title: Integrated functional analysis of engineered carbon limitation in the CO2/HCO3-uptake deficient ∆ndhD3/ndhD4/cmpA/sbtA mutant of Synechocystis sp. PCC 6803

summary: Functional analysis of engineered carbon limitation in the ∆ndhD3/ndhD4/cmpA/sbtA (= ∆4) Synechocystis mutant reveals a global phenocopy of wild type acclimation to low CO2 and multi-layered Ci-regulation.

overall_design: We analyzed gene expression in Synechocystis sp. PCC 6803 WT as well as a ∆ndhD3/ndhD4/cmpA/sbtA mutant (= ∆4) at HC (5% CO2) as well as 3h and 24h after shift to LC (air). For each strain and each sampling point, 2 biological replicates were analyzed.


title: Nanos2-regulated mRNAs in the cultured spermatogonial stem cells (SSCs)

status: Public on Sep 25 2015

city: Mishima

first: ZHI

last: ZHOU

address: Yata 1111

department: Division of Mammalian Development

country: Japan

institute: National Institute of Genetics, Japan

summary: Spermatogonial stem cells are foundation of spermatogenesis. In our previous study, we observed a rapid degeneration of spermatogenesis by conditional knockout (cKO) of Nanos2 in adult spermatogonia, but the underlying mechanisms are largely unknown. While, conditional overexpression (cOE) of Nanos2 also inhibited germ cell development and stayed in undifferentiation status. Here we used cultured germline stem cells (GSCs) to study the mechanisms of Nanos2 in spermatogonia. We compared Nanos2 expression in cultured GSCs with in vivo isolated Nanos2 positive cells, and found the level of Nanos2 is significantly lower in GSCs as compared to Nanos2 positive cells. Thus we generated Nano2 cOE GSCs lines. By conditional inducing expression of Nanos2 we compared gene expression profile to control GSCs. These data provide the first evidence of Nanos2 regulating genes in spermatogonial stem cells.

overall_design: Ectopic induction of Nanos2 in cultured GSCs. Duplicated control (Roa-CreERT2;CAG-CAT-3FlagNanos2-pA, DMSO) and experiment (Roa-CreERT2;CAG-CAT-3FlagNanos2-pA, Tamoxifen)

first: Zhi

last: Zhou

first: Saga

last: Yumiko


title: Development of gene expression signatures for mouse macrophages polarization

status: Public on Sep 30 2015

city: Hangzhou

first: Qian

address: Yuhang Road 866

country: China

institute: College of Pharmaceutical Sciences, Zhejiang University

summary: To further development of our gene expression approach to macrophages polarization, we have employed whole genome microarray expression profiling as a discovery platform to identify genes with the potential mechanism of ATRA-inhibited M2 macrophages. RAW264.7 cells were treated with ATRA or IL-13 alone or together for 12h or 24h, then the cells were collected with trizol.

overall_design: Overall gene expression in mouse macrophages were measured after raw264.7 cells were treated with ATRA or IL-13 alone or together for 12h or 24h.

first: Zhou

last: Qian

first: Liang

last: Guikai


title: 1918 pandemic influenza virus and pneumococcus co-infection results in activation of coagulation and widespread pulmonary microvascular thrombosis in mice and humans

status: Public on Sep 20 2015

city: Seattle

first: kathie

last: walters

state: WA

address: 401 Terry Ave N

country: USA

institute: Institute for Systems Biology

summary: To study the effects of secondary bacterial infection during 1918 pandemic H1N1 influenza virus infection, BALB/c mice were inoculated with the fully reconstructed 1918 influenza virus followed by inoculation with pneumococcus 72h later.

first: Kathie-Anne

last: Walters

first: John

last: Kash

first: Jeffery

last: Taubenberger


title: Transformation of enriched mammary cell populations with Polyoma Middle T Antigen influences tumor subtype and metastatic potential

status: Public on Sep 08 2015

city: Salt Lake City

first: Brett

last: Milash

state: UT

department: Center for High Performance Computing

institute: University of Utah

summary: Breast cancer is a multifaceted disease, exhibiting significant molecular, histological, and pathological diversity. Factors that impact this heterogeneity are poorly understood; however, transformation of distinct normal cell populations of the breast may generate different tumor phenotypes. Our previous study demonstrates that the polyomavirus middle T antigen (PyMT) oncogene can establish diverse tumor subtypes when broadly expressed within mouse mammary epithelial cells. Herein, we assess the molecular, histological, and metastatic outcomes from distinct mammary cell populations transformed with PyMT. By combining several methodologies, including lentiviral infection, cell sorting, and transplantation, we have characterized tumors arising from enriched populations of mammary epithelial cells. We have found that expression of PyMT within different cell populations influences tumor histology, molecular subtype, and metastatic potential.

overall_design: 32 samples, 1 from each of 32 mouse mammary tumors arising from transplanted mouse mamary epithelial cells (MMECs) transduced with PyMT-expressing  lentivirus. MMECs were sorted into four different types prior to transplant: luminal CD133+ (8 samples), luminal CD133- (11 samples), stem (6 samples), and  basal (7 samples). The background for the cell donor and transplant recipients mice was FVB/NJ obtained from Jackson Laboratories.

first: Daria

last: Drobysheva

first: Brittni

middle: A

last: Smith

first: Huseyin

last: Ekiz

first: Bryan

middle: E

last: Welm


title: Nanos2-associated mRNAs in the postnatal testis

summary: To identify Nanos2-associated mRNAs, we performed microarray analysis of mRNAs coprecipitated with FLAG-tagged NANOS2 with postnatal testis from Tg-Nanos2 enhancer-3xFLAG-Nanos2-3'UTR at P7.

overall_design: Biological duplicates were examined at each sample.


title: Profiles of cytokines in heart after β-adrenergic stimulation in different time point

status: Public on Sep 09 2015

city: Beijing

first: Hao

last: LI

address: No. 49, Huayuan Bei Road, Haidian District

department: Institute of Vascular Medicine

institute: Peking University Third Hospital

summary: To identify the dynamic changes of cytokines in the heart upon β-adrenergic stimulation (isoproterenol, 5 mg/kg body weight) at 3hrs, 6hrs, 12hrs, 24hrs and 3days using mouse cytokine antibody arrays

overall_design: 27 samples. There are 6 groups: vehicle group, mice were subcutaneous injected with a single dose of saline (10 ml/kg body weight), ISO groups, mice were subcutaneous injected with a single dose of isoproterenol (5 mg/kg body weight) after 3hrs, 6hrs, 12hrs, 24hrs and 3days (5 groups by different pionts)

first: Youyi

last: ZHANG


title: Interspecies Comparative Genomics Identifies Optimal Mouse Models of Scleroderma

status: Public on Aug 13 2015

city: Hanover

first: Michael

last: Whitfield

state: New Hampshire

address: 710 Remsen 74 College Street

department: Genetics

institute: Geisel School of Medicine at Dartmouth

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

overall_design: Refer to individual Series


title: Interspecies Comparative Genomics Identifies Optimal Mouse Models of Scleroderma (Tsk2)

summary: Systemic sclerosis (SSc) is confounded by considerable disease heterogeneity.  Animal models of SSc that recapitulate distinct subsets of disease at the molecular level have not delineated. We applied interspecies comparative analysis of genomic data from multiple mouse models of SSc and patients with SSc to determine which animal models best reflect the SSc intrinsic gene expression subsets.

