title: Gene expression profiling of Human Umbilical Vein Endothelial Cells (HUVEC) after treatment with Erg or control antisense (GeneBloc)

status: Public on Feb 27 2012

city: London

first: Graeme

middle: Miles

last: Birdsey

address: Hammersmith Hospital, Du Cane Road

department: National Heart and Lung Institute

institute: Imperial College London

summary: The endothelial transcription factor Erg (Ets Related Gene) plays an important role in homeostasis and angiogenesis by regulating many endothelial functions including survival and junction stability. Here we show that Erg regulates endothelial cell migration. Transcriptome profiling of Erg-deficient endothelial cells (EC) identified 80 genes involved in cell migration as candidate Erg targets, including regulators of the Rho GTPases. Inhibition of Erg expression in human umbilical vein endothelial cells (HUVEC) resulted in decreased migration in vitro, whilst Erg over-expression using adenovirus caused increased migration. Live-cell imaging of Erg-deficient HUVEC showed a reduction in lamellipodia, in line with decreased motility. Both actin and tubulin cytoskeletons were disrupted in Erg-deficient EC, with a dramatic increase in tubulin acetylation. Amongst the most significant microarray hit was the cytosolic histone deacetylase (HDAC)-6, a regulator of cell migration. Rescue experiments confirmed that HDAC6 mediates the Erg-dependent regulation of tubulin acetylation and actin localization.

overall_design: The functional role of Erg in EC was studied by gene expressing profiling using three separate HUVEC isolates treated with either control antisense or Erg-specific antisense for 24 or 48 hours.

first: Nicola

middle: H

last: Dryden

first: Aarti

last: Shah

first: Rebecca

last: Hannah

first: Matthew

last: Hall

first: Dorian

middle: O

last: Haskard

first: Maddy

last: Parsons

first: Justin

last: Mason

first: Marketa

last: Zvelebil

first: Berthold

last: Gottgens

first: Anne

last: Ridley

first: Anna

last: Randi


title: Profiling of cell cycle-related or cancer-related genes dysregulated by knockdown of MYC or lncRNAs using Nanostring Gene Expression Assay

status: Public on Jul 04 2012

city: Columbus

first: Taewan

last: Kim

state: OH

country: USA

institute: The Ohio State University

summary: Identification of cell cycle-related or cancer-related genes dysregulated by knockdown of MYC or lncRNAs in colorectal cancer-derived HCT116 or prostate cancer-derived PC3.

overall_design: Using siRNAs targeting MYCLos, the cells were transfected and RNA samples from the treated cells were subjected to Nanostring Gene Expression Assay.

first: Hansjuerg

last: Alder


title: microRNA expression patterns of lung metastasis samples distinguish patients with high vs. low rates of metastasis

status: Public on Jun 13 2012

city: Chicago

first: Jianrong

last: Li

state: IL

address: 909 S Wolcott Avenue

department: Medicine

institute: University of Illinois at Chicago

summary:
Background: Many strategies to define subtypes and treat cancer relies on a presumption of either localized or widespread (poly)metastatic disease. We proposed an intermediate state of metastasis termed oligometastasis(es) characterized by limited metastatic progression and amenable to treatment by localized methods e.g. surgery or radiotherapy.
Methods: To understand the biological basis of oligometastatic and polymetastatic progression, we analyzed microRNA expression patterns from lung tumor samples of patients with less than five metastases at first metastasis presentation and treated with metastasis-directed surgery.
Results: Patients were stratified into four subgroups of oligo- and poly-metastatic progression based on the rate of metastatic progression over follow-up period. We prioritized microRNAs between the extremes of oligo- vs. poly-metastatic progression and validated their capacity to distinguish these phenotypes and predict survival in an independent validation dataset.
Conclusions: Our results provide further evidence for the biological underpinnings of oligometastasis(es) and potential microRNA candidates to predict progression trajectories of patients and optimize corresponding metastasis-directed treatment.

overall_design: We collected tumor samples from 63 patients that (i) had between one and five metastasis(es) at first metastatic presentation and no clinical or radiologic evidence of metastases in the pleural, peritoneal, pericardial or retroperitoneal cavities,(ii) at the time of lung surgery, had every site of known metastases  treated with definitive intent, and (iii) had a minimum of 16 months of follow-up after surgery was required. Total RNA were derived from FFPE metastatic tissue samples. Patient samples were subsequently classified into 3 groups: those from patients with high, intermediate and low rates of progression.

first: Yves

middle: A

last: Lussier

first: Nikolai

middle: N

last: Khodarev

first: Kelly

last: Regan

first: Kimberly

last: Corbin

first: Haiquan

first: Sajid

last: Khan

first: Sabha

last: Ganai

first: Jennifer

last: Gnerlich

first: Thomas

middle: E

last: Darga

first: Hanli

last: Fan

first: Yong

last: Huang

first: Oleksiy

last: Karpenko

first: Mitchell

middle: C

last: Posner

first: Steven

middle: J

last: Chmura

first: Samuel

last: Hellman

first: Mark

middle: K

last: Ferguson

first: Ralph

middle: R

last: Weichselbaum


title: Expression of RpoN molecular roadblock in Pseudomonas aeruginosa PAO1 in rich media

status: Public on Feb 09 2012

city: Syracuse

first: Christopher

last: Nomura

state: NY

address: 1 Forestry Dr.

department: Chemistry

institute: SUNY-ESF

summary:
The bacterial transcription factor RpoN regulates an extensive network of genes whose products are involved in diverse biological functions.  We constructed a small peptide termed the RpoN molecular roadblock, which binds to and blocks transcription from RpoN promoters.  This RpoN molecular roadblock can be used in any bacterium to obtain information on the RpoN regulon.
We expressed the RpoN molecular roadblock in P. aeruginosa PAO1 and used microarrays to identify genes that were differentially transcribed due to the RpoN molecular roadblock.

overall_design: The RpoN molecular roadblock was expressed in P. aeruginosa PAO1 in mid-exponential phase in rich media.  Total RNA was isolated and prepped for Affymetrix GeneChips.

first: Benjamin

last: Lundgren

middle: T


title: DUX4 activates germline genes, retroelements and immune-mediators: Implications for facioscapulohumeral dystrophy

status: Public on Jan 03 2012

city: Seattle

first: Stephen

last: Tapscott

state: WASHINGTON

address: 1100 Fairview N. Ave

department: Human Biology

institute: Fred Hutch Cancer Research Center

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Facioscapulohumeral dystrophy (FSHD) is one of the most common inherited muscular dystrophies. The causative gene remains controversial and the mechanism of pathophysiology unknown. Here we identify genes associated with germline and early stem cell development as targets of the DUX4 transcription factor, a leading candidate gene for FSHD. The genes regulated by DUX4 are reliably detected in FSHD muscle but not in controls, providing direct support for the model that misexpression of DUX4 is a causal factor for FSHD. Additionally, we show that DUX4 binds and activates LTR elements from a class of MaLR endogenous primate retrotransposons and suppresses the innate immune response to viral infection, at least in part through the activation of DEFB103, a human defensin that can inhibit muscle differentiation. These findings suggest specific mechanisms of FSHD pathology and identify candidate biomarkers for disease diagnosis and progression.

overall_design: Examine Dux4 full isoform binding sites in human fibroblast.

first: Linda

last: Geng

first: Zizhen

last: Yao


title: Gene expression analysis of Chronic rhinosinusitis

status: Public on Mar 28 2012

first: Atsushi

last: Kato

address: 240 E. Huron St.

department: Allergy-Immunology Division

institute: Northwestern University Feinberg School of Medicine

summary: Chronic rhinosinusitis (CRS) is a heterogeneous disease characterized by local inflammation of the upper airways which persists for at least 12 weeks. CRS is one of the most common chronic diseases in adults in the United States, affecting over 30 million Americans. CRS is frequently divided into 2 types: CRS with nasal polyps (CRSwNP) and CRS without nasal polyps (CRSsNP). Histologic studies have demonstrated significant tissue eosinophilia in CRSwNP. T cells in the mucosa are elevated in both forms of CRS and are skewed towards Th2 cytokine expression in CRSwNP.  However pathogenic role of CRS has not been fully explored. To screen for pathogenic factors in CRS, we performed a microarray study. We collected uncinate tissues (UT) from 6 subjects with CRSsNP, 6 subjects with CRSwNP and 6 control subjects and nasal polyp (NP) tissues from 6 subjects with CRSwNP and then evaluated gene expression profiles using Affymetrix Human Genome U133 plus 2.0 array.

overall_design: We collected UT from control subjects and pathients with CRSsNP and CRSwNP, and nasal polyp tissues from  patients with CRSwNP. Gene expression profiles were evaluated using  Human Genome U133 plus 2.0 array (Affymetrix).

first: Chris

first: Anuk

last: Das

first: Robert

last: Kern

middle: P

last: Schleimer


title: Identification of a responsive gene set to evaluate the potential impact of seismic exposure on Atlantic salmon (Salmo salar) inner ear

status: Public on Feb 28 2012

city: St. John's

first: Catherine

middle: Dawn

last: Andrews

state: NL

address: 80 East White Hills Road

department: Science Branch

country: Canada

institute: Fisheries and Oceans Canada

summary: Considerable interest and controversy has arisen over the potential effects of seismic surveys carried out during exploration for oil and gas deposits. Regarding fish, there is a concern that intense sound sources, such as seismic airguns, may injure their auditory system. In this study, salmonid cDNA microarrays and quantitative reverse transcription – polymerase chain reaction (QPCR) were used to identify and study a responsive gene set in the inner ear of Atlantic salmon (Salmo salar) following seismic airgun exposure. Microarray analyses on pooled seismic exposed inner ear RNA versus pooled control inner ear RNA revealed 79 unique transcripts (passing background threshold) that were greater than 1.75-fold differentially-regulated by acoustic stress on at least 3 of the 4 slides in the study (including at least one dye-swap). QPCR analyses of 8 microarray-identified transcripts of interest revealed a significant up-regulation (P<0.05) of transcripts encoding nicotinamide riboside kinase 2 (1.89-fold) and hemoglobin subunit alpha-4 (3.78-fold), and a significant down-regulation (P<0.05) of a transcript encoding C14orf159 protein (1.35-fold). QPCR analyses also confirmed an overall up-regulation of transcripts encoding growth hormone I (7.78-fold), c-type lectin receptor A (2.20-fold) and retinol binding protein I (1.24-fold), however these differences were not considered to be statistically significant (P<0.05) due to the high biological variability in the seismic exposed group for these transcripts of interest. Initial results demonstrate that genomics has the potential to greatly enhance our understanding of the impact of seismic airguns on gene and molecular pathways involved in hearing, and provide valuable molecular biomarkers that can act as an early warning sensor to acoustic stress.

