title: Validation of an Airway Gene Expression Classifier for Lung Cancer in Patients Undergoing Diagnostic Bronchoscopy

status: Public on May 17 2015

city: South San Francisco

first: James

last: Diggans

address: 7000 Shoreline Ct

institute: Veracyte Inc.

summary: BACKGROUND: In patients with suspicious pulmonary lesions, bronchoscopy is frequently non-diagnostic. This often results in additional invasive testing, including surgical biopsy, although many patients have benign disease.  We sought to validate an airway gene-expression classifier for lung cancer in patients undergoing diagnostic bronchoscopy.   METHODS: Two multicenter prospective studies (AEGIS 1 and 2) enrolled 1357 current or former smokers undergoing bronchoscopy for suspected lung cancer.  Bronchial epithelial cells were collected from normal appearing mucosa in the mainstem bronchus during bronchoscopy. Patients without a definitive diagnosis from bronchoscopy were followed for 12 months. A gene-expression classifier was used to assess the risk of lung cancer, and its performance was evaluated.  RESULTS: A total of 298 patients from AEGIS 1 and 341 from AEGIS 2 met criteria for analysis.  Bronchoscopy was non-diagnostic for cancer in 272 of 639 patients (43%; 95%CI, 39-46%). The gene expression classifier correctly identified 431 of 487 patients with cancer (89% sensitivity; 95%CI, 85-91%), and 72 of 152 patients without cancer (47% specificity; 95%CI, 40-55%). The combination of the classifier and bronchoscopy had a sensitivity of 97% (95%CI, 95-98%), which was independent of size, location, stage, and histological subtype of lung cancer.  In patients with an intermediate pre-test risk (10-60%) of lung cancer, the NPV of the classifier was 91% (95%CI 75-98%).  CONCLUSIONS: In patients with an intermediate risk of lung cancer and a non-diagnostic bronchoscopy, a gene-expression classification of “low-risk” warrants consideration of a more conservative diagnostic approach that could reduce unnecessary invasive testing in patients with benign disease.

overall_design: 680 CEL files from 639 BEC specimens, 152 benign and 487 malignant samples

first: Gerard

last: Silvestri

first: Anil

last: Vachani

first: Duncan

last: Whitney

first: Michael

last: Elashoff

first: Kate

last: Porta

first: J

last: Ferguson

first: Edward

last: Parsons

first: Jerome

last: Brody

first: Marc

last: Lenburg

first: Avrum

last: Spira


title: Unexposed control & 3 VOCs exposed workers

status: Public on Mar 28 2015

city: Seoul

first: Mi-Kyung

last: Song

address: 39-1 Hwawol-gok-dong, Wolsong-gil5, Seongbuk-gu-seoul

country: South Korea

institute: Korea Institute of Science & Technology

summary: We identified and validated characteristic miRNA expression profiles of human whole blood in workers exposed to volatile organic compounds (VOCs) and compared the usefulness of miRNA indicator of VOCs with the effectiveness of the already used urinary biomarkers of occupational exposure.

overall_design: Using a microarray based approach, we screened and detected deregulated miRNAs in their expression in workers exposed to VOCs (toluene [TOL], xylene [XYL] and ethylbenzene [EBZ]). Total 169 workers from four dockyards were enrolled in current study, and 50 subjects of them were used for miRNA microarray analysis.

first: M-Kyung

first: Jae-Chun

last: Ryu


title: Expression data from MDA-MB-231 breast cancer cell lines exposed to DMSO control and UF010

status: Public on Feb 19 2015

city: Gainesville

first: Daiqing

last: Liao

state: FLORIDA

address: 1333 Center Drive

department: Anatomy and Cell Biology

country: USA

institute: University of Florida

summary:
Breast cancer cell line MDA-MB-231 was treated with DMSO or UF010, a novel HDAC inhibitor for 24 hours. The impact of UF010 treatment on global gene expression was determined.
We used Affymetrix Human Transcriptome Array 2.0 (HTA-2_0) to analyze genes that were up or downregulated upon UF010 exposure.

overall_design: MDA-MB-231 cells were treated with DMSO (control) or 1.0 µM of UF010 for 24 hours.Total RNAs were isolated for hybridization on Affymetrix microarrays.

first: Guimei

last: Tian

first: Yanping

last: Zhang


title: Array analysis of wound induced hair neogenesis (early stage)

status: Public on Aug 05 2015

city: Baltimore

first: Luis

middle: Andres

last: Garza

state: MD

address: 1550 Orleans St. Suite 204 CRBII Koch

department: Dermatology

institute: Johns Hopkins School of Medicine

summary: Mice were wounded and skin samples of the scar  collected on the day of wound closure. We compared Mixed mice (B6/FVB/SJL), a strain of  high regeneration, versus  C57bl mice, a strain of low regeneration.

overall_design: Whole skin  biopsies of wound scars were submitted for Affymetrix Exon arrays. 4 mice each of 2 distinct strains of differing regeneration levels were collected.

middle: A

first: Amanda

middle: M

last: Nelson


title: 4 mutants-Transcriptome sup62 and cpsf30 mpk4

status: Public on Apr 01 2015

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

country: France

institute: INRA

summary: AU13_15_sup62 - 4 mutants - Transcriptome analysis of the mutant sup62, cpsf30, two suppressors of programmed cell death in A. thaliana - Plants Col-0, mips1, sup62 and sup62 mips1 were grown for 3 weeks in Short-Day condition and subsequently transfered in Long-Day condition. Rosette leaves were sampled after 4 days in Long-Day condition.

overall_design: 8 dye-swap - gene knock out,genotype comparaison

first: Sandrine

last: Balzergue

first: Ludivine

last: Taconnat

first: Marianne

last: Delarue

first: Marie-Laure

last: Martin-Magniette


title: Expression data from glioblastoma tissue and matched adjacent normal tissue

status: Public on Feb 04 2015

city: Beijing

first: Weitao

last: Man

address: Fuxing Hospital affiliated to Capital Medical University,Beijing,China

country: China

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

summary:
Glioblastoma (GBM) is the most common and lethal primary malignancy of the central nervous system in adult. In order to improve the diagnosis, prevention and treatment of GBM, the details of molecular mechanisms underlying the tumorigenesis and development needs to be clarified. This is a nalysis of glioblastoma tissues and matched adjacent normal brain tissues from 3 patients. Results provide insight into molecular mechanisms underlying the non-coding and coding genes interactions in glioblastoma.
3 human GBM tissues and the matched adjacent normal brain tissues were analyzed using microarray. The aberrant lncRNAs, miRNAs and mRNAs between the 2 groups were detected.

platform_organism:
Homo sapiens
synthetic construct

overall_design: A total of 3 GBM tissues and the matched adjacent normal brain tissues were obtained for RNA extraction and hybridization from patients who underwent primary surgical treatment according to clinical protocols. No chemotherapy or radiotherapy was performed on the patients before therapeutic resection. All cases were reviewed by two neuropathologist for confirming the diagnosis of GBM as per 2007 World Health Organization criteria. We sought to obtain the aberrant lncRNAs, miRNAs and mRNAs between tissues and the matched adjacent normal brain tissues.

first: Jun

last: Yang

first: Yiping

last: Li

first: Fusheng

last: Liu

first: Ying

last: Huang

first: Shunchang

last: Ma


title: Profiling of iPSC-derived keratinocytes

status: Public on Dec 01 2014

city: New York

first: Jane

middle: E.

last: Cerise

state: NY

address: 1150 St. Nicholas Avenue

institute: Columbia University

summary:
Our goal was to demonstrate the similarity between the original keratinocytes and iPSC-derived keratinocytes from the same individual
Profiles of original keratinocytes, iPSCs, IPSC-derived keratinocytes, iPSC-derived fibroblasts from a single individual and normal fibroblasts from a second individual were compared

overall_design: Three technical replicates were prepared for revertant-iPSC-FB, two technical replicates for normal FB and one for iPSC, revertant-iPSC-KC and the original keratinocytes

first: Noriko

last: Umegaki-Arao

middle: E

first: Angela

last: Christiano


title: GATA2 facilitates steroid receptor coactivator (SRC) recruitment to the androgen receptor (AR) complex

status: Public on Jan 21 2015

city: Houston

first: Nicholas

last: Mitsiades

state: Texas

address: One Baylor Plaza

department: Medicine-Hematology & Oncology

institute: Baylor College of Medicine

summary: The androgen receptor (AR) is a key driver of prostate cancer (PC), even in the state of castration-resistant PC (CRPC), and frequently even after treatment with second-line hormonal therapies such as abiraterone and enzalutamide. The persistence of AR activity via both ligand-dependent and ligand-independent (including constitutively active AR splice variants) mechanisms highlights the unmet need for alternative approaches to block AR signaling in CRPC. We investigated the transcription factor GATA2 as a regulator of AR signaling and a novel therapeutic target in PC. We demonstrate that GATA2 directly promotes AR expression (both full-length and splice variant), resulting in a strong positive correlation between GATA2 and AR expression in PC (cell lines and patient specimens). Conversely, GATA2 expression is repressed by androgen and AR, suggesting a negative feedback regulatory loop that, upon androgen deprivation, derepresses GATA2 to contribute to AR overexpression in CRPC. Simultaneously, GATA2 is necessary for optimal transcriptional activity of AR (both full-length and splice variant). GATA2 co-localizes with AR and FOXA1 on chromatin to enhance recruitment of steroid receptor coactivators (SRCs) and formation of the transcriptional holocomplex. In agreement with these important functions, high GATA2 expression and transcriptional activity predicted for worse clinical outcome in PC patients. A GATA2 small molecule inhibitor suppressed the expression and transcriptional function of AR (both full-length and splice variant) and exerted potent anticancer activity against PC cell lines. We propose pharmacological inhibition of GATA2 as a “first-in-field” approach to target AR expression and function and improve outcomes in CRPC.

overall_design: LNCaP cells were transfected with control siRNA (3), GATA2 siRNA (3) or AR siRNA for 72 hours.

first: Cristian

last: Coarfa


title: Gene expression of human keratinocyte (HaCaT) under the stress of high sodium concentration

status: Public on Jan 29 2015

city: Chicago

first: Wei

last: Xu

state: IL

address: 303 E Chicago Ave, Tarry 4-714

department: Surgery

institute: Northwestern University, Feinberg School of Medicine

summary:
The mechanisms by which the epidermis responds to disturbances in barrier function and restores homeostasis are unknown. With a disruption of the epidermal barrier, water is lost resulting in an increase in extracellular sodium concentration. We demonstrate that the sodium channel Nax functions as the sodium sensor. With increased extracellular sodium, Nax up-regulates prostasin which results in activation of the sodium channel ENaC, resulting in increased sodium flux and increased downstream mRNA synthesis of inflammatory mediators. The same pathways are present in lung epithelial cells.
A signal transduction pathway mediated directly through Nax and secondarily through ENaC results in production of secretory inflammatory mediators. These mediators result in epithelial proliferation and restoration of epidermal homeostasis, but can also have negative effects including excess inflammation and ultimately leads to activation of fibroblasts.

overall_design: Both wild type and Nax knockdown HaCaT cells were seeded in 12-well plates. 70-80% confluent cells were starved with fetal bovine serum (FBS) free Dulbecco's modiﬁed Eagle's medium (DMEM) overnight followed by a treatment with control medium (final150 mM sodium) or medium plus 10% more sodium (final 165 mM sodium). Cells were harvested at time point 0, 4, and 16 hours post treatment.

