio lymphatic invasion: No


title: Prostate tumor patient 44 (HG-U133A 2.0 Array)

description: Race: Caucasian, Smoking Status: Unknown, Gleason Sum: 7, PT Stage: 3, Extraprostatic Extension: Focal, Perineural Invasion: Yes, Seminal vesicle invasion: No, Are Surgical margins involved: All surgical margins are free of tumor, Angio lymphatic invasion: No


title: Prostate tumor patient 70 (HG-U133A 2.0 Array)

description: Race: Caucasian, Smoking Status: Never, Gleason Sum: 5, PT Stage: 2, Extraprostatic Extension: NA, Perineural Invasion: NA, Seminal vesicle invasion: NA, Are Surgical margins involved: NA, Angio lymphatic invasion: NA


title: Prostate tumor patient 43 (HG-U133A 2.0 Array)

description: Race: African American, Smoking Status: Current, Gleason Sum: 8, PT Stage: 3, Extraprostatic Extension: Established, Perineural Invasion: Yes, Seminal vesicle invasion: Yes, Are Surgical margins involved: Tumor focal at margin, Angio lymphatic invasion: No


title: Prostate tumor patient 42 (HG-U133A 2.0 Array)

description: Race: Caucasian, Smoking Status: Past, Gleason Sum: 7, PT Stage: 2, Extraprostatic Extension: None, Perineural Invasion: Yes, Seminal vesicle invasion: No, Are Surgical margins involved: All surgical margins are free of tumor, Angio lymphatic invasion: No


title: Prostate tumor patient 40 (HG-U133A 2.0 Array)

description: Race: Caucasian, Smoking Status: Current, Gleason Sum: 7, PT Stage: 3, Extraprostatic Extension: Multifocal, Perineural Invasion: Yes, Seminal vesicle invasion: No, Are Surgical margins involved: Tumor focal at margin, Angio lymphatic invasion: No


title: Prostate tumor patient 39 (HG-U133A 2.0 Array)

description: Race: Caucasian, Smoking Status: Never, Gleason Sum: 7, PT Stage: 3, Extraprostatic Extension: Focal, Perineural Invasion: Yes, Seminal vesicle invasion: No, Are Surgical margins involved: All surgical margins are free of tumor, Angio lymphatic invasion: No


title: Prostate tumor patient 41 (HG-U133A 2.0 Array)


title: Prostate tumor patient 35 (HG-U133A 2.0 Array)

description: Race: African American, Smoking Status: Unknown, Gleason Sum: 7, PT Stage: 3, Extraprostatic Extension: Multifocal, Perineural Invasion: Yes, Seminal vesicle invasion: No, Are Surgical margins involved: All surgical margins are free of tumor, Angio lymphatic invasion: No


title: Prostate tumor patient 33 (HG-U133A 2.0 Array)


title: Prostate tumor patient 36 (HG-U133A 2.0 Array)


title: Prostate tumor patient 34 (HG-U133A 2.0 Array)

description: Race: African American, Smoking Status: Past, Gleason Sum: 7, PT Stage: 3, Extraprostatic Extension: Multifocal, Perineural Invasion: Yes, Seminal vesicle invasion: No, Are Surgical margins involved: Tumor focal at margin, Angio lymphatic invasion: No


title: Prostate tumor patient 24 (HG-U133A 2.0 Array)

description: Race: Caucasian, Smoking Status: Unknown, Gleason Sum: 9, PT Stage: 3, Extraprostatic Extension: Focal, Perineural Invasion: Yes, Seminal vesicle invasion: No, Are Surgical margins involved: Tumor focal at margin, Angio lymphatic invasion: No


title: Prostate tumor patient 26 (HG-U133A 2.0 Array)

description: Race: Caucasian, Smoking Status: Never, Gleason Sum: 6, PT Stage: 2, Extraprostatic Extension: None, Perineural Invasion: Yes, Seminal vesicle invasion: No, Are Surgical margins involved: All surgical margins are free of tumor, Angio lymphatic invasion: No


title: Prostate tumor patient 37 (HG-U133A 2.0 Array)

description: Race: African American, Smoking Status: Unknown, Gleason Sum: 7, PT Stage: 3, Extraprostatic Extension: None, Perineural Invasion: Yes, Seminal vesicle invasion: Yes, Are Surgical margins involved: All surgical margins are free of tumor, Angio lymphatic invasion: No


title: Prostate tumor patient 32 (HG-U133A 2.0 Array)

description: Race: African American, Smoking Status: Past, Gleason Sum: 9, PT Stage: 3, Extraprostatic Extension: Established, Perineural Invasion: Yes, Seminal vesicle invasion: No, Are Surgical margins involved: Tumor focal at margin, Angio lymphatic invasion: Yes


title: Prostate tumor patient 28 (HG-U133A 2.0 Array)

description: Race: Caucasian, Smoking Status: Unknown, Gleason Sum: 7, PT Stage: 2, Extraprostatic Extension: None, Perineural Invasion: Yes, Seminal vesicle invasion: No, Are Surgical margins involved: All surgical margins are free of tumor, Angio lymphatic invasion: No