platform_organism:
Osmerus mordax
Oncorhynchus mykiss
Salmo salar
Coregonus clupeaformis
Oncorhynchus tshawytscha

overall_design: Juvenile Atlantic salmon (Salmo salar) smolt were obtained from North Water Products Ltd., Daniel’s Harbour, NL and held at ambient seawater temperature, in a flow-through system supplied with air at the Northwest Atlantic Fisheries Centre, St. John’s, NL. Two weeks prior to seismic airgun exposures, fish were divided into two 1m3 cages, one each for control (non-exposed) and exposed groups, in a 15,000L aquarium at ambient seawater temperature (0.2°C). Each cage was placed the same distance from the water intake and airstones were placed next to each cage. Fish were fasted for two days prior to exposure. Sixteen control (non-exposed) fish from one cage were sampled prior to seismic activity. Immediately following sampling of control fish, seventeen fish in the remaining cage were placed 2m from a 10in3 Texas Instruments airgun. Fish were subjected to 50 exposures, 1 exposure every 10 seconds, at an average sound pressure level of 204 dB peak-to-peak relative to 1µPa; considered to be a worse case scenario within a few hundred meters of a survey vessel. Seventeen seismic exposed fish were sampled 16 h following exposure. The only aquarium available that was suitable for seismic airgun exposures was not designed to have a regulated photoperiod. For this reason the fish were held under a constant daylight regime. Fish were collected by dip-net and euthanized by severing the spinal cord. The inner ears from each salmon were removed, placed immediately in RNase-free 2 ml tubes, and then flash frozen in liquid nitrogen. RNA isolated from the right inner ear of the 12 seismic exposed and 12 control individuals that gave the highest total RNA yields were used to generate 2 mRNA pools (a “seismic” pool and a “control” pool). Each sample contributed 4.0 µg column purified total RNA to each pool. Comparisons were made for the seismic exposed mRNA pool compared to the control (non-exposed) mRNA pool using the consortium for Genomic Research on All Salmonids Project (cGRASP) 16K (salmonid) cDNA array and the 3DNA Array 900 Detection Kit and instructions (Genisphere). Technical quadruplicate slides including 2 dye-swaps were run for the comparison.     Slide GG003_011: Cy5-labeled control ear, Cy3-labeled seismic  Slide GG003_012: Cy5-labeled control ear, Cy3-labeled seismic  Slide GG003_013: Cy3-labeled control ear, Cy5-labeled seismic  Slide GG003_014: Cy3-labeled control ear, Cy5-labeled seismic

middle: D

first: Jerry

middle: F

last: Payne

first: Matthew

middle: L

last: Rise


title: Microarray analysis of Atelp2, npr1 and wild type (Col-0) infected with the avirulent bacterial pathogen  Pst DC3000/avrRpt2

status: Public on Jun 30 2012

city: Gainesville

first: Zhonglin

last: Mou

state: FL

address: 981 Museum Road

department: Microbiology and Cell Science & Plant Molecular and Cellular  Biology

institute: University of Florida

summary: The goal of the microarray experiment was to determine the induction kinetics of transcriptome changes in the Arabidopsis mutant Atelp2, npr1 and wild type in response to infection of the avirulent bacterial pathogen Pst DC3000/avrRpt2.  Results indicated that Atelp2 exhibited slower kinetcis of transcriptional changes than the wild type after Pst DC3000/avrRpt2 infection, whereas npr1 did not show significant alteration in the induction kinetics.

overall_design: Three biological replicates with leaves from 8 plants per sample were collected at 0, 4, 8, and 12 hours after inoculation with the avirulent bacterial pathogen Pst DC3000/avrRpt2.  After extraction, RNA concentration was determined on a NanoDrop Spectrophotometer (Thermofisher Scientific, Waltham, MA) and sample quality was assessed using the 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).  Each replicate was used as one sample for microarray analysis.

first: Yongsheng

last: Wang

first: Yanping

last: Zhang

first: Jin

first: Yijun

last: Sun


title: HIV/HCV coinfection activates a type 1 interferon response in monocytes that correlates with cognitive impairment

status: Public on Jun 07 2012

city: San Francisco

first: Bing

state: CA

address: B1, R103, 4150 Clement St

institute: San Francisco VA Medical Center

summary: Chronic immune activation is a hallmark of human immunodeficiency virus (HIV) infection and the best prognostic indicator of disease progression. Suppressing HIV viremia by antiretroviral therapy (ART) restores normal immune response and effectively prolongs life. In HIV-infected individuals who are coinfected with hepatitis C virus (HCV) the immune system is activated despite effective HIV antiretroviral therapy controlling viral load. Here we examined CD14+ monocyte gene expression by high-density microarray analysis and T cell subsets, CD4 and CD8, by flow cytometry to characterize immune activation in monoinfected HCV, monoinfected HIV and HIV/HCV coinfected subjects with undetected HIV viral load. To determine the impact of coinfection on cognition, subjects were evaluated in 7 domains for neuropsychological (NP) performance, which was summarized as global deficit scores (GDS). Gene expression analysis of CD14+ monocytes from coinfected subjects revealed an elevated type 1 interferon (IFN) response profile unique to coinfection. For both CD4 and CD8 T cells, coinfection triggered significantly increased expression of activation markers CD38 and HLA-DR. In the coinfected group, mild cognitive impairment was associated with a type 1 IFN monocyte response but not plasma lipopolysaccharide. These observations raise the possibility that cognitive impairment evident in the HIV/HCV population is associated with the IFN response detected in coinfected individuals.

overall_design: Monocytes isolated from healthy controls (n=17), HCV monoinfected (n=19) and HIV/HCV coinfected (n=17) were analyzed for gene expression using high-density microarrays. Whole blood was collected in Vacutainer CPT tubes (BD Biosciences) and PBMCs were enriched by centrifugation. Typically, three million CD14+ monocytes were isolated from 30 ml of whole blood using an anti-CD14 monoclonal antibody immunomagnetic - ferrous bead conjugate according to the manufacturer’s instructions (Miltenyi Biotech). Monocyte purity exceeded 97% with <1% T or B cell contamination as determined by flow cytometry. Monocyte RNA was isolated using a Qiagen RNeasy Micro Kit with an RNA integrity value exceeding 9. Complementary DNA was synthesized and labeled with biotin (iExpress iAmplify kit, Applied Microarrays) and hybridized to Codelink Whole Human Genome Bioarrays (55K probes, Applied Microarrays). Slides were scanned (Axon GenePix 4000B, Molecular Devices), analyzed (CodeLink Expression Software Kit v4.1) and microarray data were normalized with loess normalization using R and Bioconductor package. Determination of differential gene expression and multiple testing correction / false discovery rate adjustments were performed using GeneSpring GX 7.3 software package (Agilent). Microarray data was analyzed using a variety of custom data analytic techniques for gene expression profile identification as described previously. Correlations were determined by Spearman rank correlation coefficient.

first: Hans

last: Rempel

first: Lynn

last: Pulliam


title: Expression data from patients with Essentiel Thrombocythemia (ET), Polycythemia Vera (PV), Primary Myelofibrosis (PMF) and control subjects

status: Public on Jan 10 2012

city: Roskilde

first: Vibe

last: Skov

address: Koegevej 7-13

department: Hematology

country: Denmark

institute: Roskilde Hospital

summary: We used microarrays to assess gene expression in patients with ET, PV, and PMF compared to control subjects

overall_design: Total RNA was purified from whole blood and amplified to biotin-labeled aRNA and hybridized to microarray chips.

first: Hans-Carl

last: Hasselbalch


title: Gene expression in primate postnatal brain through lifespan

status: Public on Dec 09 2011

city: Leipzig

first: Mehmet

last: Somel

address: Deutscher Platz 6

department: Evolutionary Genetics

country: Germany

institute: Max Planck Institute for Evolutionary Anthropology

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

sample_organism:
Macaca mulatta
Pan troglodytes
Homo sapiens

overall_design: Refer to individual Series


title: Global microRNA expression profiling of high-risk ER+ breast cancers from patients receiving adjuvant Tamoxifen mono-therapy: a DBCG study

status: Public on Apr 19 2012

city: Lund

first: Rolf

last: Søkilde

address: Scheelevägen 2

department: Department of Oncology

country: Sweden

institute: Lund University, Sweden

summary: Purpose: Despite the benefits of estrogen receptor (ER)-targeted endocrine therapies in breast cancer, many tumors develop resistance. MicroRNAs (miRNAs) have been suggested as promising biomarkers and we here evaluated whether a miRNA profile could be identified, sub-grouping ER+ breast cancer patients treated with adjuvant Tamoxifen with regards to probability of recurrence.  Experimental design: Global miRNA analysis was performed on 152 ER+ primary tumors from high-risk breast cancer patients with an initial discovery set of 52 patients, followed by 2 independent test sets (N=60 and N=40). All patients had received adjuvant Tamoxifen as mono-therapy (median clinical follow-up: 4.6 years) and half had developed distant recurrence (median time-to-recurrence: 3.5 years). MiRNA expression was examined by unsupervised hierarchical clustering and supervised analysis, including clinical parameters as co-variables.

platform_organism:
Homo sapiens
Human alphaherpesvirus 1
Human betaherpesvirus 5
Murid betaherpesvirus 1
human gammaherpesvirus 4
JC polyomavirus
Human immunodeficiency virus 1
Murid gammaherpesvirus 4
Human gammaherpesvirus 8
Betapolyomavirus hominis
Betapolyomavirus macacae

overall_design: 3 parts of microRNA profiling of ER+ breast cancer samples

first: Maria

middle: B

last: Lyng

first: Anne-Vibeke

last: Lænkholm

first: Karina

last: Gravgaard

first: Thomas

last: LItman

first: Henrik

last: Ditzel


title: Noncoding RNA expression in myocardium from infants with tetralogy of Fallot

status: Public on Jul 12 2012

city: Kansas City

first: Douglas

last: Bittel

state: MO

address: 2401 Gillham Rd

department: Genetics research

institute: Childrens Mercy Hospital

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

platform_organism:
Homo sapiens
synthetic construct


title: Gene regulation in macrophages from irradiated tumors

status: Public on Dec 07 2011

city: Portland

first: Michael

last: Gough

state: OR

address: 4805 NE Glisan St

department: Earle A Chiles Research Institute

institute: Providence Cancer Center

summary:
Tumors engender an environment dominated by M2 differentiated tumor macrophages that support tumor invasion, metastases and escape from immune control. In this study, we demonstrate that following radiation therapy of tumors in mice there is an influx of tumor macrophages that polarize towards wound repair and immune suppression.
To investigate changes in the phenotype of tumor macrophages following radiation therapy, we FACS sorted tumor macrophages from Panc02 tumors. We have previously shown that we can distinguish mature tumor macrophages from immature myeloid and MDSC populations by expression of Gr1 and IA (MHC class II). To isolate these sub-populations, we first gated CD11b+ cells in the untreated or irradiated tumors, then sorted the CD11b+IA+ macrophage population and the CD11b+Gr1hi MDSC population. Cytospins of the sorted populations demonstrates that the CD11b+Gr1hi MDSC predominantly have a granulocyte morphology and the CD11b+IA+ cells have a macrophage morphology in both the untreated and irradiated tumors. RNA was purified from CD11b+IA+ macrophages from untreated or irradiated tumors 1 day or 7 days following radiation therapy and Gene Expression Microarray analysis was performed.

