title: Integrated analysis reveals microRNA networks coordinately expressed with key proteins in breast cancer [mRNA]

status: Public on Feb 02 2015

city: Oslo

first: Miriam

middle: Ragle

last: Aure

address: Ullernchauséen 70

department: Dept. of Cancer Genetics

institute: Oslo University Hospital Radiumhospitalet

summary:
BACKGROUND:
The role played by microRNAs in the deregulation of protein expression in breast cancer is only partly understood. To gain insight, the combined effect of microRNA and mRNA expression on protein expression was investigated in three independent data sets.

METHODS:
Protein expression was modeled as a multilinear function of powers of mRNA and microRNA expression. The model was first applied to mRNA and protein expression for 105 selected cancer-associated genes and to genome-wide microRNA expression from 283 breast tumors. The model considered both the effect of one microRNA at a time and all microRNAs combined. In the latter case the Lasso penalized regression method was applied to detect the simultaneous effect of multiple microRNAs.

RESULTS:
An interactome map for breast cancer representing all direct and indirect associations between the expression of microRNAs and proteins was derived. A pattern of extensive coordination between microRNA and protein expression in breast cancer emerges, with multiple clusters of microRNAs being associated with multiple clusters of proteins. Results were subsequently validated in two independent breast cancer data sets. A number of the microRNA-protein associations were functionally validated in a breast cancer cell line.

CONCLUSIONS:
A comprehensive map is derived for the co-expression in breast cancer of microRNAs and 105 proteins with known roles in cancer, after filtering out the in-cis effect of mRNA expression. The analysis suggests that group action by several microRNAs to deregulate the expression of proteins is a common modus operandi in breast cancer.

overall_design: The mRNA expression profiling of 283 breast cancer samples was performed using the SurePrint G3 Human GE 8x60K one-color microarrays from Agilent (Agilent Technologies, Santa Clara, CA, USA) according to the manufacturer’s protocol (One-Color Microarray-Based Gene Expression Analysis, Low Input Quick Amp Labeling, v.6.5, May 2010). For each sample, 100 ng of RNA was amplified and hybridized on the array. Scanning was performed with Agilent Scanner G2565A, using AgilentG3_GX_1Color as profile. Signals were extracted using FE v.10.7.3.1 and protocol GE1_107_Sep09 (Agilent Technologies). Arrays were log2-transformed, quantile normalized and hospital-adjusted by subtracting from each probe value the mean probe value among samples from the same hospital.

first: Sandra

last: Jernström

first: Marit

last: Krohn

first: Hans

last: Vollan

first: Eldri

middle: U

last: Due

first: Einar

last: Rødland

first: Rolf

last: Kåresen

first: Prahlad

last: Ram

first: Yiling

last: Lu

first: Gordon

middle: B

last: Mills

first: Anne-Lise

last: Børresen-Dale

first: Kristine

last: Sahlberg

first: Ole

last: Lingjærde

first: Vessela

middle: N

last: Kristensen


title: Characterization of global loss of imprinting in overgrowth syndrome induced by assisted reproduction