overall_design: Gene expression measured in skin from mice with sclerodermatous graft-versus-host disease, bleomycin-induced fibrosis, or Tsk1/+ and Tsk2/+ mice was mapped to human orthologs and compared to SSc skin biopsy-derived gene expression.

first: Jennifer

last: Sargent

first: Zhenghui

last: Li


title: Interspecies Comparative Genomics Identifies Optimal Mouse Models of Scleroderma (bleoskin)


title: Identification of Sox9/Pdx1-coregulated Genes During Pancreas Organogenesis

status: Public on Aug 07 2015

city: La Jolla

first: Maike

last: Sander

state: CA

address: 2880 Torrey Pines Scenic Dr.

institute: UC San Diego

summary: Sox9/Pdx1 co-regulated target genes were identified by comparing gene expression in Sox9/Pdx1-double heterozygates versus Sox9- or Pdx1-  heterozygates pancreata using microarray analysis.

overall_design: Pdx1LacZko (herein designated Pdx1-/+) (Offield et al. 1996) and one Sox9 allele was conditionally deleted in the developing pancreas via recombination of a Sox9-flox allele (Kist et al., 2002) using the Foxa3-Cre transgene (Lee et al., 2005). Total RNA was isolated and pooled from dorsal pancreatic epithelia of e12.5 Sox9fl/+; Foxa3-Cre (Sox9 het),  Pdx1-/+ (Pdx1 het) versus Sox9fl/+; Foxa3-Cre; Pdx1-/+ (Sox9/Pdx1 double hets) littermates for three biological replicates

first: Hung

middle: P

last: Shih

first: Nisha

last: Patel


title: Murine Kidney Papilla Cells: Control GFP- vs. GFP+ label retaining cells. Cell populations were separated by FACS.

status: Public on Aug 05 2015

city: New York

first: Qais

last: Al-Awqati

state: NY

department: Medicine

institute: Columbia University

summary: Transcriptional profiling of mouse kidney papilla cells comparing control GFP- cells with GFP+ labeled cells. Mouse kidney papillae were dissected. GFP- and GFP+ cell populations were isolated by FACS. The latter represent slow cycling label retaining cells (LRCs).

overall_design: Two-condition experiment, GFP- vs. GFP+ label retaining cells cells. Biological replicates: 5 control GFP- replicates, 5 GFP+ label retaining cell replicates.

first: Juan

last: Oliver


title: Galectin-3 Deficiency Exacerbates Hyperglycemia and the Endothelial Response to Diabetes

status: Public on Aug 01 2015

city: Honolulu

first: April

middle: L

last: Darrow

state: HI

address: 651 Ilalo St.

institute: University of Hawaii

summary: Microarray analyses were performed in order to determine the effect of galectin-3 ablation on the endothelial transcriptional response in a mouse model of type 2 diabetes. Galectin-3-deficient mice (KO) and wild-type C57BL/6 (WT) were fed a high-fat diet (60% fat calories) or standard chow for 8 weeks. CD105+/CD45- endothelial cells were isolated from the aortae and skeletal muscles of these mice by FACS. Whole genome microarray expression profiling revealed greater transcriptional dysregulation in the endothelium of the KO after high-fat feeding compared to WT. Transcripts dysregulated in the KO endothelium after HFD include those involved in glucose uptake and insulin signaling, oxidative stress, vasoregulation, coagulation, and atherogenesis. Real-time PCR confirmed transcriptional downregulation of the glucose transporter, Glut4, and immunofluorescence staining confirmed reduced GLUT4 protein in the endothelium and mudcle of the KO compared to WT. The transcriptional and histological data was consistent with physiological studies showing exacerbated hyperglycemia and coagulation in the KO. These results suggest that galectin-3 serves a protective role against metabolic dysregulation and endothelial dysfunction in diabetes.

overall_design: Galectin-3-deficient mice (KO) and wild-type C57BL/6 (WT) were fed either a high-fat diet (60% fat calories) or standard chow diet (12% fat calories) for 8 weeks. Three independent experiments were performed.  For each experiment, the aorta and skeletal muscle from 3-4 animals per diet/genotype group were excised and pooled for each tissue. Live, CD105+/CD45- endothelial cells  were isolated from the aortic and muscle suspensions by FACS.

first: Ralph

middle: V

last: Shohet


title: Expression data from Jurkat cells treated with SB225002 for 6h and 9h.

status: Public on Jul 23 2015

city: Campinas

first: Jaira

middle: Ferreira de

last: Vasconcellos

state: Sao Paulo

address: Rua Dr. Gabriel Porto, 1270.

country: Brazil

institute: Centro Infantil Boldrini

summary:
In our efforts to evaluate the function of the IL-8 receptor CXCR2 in Acute Lymphoblastic Leukemia (ALL) cells, we made use of SB225002 (N-(2-hydroxy-4-nitrophenyl)-N’-(2-bromophenyl)urea), a drug initially described as a CXCR2 antagonist. Although the CXCR2 receptor was found to be non-functional in ALL, B- and T-ALL cell lines were sensitive to SB225002.
We used microarray analysis to identify a transcriptional profile of genes that mediate SB225002's effects in acute lymphoblastic leukemia  cells.

overall_design: Jurkat cells were treated for 6h or 9h with SB225002 [12.5 uM] or 0.1% DMSO (vehicle control).

last: Ferreira de Vasconcellos

first: Towia

last: Libermann

first: Luiz

last: Zerbini

first: Jose

last: Yunes


title: Transcriptional profiles of embryonic stem cell derived gastrointestinal tissue.