overall_design: There are untreated and irradiated samples at time points 1 day and 7 days following radiation therapy. The experiment was repeated in entirety, generating a second gene array sample for each. For analysis, the untreated samples of 1 day and 7 days were grouped together.


title: A gene co-expression network in whole blood of schizophrenia patients is independent of antipsychotic-use and enriched for brain-expressed genes [HumanHT-12 V3.0]

status: Public on Jul 09 2012

city: Los Angeles

first: Simone

last: de Jong

state: California

address: 695 Charles E. Young Drive south

institute: UCLA

summary: Gene expression analyses in whole blood reveal a network of genes related to schizophrenia

overall_design: Weighted gene co-expression analyses applied to human whole blood gene expression data of schizophrenia cases and healthy controls

first: Marco

last: Boks

first: Tova

last: Fuller

first: Eric

last: Strengman

first: Esther

last: Janson

first: Carolien

middle: G

last: de Kovel

first: Anil

last: Ori

first: Nancy

last: Vi

first: Flip

last: Mulder

first: Jan

last: Blom

first: Birte

last: Glenthoj

first: Chris

last: Schubart

first: Wiepke

last: Cahn

first: Rene

last: Kahn

first: Steve

last: Horvath

first: Roel

last: Ophoff


title: A Map of Copy Number Variations in Chinese Populations

status: Public on Dec 31 2011

city: Shanghai

first: Haiyi

last: Lou

address: 320 Yueyang Road

country: China

institute: CAS-MPG PICB

summary:
It has been shown that the human genome contains extensive copy number variations (CNVs). Investigating the medical and evolutionary impacts of CNVs requires the knowledge of locations, sizes and frequency distribution of CNVs within and between populations. However, CNV study of Chinese populations has been underrepresented considering the same efforts in other populations.
Here we constructed a Chinese CNV map by using Affymetrix SNP 6 array. We did population analysis with other HapMap populations and identified population specific CNVs as well as candidate CNV regions under selection. Our results serve as a useful resource in further evolutionary and medical studies.

overall_design: There are 155 samples included in the analysis

first: Shilin

last: Li

first: Yajun

last: Yang

first: Xin

last: Zhang

first: Bailin

last: Wu

first: Li

last: Jin

first: Shuhua

last: Xu


title: miRNA expression signatures in gastrointestinal stromal tumors (GISTs)

status: Public on Nov 01 2011

city: Sapporo

first: Hiromu

last: Suzuki

state: Hokkaido

address: S1, W17, Chuo-ku

department: Department of Molecular Biology

country: Japan

institute: Sapporo Medical University

summary: To clarify the microRNA (miRNA) expression signatures in gastrointestinal stromal tumors (GISTs), a series of 32 GIST specimens were analyzed using Agilent miRNA microarray V3. Unsupervised hierarchical clustering revealed that GISTs can be categorized into 2 groups according to the expression of a miRNA cluster encoded on chromosome 14q32.31.

overall_design: Total RNA was extracted from 32 fresh frozen GIST specimens obtained from surgical resections. Expression of 851 miRNAs was analyzed using Human miRNA Microarray V3 (Rel 12.0 G4470C; Agilent technologies, Santa Clara, CA, USA). Risk grade was assessed according to the risk definition system proposed by Fletcher et al. (Hum Pathol. 2002;33:459-65.)

first: Minoru

last: Toyota


title: Gene expression in primate postnatal brain through lifespan - cerebellar cortex

first: Mehmet

last: Somel

summary:
We investigated molecular changes during human, chimpanzee, and rhesus macaque postnatal brain development at the transcriptome, proteome, and metabolome levels in two brain regions: the prefrontal cortex (PFC) that is involved in several human-specific cognitive processes, and the cerebellar cortex (CBC) that may be functionally more conserved. We find a nearly three-fold excess of human-specific gene expression changes in PFC compared to CBC. The most prominent human-specific mRNA expression pattern in the PFC is a developmental delay of approximately 5 years in the expression of genes associated with learning and memory, such as synaptic transmission and long-term potentiation. This pattern is supported by correlated changes in concentrations of proteins and the respective neurotransmitters and its magnitude is beyond the shift expected from the life-histories of the species. Mechanistically, it might be driven by change in timing of expression of four or more transcription factors. We speculate that delayed synaptic maturation in PFC may play a role in the emergence of human-specific cognitive abilities.

Keywords: Age series

overall_design:
Human, chimpanzee and rhesus macaque post-mortem brain samples from the cerebellar cortex were collected. The age ranges of the individuals in all three species covered the respective species' postnatal maturation period from infancy to old adulthood. RNA extracted from the dissected tissue was hybridized to Affymetrix® Human Gene 1.0 ST arrays.

CBC samples.

first: Xiling

last: Liu

first: Lin

last: Tang

first: Zheng

last: Yan

first: Song

last: Guo

first: Philipp

last: Khaitovich


title: DNA microarrays of Turner Syndrome induced pluripotent stem cells

status: Public on Oct 04 2011

city: guangzhou

first: wang

last: xianming

institute: Guangzhou Institutes of Biomedicine and Health,Chinese Academy of Sciences

summary: We have generated iPSCs from monosomy X (Turner Syndrome), trisomy 8 (Warkany Syndrome 2), trisomy 13 (Patau Syndrome) and partial trisomy 11;22 (Emanuel Syndrome), using either skin fibroblasts from affected individuals or amniocytes from antenatal diagnostic tests. These cell lines stably maintain the karyotype of the donors and behave like embryonic stem cells (ESCs) in all tested assays. Turner Syndrome iPSCs were used for further studies including global gene expression analysis and tissue-specific directed differentiation. Multiple clones displayed lower levels of the pseudoautosomal genes ASMTL and PPP2R3B than the controls. Moreover, they could be transformed into neural-like, hepatocyte-like and heart-like cells but displayed insufficient up-regulation of the pseudoautosomal placental gene CSF2RA during embryoid body (EB) formation. These data support that abnormal organogenesis and early lethality in Turner Syndrome are not caused by a tissue-specific differentiation blockade but rather involves other abnormalities including impaired placentation.

overall_design: Global gene expression profiling with DNA microarrays showed that 3 TS iPSC clones corresponding to the same patient showed a global gene expression pattern similar to ESCs and euploid iPSCs, and very different from donor cells .We detected transcriptomic changes between TS iPSCs and the other ESCs/iPSCs but these variations did not follow a pattern and in fact all pluripotent cell lines clustered together. For DNA microarray analysis, all cells were treated with Trizol, followed by RNA extraction and hybridization.

first: Wen

first: Xianming

last: Wang

first: Wenxia

last: Fan


title: Global gene expression profile of mouse ESC-2i, EpiSC-CHIR/XAV and EpiSC-FGF2/activin

status: Public on Aug 19 2011

city: los angeles

first: Qilong

last: Ying

address: 1425 san pablo st BCC509b

institute: USC

summary:
The requirements for self-renewal differ between EpiSCs and ES cells and the underlying mechanism is largely unknown. Here we show that mouse EpiSCs can be efficiently derived and robustly propagated even from single cells, using two small-molecule inhibitors: CHIR99021 and XAV939.
The whole-genome microarray analyses is performed to confirm the identity of EpiSC maintained in CHIR/XAV by comparing the expression profile in EpiSC-CHIR/XAV to those in ESC maintained in 2i and EpiSC maintained in FGF2/activin.

overall_design: Total RNA from ESC-2i, EpiSC-CHIR/XAV, and EpiSC-FGF2/activin were extracted for microarray analisys

first: Hoom

last: Kim

first: Chih-I

last: Tai


title: Gene Copy Number Aberrations are Associated with Survival in Histological Subgroups of Non-Small Cell Lung Cancer (expression data)

status: Public on Oct 28 2011

city: Uppsala

first: Anders

last: Isaksson

address: Akademiska sjukhuset ing61 3tr

institute: Uppsala University

summary:
Hypothesis: Non-small cell lung cancer (NSCLC) is characterized by a multitude of genetic aberrations with unknown clinical impact. In this study, we aimed to identify gene copy number changes that correlate with clinical outcome in NSCLC. To maximize the chance to identify clinically relevant events, we applied a strategy involving two prognostically extreme patient groups.

Results: Genetic aberrations were strongly associated with tumor histology. In adenocarcinoma (n=50), gene copy number gains on chromosome 8q21-q24.3 (177 genes) were more frequent in long-term survivors. In squamous cell carcinoma (n=28), gains on chromosome 14q23.1-24.3 (133 genes) were associated with shorter survival, whereas losses in a neighboring region, 14q31.1-32.33 (110 genes), correlated with favorable outcome. In accordance with copy number gains and losses, mRNA expression levels of corresponding genes were increased or decreased, respectively.

Conclusion: Comprehensive tumor profiling permits the integration of genomic, histologic and clinical data. We identified gene copy number gains and losses, with corresponding changes in mRNA levels, that were associated with prognosis in adenocarcinoma and squamous cell carcinoma of the lung.

overall_design: Short-term (<20 months; n=53) and long-term survivors (>58 months; n=47) were selected from a clinically well-characterized NSCLC patient cohort with available fresh-frozen tumor specimens. The samples were analyzed using array-based gene expression profiling. The molecular data was combined with information on clinical parameters.

first: Patrick

last: Micke

first: Lars

last: Holmberg

first: Karolina

last: Edlund

first: Hanna

last: Göransson

first: Simon

last: Ekman

first: Michael

last: Bergqvist

first: Lena

last: Scheibenflug

first: Kristina

last: Lamberg

first: Gunnar

last: Myrdal

last: Berglund

first: Mats

last: Lambe

first: Fredrik

last: Nyberg

first: Andrew

last: Thomas

first: Johan

last: Botling


title: Dermal reprogramming through epidermal activation of beta-catenin

status: Public on Oct 13 2011

city: Cambridge

first: Kai

last: Kretzschmar

state: Cambridgeshire

address: Tennis Court Road

department: Wellcome Trust Centre for Stem Cell Research

country: United Kingdom

institute: University of Cambridge

summary: Hair follicle formation depends on reciprocal epidermal-dermal interactions and occurs during skin development, but not in adult life. This suggests that the properties of dermal fibroblasts change during postnatal development. To examine this, we used a PdgfraEGFP mouse line to isolate GFP-positive fibroblasts from neonatal skin, adult telogen and anagen skin and adult skin in which ectopic hair follicles had been induced (EF skin) by transgenic epidermal activation of beta-catenin. We also isolated epidermal cells from each mouse. The gene expression profile of EF epidermis was most similar to that of anagen epidermis, consistent with activation of beta-catenin signalling. In contrast, adult dermis with ectopic hair follicles more closely resembled neonatal dermis than adult telogen or anagen dermis. In particular, genes associated with mitosis were upregulated and extracellular matrix-associated genes were downregulated in neonatal and EF fibroblasts. We confirmed that sustained epidermal beta-catenin activation stimulated fibroblasts to proliferate to reach the high cell density of neonatal skin. In addition, the extracellular matrix was comprehensively remodelled, with mature collagen being replaced by collagen subtypes normally present only in developing skin. The changes in proliferation and extracellular matrix composition originated from a specific subpopulation of fibroblasts located beneath the sebaceous gland. Our results show that adult dermis is an unexpectedly plastic tissue that can be reprogrammed to acquire the molecular, cellular and structural characteristics of neonatal dermis in response to cues from the overlying epidermis.