status: Public on Mar 06 2015

city: Columbia

first: Rocio

middle: Melissa

last: Rivera

state: MO

address: 920 East Campus Drive

department: Division of Animal Sciences

country: USA

institute: University of Missouri, Columbia

type: Expression profiling by high throughput sequencing

summary: Embryos generated with the use of assisted reproductive technologies (ART) can develop overgrowth syndromes. In ruminants, the condition is referred to as large offspring syndrome (LOS) and exhibits variable phenotypic abnormalities including overgrowth, enlarged tongue, and abdominal wall defects. These characteristics recapitulate those observed in the human loss-of-imprinting (LOI) overgrowth syndrome Beckwith-Wiedemann (BWS).  We have recently shown LOI at the KCNQ1 locus in LOS, the most common epimutation in BWS.  Although the first case of ART-induced LOS was reported in 1995, studies have not yet determined the extent of LOI in this condition.   Here, we determined allele-specific expression of imprinted genes previously identified in human and/or mouse in day 105 Bos taurus indicus X Bos taurus taurus F1 hybrid control and LOS fetuses using RNAseq.  Our analysis allowed us to determine the monoallelic expression of 20 genes in tissues of control fetuses.  LOS fetuses displayed variable LOI when compared to controls.  Biallelic expression of imprinted genes in LOS was associated with tissue-specific hypomethylation of the normally methylated parental allele. In addition, a positive correlation was observed between bodyweight and the number of biallelically expressed imprinted genes in LOS fetuses.  Further, not only was there loss of allele-specific expression of imprinted genes in LOS, but we also observed differential transcript amounts of these genes between control and overgrown fetuses.  In summary, we characterized previously unidentified imprinted genes in bovine and identified misregulation of imprinting at multiple loci in LOS.  We concluded that LOS is a multi-locus loss-of-imprinting syndrome, as is BWS.

overall_design: Imprinted gene expression in kidney, skeletal muscle, liver, and brain of four control and large offspring syndrome(LOS) fetuses were studied using RNAseq

first: Zhiyuan

last: Chen

first: Darren

middle: E

last: Hagen

first: Christine

middle: G

last: Elsik

first: Tiemin

last: Ji

first: Collind

middle: J

last: Morris

first: Laura

last: Moon

first: Rocío

middle: M


title: Integrated analysis reveals microRNA networks coordinately expressed with key proteins in breast cancer [miRNA]

first: Miriam

last: Aure

country: Norway

overall_design: The miRNA expression profiling of 283 breast cancer samples was performed using the 8x15k “Human miRNA Microarray Kit release 14.0 (V2)” with design id 029297 from Agilent (Agilent Technologies, Santa Clara, CA, USA). In brief, 100 ng total RNA was dephosphorylated, labeled and hybridized for 20 hours, following the manufacturer’s protocol. Scanning was performed on Agilent Scanner G2565A, signals were extracted using Feature Extraction v10.7.3.1 and the subsequent data processing was performed using the GeneSpring software v11.0 (Agilent Technologies). In brief, the miRNA signal intensities were log2-transformed and normalized to the 90th percentile, and miRNAs that were detected in less than 10% of the samples were excluded. This resulted in 421 unique mature miRNAs.

middle: R

first: Sandra

last: Jernström

first: Marit

last: Krohn

first: Hans

last: Vollan

first: Eldri

last: Due

first: Einar

middle: K

middle: C


title: Integrated analysis reveals microRNA networks coordinately expressed with key proteins in breast cancer

status: Public on Jan 31 2015

type:
Non-coding RNA profiling by array
Expression profiling by array

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Transcriptomics and methylomics of human T cells [transcriptome]

status: Public on Nov 24 2014

city: Winston-Salem

first: Yongmei

last: Liu

state: NC

address: Medical Center Blvd.

institute: Wake Forest School of Medicine

summary:
The MESA Epigenomics and Transcriptomics Study has been launched to investigate potential gene expression regulatory methylation sites in humans by examining the association between CpG methylation and gene expression in purified human monocytes and T cells from a large study population (community-dwelling participants in the Multi-Ethnic Study of Atherosclerosis (MESA)).
The MESA Epigenomics and Transcriptomics Study was funded by a National Heart, Lung and Blood Institute grant (R01HL101250) through the NIH Roadmap Epigenomics Program in 2009.

overall_design:
Data includes transcriptomic and methylomic data from CD4+ samples, collected from 214 individuals.  Peripheral T cells were isolated from blood (Exam 5) with anti-CD4 coated magnetic beads, and the Illumina HumanHT-12 v4 Expression BeadChip and the Illumina HumanMethylation450 BeadChip were used to provide genome-wide coverage of mRNA expression and DNA methylation, respectively.  This data enabled us to identifyCpG loci whose degree of methylation was associated with age (age-DMR),and identify age- and expression-associated methylation sites (age-eMS), whose degree of methylation was associated with age and cis-gene expression (+/- 1Mb), after adjusting for other covariates such as race, gender, study site, and sample contaimination with B-cells, monocytes, natural killer cells, and neutrophils.