first: Seok

middle: J

last: Hong

first: Aeimei

last: Zhong

first: Shengxian

last: Jia

first: Ping

last: Xie

first: Kai

middle: P

last: Leung

first: Robert

middle: D

last: Galiano

first: Thomas

last: Mustoe


title: ISG15 in regulation of interferon responses

first: Dusan

last: Bogunovic

state: New York

address: 1468 Madison Avenue,

department: Microbiology

institute: Icahn School of Medicine at Mount Siani

summary:
We assessed how lack of ISG15 influences the levels of transcripts after IFNa stimulation.
Expression data from ISG15 deficient patients (P1, P2, P3) and control (C1, C6, C16) hTert fibroblasts

overall_design: HTert-immortalized fibroblasts from C1, C6, C16, P1, P2 and P3 were treated with 1000U of IFN-α2b for 12 h, washed with PBS and left to rest for 36 h, after which relative mRNA levels were assessed


title: Whole transcriptome analysis of laser capture microdissected tissues reveals site-specific programming of the host epithelial transcriptome by the gut microbiota

status: Public on Feb 12 2015

city: Little Rock

first: Intawat

last: Nookaew

address: 4301 W Markham St

department: Department of Biomedical Informatics

institute: University of Arkansas for Medical Sciences

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

overall_design: Refer to individual Series

first: Felix

last: Sommer

first: Nina

last: Adam

first: Per

last: Fogelstrand

first: Fredrik

last: Bäckhed


title: Microarray analysis of immunity in response to injection of non-specific long dsRNA in kuruma shrimp, Marsupenaeus japonicus

city: Tokyo

first: Hidehiro

last: Kondo

address: 4-5-7 Konan, Minato

country: Japan

institute: Tokyo University of Marine Science and Technology

summary: There is continuous interest in the anti-viral immune response of shrimp to prevent bacterial and viral infection. In this study, global expression analysis through microarray was conducted to gain insights about the mechanisms involved in the protection of non-specific double stranded RNA –injected shrimps against infectious diseases. Hemocytes were collected from different shrimp groups injected with PBS (Phosphate buffered saline), siGFP and dsGFP at 12 and 24 hour timepoints. Genes were clustered based on expression and treatment to highlight differences in expression related to the type of injection.

overall_design: Non-specific RNA induced gene expression in shrimp hemocyte was measured at 24 and 48 hours post injection of 3 ug/g of dsGFP, siGFP, or PBS. Four different shrimps were used in each treatment group.

first: Benedict

last: Maralit

first: Mami

last: Komatsu

first: Sheryll

middle: G

last: Hipolito

first: Ikuo

last: Hirono


title: Gene Expression of Prostate Cancer Cells; 22Rv1, DU-145 and LNCaP: 5-Aza-2'-deoxycytidine (DAC) Treatment vs. Control

status: Public on Nov 13 2014

city: Toronto

first: Bharati

last: Bapat

address: 60 Murray St

country: Canada

institute: Mount Sinai Hospital

summary:
Epigenetic silencing mediated by CpG methylation is a common feature of many cancers. Characterizing aberrant DNA methylation changes associated with tumor progression may identify potential prognostic markers for prostate cancer (PCa). We treated three PCa cell lines, 22Rv1, DU-145 and LNCap with the demethylating agent 5-aza 2’–deoxycitidine (DAC) and examined gene expression changes using a custom microarray (GPL16604). These data were integrated with gene methylation status (GEO Pending) in PCa cell lines and further combined with patient tumor data to identify potential novel biomarkers for PCa patients.
In order to identify genes that are methylated in PCa, we employed a genome-wide gene expression profiling approach and compared cells treated with 5-aza 2’–deoxycitidine (DAC) to untreated cells. 22Rv1, DU-145 and LNCaP PCa cell lines were incubated in culture medium with 2 μg/mL DAC for 4 days with medium change every 2 days. Total RNA was extracted and gene expression was analyzed using a custom microarray (GPL16604).

overall_design: Cells were plated in 6 cm dishes and incubated in culture medium with 2 μg/mL DAC for 4 days with medium change every 2 days. The effect of DAC on gene expression in the PCa cell lines 22Rv1, DU-145 and LNCaP was measured by gene expression array. Experiments were preformed in triplicate.

first: Nicole

last: White-Al Habeeb

first: Ken

last: Kron

first: Ekaterina

last: Olkhov-Mitsel

first: Melanie

last: Lehman

first: Lidija

last: Jovanovic

first: Colleen

middle: C

last: Nelson


title: Expression analysis of canonical and adaptive human NK cell subsets

status: Public on Mar 06 2015

city: Stockholm

first: Yenan

last: Bryceson

state: Sweden

address: Karolinska University Hospital Huddinge

department: Department of Medicine

country: Sweden

institute: Karolinska Institutet

summary: The mechanisms underlying human natural killer (NK) cell phenotypic and functional heterogeneity are unknown. Here, we have described the emergence of diverse subsets of human NK cells selectively lacking expression of signaling proteins following cytomegalovirus (CMV) infection. The absence of B and myeloid cell-related signaling protein expression in these NK cell subsets correlated with promoter DNA hypermethylation. Genome-wide DNA methylation patterns were strikingly similar between CMV-associated adaptive NK cells and cytotoxic effector T cells, but differed from those of canonical NK cells. Functional interrogation demonstrated altered cytokine responsiveness in adaptive NK cells that was linked to reduced expression of the transcription factor PLZF. Furthermore, subsets of adaptive NK cells demonstrated significantly reduced functional responses to activated autologous T cells. The present results uncover a spectrum of epigenetically unique adaptive NK cell subsets that diversify in response to viral infection and have distinct functional capabilities compared to canonical NK cell subsets.

overall_design: Donor PBMC were screened for individuals where FcεRγ- and PLZF- NK cell subsets correlated with NKG2C surface expression. For the donors used in the expression analysis, 89.3±9.5% (mean±SD) or 3.6±2.6% expressed FcεRγ and 89.0±9.8% or 1.7±1.3% expressed PLZF of the canonical CD3-CD56dimCD57+NKG2A-NKG2C- or adaptive CD3-CD56dimCD57+NKG2A-NKG2C+ populations, respectively. Based on CD57, NKG2A and NKG2C expression, CD3-CD56dim NK cell subsets were sorted from 4 donors.

first: Heinrich

last: Schlums

first: Frank

last: Cichocki

first: Bianca

last: Tesi

first: Jakob

last: Theorell

first: Tim

last: Holmes

first: Hans-Gustaf

last: Ljunggren

first: Jeffrey

middle: S

last: Miller

middle: T


title: Genomewide analysis of the human p53 transcriptional network unveils a lncRNA tumor suppressor signature (expression)

status: Public on Dec 22 2014

city: Pamplona

first: Maite

last: Huarte

state: Navarra

address: c/ Avd Pio XII, 55

country: Spain

institute: Centro de Investigación Médica Aplicada

summary: We report the application of high-throughput sequencing to performed the p53 regulated trancriptome in HCT116 colon cancer cells treated with the DNA damage 5FU. To study the direct targets of p53 we performed ChIP-seq to deterrmined the p53 biding sites and associated with the expression levels. With this study we identified the new genomic regions regulated by p53 and with special attention in those regions that are significally expressed by DNA damage and and are non- coding.

overall_design: HCT116 p53 wt cell transfected with the ASO-SC, ASO lncRNA-1 and ASO unassigned-1 for depletion of this new lncRNAs  and treated with the DNA damage drug 5FU for 12h  were analyzed in the affimetrix platform HTA2.

first: Yolanda

last: Sanchez

first: Victor

last: Segura


title: Identification of Salmonella enterica genes under the control of StdE and StdF

status: Public on Nov 25 2014

city: Sevilla

first: Lucía

middle: García

last: Pastor

state: Sevilla

address: Avda. Reina Mercedes 6

department: Genetics

institute: Universidad de Sevilla

summary: Transcriptomic analysis in a Salmonella enterica Serovar Typhimurium SL 1344 that constitutively expresses stdE and stdF compared with a strain carrying an stdEF deletion

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

overall_design: A four chip study using total RNA recovered from two separate cultures of Salmonella enterica Serovar Typhimurium SL 1344 constitutively expressing stdE and stdF and two separate cultures of Salmonella enterica Serovar Typhimurium SL 1344 lacking stdE and stdF.

last: García-Pastor

first: Elena

last: Puerta-Fernandez

first: Josep

last: Casadesús


title: microRNA expression profiling and its integration with mRNA in metastatic melanoma reveal associations with BRAF mutation status and patient prognosis

status: Public on Oct 06 2014

city: North Sydney

first: Graham

middle: J.

last: Mann

state: NSW

address: Poche Centre, 40 Rocklands Road

country: Australia

institute: Melanoma Institute Australia

summary: Objectives/experimental design

overall_design: Samples eligible for this study (n=84) were obtained from lymph node specimens (Melanoma Institute Australia (MIA) Biospecimen Bank) in which macroscopic tumor was observed, obtained from patients believed to be without distant metastases at the time of tumor banking based on clinical examination and computerised axial tomographic scanning of the brain, chest, abdomen and pelvis. Specimens were macro-dissected at time of banking and subsequently reviewed to meet minimum criteria for tumor cell content (>80%) and amount of necrosis (<30%). Linked clinical and pathologic data were obtained from the MIA research database. mRNA expression profiling information in the same samples is available: GSE54467.

first: Varsha

last: Tembe

first: Sarah-Jane

last: Schramm

first: Mitchell

last: Stark

first: Ellis

last: Patrick

first: Vivek

last: Jayaswal

first: Yue

middle: H

last: Tang

first: Andrew

last: Barbour

first: Nicholas

middle: K

last: Hayward

first: John

middle: F

last: Thompson

first: Richard

last: Scolyer

first: Yee

last: Yang


title: KAP1 promotes proliferation and metastatic progression of breast cancer cells

status: Public on Sep 23 2014

city: Morgantown

first: Alexey

middle: Virginia

last: Ivanov

state: West Virginia

address: 64 Medical Center Drive

department: Department of Biochemistry and Molecular Medicine and WVU Cancer Institute

institute: West Virginia University

summary: KAP1 (TRIM28) is a transcriptional regulator in embryonic development that controls stem cell self-renewal, chromatin organization and the DNA damage response, acting as an essential co-repressor for KRAB family zinc finger proteins (KRAB-ZNF). To gain insight into the function of this large gene family, we developed an antibody that recognizes the conserved zinc fingers linker region (ZnFL) in multiple KRAB-ZNF. Here we report that the expression of many KRAB-ZNF along with active SUMOlyated KAP1 is elevated widely in human breast cancers. KAP1 silencing in breast cancer cells reduced proliferation and inhibited the growth and metastasis of tumor xenografts. Conversely, KAP1 overexpression stimulated cell proliferation and tumor growth. In cells where KAP1 was silenced, we identified multiple downregulated genes linked to tumor progression and metastasis, including EREG/epiregulin, PTGS2/COX2, MMP1, MMP2 and CD44, along with downregulation of multiple KRAB-ZNF proteins. KAP1-dependent stabilization of KRAB-ZNF required direct interactions with KAP1. Together, our results show that KAP1-mediated stimulation of multiple KRAB-ZNF contributes to the growth and metastasis of breast cancer.