overall_design: We have isolated the following populations of cells from mouse back skin by flow cytometry: 1A) GFP+ WT neonatal dermal fibroblasts, 1B) ItgA6+ WT neonatal epidermal keratinocytes, 2A) GFP+  WT telogen dermal fibroblasts, 2B)  ItgA6+ WT telogen epidermal keratinocytes, 3A) GFP+ D2 transient activation (anagen) dermal fibroblasts, 3B) ItgA6+ D2 transient activation (anagen) epidermal keratinocytes, 4A) GFP+ D2 sustained activation (ectopic follicles) dermal fibroblasts, 4B) ItgA6+ D2 sustained activation (ectopic follicles) epidermal keratinocytes

first: Charlotte

last: Collins

first: Fiona

middle: M

last: Watt


title: H. salinarum NRC-1 vs TFB knockouts and synthetic TFB constructs

status: Public on Aug 15 2011

first: Serdar

last: Turkarslan

state: WA

address: 401 Terry Ave

institute: Institute for Systems Biology

summary:
Numerous lineage-specific expansions of the transcription factor B (TFB) family in archaea suggests an important role for expanded TFBs in encoding environment-specific gene regulatory programs.  Given the characteristics of hypersaline lakes the unusually large numbers of TFBs in halophilic archaea further suggests that they might be especially important in rapid adaptation to the challenges of a dynamically changing environment. Motivated by these observations we have investigated the implications of TFB expansions by correlating sequence variations, regulation, and physical interactions of all seven TFBs in Halobacterium salinarum NRC-1 to their fitness landscapes, functional hierarchies, and genetic interactions across 2,488 experiments covering combinatorial variations in salt, pH, temperature, and Cu-stress. This systems analysis has revealed an elegant scheme in which completely novel fitness landscapes are generated by gene conversion events that introduce subtle changes to the regulation or physical interactions of duplicated TFBs.  Based on these insights we have introduced a synthetically redesigned TFB and altered the regulation of existing TFBs to illustrate how archaea can rapidly generate novel phenotypes by simply reprogramming their TFB regulatory network.

The purpose of this gene expression study was to show that reprogrammed synthetic TFB (TFBx) variants are rewired into the gene regulatory network and create global transcriptional changes.

overall_design: The relative changes in transcript levels and transcriptome structure at 37°C and 25°C were determined for wild type, tfbD and tfbE in frame deletion knockouts and all recombinant strains transformed with a plasmid carrying the synthetic TFB constructs. The strains were batch cultured in flasks at either 25°C or 37°C with constant shaking, culture aliquots (~4 ml) were collected over early (OD600: ~0.2), mid (OD600: ~0.4) and late (OD600: ~0.8) phases of growth, centrifuged (16 000 g, 90 s), and flash frozen. Total RNA was prepared from the cell pellets using the mirVANA RNA kit (Ambion, Austin, TX) according to manufacturer's instructions. Whole-genome tiling arrays for H. salinarum NRC-1 were designed with e-Array (Agilent Technologies), using strand-specific 60 mer probes with 24nt spacing between adjacent probes for the main chromosome (NC_002607) and the plasmids pNRC200 (NC_002608) and pNRC100 (NC_001869). Altogether the array contained a total of 60K probes, including manufacturers' controls. The microarrays were printed by Agilent technologies. Labeling with Cyanine 3 (Cy3) and Cyanine5 (Cy5) dyes (Molecular Probes and Kreatech BV), hybridization, and washing were performed as described earlier (Baliga et al, 2004). Arrays were scanned in ScanArray (Perkin Elmer) and spot finding was done using Feature Extraction (Agilent Technologies). Normalization and statistical analysis were performed as described before (Koide et al, 2009).

first: Nitin

last: Baliga

first: Min

last: Pan


title: Microarray analyses of laser-captured hippocampus reveal distinct gray and white matter signatures associated with incipient Alzheimer’s disease

status: Public on Aug 01 2011

city: Lexington

first: Eric

last: Blalock

state: KY

address: 800 Rose St.

department: Molecular and Biomedical Pharmacology

institute: University of Kentucky

summary: Alzheimer's disease (AD) is a devastating neurodegenerative disorder that threatens to reach epidemic proportions as our population ages. Although much research has examined molecular pathways associated with AD, relatively few studies have focused on critical early stages. Our prior microarray study correlated gene expression in human hippocampus with AD markers. Results suggested a new model of early-stage AD in which pathology spreads along myelinated axons, orchestrated by upregulated transcription and epigenetic factors related to growth and tumor suppression (Blalock et al., 2004). However, the microarray analyses were performed on RNA from fresh frozen hippocampal tissue blocks containing both gray and white matter, potentially obscuring region-specific changes. In the present study, we used laser capture microdissection to exclude major white matter tracts and selectively collect CA1 hippocampal gray matter from formalin-fixed, paraffin-embedded (FFPE) hippoc ampal sections of the same subjects assessed in our prior study. Microarray analyses of this gray matter-enriched tissue revealed many correlations similar to those seen in our prior study, particularly for neuron-related genes. Nonetheless, in the laser-captured tissue, we found a striking paucity of the AD-associated epigenetic and transcription factor genes that had been strongly overrepresented in the prior tissue block study. In addition, we identified novel pathway alterations that may have considerable mechanistic implications, including downregulation of genes stabilizing ryanodine receptor Ca2+ release and upregulation of vascular development genes. We conclude that FFPE tissue can be a reliable resource for microarray studies, that upregulation of growth-related epigenetic/ transcription factors with incipient AD is predominantly localized to white matter, further supporting our prior findings and model, and that alterations in vascular and ryanodine receptor-relat ed pathways in gray matter are closely associated with incipient AD.

overall_design: RNA was extracted using RecoverAll Total Nucleic Acid Isolation Kit for FFPE (Ambion) according to manufacturer’s instructions (3h incubation at 55 C followed by glass fiber filtration). This system has recently been shown to outperform other FFPE methods/ kits regarding yield of amplifiable RNA (Okello et al., 2010). Quality assessment of extracted material was performed with the Paradise Reagent Quality Assessment Kit (Molecular Devices), as well as via NanoDrop (Thermoscientific). All samples yielded sufficient genetic material (>50 ng) for subsequent reactions. 50 ng of extracted purified nucleic acid underwent RNA amplification using WT-Ovation FFPE System (NuGen) followed by FL-Ovation cDNA Biotin Module V2 (NuGen) for labeling and microarray (Affymetrix HGU133 v2) hybridization. All 30 microarrays (one per specimen) performed within acceptable limits (Scaling factor: 32.6 +/- 3.7; RawQ: 1.28 +/- 0.01; GapDH 3’:5’: 1.48 +/- 0.08; % present 35.4 +/- 1.5) and were not significantly different across treatment (p < 0.5 for all measures, 1-ANOVA). In general, these results indicate a smaller signal in laser captured FFPE samples than in prior fresh frozen samples (Scaling factor: 5.9 +/- 0.6; RawQ 2.7 +/- 0.04; GapDH 3’:5’: 3.65 +/- 0.55; % present: 44.6 +/- 1.1) with an increased scaling factor decreased RawQ and reduced % present all indicating reduced signal volume, while the smaller GapDH ratio suggests more degraded material- consistent with other reports of the dynamics of small FFPE sample results. Further, the % present call, while lower than found in fresh frozen tissue, is much greater than would be expected by chance (5%).This suggests that the extracted genetic material still contains a large amount of valid data. Probe sets were annotated, and transcriptional profiles were generated, using the MAS5 algorithm and annotation data sets (Affymetrix Expression Console v. 1.1; HGU133 annotation October, 2003) in order to facilitate comparison with prior work. Results were filtered for presence, redundancy, and annotation status and analyzed by Pearson’s test for correlation with each subject’s Mini-Mental Status Exam (MMSE) score and Neurofibrillary Tangle (NFT) counts. The false discovery rate (FDR) (Hochberg and Benjamini, 1990) was used to estimate the error of multiple testing’s contribution to False Positives and the DAVID suite of bioinformatic tools was used to identify transcriptional pathways using the ‘table cluster’ option.

first: Heather

last: Buechel

first: Jelena

last: Popovic

first: James

middle: W

last: Geddes

first: Philip

last: Landfield


title: Identification of Novel and Conserved MicroRNAs of Root-knot Nematode Using a Deep-sequencing Approach

status: Public on Jul 21 2011

city: Changsha

first: Yunsheng

last: Wang

state: Hunan

address: Nongda road 1

department: Bioinformatics

institute: Hunan Agricultural University

type: Non-coding RNA profiling by high throughput sequencing

summary: 111,556,278 high-quality reads were obtained by a deep-sequencing approach that show an exact match to the genome of Meloidogyne incognita from the library of J2 juveniles of M. incognita (Mi). Based on these Solexa reads, 89 M. incognita microRNA genes were identified, which grouped into 67 non-redundant miRNAs with mature sequences. All of these candidate miRNAs were confirmed by qRT-PCR, and 26 of them could be detected in the library of the galls of cucumber root infected by M. incognita (GC). MiR-100 was found in a cluster with let-7, which is similar with B. malayi, a human parasitic nematode. Based on the results of deep sequencing, the expression of miR-100 was much more abundant than that of let-7, which indicated that they may not be co-expressed. The ortholog of let-7, a key regulator that controls the nematode from L4 to adult in C. elegans, could be frequently sequenced in the GC library, the later stages of development of M. incognita, while it had a relative low expression level in J2, which indicated that let-7 may have a similar role in the development regulation in plant parasitic nematodes. Frequently sequenced microRNAs, including miR-71, miR-100 and miR-124, should play an important role in the growth and proliferation of M. incognita.

sample_organism:
Capsicum annuum
Meloidogyne incognita

platform_organism:
Capsicum annuum
Meloidogyne incognita

overall_design: Identifying microRNAs of M. incognita based on deep-sequencing of the small RNAs of an Mi library, the J2 juveniles, and comparing their expression levels with those in a GC library, the gall of cucumber root infected with M. incognita.

first: Binyan

last: Xie


title: Leptosphaeria maculans gene expression during in vitro growth and primary oilseed rape leaf infection

status: Public on Feb 09 2011

city: Thiverval-Grignon

first: Isabelle

last: Fudal

address: avenue Lucien Bretignieres

country: France

institute: INRA

summary: The transcriptome of Leptosphaeria maculans was analyzed in mycelium and during oilseed rape (Brassica napus) leaf infection. The array probes were designed from gene models from the L. maculans whole genome annotation. One aim of this study was to verify the expression of the automatically annotated gene models in various conditions. Another goal was to monitor gene expression profiles during oilseed rape leaf infection and to highlight tissue-specific transcripts, e.g. in plant up-regulated transcripts, for further analyses.

sample_organism:
Brassica napus
Plenodomus lingam

overall_design: We performed 9 hybridizations (NimbleGen) with samples derived from mycelium and infected oilseed rape leaves. Samples from infected oilseed rape leaves were harvested 7 and 14 days post infection. Three replicates each. All samples were labeled with Cy3.