To estimate residual sample contamination for monocyte data analysis, separate enrichment scores for neutrophils, B cells, T cells, and natural killer cells were calculated and provided as sample characteristics.
The participant race, gender, and study site were provided as 'raceGenderSite variable' which represents a combination of those factors.

A detailed description of each sample characteristics is included in the 'README.txt'.


title: Transcriptomic profiling maps anatomically patterned subpopulations among single embryonic cardiac cells [RNA-seq]

status: Public on Nov 10 2016

city: Pittsburgh

first: Guang

last: Li

state: PA

address: 530 45th St. 8116 Rangos Research Center

department: Developmental Biology

institute: University of Pittsburgh

summary: Embryonic gene expression intricately reflects anatomical context, developmental stage, and cell type. To address whether the precise spatial origins of cardiac cells can be deduced solely from their transcriptional profiles, we established a genome-wide expression database from 118, 949, and 1166 single murine heart cells at embryonic days (e)8.5, 9.5, and 10.5, respectively. We segregated these cells by type using unsupervised bioinformatic analysis and identified novel chamber-specific genes. Using a random forest algorithm, we reconstructed the spatial origin of single e9.5 and e10.5 cardiomyocytes with 92.0+/-3.2% and 91.2+/-2.8% accuracy respectively (99.4+/-1.0% and 99.1+/-1.1% if a +/-1 zone margin is permitted) and predicted the second heart field distribution of Isl1-lineage descendants. When applied to Nkx2-5-/- cardiomyocytes from murine e9.5 hearts, we showed their transcriptional alteration and lack of ventricular phenotype. Our database and zone classification algorithm will enable the discovery of novel mechanisms in early cardiac development and disease.

overall_design: Genome-wide transcriptional analysis of single cardiac cells from three sequential developmental stages.

first: Adele

last: Xu

first: Sean

last: Wu


title: Transcriptomics and methylomics of human T cells [methylome]

type: Methylation profiling by genome tiling array


title: Genome-wide DNA methylation profiles in progression to in situ and invasive carcinoma of the breast with impact on gene transcription and prognosis

status: Public on Aug 08 2014

first: Thomas

last: Fleischer

address: Ullernchausséen 70

department: Department of Cancer Genetics, Institute for Cancer Research

institute: Oslo University Hospital

summary: Ductal carcinoma in situ (DCIS) of the breast is a precursor of invasive breast carcinoma (IBC). DNA methylation alterations are thought to be an early event in progression of cancer, and may prove valuable as a tool in clinical decision making and for understanding neoplastic development. Genome-wide DNA methylation profiles of 285 breast tissue samples representing progression of cancer were generated using Illumina HumanMethylation450. Validation of methylation changes between normal and DCIS was performed in an independent dataset of 15 normal and 40 DCIS samples, and validation of a prognostic signature was performed on 583 breast cancer samples from The Cancer Genome Atlas. Using two independent datasets of normal breast tissue and DCIS revealed that DNA methylation profiles of DCIS were radically altered compared to normal breast tissue, involving almost 7000 genes (including CUL7 and ICAM2).  Changes between DCIS and IBC involved around 1000 genes. In tumors, DNA methylation was associated with gene expression of almost 3000 genes (p<0.05, Bonferroni corrected) including both negative and positive correlations. A prognostic signature based on methylation level of 18 CpGs (representing genes such as IRF6, TBX5, ZNF259, KCTD21, EPN3, MACF1 and CSNK1G2) was associated to survival of breast cancer patients with invasive tumors, as well as to survival of patients with DCIS and mixed lesions of DCIS and IBC. This work demonstrates that changes in the epigenome occurs early in the neoplastic progression, provide evidence for the possible utilization of DNA methylation based markers of progression in the clinic, and highlights the importance of epigenetic changes in carcinogenesis.