title: Prostate tumor patient 31 (HG-U133A 2.0 Array)


title: Prostate tumor patient 30 (HG-U133A 2.0 Array)

description: Race: African American, Smoking Status: Unknown, Gleason Sum: 7, PT Stage: 2, Extraprostatic Extension: None, Perineural Invasion: Yes, Seminal vesicle invasion: No, Are Surgical margins involved: All surgical margins are free of tumor, Angio lymphatic invasion: No


title: Prostate tumor patient 29 (HG-U133A 2.0 Array)

description: Race: African American, Smoking Status: Past, Gleason Sum: 7, PT Stage: 3, Extraprostatic Extension: None, Perineural Invasion: Yes, Seminal vesicle invasion: Yes, Are Surgical margins involved: All surgical margins are free of tumor, Angio lymphatic invasion: Yes


title: Prostate tumor patient 17 (HG-U133A 2.0 Array)


title: Prostate tumor patient 13 (HG-U133A 2.0 Array)

description: Race: African American, Smoking Status: Current, Gleason Sum: 6, PT Stage: 2, Extraprostatic Extension: None, Perineural Invasion: Yes, Seminal vesicle invasion: No, Are Surgical margins involved: All surgical margins are free of tumor, Angio lymphatic invasion: No


title: Prostate tumor patient 18 (HG-U133A 2.0 Array)

description: Race: Caucasian, Smoking Status: Unknown, Gleason Sum: 7, PT Stage: 3, Extraprostatic Extension: Focal, Perineural Invasion: Yes, Seminal vesicle invasion: No, Are Surgical margins involved: Tumor focal at margin, Angio lymphatic invasion: No


title: Prostate tumor patient 14 (HG-U133A 2.0 Array)

description: Race: African American, Smoking Status: Unknown, Gleason Sum: 6, PT Stage: 2, Extraprostatic Extension: None, Perineural Invasion: No, Seminal vesicle invasion: No, Are Surgical margins involved: Tumor focal at margin, Angio lymphatic invasion: No


title: Prostate tumor patient 21 (HG-U133A 2.0 Array)

description: Race: African American, Smoking Status: Unknown, Gleason Sum: 7, PT Stage: 3, Extraprostatic Extension: Multifocal, Perineural Invasion: Yes, Seminal vesicle invasion: Yes, Are Surgical margins involved: Tumor focal at margin, Angio lymphatic invasion: No


title: Prostate tumor patient 22 (HG-U133A 2.0 Array)

description: Race: African American, Smoking Status: Never, Gleason Sum: 6, PT Stage: 3, Extraprostatic Extension: Focal, Perineural Invasion: Yes, Seminal vesicle invasion: No, Are Surgical margins involved: All surgical margins are free of tumor, Angio lymphatic invasion: No


title: Prostate tumor patient 25 (HG-U133A 2.0 Array)

description: Race: Caucasian, Smoking Status: Past, Gleason Sum: 6, PT Stage: 2, Extraprostatic Extension: None, Perineural Invasion: No, Seminal vesicle invasion: No, Are Surgical margins involved: All surgical margins are free of tumor, Angio lymphatic invasion: No


title: Prostate tumor patient 10 (HG-U133A 2.0 Array)

description: Race: African American, Smoking Status: Never, Gleason Sum: 7, PT Stage: 3, Extraprostatic Extension: Focal, Perineural Invasion: Yes, Seminal vesicle invasion: No, Are Surgical margins involved: Tumor focal at margin, Angio lymphatic invasion: No


title: Prostate tumor patient 16 (HG-U133A 2.0 Array)

description: Race: African American, Smoking Status: Past, Gleason Sum: 7, PT Stage: 2, Extraprostatic Extension: None, Perineural Invasion: No, Seminal vesicle invasion: No, Are Surgical margins involved: All surgical margins are free of tumor, Angio lymphatic invasion: No


title: Prostate tumor patient 27 (HG-U133A 2.0 Array)

description: Race: African American, Smoking Status: Past, Gleason Sum: 7, PT Stage: 2, Extraprostatic Extension: None, Perineural Invasion: Yes, Seminal vesicle invasion: No, Are Surgical margins involved: All surgical margins are free of tumor, Angio lymphatic invasion: No


title: Prostate tumor patient 20 (HG-U133A 2.0 Array)

description: Race: African American, Smoking Status: Current, Gleason Sum: 7, PT Stage: 3, Extraprostatic Extension: Focal, Perineural Invasion: Yes, Seminal vesicle invasion: No, Are Surgical margins involved: All surgical margins are free of tumor, Angio lymphatic invasion: No


title: Prostate tumor patient 9 (HG-U133A 2.0 Array)

description: Race: Caucasian, Smoking Status: Past, Gleason Sum: 6, PT Stage: 3, Extraprostatic Extension: Focal, Perineural Invasion: Yes, Seminal vesicle invasion: No, Are Surgical margins involved: Tumor widespread at margin, Angio lymphatic invasion: No