first: Juliette

last: Linglin


title: Molecular Characterization of Breast Carcinoma Associate fibroblasts

status: Public on Oct 25 2011

city: Montreal

first: Mark

last: Basik

state: QC

address: 3755 Cote Ste Catherine

department: Oncology

institute: Lady Davis Institute

summary: Normal breast fibroblasts, breast cancer associated fibroblasts, fibroblasts taken at least 2cm from cancer margins and femur-derived human mesenchymal stem cells were profiled for comparative purposes

overall_design: Ex vivo cultured primary cells of different anatomical origin were expression profiled under low serum conditions: cancer-associated fibroblasts, fibroblasts from a distance of at least 2cm from the cancers' edge, fibroblasts from cancer-free breasts and mesenchymal stromal cells from the marrow of femurs.  Biological Replicates= 46.  Technical Replicates= 17

first: Abde

middle: l

last: Hosein


title: MicroRNA-Based Classification of Hepatocellular Carcinoma and Oncogenic Role of miR-517a

status: Public on Feb 17 2011

city: Dallas

first: Yujin

last: Hoshida

state: TX

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

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

summary:
Hepatocellular carcinoma (HCC) is a complex and heterogeneous tumor due to activation of multiple cellular pathways and molecular alterations. Herein, we report the first molecular classification of 89 HCC based on the expression of 358 microRNAs and integrative genomic analysis. Three main subclasses of HCC were identified : two of them were associated with beta-catenin mutations or aggressive phenotype. A subset of the subclass of aggressive tumors (8/89, 9%) showed overexpression of a cluster of microRNAs located on chr19q13.41 (C19MC locus. We showed that miR 517a, representing C19MC, promoted cell proliferation, migration and invasion in vitro and induced the development of aggressive tumors in vivo suggesting its role as a novel oncogenic driver in HCC.

This SuperSeries is composed of the SubSeries listed below.


title: Musashi 2 regulates normal hematopoiesis and accelerates leukemogenesis (LSK and LK)

status: Public on Jul 22 2010

first: Fatima

last: Al-Shahrour

state: MA

address: 7 Cambridge Center

department: Cancer program

institute: Broad Institute of MIT and Harvard

summary: We demonstrate that Msi2 is the predominant form expressed in hematopoietic stem cells (HSC), and its knockdown leads to reduced engraftment and depletion of HSCs in vivo. Overexpression of Msi2 in a mouse model increases HSC cell cycle progression and cooperates with BCR-ABL1 to induce an aggressive leukemia. MSI2 is over-expressed in human myeloid leukemia, and expression levels directly correlate with decreased patient survival, thereby defining MSI2 expression as a novel prognostic marker in acute myeloid leukemia (AML). Depletion of MSI2 in human myeloid leukemia cells leads to decreased proliferation and apoptosis. These data implicate the MSI2 RNA binding protein in myeloid leukemogenesis and identify a novel potential target for therapy in AML.

overall_design: Mouse hematopoietic stem cells (defined as LineageLow, Sca1+, Kit+; LSK; n=3) as well as committed progenitor cells (LineageLow, Sca1-, Kit+; LK; n=3) were sorted and RNA was extracted using Qiagen RNeasy Micro Kit according to manufacturers instruction. cDNA was fragmented and biotinylated before hybridization onto Affymetrix Mouse Expression Array 430 2.0.

first: Michael

last: Kharas

first: Christopher

last: Lengner

first: Lars

last: Bullinger

first: Brian

last: Ball

first: Samir

last: Zaidi

first: Kelly

last: Morgan

first: Winnie

last: Tam

first: Mahnaz

last: Paktinat

first: Rachel

last: Okabe

first: Maricel

last: Gozo

first: William

last: Einhorn

first: Steven

last: Lane

first: Claudia

last: Scholl

first: Stefan

last: Fröhling

last: Fleming

first: Benjamin

last: Ebert

first: D

last: Gilliland

first: Rudolf

last: Jaenisch

first: George

middle: Q

last: Daley


title: Transcriptional Mediator Subunit MED1/TRAP220 in Stromal Cells Is Involved in Hematopoietic Stem/Progenitor Cell Support through Osteopontin Expression

status: Public on Aug 31 2010

city: Kobe

first: Mitsuhiro

last: Ito

address: 7-10-2 Tomogaoka, Suma-ku

institute: Kobe University Graduate School of Medicine

summary: MED1/TRAP220, a subunit of the transcriptional Mediator/TRAP complex, is crucial for various biological events through its interaction with distinct activators such as nuclear receptors and GATA family activators. In hematopoiesis, MED1 plays a pivotal role in optimal nuclear receptor-mediated myelomonopoiesis and GATA-1-induced erythropoiesis. In this study, we present evidence that MED1 in stromal cells is involved in supporting hematopoietic stem and/or progenitor cells (HSPCs) through osteopontin (OPN) expression. We found that the proliferation of bone marrow (BM) cells cocultured with MED1 knockout (Med1-/-) mouse embryonic fibroblasts (MEFs) was significantly suppressed when compared to the control. Furthermore, the number of long-term culture-initiating cells (LTC-ICs) was attenuated for BM cells cocultured with Med1-/- MEFs. The vitamin D receptor (VDR)- and Runx2-mediated expression of OPN, as well as Mediator recruitment to the Opn promoter, was specifically attenuated in the Med1-/- MEFs. Addition of OPN to these MEFs restored the growth of cocultured BM cells and the number of LTC-ICs, both of which were attenuated by the addition of the anti-OPN antibody to Med1+/+ MEFs and to BM stromal cells. Consequently, MED1 in niche appears to play an important role in supporting HSPCs, by upregulating VDR- and Runx2-mediated transcription on the Opn promoter.

overall_design: Total RNAs of mouse embryonic fibroblasts (MEFs) derived from Med1-/-/p53-/- and Med1+/+/p53-/- E10.0 embryos were compared. Duplicate samples for each MEF type were analyzed.

first: Akiko

last: Sumitomo

first: Ruri

last: Ishino

first: Norinaga

last: Urahama

first: Kana

last: Inoue

first: Kenji

last: Yonezawa

first: Natsumi

last: Hasegawa

first: Osamu

last: Horie

first: Hiroshi

last: Matsuoka

first: Toru

last: Kondo

first: Robert

last: Roeder


title: microRNA profiling of human hepatocellular carcinoma

first: Yujin

last: Hoshida

summary: microRNA profiling of 89 human hepatocellular carcinoma tissues using bead-based technology.

overall_design: microRNA expression profiling was performed using freshly frozen hepatocellular carcinoma tissues obtained at the time of surgical treatment.

first: Sara

last: Toffanin

first: Anja

last: Lachenmayer

first: Augusto

last: Villanueva

first: Laia

last: Cabellos

first: Beatriz

last: Minguez

first: Stephen

last: Ward

first: Swan

last: Thung

first: Radoslav

last: Savic

first: Derek

middle: Y

last: Chiang

first: Clara

middle: A

last: Armengol

first: Victoria

last: Tovar

first: Sasan

last: Roayaie

first: Craig

last: April

first: Jian-Bing

last: Fan

first: Myron

last: Schwartz

first: Jordi

last: Bruix

first: Scott

last: Friedman

first: Todd

last: Golub

first: Vincenzo

last: Mazzaferro

first: Josep

last: Llovet


title: Uncoupling growth and product formation kinetics to design improved strains for recombinant protein production in escherichia coli

status: Public on Jun 01 2011

city: New Delhi

first: Krishna

middle: Jyoti

last: Mukherjee

email: anuradha.bharara@gmail.com, ashishji101@gmail.com, shubhashreemahalik@gmail.com, kjmukherjee@mail.jnu.ac.in

state: delhi

address: New Mehrauli Road

department: School Of Biotechnology

country: India

institute: Jawaharlal Nehru University

summary: The ability to control the synthesis of products in the absence of cell division remains an attractive alternative for the optimization of microbial processes.  If this could be achieved, it would dramatically expand the productivity of many microbial processes by increasing product synthesis in the absence of an increase in cell mass. In the present work we have looked at the factors involved in the design of a host where the fluxes would be channeled towards product formation rather than biomass synthesis. To identify the genes responsible for diverting the metabolic flux specifically towards product formation we have used for this study is quiescent-cell (Q-cell) expression system, in which a plasmid-encoded protein is expressed in nongrowing but metabolically active cells. These cells channel the metabolic flux towards recombinant protein production and therefore the specific product yield per unit biomass is significantly higher. Indole which is previously known to be a signalling molecule is here used as an inducer of Quiescence. E.coli L-Asparaginase is used as a model protein in this work.

overall_design: Fed batch cultures were carried out in Sartorius BIOSTAT B plus 5liter bioreactor. The data acquisition was done with the MFCS Shell software (version) provided with the bioreactor. The Sartorius BIOSTAT B plus had proportional integral derivative-based control loops for temperature, pH, antifoam, and dissolved-oxygen (DO) regulation. The culture was grown in a batch mode till 10-12 OD (µ=0.5) and then the feed was attached. In the next hour the culture was induced for product formation with 1M IPTG. In case of Q culture quiescence was induced with 0.5M Indole just 5min after induction with IPTG. Post induction every hour samples were collected and frozen with liquid nitrogen and stored at -80ºC for further analytical use. Total RNA extraction, RNA quality control (Agilent BioAnalyser), total RNA labeling, microarray hybridization and scanning were performed according to the Affymetrix GeneChip Expression analysis .

first: Shubhashree

last: Mahalik

first: Ashish

last: Sharma

middle: J


title: Gene Copy Number Aberrations are Associated with Survival in Histological Subgroups of Non-Small Cell Lung Cancer

first: Anders

last: Isaksson

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

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

overall_design: Refer to individual Series


title: Genome-wide analysis of gene expression profiles of 21 European maize (Zea mays L.) inbred lines.

status: Public on Aug 21 2010

city: Hamburg

first: Stefan

last: Scholten

address: Ohnhorststrasse 18

department: Biocenter Klein Flottbek

institute: University of Hamburg

summary: In the current study a microarray (46k, University of Arizona, USA) analysis of 21 European maize (Zea mays L.) parental inbred lines (14 dent and 7 flint) was applied. The aim was the identification of parental genes which expression levels are correlated to heterosis and/or hybrid performance for grain yield (GY) and grain dry matter content (GDMC) in the hybrid progeny (F1). Therefore gene expression profiles of differentially expressed genes of the parental inbred lines at the seedling stage were correlated with GY- and GDMC-field data of 98 flint x dent factorial crosses gained at six different locations in Germany. The identification of heterosis-correlated genes is an approach for the characterization and also for the prediction of this phenomenon. For the analyses total RNA of seven days old seedlings was extracted and aminoallyl-labeled RNA probes were synthesized. RNA labeling (Cy3, Cy5) and hybridizations were performed according to the protocol of the maize oligonucleotide array project (http://www.maizearray.org). The microarrays were scanned (AppliedPrecision ArrayWorx Scanner, Applied Precision Inc., USA) and data were evaluated using the Software GenePix Pro 4.0 (Molecular Devices, Sunnyvale, USA). An experimental interwoven loop design was developed aiming to yield in a preferably low average variance among the hybridizations, especially between intergroup (dent lines vs. flint lines) hybridizations. As a result 12288 (28.3%) of the genes showed differential expression between any combination of inbred lines. These differentially expressed genes were used for subsequent field data correlation analyses.