overall_design: Bisulphite converted DNA from the 285 samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip

first: Arnoldo

last: Frigessi

first: Kevin

last: Johnson

first: Hege

last: Edvardsen

first: Nizar

last: Touleimat

first: Jovana

last: Klajic

first: Margit

middle: L

last: Riis

first: Vilde

middle: D

last: Haakensen

first: Fredrik

last: Wärnberg

first: Bjørn

last: Naume

first: Åslaug

last: Helland

first: Anne-Lise

last: Børresen-Dale

first: Jörg

last: Tost

first: Brock

last: Christensen

first: Vessela

last: Kristensen


title: Stability of miRNA in FFPE tumour samples exhibiting degraded mRNA [Cervix samples series 2]

status: Public on Jul 04 2012

city: Manchester

first: Jan

last: Taylor

address: Wilmslow Road

department: Bioinformatics

country: United Kingdom

institute: Paterson Institute for Cancer Research

summary:
Background: As degradation of formalin-fixed paraffin-embedded (FFPE) samples limits ability to expression profile, we explored factors predicting success for FFPE profiling and investigated an approach overcoming this limitation.

Methods: Bladder (n=141, stored 3-8 years) and cervix (n=160, stored 8-23 years) carcinoma FFPE samples were hybridised to Affymetrix Exon1.0ST arrays. Percent detection above background (%DABG) measured technical success. Biological signal was assessed by distinguishing cervix squamous cell carcinoma (SCC) and adenocarcinoma (AC) using a gene signature. Precursor mir-205 was measured by Exon array and mature miR-205 by qRT-PCR. Eight-old and -young cervix samples were compared using Affymetrix miRNA 2.0 arrays.
For comparison, the 'cervix_tumour_cs1_113' (previsously submitted GSM677307) was included and re-analyzed with the samples from the current study (total 161 Cervix samples).

Results: RNA quality controls (e.g. RNA integrity number) failed to predict profiling success, but sample age correlated with %DABG in bladder (R2=-0.30, p<0.01) and cervix (R2=-0.69, p<0.01). Biological signal was lost in older samples and neither a signature nor precursor mir-205 separated samples by histology. miR-205 qRT-PCR discriminated SCC from AC, validated by miRNA profiling (26-fold higher in SCC; p=1.10x10-5). Median miRNA probeset expression of eight-old and eight-young cervix samples correlated well (R2=0.95) overcoming the age-related bias of mRNA probesets, suggesting miR-205 stability generalises across microRNA.

Conclusions: microRNA profiling overcomes the limitation of degraded FFPE samples

overall_design: 48 Cervix tumour FFPE samples hybridised to exon arrays

first: John

middle: S

last: Hall

first: Janet

first: Amanda

last: Eustace

first: Helen

last: Valentine

first: Joely

last: Irlam

first: Crispin

last: Miller

first: Catharine

last: West


title: Stability of miRNA in FFPE tumour samples exhibiting degraded mRNA [cell lines]

overall_design: 16 cervix tumour cell lines hybridised to exon arrays


title: Stability of miRNA in FFPE tumour samples exhibiting degraded mRNA [Cervix samples series 1]

overall_design: 113 Cervix tumour FFPE samples hybridized to exon arrays


title: Small RNAs and RNA chaperone Hfq in enterohemorrhagic E. coli

status: Public on May 22 2014

city: Sydney

first: Jai

middle: Justin

last: Tree

state: NSW

address: Rm s110 Bldg F25, UNSW, Gate 11 Botany St

department: School of Biotechnology and Biomolecular Sciences

country: Australia

institute: University of New South Wales

sample_organism: Escherichia coli str. K-12 substr. MG1655


title: Transcriptomic profiling maps anatomically patterned subpopulations among single embryonic cardiac cells

first: Guang

last: Li


title: UV-crosslinking and high throughput sequencing of cDNAs (CRAC) of the RNA chaperone Hfq in enterohaemorhaggic E. coli

summary: UV-crosslinking and high througput sequencing of cDNAs (CRAC) was used to map the binding sites Hfq in enterohaemorhaggic E. coli (EHEC). Hfq was tagged with a His-FLAG dual affintiy tag and UV crosslinked after growth in the MEM-HEPES media essentailly as per Granneman et al (2009) PNAS. We additionally crosslinked Hfq in non-pathogenic E. coli K12 str. MG1655 grown in LE media. Hfq-RNA complexes were purified and trimmed using RNase A/T1. RNA fragments were isolated and converted to cDNA, PCR amplified and sequenced using Illumina Solexa GAxII and HiSeq2000 platforms.