title: Prostate tumor patient 11 (HG-U133A 2.0 Array)


title: Prostate tumor patient 8 (HG-U133A 2.0 Array)

description: Race: Caucasian, Smoking Status: Never, Gleason Sum: 7, PT Stage: 2, Extraprostatic Extension: None, Perineural Invasion: No, Seminal vesicle invasion: No, Are Surgical margins involved: Tumor focal at margin, Angio lymphatic invasion: No


title: Prostate tumor patient 13 (MicroRNA Array)

description: Race: African American, Smoking Status: Current, Gleason Sum: 6, PT Stage: 2, Extraprostatic Extension: None, Perineural Invasion: Yes, Seminal vesicle invasion: No, Are Surgical margins involved: All surgical margins are free of tumor, Angio lymphatic invasion:No


title: Prostate tumor patient 15 (HG-U133A 2.0 Array)

description: Race: African American, Smoking Status: Past, Gleason Sum: 6, PT Stage: 2, Extraprostatic Extension: None, Perineural Invasion: Yes, Seminal vesicle invasion: No, Are Surgical margins involved: All surgical margins are free of tumor, Angio lymphatic invasion: No


title: Prostate tumor patient 7 (HG-U133A 2.0 Array)

description: Race: Caucasian, Smoking Status: Past, Gleason Sum: 7, PT Stage: 2, Extraprostatic Extension: None, Perineural Invasion: Yes, Seminal vesicle invasion: No, Are Surgical margins involved: Tumor widespread at margin, Angio lymphatic invasion: No


title: Prostate tumor patient 12 (HG-U133A 2.0 Array)

description: Race: African American, Smoking Status: Unknown, Gleason Sum: 6, PT Stage: 2, Extraprostatic Extension: None, Perineural Invasion: Yes, Seminal vesicle invasion: No, Are Surgical margins involved: Tumor focal at margin, Angio lymphatic invasion: No


title: Prostate tumor patient 23 (HG-U133A 2.0 Array)

description: Race: Caucasian, Smoking Status: Never, Gleason Sum: 7, PT Stage: 2, Extraprostatic Extension: None, Perineural Invasion: Yes, Seminal vesicle invasion: No, Are Surgical margins involved: All surgical margins are free of tumor, Angio lymphatic invasion: No


title: Prostate tumor patient 6 (HG-U133A 2.0 Array)

description: Race: African American, Smoking Status: Never, Gleason Sum: 7, PT Stage: 2, Extraprostatic Extension: None, Perineural Invasion: Yes, Seminal vesicle invasion: No, Are Surgical margins involved: All surgical margins are free of tumor, Angio lymphatic invasion: No


title: Prostate tumor patient 5 (HG-U133A 2.0 Array)

description: Race: Caucasian, Smoking Status: Never, Gleason Sum: 7, PT Stage: 2, Extraprostatic Extension: None, Perineural Invasion: Yes, Seminal vesicle invasion: No, Are Surgical margins involved: Tumor focal at margin, Angio lymphatic invasion: Yes


title: Prostate tumor patient 4 (HG-U133A 2.0 Array)

description: Race: Caucasian, Smoking Status: Past, Gleason Sum: 7, PT Stage: 2, Extraprostatic Extension: None, Perineural Invasion: Yes, Seminal vesicle invasion: No, Are Surgical margins involved: Tumor focal at margin, Angio lymphatic invasion: No


title: Prostate tumor patient 3 (HG-U133A 2.0 Array)

description: Race: African American, Smoking Status: Past, Gleason Sum: 6, PT Stage: 3, Extraprostatic Extension: Focal, Perineural Invasion: Yes, Seminal vesicle invasion: No, Are Surgical margins involved: Tumor widespread a surgical margins, Angio lymphatic invasion: No


title: Prostate tumor patient 38 (HG-U133A 2.0 Array)

description: Race: Caucasian, Smoking Status: Unknown, Gleason Sum: 7, PT Stage: 3, Extraprostatic Extension: Established, Perineural Invasion: Yes, Seminal vesicle invasion: Yes, Are Surgical margins involved: Tumor focal at margin, Angio lymphatic invasion: No


title: Prostate tumor patient 1 (HG-U133A 2.0 Array)

description: Race: Caucasian, Smoking Status: Past, Gleason Sum: 7, PT Stage: 3, Extraprostatic Extension: Focal, Perineural Invasion: Yes, Seminal vesicle invasion: No, Are Surgical margins involved: Unknown, Angio lymphatic invasion: No


title: Prostate tumor patient 2 (HG-U133A 2.0 Array)

description: Race: Caucasian, Smoking Status: Unknown, Gleason Sum: 6, PT Stage: 3, Extraprostatic Extension: Focal, Perineural Invasion: Yes, Seminal vesicle invasion: Yes, Are Surgical margins involved: All surgical margins are free of tumor, Angio lymphatic invasion: No