overall_design: Five plants of each of the 21 inbred lines (7 flint lines: F037, F039, F043, F047, L024, L035, L043; 14 dent lines: P033, P040, P046, P048, P063, P066, S028, S036, S044, S046, S049, S050, S058, S067) were grown for seven days in a climate chamber (Percival Scientific Inc., Perry, USA)  under regulated growth conditions (25℃ 16h-day, 21℃ 8h-night, 70% air humidity). Since we aimed for the identification of genotype-dependent expression differences in inbred lines and for diminishing individual expression variations, the five biological replicates were pooled before target labeling and hybridization. Whole tissue of 7-days old seedlings was used. The pooled tissue was frozen in liquid nitrogen and finely pounded. The complete RNA was isolated and used to synthesize aminoallyl-labeled RNA (aaRNA) following the "Amino Allyl MessageAmp II aRNA Amplification Kit" protocol (Applied Biosystems/Ambion, Austin, USA). Synthesised aaRNA was coupled with fluorescence dyes Cy3 or Cy5. In total 63 hybridizations were realized in an interwoven loop design, in which the dye used for each genotype was alternated to reduce systematic bias. The loop was designed in a way that each dent line was sampled 5 times and each flint line 8 times. In addition to every direct connection between dent and flint lines, multiple indirect connections of three or more hybridizations were realized.

first: Alexander

last: Thiemann

first: Junjie

last: Fu

first: Tobias

last: Schrag

first: Albrecht

middle: E

last: Melchinger

first: Matthias

last: Frisch


title: Musashi 2 regulates normal hematopoiesis and accelerates leukemogenesis (Leukemia cell lines)

status: Public on Jul 21 2010

first: Fatima

last: Al-Shahrour

overall_design: We transduced four human leukemia cell lines with lentiviral shRNA vectors targeting MSI2. Hybridizations of treated and control samples from each cell line were dye swap replicated

first: Michael

last: Kharas

first: Christopher

last: Lengner

first: Lars

last: Bullinger

first: Brian

last: Ball

first: Samir

last: Zaidi

first: Kelly

last: Morgan

first: Winnie

last: Tam

first: Mahnaz

last: Paktinat

first: Rachel

last: Okabe

first: Maricel

last: Gozo

first: William

last: Einhorn

first: Steven

last: Lane

first: Claudia

last: Scholl

last: Fröhling

first: Mark

last: Fleming

first: Benjamin

last: Ebert

first: D

last: Gilliland

first: Rudolf

last: Jaenisch

first: George

last: Daley


title: Musashi 2 regulates normal hematopoiesis and accelerates leukemogenesis (LK and MS12-inducible)

first: Fatima

last: Al-Shahrour

overall_design: Hematopoietic stem cells and progenitor cells (LineageLow, Sca1-, Kit+; LK) from control and transgenic MSI2-inducible mice were isolated and RNA was extracted using Qiagen RNeasy Micro Kit according to manufacturers instruction. cDNA was fragmented and biotinylated before hybridization onto Affymetrix Mouse Expression Array 430 2.0.

first: Michael

last: Kharas

first: Christopher

last: Lengner

last: Bullinger

first: Stefan


title: Global gene expression profiling and validation in esophageal squamous cell carcinoma (ESCC)

status: Public on Sep 01 2010

city: Bethesda

first: Howard

last: Yang

state: MD

address: 37 CONVENT DR, Room 5120

department: CCR

institute: NCI

summary:
Esophageal squamous cell carcinoma (ESCC) is an aggressive tumor with poor prognosis.  Understanding molecular changes in ESCC should improve identification of risk factors in molecular subtypes and provide potential targets for early detection and therapy.  To better characterize molecular changes in ESCC, we followed up a previous cDNA array study with additional discovery and confirmatory studies in new ESCC cases using alternative methods.  We profiled global gene expression (Affymetrix U133A/B chip) for discovery and confirmation, and validated selected dysregulated genes with additional RNA (qRT-PCR, N=51) or protein studies (immunohistochemistry [IHC] of tumor tissue microarray [TMA], N=275).We also found genes associated with survival.
The dysregulated genes should aid in identifying risk factors in ESCC, as well as potential targets for early detection, and outcome prediction and therapy.

overall_design:
53 ESCC samples and 53 matched normal samples were analyzed (samples AE43 and AE45 were not run on HG-U133B due to not having enough material).

Contributors have chosen not to include the clinical phenotypes in their GEO submission.

first: Hua

last: Su

last: Hu

middle: H


title: microRNA epxression patterns can discriminate between patients with oligometastatic and polymetastatic progression

status: Public on Dec 09 2010

city: Charlottesville

first: Yong

last: Huang

state: VA

address: 1340 Jefferson Park Ave

department: Medicine

institute: University of Viginia

first: Yves

last: Lussier

first: Rosie

last: Xing

first: Joseph

middle: K

last: Salama

first: Nikolai

middle: N

last: Khodarev

first: Qingbei

last: Zhang

first: Sajid

last: Khan

first: Xinan

last: Hasselle

first: Thomas

last: Darga

first: Renuka

last: Malik

first: Hanli

last: Fan

first: Samantha

last: Perakis

first: Matthew

last: Filippo

first: Kimberly

last: Corbin

first: Younghee

last: Lee

first: Mitchell

middle: C

last: Posner

last: Chmura

first: Samuel

last: Hellman

first: Ralph

middle: R

last: Weichselbaum


title: Differential Transcriptional Changes in Mice Exposed to Chemically Distinct Diesel Samples

status: Public on Jul 10 2010

city: carrboro

first: Tina

last: Stevens

state: NC

address: 138 marlowe ct

institute: UNC

summary: Epidemiological studies have linked exposure to ambient particulate matter (PM) with increased asthmatic symptoms. Diesel exhaust particles (DEP) are a predominant source of vehicle derived ambient PM, and experimental studies have demonstrated that they may have adjuvant potential when given with an antigen. We previously compared 3 DEP samples: N-DEP, A-DEP, and C-DEP in a murine ovalbumin (OVA) mucosal sensitization model and reported the adjuvant activity to be: C-DEP ≈ A-DEP > N-DEP. The present study analyzed gene expression changes from the lungs of these mice. Transcription profiling demonstrated that all the DEP samples altered cytokine and toll-like receptor pathways regardless of type, with or without antigen sensitization. Further analysis of DEP exposure with OVA showed that all DEP treatments altered networks involved in immune and inflammatory responses. The A- and C-DEP/OVA treatments induced differential expression of apoptosis pathways in association with stronger adjuvant responses, while expression of cell cycle control and DNA damage pathways were also altered in the C-DEP/OVA treatment. This comprehensive approach using gene expression analysis to examine changes at a pathway level provides detailed information on events occurring in the lung after DEP exposure, and confirms that the most bioactive sample induced many more individual genes and changes in immuno-regulatory and homeostatic pathways.

overall_design: Female BALB/C mice (8-10 weeks old) were randomly divided into 8 treatment groups containing 3 mice each and exposed to saline, 20 ug ovalbumin, 150 ug diesel exhaust particles (either C-DEP, A-DEP, or N-DEP), or diesel exhaust particles + ovalbumin by intranasal instillation on Days 0 and 13 and necropsied 18 hrs latter.

first: Susan

last: Hester

first: M

middle: I

last: Gilmour


title: Musashi-2 regulates normal hematopoiesis and promotes aggressive myeloid leukemia

status: Public on Jul 11 2010

city: Berlin

first: Lars

last: Bullinger

address: Augustenburger Platz 1

department: Hematology, Oncology and Tumorimmunology

institute: Charité

summary: RNA-binding proteins of the Musashi (Msi) family are expressed in stem cell compartments and in aggressive tumors, but they have not yet been widely explored in the blood. Here we demonstrate that Msi2 is the predominant form expressed in hematopoietic stem cells (HSCs), and its knockdown leads to reduced engraftment and depletion of HSCs in vivo. Overexpression of human MSI2 in a mouse model increases HSC cell cycle progression and cooperates with the chronic myeloid leukemia-associated BCR-ABL1 oncoprotein to induce an aggressive leukemia. MSI2 is overexpressed in human myeloid leukemia cell lines, and its depletion leads to decreased proliferation and increased apoptosis. Expression levels in human myeloid leukemia directly correlate with decreased survival in patients with the disease, thereby defining MSI2 expression as a new prognostic marker and as a new target for therapy in acute myeloid leukemia (AML).

overall_design: Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.


title: miRNA expression data from rhesus macaque postnatal brain in prefrontal cortex: time course

status: Public on Jun 10 2010

city: shanghai

first: Song

last: Guo

address: 320 Yue Yang Road

institute: PICB

summary:
Gene expression changes determine functional differentiation during development and are associated with functional decline during aging. While developmental changes are tightly regulated, regulation of aging changes is not well established. To assess the regulatory basis of age-related changes and investigate the mechanism of regulatory transition between development and aging, we measured mRNA and microRNA expression patterns in brains of humans and rhesus macaques over the entire species’ lifespan. We find that in both species, developmental and aging changes overlap in the course of lifetime with many changes found at the late age initiating in early childhood. Keywords: miRNA  Age Series

Keywords: Non-coding RNA profiling by high throughput sequencing

overall_design: rhesus macaque post-mortem brain samples from the superior frontal gyrus region of the prefrontal cortex were collected. The age ranges of the indibiual in rhesus macaque covered the  whole life span fom newborn to death.

first: Mehmet

last: Somel

first: Ning

last: Fu

first: Zheng

last: Yan

first: Haiyang

last: Hu

first: Philipp

last: Khaitovich


title: Gene Signature to Identify Vascular Invasion in Human Hepatocellular Carcinoma

status: Public on Jul 31 2011

first: Yujin

last: Hoshida


title: Gene expression data from primate postnatal brain in prefrontal cortex: time course

summary: Gene expression changes determine functional differentiation during development and are associated with functional decline during aging. While developmental changes are tightly regulated, regulation of aging changes is not well established. To assess the regulatory basis of age-related changes and investigate the mechanism of regulatory transition between development and aging, we measured mRNA and microRNA expression patterns in brains (superior frontal gyrus) of humans and rhesus macaques over the entire species’ lifespan. We find that in both species, developmental and aging changes overlap in the course of lifetime with many changes found at the late age initiating in early childhood.

sample_organism:
Macaca mulatta
Homo sapiens

overall_design:
Human post-mortem brain samples from the superior frontal gyrus region of the prefrontal cortex were collected. The age ranges of the indibiual in human covered its whole life span fom newborn to death. RNA extracted from the dissected tissue was hybridized to Affymetrix® Human Gene 1.0 ST arrays.