overall_design:
To determine KAP1 regulated genes, we performed microarray analysis of gene expression in KAP1 depleted breast cancer cells MDA-MB-231LN.
7 total samples were analyzed. Stable sublines of MDA-MB-231LN cells expressing control non-targeting shRNA (Scr, 3 biological replicates) and two different shRNAs against KAP1 (KAP1-3, 2 biological replicates and KAP1-4, 2 biological replicates) from doxycycline-inducible pTRIPZ vector were cultured in the presence of 0.5 ug/ml doxycycline for 7 days to induce shRNA expression. Cells were lysed and total RNA was isolated using mirVana miRNA isolation kit (Ambion) in the WVU Genomics Core Facility.

middle: V

first: Dongquan

last: Chen


title: The tumor-promoting receptor tyrosine kinase, eEphB4, regulates expression of integrin β8 in prostate cancer cells

status: Public on Sep 27 2014

city: Woolloongabba

first: Inga

last: Mertens-Walker

address: 37 Kent St

institute: Queensland University of Technology, TRI

type: Expression profiling by genome tiling array

summary: Knockdown of the receptor tyrosine kinase EphB4 using siRNA in LNCaP prostate cancer cells compared to negative siRNA controls

overall_design: In this study there were four replicates of EphB4 siRNA treated samples and three replicates of negative non-silencing siRNA controls

first: Bruno

last: Fernandini

first: Mohannan

last: Maharaj

first: Anja

last: Rockstroh

first: Colleen

last: Nelson

first: Adrian

last: Herington

first: Sally-Anne

last: Stephenson


title: Identification of interleukin-4 (IL-4) targets in chronic lymphocytic leukemia (CLL)

city: Murcia

first: Antonio

last: Parrado

address: Ctra. Madrid-Cartagena, s/n

institute: Hospital Clinico Universitario Virgen de la Arrixaca

summary: Gene expression profiles of CLL cells and normal B cells (NBC) treated for 18 hr with 10 ng/ml IL-4, compared with culture with nothing (Ctrl) and the basal (Pre) samples. Patient CLL01 was also treated with IL-4 plus 5 mg/ml ERK activation inhibitor peptide I, or IL-4 plus 10 µM NFkB activation inhibitor, and IL-4 plus 100 mg/ml cyclic-pifithrin-α

overall_design: 23 CLL patients (10 Pre samples, 23 Ctrl samples, 23 IL-4 samples, 1 IL-4 plus ERK inhibitor sample, 1 IL-4 plus NFkB inhibitor sample, 1 IL-4 plus Pifithrin sample), 13 NBC (10 Pre samples, 10 Ctrl samples, 13 IL-4 samples)


title: Gene expression data from human induced pluripotent stem cells, induced pluripotent stem cell-derived human neural stem/progenitor cells, and iPSC-derived cerebral cortical neurons

status: Public on Sep 12 2014

city: Cambridgeshire

first: Yichen

last: Shi

address: Suite 3, The Science Village Building, Chesterford Research Park, Little Chesterford

country: United Kingdom

institute: Axol Bioscience Limited

summary:
Embryonic stem cells are pluripotent and possess the ability to differentiate into numerous lineages during the developmental process. In similarity to embryonic stem cells, human induced pluripotent stem cells (iPSCs) possess the potential to differentiate into multiple lineages making them an excellent research tool. We generated iPSCs from multiple donors and also differentiated iPSCs from these donors into human neural stem/progenitor cells (NSCs). We used human transcriptome arrays to detail the programme of gene expression underlying NPC induction and identified distinct classes of up-regulated genes during this process.

Human induced pluripotent stem cells (iPSCs) can be used to create neurons in vitro. This microarray allows researchers to check the expression of their gene of interest in iPSC-derived neurons and compare the gene expression profile of iPSC-derived neurons to other cell types or primary human tissue.

overall_design:
Total RNAs were extracted from human induced pluripotent stem cells and induced pluripotent stem cell-derived neural stem cells. Their gene expression profiles were investigated using the Affymetrix GeneChip Human Transcriptome Array 2.0 platform.

Total RNA was extracted from iPSC-derived cerebral cortical neurons and the gene expression profile was investigated using the Affymetrix GeneChip Human Transcriptome Array 2.0

first: Jun

last: Wei

first: Claire

middle: L

last: Cox


title: Species and gene divergence in Littorina snails by aCGH

status: Public on Jul 29 2014

city: Strömstad

first: Marina

last: Panova

address: Tjärnö

department: Biol and Env Sciences

institute: Gothenburg University

summary:
Background: Array comparative genomic hybridization (aCGH) is commonly used to screen different types of genetic variation in humans and model species. Here, we performed aCGH using an oligonucleotide gene-expression array for a non-model species, the intertidal snail Littorina saxatilis. First, we tested what types of genetic variation can be detected by this method using direct re-sequencing and comparison to the Littorina genome draft. Secondly, we performed a genome-wide comparison of four closely related Littorina species: L. fabalis, L. compressa, L. arcana and L. saxatilis and of populations of L. saxatilis found in Spain, Britain and Sweden. Finally, we tested whether we could identify genetic variation underlying “Crab” and “Wave” ecotypes of L. saxatilis.
Results: We could reliably detect copy number variations, deletions and high sequence divergence (i.e. above 3%), but not single nucleotide polymorphisms. The overall hybridization pattern and number of significantly diverged genes were in close agreement with earlier phylogenetic reconstructions based on single genes. The trichotomy of L. arcana, L. compressa and L. saxatilis could not be resolved and we argue that these divergence events have occurred recently and very close in time. We found evidence for high levels of segmental duplication in the Littorina genome (10% of the transcripts represented on the array and up to 23% of the analyzed genomic fragments); duplicated genes and regions were mostly the same in all analyzed species. Finally, this method discriminated geographically distant populations of L. saxatilis, but we did not detect any significant genome divergence associated with ecotypes of L. saxatilis.
Conclusions: The present study provides new information on the sensitivity and the potential use of oligonucleotide arrays for genotyping of non-model organisms. Applying this method to Littorina species yields insights into genome evolution following the recent species radiation and supports earlier single-gene based phylogenies. Genetic differentiation of L. saxatilis ecotypes was not detected in this study, despite pronounced innate phenotypic differences. The reason may be that these differences are due to single-nucleotide polymorphisms.

sample_organism:
Littorina saxatilis
Littorina arcana
Littorina fabalis
Littorina compressa

overall_design: Genomic DNA samples of L. fabalis, L. compressa, L. arcana and 3 geographic populations x 2 ecotypes of L. saxatilis (n=4 per group) have been hybridized to a transcriptomic oligoarray.


title: miRQC study, Agilent Platform data

status: Public on Jun 10 2014

city: Santa Clara

first: Stephanie

last: Fulmer-Smentek

state: CA

address: 5301 Stevens Creek Blvd

department: R&D

institute: Agilent Technologies

summary:
This data is a subset of the miRQC study, submitted for publication in summer of 2013.  The purpose of the study was to compare various aspects of miRNA profiling platform performance (reproducibility, sensitivity, accuracy, etc) using a standardized set of samples.
The data included in this submission is a subset of the study data generated on the Agilent miRNA profiling system.  The array used was designed to measure all of the human and human viral miRNAs in miRBase 16.0 and the is annotated based on miRBase 18.  Analysis for the miRQC study was based only on the human sequences present in miRBase 18 (8 sequences were deleted between 16.0 and 18.0)

sample_organism:
Homo sapiens
Escherichia phage MS2

overall_design: miRNA profiling on a standardized set of 20 samples.

first: Petula

last: D'Andrade


title: Gene expression of LNCaP cells grown in polyethlene glycol-based hydrogels alone (monocultures) and grown with human osteoblasts as tissue engineered bone (co-culture) with the presence of synthetic androgen, R1881

status: Public on May 13 2014

city: Brisbane

state: Queensland

address: 199 Ipswich Road

department: Institute of Health and Biomedical Innovation; Vancouver Prostate Centre

institute: Queensland University of Technology; University of British Columbia

summary: Analysis of LNCaP cell molecular differences in monocultures and in co-cultures in the presence of R1881. Human osteoblast molecular signatures were also identified from the tissue engineered bone monocultures. LNCaP cells molecular profile was altered by co-culturing with human osteoblasts compared to LNCaP monocultures with or without R1881 stimulations.  These results provide insights into the behavioral change of LNCaP cells in a bone-like microenvironment.

overall_design: In this study, LNCaP cells cultured in the hydrogel were prepared and co-cultured with or without human osteoblasts (in the form oftissue engineered bone). Similarly, tissue engineered bone monocultures were also prepared 4-6 weeks earlier before co-culturing with the LNCaP cells. These cultures were maintained up to  24 days in RPMI growth media (+10% FBS) before they were androgen-starved for 48 hours. Cells were either treated with 1nM R1881 or continued to be androgen-deprived (without R1881 with 0.008% ethanol) for another 48 hours prior to cell harvest for gene expression analysis. Biological triplicates were prepared for each condition.

first: Shirly

last: Sieh

first: Anna

last: Taubenberger

first: Melanie

last: Lehman

first: Judith

middle: A

last: Clements

first: Dietmar

middle: W

last: Hutmacher


title: Masseter muscle gene expression in human malocclusion subjects with and without posterior facial asymmetry

status: Public on May 20 2014

city: philadelphia

first: michael

middle: joseph

last: horton

state: pennsylvania

address: 3223 n broad st

department: orthodontics

institute: temple university school of dentistry

summary:
Non-syndromic facial asymmetry is commonly found in dentofacial deformity populations with skeletal malocclusions.  Asymmetry of this type may result from imbalanced growth and function of both the jaw and associated muscles.   Among the  multiple genes that interact to affect the craniofacial musculoskeletal complex during pre and postnatal growth and development, NODAL signaling pathwy (NSP) genes are active in adult skeletal muscle and may be key factors in development, growth and maintenance of facial asymmetry.  It is of interest to determine whether expression of NODAL pathway genes might differ in masseter muscles between individuals with malocclusion that have facial asymmetry and normal symmetry.
Human Transcriptome 2.0 GeneChips (HTA2.0) were used to examine global gene expression in masster muscles between malocclusion subjects with posterior facial asymmetry and with normal facial symmetry.

overall_design:
Eleven patients undergoing orthoganthic surgery were selected for comparison of masseter muscle gene expression on microarrays.  Two subjects had posterior facial asymmetry (one with class II open bite and one with class III open bite malocclusion) and nine subjects had normal facial symmetry (three with class II open bite, two with class III open bite and four with class II deep bite malocclusion).  RNA representative of total gene expression in masseter muscles of  the malocclusion subjects with and without posterior facial asymmetry was prepared for labeling and hybridization on HTA2.0 chips. The two subjects with facial asymmetry clustered separately from eight other malocclusion subjects by a principle component analysis (PCA), even though one had a class II and the other a class III malocclusion. Sample 4L_Open_II is from a subject who has sleep apnea.  Data from  4L_Open_II clustered independent of the asymmetry group and the eight other subjects of the symmetry group by PCA and was not included in analysis of differential expression with facial symmetry.
Masseter muscles are paired jaw muscles (i.e. right and left masseter). In some cases, there was not sufficient quantity/quality of RNA from one side, thus the other side was used.