platform_organism: Escherichia coli str. K-12 substr. MG1655

overall_design: His-FLAG tagged Hfq and untagged controls were cultured to an OD of 0.8 and crosslinked with UV-C. Five replicates of tagged EHEC Hfq and 2 replicates of untagged Hfq were crosslinked. We have additionally crosslinked 2 replicates each of E. coli K12 tagged and untagged Hfq.

first: Davif

last: Gally

first: David

last: Tollervey


title: Stability of miRNA in FFPE tumour samples exhibiting degraded mRNA [Cervix samples miRNA]

overall_design: 18 samples hybridised to miRNA microarray V2 arrays, 2 cervix cell lines and 16 clinical cervical tumour samples. There are no technical replicates.


title: Transcriptomics and methylomics of human monocytes [methylome]

first: Yongmei

last: Liu

summary:
The MESA Epigenomics and Transcriptomics Study has been launched to investigate potential gene expression regulatory methylation sites in humans by examining the association between CpG methylation and gene expression in purified human monocytes from a large study population (community-dwelling participants in the Multi-Ethnic Study of Atherosclerosis (MESA)).
The MESA Epigenomics and Transcriptomics Study was funded by a National Heart, Lung and Blood Institute grant (R01HL101250) through the NIH Roadmap Epigenomics Program in 2009.

overall_design:
The current study is particularly focused on the relationships between transcriptomics and methylomics with age.
Data includes transcriptomic and methylomic data from CD14+ samples, collected from 1,202 individuals ranging 44 - 83 years of age (Exam 1).  Peripheral monocytes were isolated from blood (Exam 5) with anti-CD14 coated magnetic beads, and the Illumina HumanHT-12 v4 Expression BeadChip and the Illumina HumanMethylation450 BeadChip were used to provide genome-wide coverage of mRNA expression and DNA methylation, respectively.  This data enabled us to identify CpG loci whose degree of methylation was associated with age (age-DMR),and identify age- and expression-associated methylation sites (age-eMS), whose degree of methylation was associated with age and cis-gene expression (+/- 1Mb), after adjusting for other covariates such as race, gender, study site, and sample contaimination with B-cells, T-cells, natural killer cells, and neutrophils.

To estimate residual sample contamination for monocyte data analysis, separate enrichment scores for neutrophils, B cells, T cells, and natural killer cells were calculated and provided as sample characteristics.
The participant race, gender, and study site were provided as 'raceGenderSite variable' which represents a combination of those factors.

A detailed description of each sample characteristics is included in the 'README.txt'.


title: Gene expression in human subcutaneous adipose tissue after administration of Gastric Insulinotropic Peptide (GIP)

status: Public on Sep 05 2012

city: Nuthetal

first: Martin

middle: A

last: Osterhoff

address: Arthur-Scheunert-Allee 155

department: Clinical Nutrition

country: Germany

institute: German Institute of Human Nutrition

summary: The intention of this clinical study was to investigate the effect of GIP administration for 240 min on gene expression in human subcutaneous adipose tissue. Three conditions have been tersted: 1. Sole infusion of GIP or NaCl as control; 2. GIP or NaCl administration under euglycemic-hyperinsulinemic clamp conditions; 3. GIP or NaCl administration under hyperglycemic-hyperinsulinemic clamp conditions to mimic the postprandial state.

overall_design: In each participant a complete physical examination and evaluation of medical history was performed, including an oral glucose tolerance test (oGTT) with 75 g glucose after overnight fast to ensure the metabolic state. Standard fasting laboratory and clinical chemistry evaluations were done. Synthetic human GIP (1-42) was dissolved in saline (0.9% NaCl-solution) under sterile conditions. All studies were done in the morning in the overnight fasted state (>10h since last meal). The effect of GIP administration on gene expression in subcutaneous adipose tissue was studied under 3 different conditions in a single blind design. Either the participants received only a GIP- or a saline- infusion (0.9% NaCl-isotonic solution, Fresenius, Germany) for 240 min. At different investigation days participants underwent euglycemic (EU)- and hyperglycemic (HC), hyperinsulinemic clamps combined with GIP- or placebo-infusions for 240 min at different examination days in a randomized, single-blind, crossover design. The capillary glucose concentration was 80mg/dl during EU-clamp and 140mg/dl during HC-clamp. The following numbers of treatments were performed: EU with GIP-infusion (N=9); EU with NaCl-infusion (N=9); HC with GIP-infusion (N=8), HC with NaCl-infusion (N=8); sole GIP-infusion (N=11) and sole placebo-infusion (N=11). Between examination days an intermission time of at least 7 days was maintained.