Rhesus macaque post-mortem brain samples from the superior frontal gyrus region of the prefrontal cortex were collected. The age ranges of the indibiual in rhesus macaque covered the  whole life span fom newborn to death. RNA extracted from the dissected tissue was hybridized to Affymetrix® Human Gene 1.0 ST arrays.


title: miRNA expression data from human postnatal brain in prefrontal cortex: time course

overall_design: Human post-mortem brain samples from the superior frontal gyrus region of the prefrontal cortex were collected. The age ranges of the indibiual in rhesus macaque covered the  whole life span fom newborn to death.


title: [E-MTAB-513] Illumina Human Body Map 2.0 Project

status: Public on Jul 14 2011

city: Hinxton

first: ArrayExpress

last: EBI

address: Wellcome Trust Genome Campus

institute: European Bioinformatics Institute

type: Expression profiling by high throughput sequencing

summary:
Illumina bodyMap2 transcriptome
Transcription profiling by high throughput sequencing of individual and mixture of 16 human tissues RNA. Additional supplementary files available at foot of this record.
Additional information available as supplementary files at the foot of this record.

ArrayExpress Release Date: 2011-03-17

Person Roles: submitter
Person Last Name: Khrebtukova
Person First Name: Irina
Person Mid Initials:
Person Email: ikhrebtukova@illumina.com
Person Phone: 1-510-723-9219
Person Address: 25861 Industrial Blvd, Hayward CA 94545, USA
Person Affiliation: Illumina

overall_design:
Experimental Design: organism_part_comparison_design
Experimental Design: co-expression_design
Experimental Design: optimization_design
Experimental Factor Name: ORGANISMPART
Experimental Factor Name: LIBRARYPREP
Experimental Factor Name: PHENOTYPE
Experimental Factor Type: organism_part
Experimental Factor Type: protocol
Experimental Factor Type: phenotype


title: mRNA and  miRNA expression in parietal lobe cortex in Alzheimer's disease

status: Public on Jan 31 2010

city: Los Angeles

first: Juan

last: Nunez-Iglesias

address: 1050 Childs Way, RRI-201

department: Computational Biology

institute: University of Southern California

summary: In this study, we jointly profiled mRNA and miRNA expression to determine the role of miRNAs in AD, and whether the levels of miRNAs are related to those of target mRNAs. We found a bias towards positive correlation between levels of miRNAs and those of their targets.

overall_design: We profiled parietal lobe tissue from 4 AD patients and 4 age-matched controls.

first: Xianghong

last: Zhou

first: Caleb

last: Finch

first: Chun-Chi

last: Liu

first: Todd

last: Morgan


title: Combining Clinical, Pathology, and Gene Expression Data to Predict Recurrence of Hepatocellular Carcinoma

summary:
Background:
Hepatocellular carcinoma (HCC) is among the top-five cancer killers worldwide. Here, we describe our analysis of 20 gene signatures with reported prognostic value in a cohort of patients with early stage HCC treated with surgical resection.
Methods:
We performed gene-expression profiling of 164 formalin-fixed, paraffin-embedded HCC from three hepatology centers participating the HCC Genomic Consortium. We utilized Illumina’s whole-genome DASL assay measuring ~24,000 annotated human genes. We evaluated genomic concordance and prognostic performance of 20 already reported prognostic gene signatures. Additionally, since only the largest nodule was profiled, we also excluded patients with multiple tumors to avoid biases related to intra-individual genomic tumor heterogeneity.
Results:
Among the 20 signatures evaluated, 15 were able to confidently allocate patients (FDR<0.05) within their predicted poor-outcome subclass. Pairwise comparisons showed a significant overlap between almost all poor-outcome signatures derived from the tumor (P<0.001), except for the metastatic HCC signature. Interestingly, poor-outcome signatures from the tumor were not significantly associated with those obtained from non-tumor adjacent tissue in the same patient. The prognosis analysis for earliest stages (BCLC 0 or A) with single nodules revealed that the G3 signature reported by Boyault et al. Conclusions:
We present a composite genomic model for prediction of tumor recurrence in early HCC. It will allow risk stratification, personalized surveillance, and eventually customized interventions in patients with early HCC candidates for resection.
Samples with "used for prognostic prediction: yes" were included in the study.

This SuperSeries is composed of the SubSeries listed below.


title: Expression from C. elegans L4 animals

status: Public on Jan 01 2010

first: Michael

last: Krause

address: 5 Center Drive

department: LMB/NIDDK

institute: NIH

summary:
Nutrient-driven O-GlcNAcylation of key components of the transcription machinery may epigenetically modulate gene expression in metazoans. Knockouts of the O-GlcNAc cycling enzymes in C. elegans are viable and fertile, allowing a global analysis of the impact of GlcNAcylation.
Whole genome transcriptional profiling of the O-GlcNAc cycling mutants confirmed dramatic deregulation of genes in these key pathways. As predicted, the O-GlcNAc cycling mutants show phenotypically altered lifespan and susceptibility to UV stress.

overall_design: Similarly aged L4 animals (20) staged by degree of vulval development were hand picked.  Wild type and mutant animals were collected and total RNA isolated for gene expression analysis

first: John

last: Hanover


title: microRNA epxression patterns can discriminate between patients with oligometastatic and polymetastatic progression: tissues

status: Public on Nov 25 2010

first: Yong

last: Huang

summary:
Background
Cancer staging and treatment presumes a division into localized or metastatic disease. We proposed an intermediate state defined by ≤5 cumulative metastasis(es), termed oligometastases. In contrast to widespread polymetastases, oligometastatic patients may benefit from metastasis-directed local treatments. However, many patients who initially present with oligometastases progress to polymetastases. Predictors of progression could improve patient selection for metastasis-directed therapy.
Methods
Here, we identified patterns of microRNA expression of tumor samples from oligometastatic patients treated with high-dose radiotherapy.
Results
Patients who failed to develop polymetastases are characterized by unique prioritized features of a microRNA classifier that includes the microRNA-200 family. We created an oligometastatic-polymetastatic xenograft model in which the patient-derived microRNAs discriminated between the two metastatic outcomes. MicroRNA-200c enhancement in an oligometastatic cell line resulted in polymetastatic progression.
Conclusions
These results demonstrate a biological basis for oligometastases and a potential for using microRNA expression to identify patients most likely to remain oligometastatic after metastasis-directed treatment.

overall_design: Tissues: We collected samples from 5 patients with both primary and metastatic tumors available for analysis, 20 patients with primary tumors only, and 9 patients with metastatic tumors only.  Eleven of these patients were analyzed retrospectively, while 23 patients were included prospectively from a previously reported radiotherapy protocol for oligometastatsis. Total RNA were derived from FFPE primary and metastatic tissue samples.

first: Yves

last: Lussier

first: Rosie

middle: X

last: Xing

first: Joseph

last: Salama

first: Nikolai

last: Khodarev

first: Qingbei

last: Zhang

first: Sajid

last: Khan

first: Xinan

last: Yang

middle: D

last: Hasselle

first: Thomas

last: Darga

first: Renuka

last: Malik

first: Hanli

last: Fan

first: Samantha

last: Perakis

first: Matthew

last: Filippo

first: Kimberly

last: Corbin

first: Younghee

last: Lee

first: Mitchell

last: Posner

first: Steven

last: Chmura

first: Samuel

last: Hellman

first: Ralph

last: Weichselbaum


title: Transcriptional profiling of P. yoelii SAP1 knockout

status: Public on Aug 01 2009

city: Seattle

first: Stefan

middle: H. I.

last: Kappe

address: 307 Westlake Ave N, Suite 500

institute: Seattle Biomedical Research Institute

summary: To study the function of gene SAP1. We knocked out SAP1 gene in P. yoelii, and compared the global gene expression profiles of the P. yoelii SAP1 knockout parasites isolated from mosquito salivary gland to that of wild type P. yoelii parasites.

overall_design: RNA samples from SAP1 knock out (SAP1ko) were directly hybridized to RNA samples obtained from mosquito salivary gland (sgSpz). Two independent biological replicates with dye swaps for each pairs of biological replicates were performed.  Also we included in the analysis two direct hybridizations between sgSpz and ooSpz from our previous study.

first: Ahmed

last: Aly

first: Xinxia

last: Peng

first: Hilda

last: Silva-Rivera


title: Renormalized GSE5509 by using the parametric method

status: Public on Aug 12 2011

city: Akita

first: Tomokazu

last: Konishi

state: Akita

address: Shimoshinjyo Nishi

department: Bioresource Sciences

institute: Akita Prefectural University

type:
Third-party reanalysis
Expression profiling by array

summary:
Although principal component analysis is frequently used in multivariate/ analysis, it has disadvantages when applied to experimental or diagnostic data. First, the identified principal components have poor generality; since the size and directions of the components are dependent on the particular data set, the components are valid only within the set. Second, the method is sensitive to experimental noise and bias between sample groups, since it cannot reflect the design of experiments; rather, it estimates the same weight and independence of all the samples in the matrix. Third, the resulting components are often difficult to interpret. To address these issues, several options were introduced to the methodology. The resulting components were scaled to unify their size unit. Also, the principal axes were identified using training data sets and shared among experiments. This training data reflects the design of experiments, and its preparation allows noise to be reduced and group bias to be removed. The effects of these options were observed in microarray experiments, and showed an improvement in the separation of groups and robustness to noise. Additionally, unknown samples were appropriately classified using pre-arranged axes, and principal axes well reflected the characteristics of groups in the experiments.
The summarized levels the genes are presented in the Matrix form.

overall_design: PM data of samples in GSE5509 were parametrically normalized in chip-wise manner according to the three-parameter lognormal distribution method (Konishi et. al., 2009 PLoS ONE 3: e3555. http://dx.plos.org/10.1371/journal.pone.0003555).   Expression level of a gene was estimated by summarizing the corresponding PM data. A pseudo data was then derived in a form of antilog of the z-scores; the center of the pseudo data was 256. The pseudo data, ABS_CALL, and the normalized data (z-scores) are presented in the matrix form [see Supplementary file below].  PM data were not directly used for the study.


title: Expression data from Perk wild-type and knockout mouse liver perfused without or with 2,5-di-tert-butylhydroquinone

status: Public on Nov 10 2009

city: Hershey

first: An

last: Dang Do

state: PA

address: 500 University Drive

department: Cellular and Molecular Physiology

institute: Penn State College of Medicine

summary:
In eukaryotes, regulation of mRNA translation enables a fast, localized and finely tuned expression of gene products.  Within the translation process, the first stage of translation initiation is most rigorously modulated by the actions of eukaryotic initiation factors (eIFs) and their associated proteins.  These 11 eIFs catalyze the joining of the tRNA, mRNA and rRNA into a functional translation complex.  Their activity is influenced by a wide variety of extra- and intracellular signals, ranging from global, such as hormone signaling and unfolded proteins, to specific, such as single amino acid imbalance and iron deficiency.  Their action is correspondingly comprehensive, in increasing or decreasing recruitment and translation of most cellular mRNAs, and specialized, in targeting translation of mRNAs with regulatory features such as a 5’ terminal oligopyrimidine tract (TOP), upstream open reading frames (uORFs), or an internal ribosomal entry site (IRES).  In mammals, two major pathways are linked to targeted mRNA translation.  The target of rapamycin (TOR) kinase induces translation of TOP and perhaps other subsets of mRNAs, whereas a family of eIF2 kinases does so with mRNAs containing uORFs or an IRES.  TOR targets translation of mRNAs that code for proteins involved in translation, an action compatible with its widely accepted role in regulating cellular growth.  The four members of the eIF2 kinase family increase translation of mRNAs coding for stress response proteins such as transcription factors and chaperones.  Though all four kinases act on one main substrate, eIF2, published literature demonstrates both common and unique effects by each kinase in response to its specific activating stress.  This suggests that the activated eIF2 kinases regulate the translation of both a global and a specific set of mRNAs.  Up to now, few studies have attempted to test such a hypothesis; none has been done in mammals.
We use array analysis to determine the global mRNA shift into polysomes following a stress response, and to compare the translational response following activation of GCN2 versus PERK, two of the four eIF2alpha kinases.