status: Public on Jul 20 2015

city: Tsukuba city

first: Takaaki

middle: K

last: Noguchi

state: Ibaraki prefecture

department: Life and environmental sciences

institute: The University of Tsukuba

summary: Successful differentiation methods have been developed in several endodermal organs, including liver, pancreas, and intestine from embryonic stem cell and induced pluripotent stem cells. Compare to these organs, however, little has been known in gastric differentiation from embryonic stem cells. Here, we established a method of  gastrointestinal tissue differentiation methods, including stomach regions from embryonic stem cells. These gastrointestinal tissue built gut primordium-like spheroids, which is also able to mature into adult tissue containing all differentiated cells in three-dimensional culture. These embryonic stem cells derived gastrointestinal tissue possessed the similar gene expression profile that of adult stomach. These data indicated that functional gastrointestinal tissue can be derived from embryonic stem cells by mimicking in vivo development and could be useful for investigating gastrointestinal study such as disease modeling.

overall_design: We generated arrays from embryonic stem cells-derived stomach tissue cells cultured in FGF10, WNT3A, NOGGIN and R-SPONDIN1 for 42 days, 46 days, and 5 months, or SHH and BMP4 for 4 days after cultured in FGF10, WNT3A, NOGGIN, and R-SPONDIN1 for 42 days. In addition, we also generated arrays from adult mouse stomach, esophagus, lung, intestine, and embryonic stomach as controls. All the datas were normalized to 75% tile shift.

first: Naoto

last: Ninomiya


title: Interspecies Comparative Genomics Identifies Optimal Mouse Models of Scleroderma (Tsk1/+)

last: Whitfield


title: Effect of PML/RARA on the transcriptome of preleukemic early promyelocytes vs PML/RARA-Flt3ITD leukemic promyelocytes

status: Public on Jul 15 2015

city: San Francisco

first: Scott

last: Kogan

address: 513 Parnassus, S-561, Box 0451

department: Laboratory Medicine

institute: UCSF

summary: Transcriptional profiling of murine cells expressing PML/RARA at the early promyelocyte stage (4 weeks old, preleukemic) and in full blown PML/RARA leukemia generated by transducing PML/RARA bone marrow with a Flt3-ITD retroviral vector

overall_design: Two-conditions experiment: preleukemic early promyelocytes vs leukemic promyelocytes

first: Coline

last: Gaillard

middle: C


title: ATM deficiency in the absence of T cells promotes the development of NF-kB-dependent B cell lymphomas [Gene Expression]

status: Public on Jul 18 2015

city: Barcelona

first: Jordi

last: Camps

state: Catalonia

address: c/Rosselló 149-153 4th floor, Center Esther Koplowitz

department: Gastroenterology

country: Spain

institute: IDIBAPS / Hospital Clinic

summary:
Our model removes T cells as targets for lymphomagenesis as well as eliminating T cell-dependent immune surveillance. These mice  exclusively develop early onset IgM+ B cell lymphomas that histologically and genetically resemble the activated B cell-like (ABC) subset of human diffuse large B cell lymphomas (DLBCL).
This dataset includes the comparison of B-cell lymphomas (tumors) from ATMKO.CD3eKO RNA expression levels with normal spleens from both ATMKO.CD3eKO and ATMWT.CD3eKO non-tumor bearing mice.

overall_design: Ten ATMKO.CD3εKO B cell lymphoma cell lines were established from tumor-bearing spleen cells. As per comparison to normal tissue, seven spleens from  ATMWT.CD3eKO mice and six non-tumor bearing spleens from a ATMKO.CD3eKO mice were used. RNA quality was assessed by Bioanalyzer and only those samples with RIN higher than 8 were used.

first: Karen

middle: S

last: Hathcock

first: Hesed

middle: M

last: Padilla-Nash

first: Dong-Mi

last: Shin

first: Daniel

last: Triner

first: Robert

middle: W

last: Maul

first: Seth

last: Steinberg

first: Patricia

middle: J

last: Gearhart

first: Herbert

last: Morse III

first: Thomas

last: Ried

first: Richard

last: Hodes


title: Gene expression analysis of synovial sarcoma, clinical samples

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

summary: To identify molecular biomarkers that are useful for diagnosis and its targeting treatment, we analysed expression profile of synovial sarcoma tissue.

overall_design: In the present study, we studied gene expression profiles comparing 11 cases of synovial sarcoma.

first: Akira

last: Maekawa

first: Yoshinao

last: Oda


title: ATM deficiency in the absence of T cells promotes the development of NF-kB-dependent B cell lymphomas

type: Genome variation profiling by genome tiling array


title: Beta 1 blockers improve survival and provide cardioprotection in septic mice

status: Public on Aug 03 2015

city: Garches

first: Arnaud

last: Mansart

address: 104 boulevard Raymond Poincaré

country: France

institute: Université de Versailles

summary: Septic cardiac dysfunction is a key feature of severe sepsis and septic shock, contributing to multiorgan dysfunction syndrome and death. It has been established that persistent beta adrenergic stimulation is detrimental in sepsis, and that specific beta 1 blockade mitigates excessive systemic inflammation and improves myocardial function. The aim of this study was to investigate the effects of specific beta 1 blocker esmolol on septic mouse myocardium by genomic and proteomic techniques. We also evaluated survival of septic mice and systemic inflammation under esmolol treatment.

overall_design: C57BL/6 mice were rendered septic by 2 models: cecal ligature and perforation (CLP) and intraperitoneal injection of lipopolysaccharides (LPS). Effects of esmolol on myocardium were assessed by microarray technique. Total RNA were isolated and purified from a 30mg sample of the heart of 6 groups of 8 animals, depending on the sepsis model and the treatment. The labeled cDNA from the treated animals were hybridized against the labeled cDNA from the untreated animals with 2 dye-swaps done for each sepsis model.

first: Etienne

last: de Montmollin

first: Alexandre

last: Pawlik

first: Djillali

last: Annane


title: Acute hepatic transcriptional response in male mice following oral exposure to benzo(a)pyrene

status: Public on Jul 01 2015

city: Ottawa

first: Sarah

last: Labib

state: Ontario

address: 204b-50 Colombine

country: Canada

institute: Health Canada

summary: Benzo(a)pyrene is a well-established human carcinogen in humans and rodents. In the present study, we sought to determine the dose- and time-dependent changes in gene expression upon oral exposure to benzo(a)pyrene. Adult male B6C3F1 mice were exposed to four doses of benzo(a)pyrene or vehicle control for three days and sacrificed 4 or 24 hours after the final exposure.

overall_design: This experiment examined the hepatic transcriptional response of male mice exposed to BaP for 3 days at four different doses, including D1 (300 mg/kg BW/day), D2 (150 mg/kg BW/day), D3 (50 mg/kg BW/day) and D4 (5 mg/kg BW/day), and one control.  Each dose group was further examined at 2 time points,  4 hours and 24 hours, following the final exposure.  Each dose group and time point had 4-5 biological replicates. There were a total 46 samples (arrays) included in the final analysis using a two-colour reference design.