Please note that the following information is provided in the 'source name' field of each sample record;
subject ID number; either left or right masseter; J CRANIOFAC SURG_ID# corresponding to the data presented in the manuscript

first: James

middle: J

last: Sciote

first: Michael

last: Horton

first: Elisabeth

middle: R

last: Barton


title: HepG2-MEK Inhibition with PD98059

status: Public on Sep 02 2014

city: Gainesville

last: Kilberg

state: Florida

address: 1600 SW Archer Road

department: Biochemistry & Molecular Biology

institute: University of Florida

summary: Transcripts (mRNA) during amino acid limitation after MEK was inhibited were analyzed.

overall_design: HepG2 cells were pretreated with MEK inhibitor, PD98059 for 1 hour, then incubated in complete medium and a medium depleted for Histidine for 8 hours. For Inhibitor treated cells, PD98059 was included in the medium during the following 8 hours-incubation.

first: Jixiu

last: Shan


title: DC-specific lincRNA controls dendritic cell development and function through interacting with STAT3

status: Public on May 02 2014

city: Shanghai

first: PIN

last: WANG

address: Xiangyin Road 800

institute: SMMU

summary: To identify the functional non-coding RNAs in human DC development, we explored the gene expression profiles during DC development from peripheral monocytes. Using microarray technique, we identified many annotated lncRNAs with markedly altered expressions during human DC differentiation and maturation.

overall_design: RNA samples from cells during the process of DC development from human peripheral blood monocytes were collected. Each time point sample was the pool of RNA from 3 donors.

first: Pin

last: Wang

first: Xuetao

last: Cao


title: Dextran sodium sulfate treatment of Pirc rats alters colonic and tumor gene expression

status: Public on Jan 14 2014

city: Madison

first: Amy

last: Irving

state: WI

address: 1400 University Avenue

department: McArdle Laboratory for Cancer Research

institute: University of Wisconsin-Madison

summary: Dextran sodium sulfate (DSS) causes inflammation in the gut similar to ulcerative colitis in humans.  Patients with ulcerative colitis have increased risk of developing colon cancer.  We sought to determine whether genes altered in the normal colonic epithelium or tumor differed between sporadic and inflammation-associated tumor development.

overall_design: 97 day old (ACIxF344)F1-Pirc male rats either untreated or given 4% DSS in the drinking water from 40-47 and 54-61 days of age, housed in 12 hour light:12 dark, ad lib feeding and drinking conditions.  Normal colonic tissue and tumors were harvested from the distal colon at 97 days of age.  A two color, reference design experiment hybridized according to Agilent protocols against a reference pool of RNA made up from colon tissue taken from pooled wild type rats which was labeled with Cy5.

first: William

last: Dove


title: Effects of dextran sodium sulfate on normal colonic tissue and tumors in wild type and Apc-Pirc/+ rats.

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

overall_design: Refer to individual Series


title: Effects of Th1- and Th17-derived factors on microglia.

status: Public on Dec 31 2013

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

country: Germany

institute: HCI - Helmholtz Centre for Infection Research

summary: There is evidence that microglia interact with infiltrating Th1 and Th17 cells and this interaction results in mutual activation. However, the potential of a distinct cytokine milieu generated by these effector T cell subsets to activate microglia is poorly understood. In this study, we tested the ability of factors secreted by Th1 and Th17 cells to induce microglial activation. Interestingly, we found that only Th1-associated factors had the potential to activate microglia while the Th17-associated factors as well as direct contact of Th17 cells with microglia only had a minimal effect. Further Th1-derived factors triggered a proinflammatory M1-type gene expression profile in microglia

overall_design:
Microglia harvested from mixed glial cultures were treated with supernatants from Th1- or Th17 cultures. Microglia cultured in medium was used as controls. At 16h post treatment RNA was isolated from the microglia and probed on Agilent´s murine 4x44k microarrays. RNA isolated from four independent experiments were used for the gene expression profiling.
Microglia, Th1, Th17

first: R

first: S

last: Floess

first: J

last: Huehn


title: Prenatal arsenic exposure and the epigenome: altered miRNA expression profiles in newborn cord blood

status: Public on Jan 22 2014

city: Chapel Hill

first: Rebecca

middle: Catherine

last: Fry

address: 1213 MHRC

department: Environmental Sciences and Engineering

institute: UNC-Chapel Hill

summary: The Biomarkers of Exposure to ARsenic (BEAR) pregnancy cohort in Gómez Palacio, Mexico was recently established to better understand the impacts of prenatal exposure to inorganic arsenic (iAs). In this study, we examined a subset (n = 40) of newborn cord blood samples for microRNA (miRNA) expression changes associated with in utero arsenic exposure. Levels of iAs in maternal drinking water (DW-iAs) and maternal urine were assessed. Levels of DW-iAs ranged from below detectable values to 236 µg/L (mean = 51.7 µg/L). Total arsenic in maternal urine (U-tAs) was defined as the sum of iAs and its monomethylated and dimethylated metabolites (MMAs and DMAs, respectively) and ranged from 6.2 to 319.7 µg/L (mean = 64.5 µg/L). Genome-wide miRNA expression analysis of cord blood revealed 12 miRNAs with increasing expression associated with U-tAs. Transcriptional targets of the miRNAs were computationally predicted and subsequently assessed using transcriptional profiling. Pathway analysis demonstrated that the U-tAs-associated miRNAs are involved in signaling pathways related to known health outcomes of iAs exposure including cancer and diabetes mellitus. Immune response-related mRNAs were also identified with decreased expression levels associated with U-tAs, and predicted to be mediated in part by the arsenic-responsive miRNAs. Results of this study highlight miRNAs as novel responders to prenatal arsenic exposure that may contribute to associated immune response perturbations.

overall_design: We assessed the impact of prenatal exposure to arsenic on genome-wide miRNA expression profiles and their potential influence on gene expression patterns in the Biomarkers of Exposure to ARsenic (BEAR) prospective pregnancy cohort. This cohort includes residents from Gómez Palacio, located in the state of Durango in the Lagunera region of Northern Mexico. A total of 200 pregnant women residing in Gómez Palacio, State of Durango, Mexico, were recruited at the General Hospital of Gómez Palacio to participate in the BEAR prospective pregnancy cohort. The present study focuses on miRNA expression profiles and utilizes 40 samples obtained from mother-newborn pairs selected from the larger cohort (n=200). The subcohort was selected to include subjects exposed to varying levels of arsenic as determined by both total arsenic in maternal urine (U-tAs) and inorganic arsenic in drinking water (DW-iAs). Cord blood samples were collected from the newborns immediately after infant delivery. Blood samples were collected using PreAnalytix PaxGene RNA tubes and extracted using the PAXgene RNA Kit, per standard protocol (Qiagen, Valencia, CA). Isolated RNA used for microarray analysis were amplified and labeled using the NuGEN Ovation Pico WTA System V2 and Encore Biotin Module, respectively (NuGEN, San Carlos, CA). RNA isolated from 40 cord blood samples were labeled and hybridized to the Agilent Human miRNA Microarray, based off miRBase v16.0.

first: Julia

middle: E

last: Rager


title: Stump project -- methylation whole tissue; volar versus non-volar acral skin gene expression

status: Public on Jul 03 2013

city: Baltimore

first: Luis

middle: Andres

last: Garza

address: 1550 Orleans St. Suite 204 CRBII Koch

department: Dermatology

institute: Johns Hopkins School of Medicine

summary: To broaden our understanding of the gene expression common to volar skin, we biopsied the dorsum of the hand, palm, dorsum of the foot and sole and collected DNA for methylation chip anlayses

overall_design:
Total of 12 skin biopsy samples with 3 repeats from distinct individuals of each site: dorsum of hand, palm, dorstum of foot and sole.
The samples below represent methylation data only.


title: Gene expression analysis of stimulated primary ASM cells [microRNA]

status: Public on May 28 2014

city: London

first: Mark

last: Perry

address: Dovehouse Street

department: Airway Disease

institute: NHLI, Imperial College London

summary: miRNA expression was determined using the Agilent Human miRNA Microarray G4870A (miRNA ID version)

overall_design: One-channel experiment: Control cells, 2.5%FCS, 2.5% FCS + Dex;  Biological replicates: 4


title: Dextran sodium sulfate treatment of wild type and Pirc rats alters colonic normal tissue gene expression

summary: Dextran sodium sulfate (DSS) causes inflammation in the gut similar to ulcerative colitis in humans.  Patients with ulcerative colitis have increased risk of developing colon cancer.  We sought to determine which genes are altered in the normal colonic epithelium, and which changes depend on the Pirc mutation.

overall_design: 97 day old (ACIxF344)F1 wild type and Pirc male rats either untreated or given 4% DSS in the drinking water from 40-47 and 54-61 days of age, housed in 12 hour light:12 dark, ad lib feeding.  Normal colonic tissue was collected from the distal colon at 97 days of age.


title: Identification of microRNAs differentially expressed in prostatic secretions of patients with prostate cancer

status: Public on Sep 27 2013

city: Istanbul

first: Mustafa

last: Ozen

address: Fatih

department: Medical Genetics

country: Turkey

institute: Istanbul University

summary: In this study, we aimed to identify a miRNA expression signature that could be used to distinguish PCa from BPH. We have shown for the first time in the literature the presence of miRNAs in the PSS. We suggest PSS as a powerful non-invasive source for evaluation of prognosis in PCa, since prostate massages can be easily applied during routine examination. Our results showed that certain differentially expressed miRNAs in PSS could be used as diagnostics markers.

overall_design: Prostate secretion samples (PSS) from 23 PCa and 25 benign prostate hyperplasia (BPH) patients were obtained from Urology Department of Bagcilar Educational and Research Hospital (Istanbul). MicroRNA (miRNA) profiling of eight PSS (four from BPH, four from PCa patients) were performed using microarray. Four of significantly deregulated miRNAs were further confirmed using quantitative reverse-transcription PCR (qRT-PCR). Statistical analysis was performed using Student’s t-test. ROC curves were plotted with SPSS-15.0.

first: Esra

last: Guzel

first: Omer

last: Karatas

first: Atilla

last: Semercioz

first: Sinan

last: Ekici

first: Serdar

last: Aykan

first: Serhat

last: Yentur

first: Chad

last: Creighton

last: Mittmann


title: Clinical Utility of Circulating MicroRNA Signatures for Breast Cancer Diagnosis (Gene expression)

status: Public on Sep 06 2013

city: Singapore

first: Maurice

last: Chan

address: 11 Hospital Drive

department: Division of Medical Sciences

country: Singapore

institute: National Cancer Centre

summary:
Purpose: There is a quest for novel non-invasive diagnostic markers for the detection of breast cancer. The goal of this study is to identify circulating microRNA signatures using a cohort of Asian Chinese breast cancer patients, and to compare microRNA profiles between  tumour and serum samples.  Experimental design: MicroRNAs from paired breast cancer tumours, normal tissue and serum samples derived from 32 patients were comprehensively profiled using microarrays (1300 microRNAs against tumour and normal tissues) or LNA RT-PCR panels (742 microRNAs against serum samples). Serum samples from healthy individuals (n=22) were also employed as normal controls. Significant serum microRNAs, identified by logistic regression, were validated in an independent set of serum samples from patients (n=82) and healthy controls (n=53).  Results: The 20 most significant microRNAs differentially expressed in breast cancer tumours included miR-21, miR-10b, and miR-145, previously shown to be dysregulated in breast cancer. Interestingly, 16 of the 20 most significant microRNAs differentially expressed in serum samples were novel. MiR-1, miR-92a, miR-133a and miR-133b were identified as the most important diagnostic markers, and were successfully validated; receiver operating characteristic curves derived from combinations of these microRNAs exhibited areas under the curves of 0.944-0.946. Only seven microRNAs were overexpressed in both tumours and serum, suggesting that microRNAs may be released into the serum selectively.   Conclusion: The clinical employment of microRNA signatures as a non-invasive diagnostic strategy is promising, but should be further validated for different subtypes of breast cancers.
"_A" and "_B" are two tissue sections of the same sample; "_1" and "_2" represents 2 runs of the same sample; na = not available

overall_design: All tissue samples were histologically confirmed by a pathologist using hematoxylin and eosin staining of cryosectioned specimens. One tumour sample was rejected due to failure to detect any tumour cells. Except for two samples (with 30% and 40% tumour cells), all tumour tissues employed had a minimum of 60% tumour cells, as estimated microscopically. Overall, the breast cancer tumour samples had an average of 71% tumour cells. The criteria for adjacent normal tissue were absence of tumour cells and presence of epithelial cells. Hence, after histological confirmation, 31 breast cancer tumours and 23 matched normal tissues were employed for microRNA extraction and profiling using microarray.