first: Andreas

middle: F

last: Pfeiffer

first: Oezlem

last: Goegebakan

first: Natalia

last: Rudovich


title: A 13-gene signature prognostic of HPV-negative OSCC: discovery and external validation

status: Public on Mar 07 2013

city: Seattle

first: Chu

last: Chen

state: Washington

address: 1100 Fairview Ave. N, PO Box 19024, M/S M5-C800

department: PHS

institute: Fred Hutchinson Cancer Research Center

summary:
OSCC is associated with substantial mortality and morbidity. In this study, we built on our previous molecular work to identify and validate a prognostic 13-gene signature that showed a higher ability than tumor stage in predicting survival for patients with
HPV-negative oral squamous cell carcinoma (OSCC).

overall_design: We previously reported 131 genes to be associated with survival in OSCC patients. In this study, we applied L1/L2-penalized Cox regression models to the Affymetrix array data from 97 HPV-negative OSCC patients on the 131 gene to identify a model for prediction of OSCC-specific survival. We then tested the model in an independent dataset and compared to tumor stage.

first: Pawadee

last: Lohavanichbutr

first: Eduardo

last: Mendez

first: F

last: Holsinger

first: Tessa

last: Rue

first: Yuzheng

last: Zhang

last: Houck

first: Melissa

middle: P

last: Upton

first: Neal

last: Futran

first: Stephen

last: Schwartz


title: Axiom® Exome 319 Array data to identify susceptible genetic variations of gastric cancer

status: Public on Jun 11 2014

city: Gyeonggi-do

first: Boyoung

last: Park

address: 323 Ilsan-ro, Ilsandong-gu, Goyang-si

country: South Korea

institute: National Cancer Centerm Korea

type:
SNP genotyping by SNP array
Genome variation profiling by SNP array

summary: To efficiently identify genetic susceptibility variants for gastric cancer, including rare coding variants, we performed an exome chip-based array study. We found that a linkage disequilibrium (LD) block containing 2 significant variants in PSCA gene increased the risk and two blocks that included 15 suggested variants including TRIM31, TRIM 40, TRIM 10, and TRIM26 regions, and included one suggested variant and OR2H2 gene showed protective associations with gastric cancer susceptibility. In addition, the PLEC region (rs200893203), FBLN2 region (rs201192415), and EPHA2 region (rs3754334) were associated with increased susceptibility

overall_design: We performed an exome chip-based array study in 329 gastric cancer cases and 683 controls.

first: Jeongseon

last: Kim

first: Jeonghee

last: Lee

first: Young

last: Cho

first: Hae

last: Woo

first: Seung

middle: H

last: Jeong

first: Jong

first: Eun

last: Shin

first: Il

last: Choi

middle: W


title: [miRNA Validation Set] Protein-coding and MicroRNA Biomarkers of Recurrence of Prostate Cancer Following Radical Prostatectomy

status: Public on Jun 01 2011

city: Atlanta

first: Gregory

last: Doho

state: GA

address: 1365B Clifton Rd NE

institute: Emory University

summary: To identify biomarkers predictive of biochemical recurrence, we isolated the RNA from 70 formalin-fixed paraffin-embedded (FFPE) radical prostatectomy specimens with known long term outcome to perform DASL expression profiling with a custom-designed panel of 522 prostate cancer relevant genes that we designed.  We identified a panel of ten protein-coding genes and two miRNA genes that could be used to separate patients with and without biochemical recurrence (p < 0.001), as well as for the subset of 42 Gleason score 7 patients (p < 0.001). We performed an independent validation analysis on 40 samples and found that the biomarker panel was also significant at prediction of recurrence for all cases (p = 0.013) and for a subset of 19 Gleason score 7 cases (p = 0.010), both of which were adjusted for relevant clinical information including T-stage, PSA and Gleason score.  Importantly, these biomarkers could significantly predict clinical recurrence for Gleason 7 patients.  These biomarkers may increase the accuracy of prognostication following radical prostatectomy using formalin-fixed specimens.