first: Julie

last: Buick

first: Kelly

last: Jackson

first: Andrew

last: Williams

first: Ivy

middle: D

last: Moffat

first: Nikolai

last: Chepelev

last: Bourdon

first: Byron

last: Kuo

first: France

last: Lemieux

first: Amal

middle: I

last: Malik

first: Sabina

last: Halappanavar

first: Mirjam

last: Luijten

first: Carole

last: Yauk


title: Spatial dissection of the Arabidopsis response to downy mildew using Fluorescence Activated Cell Sorting

status: Public on Jul 13 2015

city: Coventry

first: Miriam

last: Gifford

address: Gibbet Hill Road

department: School of Life Sciences

country: United Kingdom

institute: University of Warwick

summary: Changes in gene expression form a crucial part of the plant response to pathogen infection. Whole-leaf expression profiling has played a valuable role in identifying genes and processes that contribute to the interactions between the model plant Arabidopsis thaliana and a diverse range of pathogens. However, for highly localised infections, such as downy mildew caused by the biotrophic oomycete pathogen Hyaloperonospora arabidopsidis (Hpa), whole-leaf profiling may fail to capture the complete Arabidopsis response. Highly localised expression changes may be diluted by the comparative abundance of non-responding leaf cells or the Hpa oomycete evading detection by cells. Furthermore, local and systemic Hpa responses of a differing nature may become convoluted. To address this we applied the technique of Fluorescence Activated Cell Sorting (FACS), typically used for analyzing plant abiotic responses, to the study of plant-pathogen interactions. Using the promoter of Downy Mildew Resistant 6 (DMR6) linked to GFP as a fluorescent marker of pathogen-contacting cells, we isolated Hpa-proximal and Hpa-distal cells from infected leaf samples using FACS, and measured global gene expression.

overall_design: The whole experiment was carried out in triplicate, with two time points (5 and 7 days post-inoculation) and three cell types (pathogen-proximal, pathogen-distal and uninfected control), totalling 18 microarrays. Transgenic Arabidopsis thaliana Col-0 with the transgene pDMR6:GFP was used for all experiments. Seedling populations were inoculated with 30,000-60,000 spores/ml of Hyaloperonospora arabidopsis strain Noks1 at 7 days old, and overground tissue sampled at 5 and 7 days post-inoculation. Protoplasts were generated from these samples according to Grønlund et al. 2012 JOVE, and sorted by fluorescence activated cell sorting into a GFP-positive (pathogen-proximal) and GFP-negative (pathogen-distal) population. As a control, uninfected seedlings were also sampled at 12 and 14 days old (equivalent age of 5 and 7 days post-inoculation), protoplasts generated and sorted to yield a GFP-negative population of uninfected control cells. Gene expression was analysed using NimbleGen 12 x 135K microarrays, designed for the TAIR10 genome. Data was normalised using the Robust Multichip Averaging algorithm.

first: Timothy

middle: R

last: Coker

first: Volkan

last: Cevik

first: Jim

last: Beynon


title: Otx2 controls regional patterning within the MGE and regional identity of the septum [Agilent]

status: Public on Jun 03 2015

first: John

last: Rubenstein

address: 1550 4th Street

department: Psychiatry

summary: The Otx2 homeobox transcription factor is essential for gastrulation and early neural development. We generated Otx2 conditional knockout (cKO) mice to investigate its roles in telencephalon development after E9.0. We conducted transcriptional profiling and in situ hybridization to identify genes de-regulated in Otx2 cKO ventral forebrain. In parallel, we used ChIP-seq to identify enhancer elements, OTX2 binding motif, and which de-regulated genes are likely direct targets of Otx2 transcriptional regulation. We found that Otx2 was essential in septum specification; regulation of Fgf signaling in the rostral telencephalon; and medial ganglionic eminence (MGE) patterning, neurogenesis, and oligodendrogenesis. Within the MGE, Otx2 was required for ventral but not dorsal identity; this is the first demonstration of a transcription factor that contributes to regional patterning within the MGE.

overall_design: We used an Otx2flox (Otx2f) allele with RxCre, Cre-line, to abrogate Otx2 expression ~E8.5 and ~E10.0. RxCre mice express Cre throughout the forebrain, except in the caudal dorsomedial domain that includes the choroid plexus and cortical hem. We compared mRNA expression in the ganglionic eminences and septum of RxCre conditional knock out (cKO) and control mouse embryos at E12.5.

first: Renée

last: Hoch

first: Susan

last: Lindtner

first: James

last: Price


status: Public on Jun 02 2015

city: South San Francisco

first: Matthew

last: Brauer

state: California

address: 1 DNA Way

department: Bioinformatics

institute: Genentech, Inc.

summary:
GCGR wt and ko mice
Glucagon receptor signaling in GCGR KO mice: fig 2a in Solloway et al.

overall_design: Gene expression comparison of livers from 5 WT and 5 GCGR KO mice.

first: Mark

last: Solloway


title: Myocardial gene expression in response to pressure overload

city: Cleveland

first: Mukesh

last: Jain

state: OH

address: 2103 Cornell Rd

institute: Case Western Reserve University

summary: Myocardial deletion of klf4 sensitizes mouse to pressure overload. In order to gain a better understanding of molecular mechanisms of such alterations, we profiled gene expression before and after 3-day of pressure overload (induced by transverse aortic constriction -TAC) in the hearts from MHC-cre (Cre) control and MHC-cre-klf4-deficient (KO) mice.

overall_design: 10wk old male mice was subjected to transverse aortic constriction (TAC) to induce pressure overload or sham operation as control group. After 3 days, heart was removed and total RNA was extracted from apex and subjected for array analysis. Four animals in each group.

first: Xudong

last: Liao


title: An ultrasensitive mechanism regulates influenza virus-induced inflammation

status: Public on Jun 12 2015

city: Minato

first: Yoshihiro

last: Kawaoka

state: Tokyo

address: Shirokanedai 4-6-1

department: ERATO Influenza-induced Host Responses Project

institute: Japanese Science and Technology Agency

summary: Whole-genome, time-course data was developed from the lungs of influenza infected mice to better characterize the dynamics of the host immune response during infection.

overall_design: Lung  for microarray studies were obtained from female, five-week old C57BL/6Js infected with influenza viruses. Forty-two animals per group were inoculated with 10^5 PFU of A/Kawasaki/UTK-4/09 H1N1 virus [Kawasaki], A/California/04/09 (H1N1) virus (pH1N1) [SOIV], A/Vietnam/1203/04 H5N1 virus (H5N1), 10^3 PFU A/Vietnam/1203/04 H5N1 virus (H5N1) [VN1203] or mock-infected with PBS. Spanning the first week of the infections, three animals per infection group were sacrificed at 14 predetermined time points, lungs isolated and the homogenate was used to assess changes in genes expression over time and between infections.