title: COHCAP MIRA / 450k Comparison [MIRA]

status: Public on Jun 08 2013

city: Duarte

first: Charles

middle: David

last: Warden

address: 1500 East Duarte Rd

department: Department of Molecular and Cellular Biology

institute: City of Hope

type: Methylation profiling by genome tiling array

summary: Compare a single sample run with two different technologies: Illumina 450k methylation array and MIRA on NimbleGen

overall_design:
This data is being published as a technical test of utility for a novel integrative genomic algorithm (COHCAP)
Keywords: HES-2

first: Joshua

last: Tompkins

first: Art

last: Riggs


title: COHCAP HCT116 Mutant Comparison [expression]

summary: Genome-wide expression and methylation differences are compared for a normal HCT116 cell line and a derived mutant with altered DNA methylation patterns.

overall_design:
The data compares the effect of a gene mutation on genome-wide expression (and methylation).  This data is being published as a technical test of utility for a novel integrative genomic algorithm (COHCAP)
Keywords: parental, mutant

first: Hua

last: Yu

first: Heehyoung

last: Lee

first: Richard

last: Jove


title: Circulating miRNA microarray analysis from archival plasma samples

status: Public on Apr 23 2013

city: Milan

first: Maurizio

last: Callari

address: Via Amadeo, 42

country: Italy

institute: Fondazione IRCCS Istituto Nazionale dei Tumori

summary: Using a microarray-based method we report on: i) adequate intra- and interarray reproducibility of miRNA profiling; ii) feasibility of using archival plasma samples stored for an extended period of time and available in limited amounts; and iii) good correlation between different batches.

overall_design: A total of 11 archived plasma samples collected between 1988 and 1999 were evaluated in this study. Firstly, RNA extracted from two samples (S1 and S2) were hybridized in triplicate. The same samples were also hybridized in triplicate after increasing the starting material volume from 2 to 2.5. Nine additional plasma samples were processed and RNA was hybridized on two different batches of arrays. Finally, two samples (S3 and S4) were re-hybridized on an array of the same batch of the first hybridization but close to the chip expiration date.


title: Stump project-- miRNA whole tissue; Volar versus non-volar acral skin gene expression

first: Luis

last: Garza

summary: To broaden our understanding of the gene expression common to volar skin, we biopsied the dorsum of the hand, palm, dorsum of the foot and sole and collected miRNA for chip anlayses

overall_design: total of 16 skin biopsy samples with 4 repeats from distinct individuals of each site: dorsum of hand, palm, dorstum of foot and sole


title: Identification of metabolic pathways in Daphnia magna exposed to selective serotonin reuptake inhibitors using transcriptomic, immunocytochemistry and physiological responses.

status: Public on Mar 15 2013

city: Doha

first: Tanwir

last: Habib

address: Al Luqta Street

country: Qatar

institute: Weill Cornell Medicine Qatar

summary: Assessing the risks of long-term exposure to low doses of pharmaceuticals is an identified research need, particularly for those that may act as neural disruptors in non-vertebrate species. Selective serotonin reuptake inhibitors (SSRIs) act by blocking the re-uptake of serotonin in the nerve synapses, increasing the effective concentration of serotonin in the intra-synaptic space and therefore stimulating serotoninergic neurons. This effect is used worldwide to treat clinical depression in humans, with the consequence of their widespread release into the environment. SSRIs have been found to alter the reproductive physiology of D. magna and other invertebrates in a biphasic way. Low levels of fluoxetine stimulated offspring production in Daphnia magna and Ceriodaphnia dubia at 36 and 50 µg/l, respectively, but higher exposure levels inhibited reproduction in the same species.

overall_design: In this study we explore the hypothesis that SSRI can affect D. magna juvenile developmental rates and offspring production disrupting serotonin activity that is known to regulate carbohydrate and oxidative metabolic pathways. The primary mode of action was tested using transcriptomic analyses of juveniles and adults exposed to SSRIs (fluoxetine 80 ppbs, fluovoxamine 30 ppbs) and serotonin-immunocytochemistry assays of D. magna brains.  Reproduction, respirometry and biochemical measurements allowed to related gene and immunological base effects to phenotypic responses.

first: Natàlia

last: Garcia-Reyero

first: Bruno

last: Campos

first: Lynn

last: Escalon

first: Henri

last: Dickensen

first: Stefan

last: Tsakovski

first: Benjamín

last: Piña

first: Romá

last: Tauler

first: Carlos

last: Barata


title: The E3 ubiquitin ligase Siah2 contributes to castration-resistant prostate cancer by regulation of androgen receptor transcriptional activity cancer.

status: Public on Feb 15 2013

city: Vancouver

first: Shawn

last: Anderson

state: BC

address: 2660 Oak Street

institute: Vancouver Prostate Centre

summary: The androgen receptor (AR) plays a central role in the development of castration resistant prostate cancer (CRPC). Here, we demonstrate that the ubiquitin ligase Siah2 targets a select pool of NCOR1-bound, transcriptionally inactive AR for ubiquitination dependent degradation, thereby promoting the expression of ~13% of AR target genes. The Siah2 binding sites located within the AR ligand-binding domain are mutated in PCa, resulting in attenuation of Siah2-mediated regulation. Siah2 is required for growth of PCa cells under androgen-deprivation conditions in vitro and in vivo. Significantly, inhibition of Siah2 promotes PCa regression upon castration and Siah2 expression is markedly increased in human CRPCs. Collectively our findings identify a key role for Siah2 in CRPC through the selective regulation of AR transcriptional activity.

overall_design: Tumor Harvest. When tumor size reached approximately 1.5 cm in diameter (6-8 weeks after injection), and the serum PSA was greater than 50 ng/ml, animals were surgically castrated under methoxyfluorane anesthesia and monitored for PSA levels for several weeks. Animals were sacrificed by carbon dioxide asphyxiation when tumors were harvested at several points along the PSA curve (pre-castrate (11), regressing (6), nadir (10), recurring (6) and castration resistant (12).  Tumor segments were placed in RNALater (Qiagen) and frozen immediately at -80°C.weeks. Tumors were harvested at several points along the PSA curve. The epithelial:stromal ratio is consistent within this tumor model and varies 10% between tumors, as assessed by immunohistochemistry of cytokeratin 14 (epithelium) and vimentin (stroma).

first: Jianfei

last: Qi

first: Manisha

last: Tripathi

first: Natasha

last: Sahgal

first: Susan

last: Ettinger

first: Ladan

last: Fazli

first: William

last: Placzek

first: Giuseppina

last: Claps

first: Leland

last: Chung

first: David

last: Bowtell

first: Martin

last: Gleave

first: Neil

last: Bhowmick

first: Ze’ev

last: Ronai


title: THE GOOD, THE BAD, AND THE TOXIC: DECIPHERING HORMESIS IN DAPHNIA MAGNA EXPOSED TO AN ENERGETIC COMPOUND

status: Public on Feb 01 2013

first: Tanwir

last: Habib

summary: Hormesis is a dose response phenomenon characterized by a stimulation of an organismal response at low doses of a chemical and inhibition of the response (toxicity) at a higher dose.  In the present study, Daphnia magna were exposed to the energetic compound 2,4,6-trinitrotoluene (TNT) for 21 days, and the endpoints survival, growth (length and dry weight), and reproduction (number of neonates per survivor) were assesed, identifying hormetic responses at the lower treatment levels. In order to elucidate the mechanisms leading to hormesis, microarray analysis was performed at 0.004 (hormetic), 0.12 (sometimes hormetic), and 1.85 (toxic) mg/L TNT. Functional and transcriptional benchmark dose analyses performed on differentially expressed genes suggested the involvement of lipid metabolism in hormetic responses and subsequently lipidomic analysis was performed on the same treatments. Lipid analysis supported the hypothesis that TNT exposure affected lipid metabolism, and showed that hormetic effects could be related to increases in some polyunsaturated fatty acids and ecosanoids known to be involved in Daphnia growth and reproduction.

overall_design: Chronic toxicity tests was designed to identify the hormetic range of D. magna responses to TNT. Daphnia magna younger than 24 h old and obtained from in-house cultures at the U.S. Army Engineer Research and Development Center, Environmental Laboratory (Vicksburg, MS) were used to initiate the bioassay. The experimental design consisted of one D. magna per test chamber and 10 test chambers per treatment level. In the microarray mass exposure, nominal treatment levels were 0.004, 0.02, 0.12, 0.44, and 1.85 mg/L. Based on the results of the testing in the 50 ml beakers, organisms from three treatments were selected for analysis of gene expression: 0.004, 0.12, and 1.85 mg/L. These treatments were selected to represent a hormetic concentration (0.004 mg/L), a toxic concentration (1.85 mg/L), and an intermediate concentration (0.12 mg/L). A total of 23 arrays used, with 5-6 replicates per each dose (solvent control, 0.004 mg/L, 0.12 mg/L, and 1.85 mg/L).

first: Jacob

last: Stanley

first: Edward

last: Perkins

first: Jerre

middle: G

last: Sims

first: Pornsawan

last: Chappell

first: Lynn

last: Escalon

first: Mitchell

last: Willbanks

first: Natalia

last: Garcia-Reyero


title: Clinical Utility of Circulating MicroRNA Signatures for Breast Cancer Diagnosis

first: Maurice

last: Chan

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


title: Gene expression profile on the penile tissue of erectile dysfunction (ED)  in cavernous nerve injury (CNI) RAT model

status: Public on Dec 31 2012

city: Seoul

first: SungWon

last: Lee

state: Seoul

address: 50 Irwon-dong

department: Urology

institute: Samsung Medical Center

summary:
(Erectile dysfunction) ED during the radical prostatectomy (RP) treatment is caused by surgical injury of the cavernous nerve which is the final neuronal pathways of penile erection.
We performed microarray experiment focused on theto understanding the gene signature alteration in the corporal cavernous tissue of the CNI-induced ED rat model.

overall_design: A total of 6 adult male Sprague-Dawley rats were randomly divided into two groups, sham operation (n=3) and bilateral CN resection (n=3) group. At 12 weeks after CN resection, penile tissue was harvested and microarray experiment was performed.

first: Sung

first: Chae

last: Meeree

first: Sanghoon


title: SM001: SARS CoV MA15 infection of C57Bl/6 mouse model – Data from 4 viral doses at 1, 2, 4 and 7 days post infection.