Keywords: stress response, comparative genomic

overall_design: Perk wild-type or knockout mouse liver were perfused without or with 2,4-di-tert-butylhydroquinone (tBuHQ) for RNA extraction and hybridization of Affymetrix microarrays.  RNA was extracted from unfractionated liver samples and polysome fraction of samples separated on sucrose density gradient.  To minimize biological variations, we pooled RNA from two perfused liver samples to use in each array analysis.  The conditions were total and polysome fraction of Perk+/+, -tBuHQ or +tBuHQ; total and polysome fraction of Perk-/-, -tBuHQ or +tBuHQ.  Each array analysis was done in duplicate.

first: Scot

last: Kimball

first: Douglas

last: Cavener

first: Leonard

middle: S

last: Jefferson


title: Whole genome analysis of nicotine-exposed cells from the brainstem of spontaneously hypertensive and Wistar Kyoto rats

status: Public on Sep 16 2009

city: São Paulo

first: Eduardo

middle: Moraes

last: Reis

state: SP

address: Av. Prof. Lineu Prestes, 748

department: Biochemistry

country: Brazil

institute: University of São Paulo

summary: The development of hypertension may be highly influenced by the use of nicotine especially in genetically susceptible subjects. In this study the effects of nicotine on gene expression of cultured cells from the brainstem of spontaneously hypertensive (SHR) and Wistar Kyoto (WKY) rats were evaluated using whole genome microarray platforms. It was described for the first time that nicotine may act differentially on the gene expression profile of SHR and WKY. The influence of strain was present in 348 genes that were differentially expressed in SHR as compared to WKY brainstem cells independently of the nicotine treatment. 176 genes had their expression altered in both strains after nicotine exposure. Interaction between nicotine treatment and the strain was observed for the expression of 269 genes which participate of cellular pathways related to neurotrabnsmitter secretion, intracellular trafficking and cell communication. In conclusion, this study leaves a list of genes whose expression shall be better studied since they are good candidates to the phenotypic differentiation between SHR and WKY, including hypertension as well as demonstrated that alterations in the systems of intracellular trafficking and neurotransmission may be relevant to the development of hypertension.

overall_design:
Global measurements of gene expression from normotensive and hypertensive were obtained using the CodeLink Expression Bioarray System (GE Healthcare, UK), which interrogates 34,000 annotated genes and ESTs expressed in the rat genome. Each rat strain was hybridized in three independent biological replicates. Target labeling and hybridization was performed strictly as recommended by the array manufacturer.

CodeLink Expression Analysis software (GE Healthcare) was used to extract background-subtracted spot intensities from microarray images. Measurements that were bellow the intensity of negative controls plus 2 standard deviations were excluded. Only genes with valid measurements in all three biological replicates of normotensive or hypertensive animals were further analyzed. To make experiments comparable, intensity data from different hybridizations were normalized by the quantile method

middle: M

first: Merari

last: Ferrari


title: Renormalized GSE8191 by using the parametric method

overall_design: PM data of samples in GSE8191 were parametrically normalized in chip-wise manner according to the three-parameter lognormal distribution method (Konishi et. al., 2009 PLoS ONE 3: e3555. http://dx.plos.org/10.1371/journal.pone.0003555).   Expression level of a gene was estimated by summarizing the corresponding PM data. A pseudo data was then derived in a form of antilog of the z-scores; the center of the pseudo data was 256. The pseudo data, ABS_CALL, and the normalized data (z-scores) are presented in the matrix form [see Supplementary file below].  PM data were not directly used for the study.


title: O-GlcNAc Chromatin Marks from C. elegans L1 animals

first: Michael

last: Krause

type: Genome binding/occupancy profiling by genome tiling array

summary: Nutrient-driven O-GlcNAcylation of key components of the transcription machinery may epigenetically modulate gene expression in metazoans. Knockouts of the O-GlcNAc cycling enzymes in C. elegans are viable and fertile, allowing a global analysis of the impact of GlcNAcylation. Whole genome ChIP profiling of the O-GlcNAc cycling mutants identified over 800 genes associated with GlcNAcylated chromatin.  This novel chromatin mark is preferentially found with genes involved in stress, longevity, and innate immunity, the same set of processes affected by global changes in gene expression analysis.  This experiment collected data on fed animals (3 hours) for comparisons to previoulsy collected starved data to see what acute effects nutritional flux would have on either O-GlcNAc chromatin marks or RNA Pol II distributions.

overall_design: L1 larvae were synchronized by starvation for two days after hatching in sterile buffer and then plated on NGM plates seeded with E. coli (OP50) and allowed to feed for 3 hours prior to collection.  Wild type and mutant animals were collected, washed, and chromatin isolated for immunoprecipitation with a variety of antibodies that recognize either O-GlcNAcylated substrates or RNA Pol II.

first: John

last: Hanover


title: Dynamic O-GlcNAc cycling at promoters of C. elegans genes regulating Longevity, Stress, and Immunity

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

overall_design: Refer to individual Series

first: Dona

last: Love

first: Salil

last: Ghosh

first: Michelle

last: Mondoux

first: Tetsunari

last: Fukushige

first: Peng

last: Wang

first: Mark

last: Wilson

first: Wendy

middle: B

last: Iser

first: Catherine

last: Wolkow

middle: W


title: Expression data from renal cysts of autosomal dominant polycystic kidney disease (ADPKD) patients

status: Public on Aug 14 2009

city: Toronto

first: York

middle: PC

last: Pei

state: Ontario

address: 8N838, 585 University Avenue

department: Department of Medicine

institute: University of Toronto

summary:
To elucidate the molecular pathways that modulate renal cyst growth in autosomal dominant polycystic kidney disease (ADPKD)
Keywords: Disease state analysis

overall_design: We performed global gene profiling on renal cysts of different size (small cysts: less than 1 ml, n=5; medium cysts: between 10-25 ml, n=5; large cysts: greater than 50 ml, n=3) and minimally cystic tissue (MCT, n=5) from five PKD1 polycystic kidneys. Additionally, non-cancerous renal cortical tissue from three nephrectomized kidneys with isolated renal cell carcinoma was used as normal control tissue (n=3)


title: Gene and miRNA expression data from primate postnatal brain in prefrontal cortex: time course

first: Song

last: Guo

platform_organism:
Macaca mulatta
Homo sapiens


title: Female MRL/lpr and Non-Obese Diabetic (NOD) Mice Treated with Placebo or Testosterone.

status: Public on Feb 01 2009

city: Boston

first: David

middle: A

last: Sullivan

address: 20 Staniford Street

institute: Schepens Eye Research Institute

summary:
The Influence of Testosterone on Lacrimal Gland Gene Expression in Female Mice of the MRL/lpr and Non-obese Diabetic Models of SjšgrenÕs Syndrome
Keywords: Placebo versus Testosterone Treatment.

overall_design: Female placebo and testosterone treated lacrimal glands were harvested from each mouse strain . Tissues were pooled into 3 biological replicates and were hybridized to separate microarrays.  Each cRNA prep was hybridized to a GE Healthcare/Amersham Biosciences CodeLink UniSet Mouse 20K I Bioarray and a Affymetrix GeneChip Mouse Expression Array 430A.

first: S

last: Richards

first: R

middle: V

last: Jensen

first: D


status: Public on Feb 27 2010

city: Dublin

first: Gary

middle: P.

last: Moran

address: Lincoln Place

department: Dental Science

country: Ireland

institute: Trinity College Dublin

summary:
Transcriptional response of Candida dubliniensis during hypha formation and environmental change (temperature, pH, density and nutrients).
Transcript profiling of C. dubliniensis identified a core shared transcriptional response with C. albicans during hypha formation and growth at alkaline pH. However, C. albicans expresses several unique hypha-specific genes, including ALS3, HYR1 and SAP4 and 5. Transcript profiling also revealed a novel role for NRG1 in regulating ferric reductases in C. dubliniensis.

overall_design: 8 experimental parameters were analysed, each carried out in quadruplicate. Dye-swaps were performed.

middle: P


title: Expression data from uterine endometrial tissues of Holstein-Friesian cows on days 14-16 after calving

status: Public on Apr 04 2009

city: Hatfield

first: Zhangrui

last: Cheng

state: Hertfordshire

address: Hawkshead Lane

department: Production and Population Health

institute: Royal Veterinary College

summary:
Most dairy cows suffer uterine microbial contamination postpartum. Persistent endometritis often develops, associated with reduced fertility. We used a model of differential feeding and milking regimes to produce cows in differing negative energy balance (NEB) status in early lactation.
We used Affymetrix GeneChipÒ Bovine Genome Array  to investigate  the global  gene expression underlying  negative energy balance and to  identify the significantly differentially expressed genes during this process.

overall_design: We investigate the differences of gene expression profiles in uterine endometrial tissues between the cows with mild and severe negative energy balance.

last: Wathes

first: Waliul

last: Chowdhury

last: Fenwick

first: Richard

last: Fitzpatrick

first: Dermot

middle: G

last: Morris

first: Joe

last: Patton

middle: J

last: Murphy


title: Expression data from the CTCR-OV01 study

status: Public on Apr 09 2009

city: Pieve Emanuele

first: Charlotte

middle: K Y

last: Ng

state: MI

address: Via Rita Montalcini 4

department: Biomedical Sciences

country: Italy

institute: Humanitas University

summary: All patients with suspected ovarian cancer (Raised CA 125 and a complex pelvic mass in a perimenopausal woman) were radiologically staged using CT scan and a chest x-ray. Patients with evidence of intra-abdominal metastasis and/or malignant pleural effusion were approached for entry to the study. Tissue biopsy was obtained either under radiological control (core needle biopsy) or via laparoscopic surgery (punch biopsy). Patients with histologicaly confirmed epithelial ovarian cancer were randomized to receive either three cycles of carboplatin (AUC 7) or paclitaxel (175 mg/m2).

overall_design: Patients with suspected ovarian cancer had a biopsy obtained before and after 3 cycles of either Carboplatin or Paclitaxel. Samples were immediately frozen for RNA extraction.

first: Ahmed

last: Ahmed

first: Thomas

last: Hardcastle

first: James

last: Brenton