first: Jason

last: Shoemaker

first: Satoshi

last: Fukuyama

first: Amie

last: Eisfeld

first: Dongming

last: Zhao

first: Eiryo

last: Kawakami

first: Saori

last: Sakabe

first: Tadashi

last: Maemura

first: Takeo

last: Gorai

first: Hiroaki

last: Katsura

first: Yukiko

last: Muramoto

first: Shinji

last: Watanabe

first: Tokiko

first: Ken

last: Fuji

last: Matsuoka

last: Kitano


title: SRRM4 Expression and the Loss of REST Activity May Promote the Emergence of the Neuroendocrine Phenotype in Castration-Resistant Prostate Cancer

status: Public on Jun 24 2015

city: Seattle

first: Ilsa

last: Coleman

address: 1100 Fairview Ave N, E2-112

department: Human Biology

institute: Fred Hutchinson Cancer Center

summary: The neuroendocrine (NE) phenotype is associated with the development of metastatic castration-resistant prostate cancer (CRPC). Our objective was to characterize the molecular features of the NE phenotype in CRPC. Expression of chromogranin A (CHGA), synaptophysin (SYP), androgen receptor (AR), and prostate-specific antigen (PSA) was analyzed by immunohistochemistry (IHC) in 155 CRPC metastases from 50 patients and in 24 LuCaP prostate cancer patient-derived xenografts (PDX). Co-expression of CHGA and SYP in >30% of cells was observed in 22 of 155 metastases (9 patients); 11 of the 22 metastases were AR+/PSA+ (6 patients), 11/22 were AR-/PSA- (4 patients), and 4/24 LuCaP PDXs were AR-/PSA-. Seventy-one of 155 metastases and the 24 LuCaP xenograft lines were analyzed by whole genome microarrays. By IHC, of the 71 metastases analyzed by whole genome microarrays, 5 metastases were CHGA+/SYP+/AR- and 5 were CHGA+/SYP+/AR+. Only CHGA+/SYP+ metastases had a NE transcript signature. The neuronal transcriptional regulator SRRM4 transcript was associated with the NE signature in CHGA+/SYP+ metastases and all CHGA+/SYP+ LuCaP xenografts. Additionally, expression of SRRM4 in the LuCaP NE xenografts correlated with a splice variant of REST that lacks the transcriptional repressor domain. In conclusion, (a) metastatic NE status can be heterogeneous in the same patient, (b) the CRPC NE molecular phenotype can be defined by CHGA+/SYP+ dual positivity, (c) the NE phenotype is not necessarily associated with the loss of AR activity, and (d) the splicing of REST by SRRM4 could promote the NE phenotype in CRPC.

overall_design: Custom Agilent 44K whole human genome expression oligonucleotide microarrays were used to profile 24 LuCaP PCa xenograft lines and 71 CRPC metastases from 47 patients. RNA was amplified prior to hybridization against a common reference pool of prostate tumor cell lines.

first: Xiaotun

last: Zhang

first: Lisha

middle: G

last: Brown

first: Lawrence

last: True

first: Lori

last: Kollath

first: Jared

last: Lucas

first: Hung-Ming

last: Lam

first: Ruth

last: Dumpit

first: Eva

last: Corey

first: Lisly

last: Chéry

first: Bryce

last: Lakely

first: Celestia

last: Higano

first: Bruce

last: Montgomery

first: Martine

last: Roudier

first: Paul

middle: H

last: Lange

first: Peter

last: Nelson

first: Robert

last: Vessella

first: Colm

last: Morrissey


title: Identification of LPS-responsive genes in bone marrow-derived dendritic cells

status: Public on May 21 2015

first: Jason

middle: A

last: Hackney

department: Department of Bioinformatics and Computational Biology

summary: Transcriptional profiling of in vitro generated murine dendritic cells after stimulation with LPS for various timepoints.

overall_design: 4 condition experiment - LPS stimulation at 0, 1, 6, and 24 hours.  3 independent biological replicates for each condition.

first: Bryan

last: Lugt


title: Transcriptomic profiling of regulatory effects of quercetin and resveratrol supplementation in high fat diet fed mice

status: Public on May 30 2015

city: Shanghai

first: Wang

last: Shidong

address: 151 Libing Road

institute: SBC

summary: To systemically evaluate the comprehensive alterations under the supplements of quercetin and/or resveratrol in high fat diet (HFD) fed mice, we have employed whole genome microarray expression profiling as a discovery platform to identify genes that differentially altered by different treatments. Gene expression profiles were significantly altered by long term HFD feeding. However, quercetin, resveratrol and their combination could effectively attenuate this alteration. Especially, combination use of quercetin and resveratrol showed more signifcant benefits on the changes of genes, involved in metabolic disorders, induced by HFD, which revealed a synergistic effect of quercetin and resveratrol supplementation in high fat diet fed mice.

overall_design: Thirty 7-week-old male C57/6J mice were  mice were randomly divided into 5 groups (n= 6): control group fed with standard diet (SD); HFD group; quercetin (HQ) group fed with HFD and 0.4% quercetin (4 g/kg diet); resveratrol (HR) group fed with HFD and 0.4% resveratrol (4g/kg diet); quercertin+resveratrol (HQR) group fed with HFD and 0.2% quercetin + 0.2% resveratrol (2g quercetin+ 2g resveratrol per kg diet). All mice were kept on corresponding diets for 26 weeks. Finally, total RNA of liver tissue of each mouse was extracted and hybridized to the microarry. Two RNA samples were exculded for microarry experiment due to the obvious degradation.