status: Public on Nov 01 2011

city: Seattle

first: Michael

last: Katze

state: WA

address: Rosen Building 960 Republican St.

department: Microbiology

institute: University of Washington

summary: Purpose of experiment was to perform transcriptomic analysis on C57Bl/6 mice infected with different doses of SARS CoV MA15 at 4 different days post infection.

overall_design:
Twenty-week-old C57BL/6 mice were infected by intranasal instillation of 10^2, 10^3, 10^4 or 10^5 PFU of SARS CoV MA15 in 50 µl of PBS or mock-infected with PBS alone.  At days 1, 2, 4 and 7 days post-infection, lungs were harvested and total RNA was isolated and subjected to microarray analysis.  The experimental design was for 4- 5 mice/time point/dose and 3 time-matched mocks.
The NIAID Systems Virology Center

first: Lisa

last: Gralinski

first: Armand

last: Bankhead

first: Jean

last: Chang

first: Ralph

last: Baric

first: Shannon

last: McWeeney


title: Clear-cell renal cell carcinomas tumors

status: Public on May 28 2011

city: Rennes

first: Julien

last: Edeline

address: Av prof leon Bernard

institute: CNRS-Université Rennes1

summary: Whole genome expression of 39 clear-cell renal cell carcinomas tumors

overall_design: 39 frozen tissue from recent nephrectomies for clear-cell renal cell carcinoma; association with clinical characteristics

first: Patricia

last: Fergelot

first: Nathalie

last: Rioux-Leclercq

first: Jean-Jacques

last: Patard

first: Florence

last: Jouan

first: Stéphanie

last: Mottier

first: Cécile

last: Vigneau


title: Expression data from paracrine senescence

status: Public on Jun 13 2013

first: Gopuraja

last: Dharmalingam

address: Faculty of Medicine, Imperial College, Hammersmith Hospital Campus

department: Epigenetics section

institute: MRC London Institute of Medical Sciences

summary:
Senescence can be transmitted in a paracrine way from cells undergoing  Oncogene Induced Senescence (OIS) to naïve normal cells. We define this phenomenon as “paracrine senescence”
We used microarrays to compare the trancriptome of cells undergoing paracrine senescence to the transcriptome of cells suffering OIS to unveil the common signatures defining both events and the similarities between them

overall_design: IMR90 cells were co-cultured with IMR90 ER:RAS undergoing OIS or IMR90-Vector control cells using 0.2 μm pore transwell (anopore) to allow communication of soluble factors but physical separation of the two cell populations. The total mRNA of IMR90, IMR90 ER:RAS or IMR90 cells cultured in Transwells together with IMR90 vector or IMR90 ER:RAS cells during 7 days in the presence of 200 nM 4OHT and 0.5 % FBS was extracted and hybridized on Affymetrix microarrays to compare paracrine senescence to OIS.

first: Juan

middle: C

last: Acosta

first: Jesus

last: Gil


title: Expression data from prostate cancer samples

status: Public on Oct 25 2012

city: Barcelona

first: Laia

last: Agell

address: Passeig Maritim 25-29

department: Pathology

institute: FIMIM

summary:
Although many genes have been proposed to be involved in prostate carcinogenesis, no single gene or gene profile has shown to have prognostic value. The main challenge for clinical management is to distinguish slowly growing tumors from those that will relapse. In this study, we compared expression profiles of 18 prostate samples (7 with Gleason 6, 8 with Gleason 7 and 3 with Gleason score equal or higher than 8) and 5 non-neoplastic prostate samples, using the GeneChip® Human Exon Array 1.0 ST of Affymetrix. Microarray analysis revealed 99 genes showing statistically significant differences among tumors with Gleason score 6, 7 and  8.  In addition, mRNA expression of 29 selected genes was analyzed by qRT-PCR with microfluidic cards in an extended series of 30 prostate tumors. From these, 29 were selected to be validated and the differential expression of 18 of them (62%) was independently confirmed by quantitative real-time RT-PCR (14 upregulated and 4 downregulated in higher Gleason scores) in the extended series. This list was further narrowed down to 12 genes that were differentially expressed in tumors with Gleason score of 6-7 vs  8. Finally, the protein levels of two genes from the 12-gene signature (SEC14L1 and TCEB1) were additionally validated by immunohistochemistry. Strong protein levels of both genes were correlated with Gleason score, stage, and PSA progression.
We used microarrays to detail the global programme of gene expression underlying cellularisation and identified distinct classes of up-regulated genes during this process.

overall_design: 23 Samples were analyzed.

first: Lloreta

last: Josep

first: Herdández

last: Silvia


title: An integrated study to the effects of thermal acclimation in zebrafish

status: Public on Aug 28 2010

city: Wilrijk

first: Lucia

last: Vergauwen

address: Universiteitsplein 1

department: Veterinary Sciences

country: Belgium

institute: University of Antwerp

summary:
Changes in environmental temperature can profoundly change species habitats and result in populations facing suboptimal environments. Many aquatic organisms are restricted in terms of migration by their habitat requirements. Also due to anthropogenic migration barriers (both physical as well as chemical), organisms are often left with no choice but to acclimate (or, in the long run, adapt) to their changing environment.
The scope of this study is to investigate thermal acclimation in zebrafish by combining data from several levels of biological organization. Zebrafish were acclimated to a higher temperature (8°C increase compared to controls) or a lower temperature (8°C decrease compared to controls) in an acute as well as a prolonged and a chronic scenario (4, 14 and 28 days). General condition of the fish was assessed by determining organismal (condition factor) and biochemical (energy homeostasis) parameters. Data at the transcriptome level (using printed oligonucleotide microarrays containing 15,208 probes and real time PCR) were applied to clarify the mechanisms underlying the thermal acclimation response in zebrafish.

overall_design: All three biological replicates of liver samples from acute (4 days) and chronic (28 days) controls (26°), warm acclimation (34°) and cold acclimation (18°) were analyzed using microarrays. An A-optimal interwoven loop design was used in which each sample appeared on an array twice in Cy3 and twice in Cy5, resulting in 36 arrays for 18 samples.

first: Donald

last: Benoot

first: Ronny

last: Blust

first: Dries

last: Knapen


status: Public on May 06 2010

city: Cambridge

first: Bernardo

last: Lemos

state: MA

address: 16 Divinity Avenue, Room 2105

institute: Harvard University

summary:
Transcriptional profiling of Drosophila melanogaster 2nd chromosome substitution lines; Background chromosomes are identical across lines; 2nd chromosomes are different across line and can be homozygous or heterozygous within each line

Keywords: Natural variation

overall_design: Loop design with 8 genotypes


title: Transcriptome profile of peripheral blood mononuclear cells in children with acute otitis media caused by Streptococcus pneumoniae

status: Public on Jul 26 2010

city: rochester

first: keyi

last: liu

address: 1425 portland ave

institute: Rochester General Research Institute

summary: Streptococcus pneumoniae (Spn) is the predominant causative organism of acute otitis media (AOM) in children. A human cDNA microarray comprising 30,968 human genome probes was used to evaluate the transcriptional changes that occur in peripheral blood mononuclear cells (PBMC) at the onset of clinical AOM caused by Spn infection in children after comparison of microarray results with the pre-infection healthy stage of the same children.

overall_design: Four to ten milliliters of heparinized peripheral venous blood was collected from children at 6 to 30 months of age when they were in acute otitis media (AOM) stage and pre-infection healthy stage. The diagnosis of AOM was based on symptoms and signs as well as S. pneumoniae culture positive in the middle ear fluid. Patients with polymicrobial infections, history of immunodeficiency, history of chronic or recurrent AOM, chronic disease, or receiving steroids or other immunomodulatory agents were excluded. Peripheral blood mononuclear cells (PBMCs) were isolated by the Ficoll gradient and total RNA was extracted from PBMCs using the QIAamp RNA blood Mini Kit (Qiagen, Maryland, USA) according to manufacturer’s instructions. Double-stranded cDNA generated from total RNA was labeled with Cyanine-5 and subsequently hybridized to Human OneArray glass slides according to the manufacturer's standard protocols (PhalanxBio Inc, CA, USA). Microarrays were scanned at 5 μm resolution using an Agilent scanner. Raw intensity signals for each microarray were captured using a Molecular Dynamics Axon 4100A scanner, measured using GenePixPro™ Software. The data from all microarrays in each experimental set was then analyzed using Omicsoft Array Studio software; control and missing features were removed, and the remaining signals were quantile normalized.

first: Keyi

last: Liu

first: Michael

last: Pichichero


title: Host cell-free growth of the Q fever bacterium Coxiella burnetii

status: Public on Oct 21 2009

city: Hamilton

first: Dan

last: Sturdevant

state: MT

address: 903 S 4th street

department: NIAID

institute: NIH

summary: The inability to propagate obligate intracellular pathogens under axenic (host cell-free) culture conditions imposes severe experimental constraints that have negatively impacted progress in understanding pathogen virulence and disease mechanisms. Coxiella burnetii, the causative agent of human Q (Query) fever, is an obligate intracellular bacterial pathogen that replicates exclusively in an acidified, lysosome-like vacuole. To define conditions that support C. burnetii growth, we systematically evaluated the organism’s metabolic requirements using expression microarrays, genomic reconstruction, and metabolite typing. This led to development of a complex nutrient medium that supported substantial growth (~ 3 log10) of C. burnetii in a 2.5% oxygen environment. Importantly, axenically grown C. burnetii were highly infectious for Vero cells and exhibited developmental forms characteristic of in vivo grown organisms. Axenic cultivation of C. burnetii will facilitate studies of the organism’s pathogenesis and genetics, and aid development of Q fever preventatives such as an effective subunit vaccine. Furthermore, the systematic approach used here may be broadly applicable to development of axenic media that support growth of other medically important obligate intracellular pathogens.

platform_organism:
Borreliella burgdorferi
Yersinia pestis
Coxiella burnetii
Chlamydia trachomatis
Staphylococcus aureus
Streptococcus pyogenes

overall_design: Host cell-free growth, Vero cell growth and carryover baseline of Coxiella burnetii

first: Anders

last: Omsland

first: Diane

last: Cockrell

first: Dale

last: Howe

first: Elizabeth

last: Fischer

first: Kimmo

last: Virtaneva

first: Daniel

first: Stephen

last: Porcella

first: Robert

last: Heinzen


title: Preadaptation of Yersinia pestis to resist mammalian innate immunity during transit through the flea vector

status: Public on Apr 06 2010

summary: Yersinia pestis, the agent of plague, is transmitted to mammals by infected fleas. Y. pestis exhibits a distinct life stage in the flea, where it grows in the form of a cohesive biofilm that promotes transmission. After transmission, the temperature shift to 37°C induces many known virulence factors of Y. pestis that confer resistance to innate immunity. These factors are not produced in the low-temperature environment of the flea, however, suggesting that Y. pestis is vulnerable to the initial encounter with innate immune cells at the flea bite site. In this study, we used whole-genome microarrays to compare the Y. pestis in vivo transcriptome in infective fleas to in vitro transcriptomes in temperature-matched biofilm and planktonic cultures, and to the previously characterized in vivo gene expression profile in the rat bubo. In addition to genes involved in metabolic adaptation to the flea gut and biofilm formation, several genes with known or predicted roles in resistance to innate immunity and pathogenicity in the mammal were upregulated in the flea. Y. pestis from infected fleas were more resistant to phagocytosis than in vitro-grown bacteria, which was largely attributable to a cluster of insecticidal-like toxin genes that were highly expressed only in the flea. Our results indicate that cycling through the flea vector preadapts Y. pestis to face the mammalian innate immune response that it encounters immediately after transmission.