overall_design: Total RNA prepared from FFPE cores from prostatectomy samples of 70 patients were used for the training phase (29 with biochemical recurrence and 41 controls).  All samples were analyzed by both custom Prostate DASL of 522 genes and by Illumina miRNA microarray.  Subsequently in the validation phase, samples from 40 patients were used on the same platforms (13 with biochemical recurrence and 27 controls).  For the training set, 45 cases were from Sunnybrook Health Science Center (Toronto, ON), and 25 patients from Emory University.  For the validation set, all samples were from Emory University.  Relevant clinical metadata included are PSA, T-stage, and Gleason Score.

first: Qi

last: Long

first: Brent

last: Johnson

first: Adeboye

middle: O

last: Osunkoya

first: Yu-Heng

last: Lai

first: Wei

last: Zhou

first: Mark

last: Abramovitz

first: Mingjing

last: Xia

middle: B

last: Bouzyk

first: Robert

last: Nam

first: Linda

last: Sugar

first: Aleksandra

last: Stanimirovic

first: Brian

last: Leyland-Jones

first: Arun

last: Seth

first: John

last: Petros

first: Carlos

last: Moreno


title: Mycobacterium tuberculosis H37Rv strains: Control vs. Linezolid.

status: Public on Oct 11 2011

city: Changchun

first: Lu

last: Yu

address: Xi'an Road 5333

country: China

institute: Jilin university

summary: Transcriptional profiling of Mycobacterium tuberculosis H37Rv strains comparing control DMSO treated strains with Linezolid treated strains. Goal was to determine the effects of Linezolid against Mycobacterium tuberculosis H37Rv strains.

overall_design: Two-condition experiment,control DMSO treated strains vs. Linezolid treated strains. Biological replicates: 2 control replicates, 2 Linezolid replicates.

first: Junchao

last: Liang


title: Stability of miRNA in FFPE tumour samples exhibiting degraded mRNA [Bladder samples]

first: Jan

last: Taylor

overall_design: 141 bladder cancer samples hybridised to Exon arrays

last: Hall

first: Janet

first: Amanda

last: Eustace

first: Helen

last: Valentine

first: Joely

last: Irlam

first: Crispin

last: Miller

first: Catharine

last: West


title: [Gene Expression Validation Set] Protein-coding and MicroRNA Biomarkers of Recurrence of Prostate Cancer Following Radical Prostatectomy

first: Gregory

last: Doho

first: Qi

last: Long

first: Brent

last: Johnson

first: Adeboye

last: Osunkoya

first: Yu-Heng

last: Lai

first: Wei

last: Zhou

first: Mark

last: Abramovitz

first: Mingjing

last: Xia

last: Bouzyk


title: Transcriptomic Responses of Synechocystis sp. PCC 6803 Encapsulated in Silica Gel

status: Public on Apr 24 2012

city: Corvallis

first: Markael

middle: D.

last: Luterra

state: OR

address: 116 Gilmore Hall

department: Biological and Ecological Engineering

institute: Oregon State University

summary: Global gene expression of Synechocystis sp. PCC 6803 encapsulated in silica gel was examined by microarray analysis. Cultures were encapsulated in gels derived from aqueous precursors and gels derived from alkoxide precursors and incubated under constant light for 24 hours prior to RNA extraction. Cultures suspended in liquid media were also exposed to 500 mM salt stress and incubated under identical conditions, for comparison purposes.  The expression of 414 genes was significantly altered by encapsulation in aqueous-derived gels (fold change >/= 1.5 and P-value < 0.01), the expression of 1143 genes were significantly altered by encapsulation in alkoxide derived gels, and only 243 genes were common to both encapsulation chemistries. Additional qRT-PCR analyses of four select genes; ggpS, cpcG2, slr5055, and sll5057, confirmed microarray results. These results illustrate that encapsulation stress is quite different than salt stress in terms of gene expression response. Furthermore, a number of hypothetical and unknown proteins associated with encapsulation and alcohol stress have been identified, with implications for improving encapsulation protocols and rationally engineering microorganisms for direct biofuel production.