first: Shidong

last: Wang

first: Ke

first: Qinghua

last: Zhang


title: caArray_gabri-00003: TCGA Analysis of RNA Expression for Glioblastoma Multiforme

status: Public on May 14 2015

city: Rockville

first: Mervi

last: Heiskanen

state: MD

address: 9609 Medical Center Drive, 1W378

department: CBIIT

institute: NCI

summary: TCGA Analysis of RNA Expression for Glioblastoma Multiforme Using Affymetrix HT_HG-U133A

overall_design:
gabri-00003
Assay Type: Gene Expression
Provider: Affymetrix
Array Designs: HT_HG-U133A
Organism: Homo sapiens (ncbitax)
Tissue Sites: Brain
Material Types: synthetic_RNA, organism_part, solid_tumor, total_RNA, cell
Disease States: GLIOBLASTOMA MULTIFORME, NOT SPECIFIED

first: Matthew

last: Meyerson

first: Stacey

last: Gabriel


title: Mouse lung tissue transcriptome response to a mouse-adapted strain of SARS-CoV in wild type C57BL6/NJ mice and TLR3-/- mice

status: Public on May 12 2015

city: Richland

first: Katrina

last: Waters

address: 902 Battelle Blvd; MSIN J4-18

department: Biological Sciences Division

institute: Pacific Northwest National Laboratory

summary: The purpose is to determine the role of TLR3-/- on the regulation of the host immune response during lethal SARS-CoV infection

overall_design: Groups of 10 week old C57BL6/NJ  or TLR3-/- mice were  infected with MA15 virus at a dose of 10^5 PFU or time-matched mock infected. Time points were 2, 4 and 7 days post infection. There were 4 or 5 animals/time point. Lung samples were collected for virus load, lung pathology, and transcriptional analysis. Weight loss and animal survival were also monitored.

first: Allison

last: Totura

first: Mark

last: Heise

first: Michael

last: Katze

first: Ralph

last: Baric


title: miRNA regulation by interleukin-4 (IL-4) in chronic lymphocytic leukemia (CLL)

status: Public on Jun 15 2015

city: Murcia

first: Antonio

last: Parrado

address: Ctra. Madrid-Cartagena, s/n

institute: Hospital Clinico Universitario Virgen de la Arrixaca

summary: miRNA 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.

overall_design: 16 CLL patients (8 Pre samples, 15 Ctrl samples, 15 IL-4 samples), 3 NBC (3 Ctrl samples, 3 IL-4 samples)


title: miRNAs in follicular fluid

city: Valencia

first: Juan

last: Moreno-Moya

address: Catedrático Agustín Escardino

institute: FIVI

summary: Our aim with this work is to identify and quantify the miRNA profile of the human follicular fluid using a miRNA microarray approach in young and advanced-aged women and in follicles with different oocyte quality.  Data collected in this study would be utilized in a future as a marker to predict the oocyte quality.

overall_design:
This observational prospective study includes women enrolled in the assisted reproduction program of Hospital Universitari i Politècnic la Fe (Valencia, Spain). The study was accepted by IRB of this Hospital and all couples received informed consent of our study and assisted technique according to service protocols. The study was divided in two stages:

Stage 1: Patients (n=21) who had follicles yielding oocytes with different degree of maturation were included (n=21). The follicular fluid samples from 21 patients were pooled in different groups. Expression of miRNA in the follicular fluids was compared within each patient according the degree of oocyte maturation.

Stage 2: Patients were allocated into two groups according to the patient's age: advanced age (AA; >36 years old) and  young age (YA; <36 years old). Follicular fluids from follicles containing MII oocytes were pooled and miRNA expression was subsequently compared.

Please note that the MII samples with underscore (such as MII1 vs MII_1) indicate different pools so they are not the same sample, but we maintained the number because they correspond to paired samples pools for GV and MI.

first: Maria

last: Núñez

first: Cesar

last: Díaz

first: Francisco

last: Domínguez


title: caArray_EXP-592: TCGA (LUSC): Analysis of Gene Expression for Non Small Cell Lung Cancer, Squamous Cell Carcinoma Using Affymetrix HT_HG-U133A (Broad)

status: Public on May 13 2015

summary: TCGA Analysis of RNA Expression for Non Small Cell Lung Cancer, Squamous Cell Carcinoma Using Affymetrix HT_HG-U133A

overall_design:
EXP-592
Assay Type: Gene Expression
Provider: Affymetrix
Array Designs: HT_HG-U133A
Organism: Homo sapiens (ncbitax)
Tissue Sites: Lung
Material Types: organism_part, Primary solid_tumor
Disease States: Lung Squamous Cell Carcinoma, NOT SPECIFIED


title: Gene expression profiling in the liver of 3-month old mice with a mutant Wrn protein treated with vitamin C compared to the liver of 3-month old untreated mice with a mutant Wrn protein.

status: Public on May 09 2015

city: Quebec

first: Michel

last: Lebel

state: Qc

address: 2705 Laurier Blvd, Local T-2-04

department: Centre Hospitalier de l’Université Laval (CHUL)

institute: Centre de Recherche du CHU de Québec

summary: Werner syndrome (WS) is a rare disorder characterized by the premature onset of a number of age-related diseases. The gene responsible for WS is believed to be involved in different aspects of transcription, replication, and/or DNA repair. We generated a mouse model with a deletion in the helicase domain of the murine WRN homologue that recapitulates most of the WS phenotypes including an abnormal hyaluronic acid excretion, higher reactive oxygen species (ROS) levels, increased genomic instability and cancer incidence resulting in a 10-15% decreased life span expectancy. In addition, WS patients and Wrn mutant mice show hallmarks of a metabolic syndrome including premature visceral obesity, hypertriglyceridemia, insulin-resistant diabetes type 2 and associated cardiovascular diseases. In this study, we compared the expression profile of liver tissues from 3 months old Wrn mutant mice treated with 0.4% vitamin C to untreated 3 months old Wrn mutant mice.

overall_design: Microarray analyses were performed on the liver tissues of 3 months old mice. Four independent biological replicates of this experiment (untreated Wrn mutant mice vs vitamin C treated Wrn mutant mice) were carried out on four replicates of each genotype.

first: Eric

last: Paquet


title: Specific gene expression related to epiblast development

status: Public on Apr 01 2015

city: Yonago

first: Akira

last: Hasegawa

state: Tottori

address: 36-1, Nishimachi

department: Department of Genetic Medicine and Regenerative Therapeutics

institute: Institute of Regenerative Medicine and Biofunction, Graduate School of Medical Science,Tottori University

summary: To explore genes involved in epiblast development, we have employed whole genome microarray expression profiling as a discovery platform to identify genes. Embryoid body (EB) formation induces embryonic stem (ES) cells to differentiate into germ layers via epiblasts and extra-embryonic tissues, whereas ES cells give rise only to extra-embryonic tissues in monolayer culture. We compared gene expression profiles of ES cells in each differentiation culture methods at day 1-3 or 4 of differentiation. The expression of organizer related genes (Lhx1, Cer1 and Foxa2) was specifically induced at day 3 of EBs, but not in monolayer culture. In epiblast model cells, the overexpression of Lhx1 induced gene expression of organizer and meso-endodermal markers, suggested that Lhx1 was related to epiblast differentiation.

overall_design: Gene expression related epiblast development was measured at undifferentiated state and day 1-3 or 4 of differentiation. Two independent experiments were performed at each time using different people for each experiment.