overall_design: Midlog phase vs. stationary phase vs. flowcell biofilm vs. flea biofilm.

first: Viveka

last: Vadyvaloo

first: Clayton

last: Jarrett

first: Florent

last: Sebbane

first: B

last: Hinnebusch


title: Transcriptomes of covR/S mutant strains of S. pyogenes

status: Public on Jun 06 2009

city: Reno

first: Paul

last: Sumby

state: NV

address: 1554 N. Virginia St.

department: Microbiology & Immunology

institute: University of Nevada

summary: Two covR mutant derivatives of parental strain MGAS2221 were recovered from mice experimentally infected with MGAS2221 and shown to differ in terms of the number and concentration of secreted proteins.  One of the covR mutant strains had a secretion phenotype identical to a covS mutant strain, while the other had a secretion phenotype identical to a constructed covR mutant strain.  To further investigate the potential differences between the two covR mutant strains we performed expression microarray analysis.

overall_design: Single cultures of each of the four GAS strains tested were grown in THY broth to early exponential phase (O.D. 0.2). Two volumes of RNA protect were added, the samples incubated at room temperature for 5 minutes, and the bacteria collected through centrifugation. Total RNA was isolated via a mechaniscal disruption method, converted to cDNA, fragmented, labeled, and hybridized to our Affymetrix microarray. Estimates of gene expression were calculated using GCOS software v1.4. Data represent probes for serotype M1.


title: Genome-scale analysis of Staphylococcus aureus reveals host-specific diversification of the core genome.

status: Public on Nov 19 2008

summary:
Staphylococcus aureus causes disease in humans and a wide array of animals. Of note, S. aureus mastitis of ruminants, including cows, sheep and goats, results in major economic losses worldwide. Extensive variation in genome content exists among S. aureus pathogenic clones. However, the genomic variation among S. aureus strains infecting different animal species has not been well examined. To investigate variation in the genome content of human and ruminant S. aureus we carried out whole genome PCR scanning (WGPS), comparative genomic hybridizations (CGH), and directed DNA sequence analysis of strains of human, bovine, ovine, and caprine origin. Extensive variation in genome content was discovered including host- and ruminant-specific genetic loci. Ovine and caprine strains were genetically allied whereas bovine strains were heterogenous in gene content. As expected, mobile genetic elements such as pathogenicity islands and bacteriophages contributed to the variation in genome content between strains. However, remarkably, most host-specific differences were restricted to regions of the conserved core genome, which contained allelic variation in genes encoding proteins of known and unknown function. Many of these proteins are predicted to be exported and could play a role in host-pathogen interactions. These data suggest that diversification of the core genome may be more important than acquisition of novel genes for S. aureus host-adaptation. The host-specific determinants identified by the whole-genome approaches adopted in the current study represent excellent targets for studies of the evolution and molecular basis of S. aureus host specificity.
Keywords: Strain vs strain

overall_design: eleven strains of Sa were compared at the DNA level in triplicate.

first: Nouri

middle: B

last: Zakour

first: Sergine

last: Even

first: Caitriona

last: Guinane

first: Corinne

last: Barbey

first: Priscila

middle: D

last: Alves

first: Marie-Françoise

last: Cochet

first: Michel

last: Gautier

last: Otto

first: J

last: Fitzgerald

first: Yves

last: Loir


title: Detection of chromosomal aberrations in renal tumors by virtual karyotyping with SNP microarrays

status: Public on Feb 19 2009

city: Houston

first: Federico

last: Monzon

state: TX

address: 6565 Fannin St., MS205

institute: The Methodist Hospital Research Institute

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

summary: Renal epithelial neoplasms have characteristic chromosomal imbalances that can be used for classification. We have previously shown that virtual karyotypes (v-karyotype) derived from SNP microarrays can be performed on formalin-fixed paraffin embedded (FFPE) tissue samples but a direct comparison with karyotypes obtained by conventional cytogenetics has not been done. 20 archival FFPE tumor samples were analyzed with Affymetrix 10K 2.0 or 250K Nsp SNP microarrays.

overall_design: 19 archival FFPE tumor samples were analyzed with Affymetrix 10K 2.0 or 250K Nsp SNP microarrays and virtual-karyotype results compared to those obtained by Cytogenetics.

first: Karla

last: Alvarez

first: Julia

last: Bridge

first: Marilu

last: Nelson

first: Zoran

last: Gatalica

first: Jill

last: Hagenkord


title: Determination of transcriptome of SptR in group A Streptococcus during growth in human saliva

status: Public on May 16 2009

first: Samuel

last: Shelburne

address: 1515 Holcombe Blvd

department: Infectious Diseases

institute: MD Anderson Cancer Center

summary: The molecular genetic mechanisms used by bacteria to persist in humans are poorly understood. Group A Streptococcus (GAS) causes the majority of bacterial pharyngitis cases in humans and is prone to persistently inhabit the upper respiratory tract. To gain information about how GAS survives in and infects the oropharynx, we analyzed the transcriptome of a serotype M1 strain grown in saliva. The dynamic pattern of changes in transcripts of genes [spy0874/0875, herein named sptR and sptS (sptR/S), for saliva persistence] encoding a two-component gene regulatory system of unknown function suggested that SptR/S contributed to persistence of GAS in saliva. Consistent with this idea, an isogenic nonpolar mutant strain (DeltasptR) was dramatically less able to survive in saliva compared with the parental strain. Iterative expression microarray analysis of bacteria grown in saliva revealed that transcripts of several known and putative GAS virulence factor genes were decreased significantly in the DeltasptR mutant strain. Compared with the parental strain, the isogenic mutant strain also had altered transcripts of multiple genes encoding proteins involved in complex carbohydrate acquisition and utilization pathways. Western immunoblot analysis and real-time PCR analysis of GAS in throat swabs taken from humans with pharyngitis confirmed the findings. We conclude that SptR/S optimizes persistence of GAS in human saliva, apparently by strategically influencing metabolic pathways and virulence factor production. The discovery of a genetic program that significantly increased persistence of a major human pathogen in saliva enhances understanding of how bacteria survive in the host and suggests new therapeutic strategies.

overall_design: We determined the transcriptome of SptR (spy0874) in human saliva by comparing expression microarray date for parental wild-type strain MGAS5005 and its delta-spy0874 isogenic mutant strain.  4 replicates of each strain were grown to mid-exponential and stationary growth phases in human saliva.  RNA was isolated, converted to cDNA, labeled and hybridized to a custom-made Affymetrix GeneChip.  Data was analyzed using GCOS.

last: Sumby

first: Izabela

last: Sitkiewicz

first: Chanelle

last: Granville

first: Frank

last: DeLeo

first: James

middle: M

last: Musser


title: Global transcriptome analysis of B. burgdorferi during adherence and invasion of human neuroglial cells

status: Public on Jun 20 2008

first: Dan

last: Sturdevant

summary:
As adherence and entry of a pathogen into a host cell are two key components to an infection, identifying the molecular mechanisms responsible for cellular association will provide a better understanding of a microbe’s ability for pathogenesis.  We previously established an in vitro model for B. burgdorferi invasion of human neuroglial cells.  To expand on our earlier study, we performed B. burgdorferi whole-genome expression
analysis following a 20-hour infection of human neuroglial cells to identify borrelial genes that were differentially regulated during cellular attachment and invasion as compared with cultured Borrelia in cell-free medium.  This study identifies several regulated genes, the products of which may be important mediators for cellular pathogenesis.
Keywords: in-vitro H4 neuroglial cells infected with B. burgdorferi

sample_organism:
Borreliella burgdorferi
Homo sapiens

overall_design: A 20-hour incubation was performed, and this time point included B. burgdorferi that were both intra- and extra-cellularly localized to the H4 cells (Livengood and Gilmore, 2006).  After B. burgdorferi infection of these cells, the total cellular RNA preparation (including H4 RNA, and Borrelia RNA) was enriched for prokaryotic RNA, which concentrated the bacterial message, but did not completely eliminate the eukaryotic RNA (data not shown).  Therefore, as a control in our arrays, eukaryotic RNA from the human H4 cells was also purified and hybridized to the array.  To control for Borrelia cell-free gene expression, the data from the experimental conditions (B. burgdorferi infected human cells) was normalized to borrelial expression following growth in BSK and a 20 hour incubation in DMEM tissue culture media.  As with the experimental samples, both controls were assayed in triplicate.

last: Livengood

first: Daniel

first: Virginia

last: Schmit

first: Robert

last: Gilmore JR


title: Comparison of Yersinia pestis from rat buboes and laboratory cultures

status: Public on Jul 28 2006

summary:
Yersinia pestis causes bubonic plague in humans and rats. The disease is characterized by an enlarged, painful lymph node, termed a bubo, that develops following bacterial dissemination from an intradermal flea bite injection site. In susceptible animals, the bacteria quickly overcome host innate immune defenses in the lymph node, spread systemically through the blood, and produce fatal sepsis 1,2. At the terminal stage of disease, the bubo contains massive numbers of extracellular bacteria, necrotic lymphoid tissue, hemorrhage, and fibrin 2. The extreme virulence of Y. pestis has been largely ascribed to its ability to avoid innate immunity by preventing phagocytosis, selectively killing immune cells, and down regulating the proinflammatory response 3.
Here we report that two innate immune effector mechanisms are generated during bubonic plague in the rat: iron limitation and nitrosative stress. The expression of nitric oxide synthase (iNOS) by rat polymorphonuclear neutrophils (PMNs) was induced in the bubo, and mutation of the Y. pestis hmp gene, which encodes a flavohemoglobin important for resistance to nitric oxide (NO), attenuated virulence. Thus, although Y. pestis avoids uptake and intracellular killing by phagocytes, it still encounters innate immune effector molecules, particularly phagocyte-derived reactive nitrogen species, in the extracellular environment of the bubo.
Keywords: repeat

overall_design: 6 biological replicates isolated from rat buboes compared to 6 biological replicates isolated from [1] stationary phase 37C culture, [2] stationary phase 21C culture, [3] exponential phase 37C culture and [4] exponential phase 21C culture

first: Florent

last: Sebbane

first: Nadine

last: Lemaitre

first: Roberto

last: Rebeil

first: Kimmo

last: Virtaneva

first: Stephen

last: Porcella

first: B

last: Hinnebusch


title: Microarray analysis of the development of proteinuria in the Dahl salt-sensitive rat

status: Public on Jan 01 2009

city: Leiden

first: klaas

last: koop

address: Albinusdreef 2

country: Netherlands

institute: Leiden University Medical Center

summary:
To get more insight in cause and consequences of proteinuria, we studied glomerular gene expression patterns before and after the onset of increased urinary albumin excretion in a proteinuric rat strain.
Spontaneously proteinuric Dahl salt-sensitive rats (Dahl SS) were compared to non-proteinuric, spontaneously hypertensive rats (SHR). In Dahl SS, UAE significantly increased starting from week 5 of age. Glomerular RNA profiles of 4- and 6 week-old rats were studied by Affymetrix microarrays.