overall_design: 16 samples; 4 biological replicates each of 4 treatments

first: David

last: Dickson

first: Roger

last: Ely


title: Neural Committed Progenitors SAGE library

status: Public on Dec 09 2005

city: Ottawa

first: Theodore

last: Perkins

state: ON

address: 501 Smyth Rd.

department: Cellular and Molecular Medicine

country: Canada

institute: Ottawa Hospital Research Institute

summary:
After 10-12 days in culture as neurospheres, the cells were cultured and plated on 5ug/ml poly-L-ornithine (1 hr RT, dry) and 10ug/ml laminin (O/N 4degC, dry) in stem cell differentiation medium. The cells were harvested 2 days later.
Keywords: other

overall_design: this experiment include 1 samples and 1 replicates


title: [Gene Expression Training Set] Protein-coding and MicroRNA Biomarkers of Recurrence of Prostate Cancer Following Radical Prostatectomy

overall_design:
Total RNA prepared from FFPE cores from prostatectomy samples of 70 patients were used for the training phase (29 with biochemical recurrence and 41 controls). All samples were analyzed by both custom Prostate DASL of 522 genes and by Illumina miRNA microarray. Subsequently in the validation phase, samples from 40 patients were used on the same platforms (13 with biochemical recurrence and 27 controls). For the training set, 45 cases were from Sunnybrook Health Science Center (Toronto, ON), and 25 patients from Emory University. For the validation set, all samples were from Emory University. Relevant clinical metadata included are PSA, T-stage, and Gleason Score.

***This submission represents the mRNA component of the study

first: Robert

last: Nam

first: Linda

last: Sugar

first: Aleksandra

last: Stanimirovic

first: Brian

last: Leyland-Jones

first: Arun

last: Seth

first: John

last: Petros

first: Carlos

last: Moreno


title: Protein-coding and MicroRNA Biomarkers of Recurrence of Prostate Cancer Following Radical Prostatectomy

first: Gregory

last: Doho

type:
Expression profiling by array
Non-coding RNA profiling by array

overall_design: Refer to individual Series


title: [miRNA Training Set] Protein-coding and MicroRNA Biomarkers of Recurrence of Prostate Cancer Following Radical Prostatectomy

first: Qi

last: Long

first: Brent

last: Johnson

first: Adeboye

last: Osunkoya

last: Lai


title: mRNA expression data of 62 human medulloblastoma tumors

status: Public on Sep 02 2008

city: Amsterdam

first: Richard

last: Volckmann

state: Noord-Holland

address: van der Boechorststraat 6a

department: Laboratory of Experimental Oncology and Radiobiology

country: Netherlands

institute: msterdam UMC and University of Amsterdam

summary:
To identify molecular subtypes of medulloblastoma we have profiled a series of 62 medulloblastoma tumors. Unsupervised hierarchical cluster analysis of these data identified 5 distinct molecular subtypes.
Manuscript submitted. Title: Identification of medulloblastoma subtypes with distinct genetic profiles, pathway signatures and clinicopathological features. Authors: Marcel Kool, Jan Koster, Jens Bunt, Nancy E. Hasselt, Arjan Lakeman, Peter van Sluis, Dirk Troost, Netteke Schouten – van Meeteren, Huib N. Caron, Alan Mršić, Bauke Ylstra, Wieslawa Grajkowska, Wolfgang Hartmann, Torsten Pietsch, David Ellison, Steven C. Clifford, Rogier Versteeg.
Keywords: tumor classification

overall_design: 62 human medulloblastoma samples were analzyed

first: Marcel

last: Kool

first: Torsten

last: Pietsch

first: Steven

last: Clifford

first: Rogier

last: Versteeg