first: Nobuhito

last: Ikeda

first: Ichiro

last: Hisatome

first: Yasuaki

last: Shirayoshi


title: caArray_golub-00327: Sanger cell line Affymetrix gene expression project

status: Public on May 16 2015

first: Mervi

last: Heiskanen

summary: The microarray gene expression pattern was studied using 798 different cancer cell lines. The cancer cell lines are obtained from different centers. Annotation information were provided in the supplementary file.

overall_design:
golub-00327
Assay Type: Gene Expression
Provider: Affymetrix
Array Designs: HT_HG-U133A
Organism: Homo sapiens (ncbitax)
Tissue Sites: leukemia, Urinary tract, Lung, BiliaryTract, Autonomic Ganglion, Thyroid gland, Stomach, Breast, Pancreas, Head and Neck, Lymphoma, Colorectal, Placenta, Liver, Brain, Bone, pleura, Skin, endometrium, Ovary, cervix, Oesophagus, Connective and Soft Tissue, Muscle, Kidney, Prostate, Adrenal Gland, Eye, Testis, Smooth Muscle Tissue, Vulva, Unknow
Material Types: cell, synthetic_RNA, whole_organism, total_RNA, BVG
Disease States: M3 acute myeloid leukemia, hairy cell leukemia, transitional cell carcinoma, Adenocarcinoma, B cell lymphoma unspecified, Acute Lymphoblastic Leukemia, blast phase chronic myeloid leukemia, Carcinoma, M6 acute myeloid leukemia, Neuroblastoma, follicular carcinoma, ductal carcinoma, Burkitt Lymphoma, Squamous Cell Carcinoma, M5 acute myeloid leukemia, Mycosis Fungoides and Sezary Syndrome, Acute T-Cell Lymphoblastic Leukemia, Adult T-Cell Leukemia/Lymphoma, M2 Therapy-Related Myeloid Neoplasm, Choriocarcinoma, Plasma Cell Myeloma, Hepatocellular Carcinoma, anaplastic large cell lymphoma, primitive neuroectodermal tumor-medulloblastoma, M4 acute myeloid leukemia, B Acute Lymphoblastic Leukemia, Acute Leukemia of Ambiguous Lineage, Osteosarcoma, Hodgkin Lymphoma, Mesothelioma, chondrosarcoma, Glioblastoma Multiforme, Malignant Melanoma, carcinosarcoma-malignant mesodermal mixed tumor, bronchioloalveolar adenocarcinoma, chronic lymphocytic leukemia-small lymphocytic lymphoma, micropapillary carcinoma, diffuse large B cell lymphoma, myelodysplastic syndrome, giant cell carcinoma, teratoma, multipotential sarcoma, Small Cell Carcinoma, ASTROCYTOMA, Fibrosarcoma, mucoepidermoid carcinoma, Rhabdomyosarcoma, L1 Acute T-Cell Lymphoblastic Leukemia, Glioma, Anaplastic Astrocytoma, Non-small cell carcinoma, Large Cell Carcinoma, mucinous carcinoma, Acute Myeloid Leukemia, malignant fibrous histiocytoma-pleomorphic sarcoma, clear cell carcinoma, B cell lymphoma unspecified, Anaplastic Carcinoma, Ewings sarcoma-peripheral primitive neuroectodermal tumor, undifferentiated carcinoma, Sarcoma, Embryonal Rhabdomyosarcoma, epithelioid sarcoma, renal cell carcinoma, carcinoid-endocrine tumor, Synovial Sarcoma, lymphoid neoplasm, rhabdoid tumor, Refractory Anemia with Excess Blasts, Liposarcoma, biphasic mesothelioma, adrenal cortical carcinoma, adenosquamous carcinoma, L2 Acute T-Cell Lymphoblastic Leukemia, chronic myeloid leukemia, Micropapillary Serous Carcinoma, desmoplastic, acute leukemia, Retinoblastoma, teratocarcinoma, clear cell renal cell carcinoma, Follicular Lymphoma, Wilms Tumor, M7 acute myeloid leukemia, gliosarcoma, embryonal carcinoma, Leiomyosarcoma, medullary carcinoma, granulosa cell tumor, papillary carcinoma, NS Acute Lymphoblastic Leukemia, papillary transitional cell carcinoma, small cell adenocarcinoma, epithelial dysplasia, hyperplasia, tubular adenocarcinoma, metaplasia, papillary ductal carcinoma, chronic eosinophilic leukemia-hypereosinophilic syndrome, #N/A, malignant trichilemmal cyst, Medullary Breast Carcinoma, L2 Acute Lymphoblastic Leukemia, Osteoblastic Osteosarcoma


title: Trichostatin A specifically improves the aberrant expression of transcription factor genes in embryos produced by somatic cell nuclear transfer

city: Tsukuba

first: Kimiko

last: Inoue

state: Ibaraki

address: 3-1-1 Koyadai

department: Bioresource Engineering Division

institute: BRC, RIKEN

summary: Although mammalian cloning by somatic cell nuclear transfer (SCNT) has been established in various species, the low developmental efficiency has hampered its practical applications. Treatment of SCNT-derived embryos with histone deacetylase (HDAC) inhibitors can improve their development, but the underlying mechanism is still unclear. To address this question, we analysed gene expression profiles of SCNT-derived 2-cell mouse embryos treated with trichostatin A (TSA), a potent HDAC inhibitor that is best used for mouse cloning. Unexpectedly, TSA had no effect on the numbers of aberrantly expressed genes or the overall gene expression pattern in the embryos. However, in-depth investigation by gene ontology and functional analyses revealed that TSA treatment specifically improved the expression of a small subset of genes encoding transcription factors and their regulatory factors, suggesting their positive involvement in de novo RNA synthesis. Indeed, introduction of one of such transcription factors, Spi-C, into the embryos at least partially mimicked the TSA-induced improvement in embryonic development by activating gene networks associated with transcriptional regulation. Thus, the effects of TSA treatment on embryonic gene expression did not seem to be stochastic, but more specific than expected, targeting genes that direct development and trigger zygotic genome activation at the 2-cell stage.

overall_design: Gene expression were measured in mouse unfertilized oocytes, in vitro fertilized, somatic cell cloned embryos and cumulus cells. Somatic cell cloned embryos were treated with/without TSA or Spi-C mRNA and subjected at 2-cell stage. More than four biological replicates were performed in each group.