Keywords: Time course analysis

overall_design: RNA was extracted from isolated glomeruli of 4- and 6 week-old rats from both strains. At each time point, two rats were used for each strain.

first: Klaas

last: Koop


title: Panton-Valentine Leukocidin Does Not Impact Virulence of Community-associated MRSA

status: Public on Sep 12 2008

first: Amy

last: Palazzolo-Ballance

address: 903 S. 4th Street

department: Rocky Mountain Laboratory

institute: NIH/NIAID

summary:
Panton-valentine leukocidin (PVL) has been linked to worldwide emergence of community-associated methicillin resistant Staphylococcus aureus (CA-MRSA) -- its role in virulence in unclear.  Here we show that PVL had no effect on global gene expression of prominent CA-MRSA strains nor did it
affect bacterial clearance from lungs, spleen and kidneys in a highly discriminatory rabbit bacteremia model.  These findings negate a large body of epidemiological research that implicated PVL in CA-MRSA virulence.
Keywords: mutant vs wild type in 2 different growth phases grown in 2 different medias

platform_organism:
Borreliella burgdorferi
Yersinia pestis
Coxiella burnetii
Rickettsia rickettsii
Chlamydia trachomatis
Staphylococcus aureus
Streptococcus pyogenes
Chlamydia muridarum
Chlamydia pneumoniae AR39
Staphylococcus epidermidis RP62A
Staphylococcus epidermidis ATCC 12228
Staphylococcus aureus subsp. aureus MW2
Borreliella burgdorferi B31
Coxiella burnetii RSA 493
Chlamydia caviae GPIC
Chlamydia trachomatis D/UW-3/CX
Staphylococcus haemolyticus JCSC1435
Granulibacter bethesdensis

overall_design: Wild type USA 300 (strain SF8300), wild type USA 400 (strain MW2) were compared against their respective PVL isogenic knock out strains.  Strains were compared at both mid-exponential and stationary phase and grown in both TSB and CCY to determine if PVL plays a role in gene regulation under these conditions.

first: Binh

last: Diep

first: Li

last: Basuino

first: Kevin

last: Braughton

first: Adeline

last: Whitney

first: Liang

last: Chen

first: Barry

middle: N

last: Kreiswirth

first: Michael

last: Otto

first: Henry

middle: F

last: Chambers


title: GAS gene expression from clinical samples

status: Public on Feb 01 2006

first: Paul

last: Sumby

summary:
GAS strains were grown in THY broth to early exponential phase and RNA extracted.  Targets from two biological replicates of each were generated and the expression profiles were determined using the RMLgenechip.  Comparisons between the sample groups allow the identification of genes differentially expressed between strains.
Keywords: repeat

overall_design: 2 biological replicates were analyzed for each of 9 GAS strains


title: GAS gene expression from mouse-passaged and clinical GAS strains

summary:
GAS strains were grown in THY broth to early exponential phase and RNA extracted.  cDNA was generated and the expression profiles were determined using the RMLgenechip.  Comparisons between the sample groups allow the identification of genes differentially expressed between strains.  This experiment compared pre- and post- mouse passaged GAS strains.
Keywords: GAS comparison

overall_design: 3 biological replicates were analyzed for each of the 2 clinical GAS strains, no replicates for mouse passaged derivatives


status: Public on Sep 26 2005

first: Dan

last: Sturdevant

summary:
To measure S. aureus gene expression during growth phase and/or S. aureus–PMN interaction.
Keywords: other

first: Jovanka

last: Voyich

first: Daniel

first: Battouli

last: Said-Salim

first: R

last: Long

first: David

last: Dorward

first: Donald

last: Gardner

first: James

last: Musser

first: Frank

last: DeLeo


title: Effects of diethylstilbestrol (DES) on the anterior pituitary gland of the ACI, Copenhagen and Brown Norway Rat.

status: Public on Mar 31 2006

city: Madison

last: Shull

address: 1400 University Avenue

department: McArdle Laboratory for Cancer Research

institute: University of Wisconsin-Madison

summary:
Anterior pituitary glands were isolated from 21 week old male rats either untreated or treated for 12 weeks with the synthetic estrogen diethylstilbestrol (DES). Three biological replicates were prepared for untreated, control animals and four biological replicates were prepared for DES-treated animals. This was done for each of 3 inbred rat strains: ACI, Copenhagen, and Brown Norway. Expression profiles were determined using Affymetrix Rat Genome 230 v. 2.0 arrays. Comparisons of untreated vs. treated animals within a strain will allow identification of estrogen responsive genes. Comparisons between strains, either treated or untreated, will identify strain (i.e., genetic) differences in expression.
Keywords: Estrogen Response

overall_design: 21 samples from anterior pituitary gland were analyzed. For each of 3 inbred rat strains (ACI, Copenhagen, and Brown Norway) there were 3 biological replicates of untreated, control animals, and 4 biological replicates of DES-treated animals.

first: Karen

last: Deffenbacher


title: Comparison of gene expression in MGAS315 and its isogenc mtsR mutant

status: Public on Feb 01 2009

city: Warsaw

first: Izabela

last: Sitkiewicz

address: Chełmska 30/34

department: Epidemiology and Clinical Microbiology

country: Poland

institute: National Medicines Institute

summary:
RATIONALE: mtsR is a regulator of genes involved in ion aquisition in S. pyogenes that has been suggested to be involved in development of invasive infections. We wanted to identify mtsR regulon.
EXPERIMENT: We compared global gene expression in wild type strain MGAS315 with expression in its isogenc mtsR mutant. Experiment was performed with bacteria in exponential (EXP) and at late exponential phase (Late EXP) grown in THY medium
Keywords: strain comparison

overall_design:
1. Three independent cultures of WT or mutant strain bacteria at exponential phase of growth (OD60=0.5, biological replicates) served as source of total RNA. RNA was transcribed into cDNA, fragmented and labeled using standard Affymetrix protocol for prokaryotic target preparation. Hybridization with custom Affymetrix array and scaning was performed using protocol recomended by manufacturer. Hybridizaton values aquired by GCOS (in CHP files) are normalized to global hybridization intesity.
2. Analogous experiment was performed with bacteria grown to OD600=1.2 representing late exponential growth phase

first: Benfang

last: Lei

first: Randal

last: Olsen


title: Longitudinal analysis of the group A Streptococcus  transcriptome

status: Public on Jun 17 2005

first: Steve

last: Porcella

address: 903 SOUTH 4TH Street

department: Rocky Mountain Laboratories

country: USA

institute: NIAID

summary:
Identification of the genetic events that contribute to host-pathogen interactions is important for understanding the natural history of infectious diseases and developing therapeutics. Transcriptome studies conducted on pathogens have been central to this goal in recent years. However, most of these investigations have focused on specific end points or disease phases, rather than analysis of the entire time course of infection. To gain a more complete understanding of how bacterial gene expression changes over time in a primate host, the transcriptome of group A Streptococcus (GAS) was analyzed during an 86-day infection protocol in 20 cynomolgus macaques with experimental pharyngitis. The study used 260 custom Affymetrix (Santa Clara, CA) chips, and data were confirmed by TaqMan analysis. Colonization, acute, and asymptomatic phases of disease were identified. Successful colonization and severe inflammation were significantly correlated with an early onset of superantigen gene expression. The differential expression of two-component regulators covR and spy0680 (M1_spy0874) was significantly associated with GAS colony-forming units, inflammation, and phases of disease. Prophage virulence gene expression and prophage induction occurred predominantly during high pathogen cell densities and acute inflammation. We discovered that temporal changes in the GAS transcriptome were integrally linked to the phase of clinical disease and host-defense response. Knowledge of the gene expression patterns characterizing each phase of pathogen-host interaction provides avenues for targeted investigation of proven and putative virulence factors and genes of unknown function and will assist vaccine research.
Keywords: other

sample_organism:
Streptococcus pyogenes
Macaca fascicularis

first: Kimmo

last: Virtaneva

first: Morag

last: Graham

first: Robin

last: Ireland

first: Claire

last: Johnson

first: Stacy

last: Ricklefs

first: Imran

last: Babar

first: Larye

last: Parkins

first: Romina

last: Romero

first: G

last: Corn

first: Don

first: John

last: Bailey

last: Parnell


title: Expression comparison of GAS M3 strains MGAS315 & MGAS9887 in exponential growth

status: Public on Feb 28 2006

first: Stephen

middle: B.

last: Beres

address: 6670 Bertner Ave.

department: Pathology and Genomic Medicine

institute: Houston Methodist Research Institute

summary:
Epidemiological data indicate that strains MGAS315 and MGAS9887 differ significantly in their capacity to cause necrotizing fasciitis infections.  To probe the hypothesis that this difference was associated with differences in gene expression, an expression MA comparison of the strains in exponential phase growth in rich media was conducted.
Keywords: strain comparison

overall_design: For statistical robustness in comparing the strains, total RNA was isolated from 3 independent growths (3 biological replicates), split into 2 samples (2 technical replicates) for a total of 6 replicates per strain, and 12 total samples for the investigation.

first: James

last: Musser


title: Expression data from adult wild-type and zCdx1b transgenic zebrafish (3 months old)

status: Public on Feb 18 2012

city: Camden

first: Xiaoxin

middle: Luke

last: Chen

state: NJ

address: 403 Haddon Avenue

institute: Coriell Institute for Medical Research

summary:
Cdx2 has been suggested to play an important role in Barrett's esophagus (BE), or intestinal metaplasia (IM) in the esophagus. However, in vivo data have been lacking.  The  aim  of  the  present  study  was  to  investigate  whether  transgenic overexpression of zCdx1b, the functional equivalent of mammalian Cdx2 in zebrafish, may lead to IM of squamous epithelium in zebrafish
A transgenic zebrafish system was developed by expressing zCdx1b gene under the control of zebrafish keratin 5 promoter (zK5p). zCdx1b expression in the esophageal squamous epithelium of transgenic zebrafish was analyzed by in situ hybridization, immunohistochemical staining and RT-PCR. Gene expression in the esophageal squamous epithelium of wild-type and transgenic zebrafish was analyzed by Affymetrix microarray and confirmed by in situ hybridization.

overall_design: The upper digestive tract tissue from 3 adult zebrafish (3 months old) was pooled as one sample. Three zCdx1b transgenic samples were used for microarray, and 2 wild type samples were used for control.

first: Bo

last: Hu


title: Placental gene expression profiling for the identification of clinically relevant subclasses of human preeclampsia

status: Public on May 10 2016

city: Toronto

first: Brian

last: Cox

state: Ontario

address: 1 King's College Circle

department: Physiology

institute: University of Toronto

type:
Expression profiling by array
Third-party reanalysis

summary:
Preeclampsia (PE) is a complex, heterogeneous disorder of pregnancy, demonstrating considerable variability in observed maternal symptoms and fetal outcomes. We hypothesized that this heterogeneity is due to the existence of multiple molecular forms of PE. To address our hypothesis, we created a large (N=330) human placental microarray data set consisting of seven previously published studies (GSE30186, GSE10588, GSE24129, GSE25906, GSE43942, GSE4707, and GSE44711) and 157 highly annotated samples from a BioBank (below).
Applying unsupervised clustering to this combined data set revealed multiple distinct molecular groups of placentas, including three clinically relevant potential origins of PE based on gene expression and correlating patient records.

overall_design: A total of 80 PE placentas and 77 non-PE placentas, representing a range of clinical presentations, were purchased from a BioBank. When combined with the previously-published data sets, we had access to and analyzed gene expression data for 157 PE placentas and 173 non-PE placentas.

first: Katherine

last: Leavey

first: Shannon

last: Bainbridge