first: Mami

last: Oikawa

first: Satoshi

last: Kamimura

first: Narumi

last: Ogonuki

first: Toshinobu

last: Nakamura

first: Toru

last: Nakano

first: Kuniya

last: Abe

first: Atsuo

last: Ogura


title: Gene expression profiles of adult neural stem cells with loss-of-function and gain-of-function of SIRT1

status: Public on Mar 30 2015

city: Berkeley

first: Chenyan

last: Ma

address: 230E Li Ka Shing Center

institute: UC Berkeley

summary: To elucidate the role of SIRT1 in adult neural stem cells, we have carried out a genome-wide microarray analysis on cultured adult neurospheres from wildtype (WT) and sirt1 knockout (KO) mice and WT neurospheres treated with DMSO and SIRT1 activator,resveratrol for 24 hours. Then we screened for genes that exhibited opposite changing patterns beween KO-versus-WT and resveratrol-versus-DMSO-treated groups. Our result revealed a significant enrichment of genes involved in metabolic process. And numerous genes involved in cell proliferation and differentiation were represented in these SIRT1-responsive genes. More interestingly, Notch signaling-related genes,such as Dll4, Mib1,Hes5, Heyl, Hey2 and so on, also showed a significant enrichment. Real-time PCR validated the expression of Notch signaling-related genes. These data revealed the regulation of SIRT1 on the self-renewal and differentiation of adult neural stem cells.

overall_design: Secondary neurospheres from WT and sirt1 KO adult mice, and WT neurospheres treated with DMSO and resveratrol for 24 hours were used, each in duplicate.

first: Yuan

last: Xiaobing

first: Ma

last: Chenyan


title: Transcriptome characterization of social stressed C57B6 mice exhibiting PTSD like features

status: Public on Apr 20 2015

city: Fort Detrick

first: seid

last: muhie

address: 568 Doughten Dr

department: Systems Biology Enterprise

institute: USACEHR

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

overall_design: Refer to individual Series


title: Granulocytic immune infiltrates are essential for the efficient formation of breast cancer liver metastases

status: Public on Mar 20 2015

city: Montreal

first: Peter

last: Siegel

state: Quebec

address: 1160 Pine avenue West

department: Medicine

institute: McGill University

summary:
Breast cancer cells display preferences for specific metastatic sites including the bone, lung and liver.  Metastasis is a complex process that relies, in part, on interactions between disseminated cancer cells and resident/infiltrating stromal cells that constitute the metastatic microenvironment. Distinct immune infiltrates can either impair the metastatic process or conversely, assist in the seeding, colonization and growth of disseminated cancer cells.  Using in vivo selection approaches, we previously isolated 4T1-derived breast cancer cells that preferentially metastasize to these organs and tissues. In this study, we examined whether the propensity of breast cancer cells to metastasize to the lung, liver or bone is associated with and dependent on distinct patterns of immune cell infiltration. Immunohistocytochemistry and immunohistofluorescence approaches were used to quantify granulocytic infiltrates within distinct metastases and depletion of Gr1+ cells was performed to functionally interrogate the role of myeloid/granulocytic infiltrates in promoting metastasis to these organs.
We show that T lymphocytes (CD3+), myeloid-derived/granulocytic cells (Gr-1+) cells and neutrophils (NE+) exhibit the most pronounced recruitment in lung and liver metastases, with markedly less recruitment within bone metastatic lesions. Interestingly, these infiltrating cell populations display different patterns of localization within soft tissue metastases. T lymphocytes and neutrophils are localized around the periphery of liver metastases whereas they were dispersed throughout the lung metastases. Furthermore, Gr-1+ cell-depletion studies demonstrate that infiltrating myeloid-derived/granulocytic cells, including neutrophils, are essential for the formation of breast cancer liver metastases but dispensable for metastasis to the lung and bone. Finally, we demonstrate that neutrophils that infiltrate and surround the liver metastases are polarized towards an N2 phenotype, which have previously been shown to enhance tumor growth and metastasis. Our results demonstrate that the liver metastatic potential of breast cancer cells is heavily reliant on interactions with infiltrating myeloid/granulocytic cells in the liver microenvironment.

overall_design: Gene expression profile comparison from 4T1 parental and individual in vivo selected metastatic sub-populations.

first: Sébastien

last: Tabariès

first: Véronique

last: Ouellet


title: Analysis of genes expressed differentially along the AP and ML axis of chick optic tectum

status: Public on Mar 26 2015

city: Worcester

first: Shweta

last: Kukreja

state: MA

address: Aaron Lazare Medical Research Building (LRB) 364 Plantation Street, LRB 9th Floor

department: Biochemistry and Molecular Pharmacology

institute: University of Massachusetts Medical School

summary: Comparison of transcription profiles on anterior tectum and posterior tectum at HH35 an HH37, and that of medial and lateral tectum at HH30 and HH35. The goal was to obtain summary of genes expressed differentially across the AP and DV axis.

overall_design: 60 samples pooled together to normalize for biological variations. No biological replicates taken for experiments. No technical replicates or dye swaps.

first: S

first: J

last: Sen


title: Gene expression profiling of the AD11 anti-NGF transgenic mouse model of neurodegeneration at 1, 3, 6, 15 months of age

status: Public on Feb 26 2015

city: Roma

first: Ivan

last: Arisi

address: viale Regina Elena 295

department: Bioinformatics Facility

country: Italy

institute: European Brain Research Institute

summary: We characterized the gene expression profile of brain regions at different stages of the Alzheimer’s like neurodegeneration in the anti-NGF AD11 trangenic mouse model. Total RNA was extracted from hippocampus, cortex and basal forebrain of postnatal day 30 (P30, 1 month), P90 (3 months), P180 (6 months)  and at 15 months of age. Expression profiles were studied by Agilent microarray analysis, followed by qRT-PCR validation of significant candidates. Wide changes in gene expression profiles occur already at the presymptomatic stage P30, with the most significantly affected clusters of mRNAs are linked to Inflammation and Immune Response.

overall_design: AD11 mice were compared to the trangenic VH controls. A total of 60 female AD11 mice and 59 female control VH (5 per group) mice were used for this study: 5 AD11 and 4-5 control VH mice for each time point (1,3,6,15 months of age) and brain area (HP, CTX, BFB).

first: Mara

last: D'Onofrio

first: Rossella

last: Brandi

first: Alessandra

last: Di Mambro

first: Armando

last: Felsani

first: Simona

last: Capsoni

first: Antonino

last: Cattaneo


title: The Taxonomic and Metabolic Potential Susceptibility of Microbial Community to Aeolian Grassland Soil Erosion and Deposition

status: Public on Mar 28 2015

city: Beijing

first: Yunfeng

last: Yang

address: No.1 Qinghuayuan, Haidian District

department: School of Environment

institute: Tsinghua University

summary: Aeolian soil erosion, exacerbated by anthropogenic perturbations, has become one of the most alarming processes of land degradation and desertification. By contrast, dust deposition might confer a potential fertilization effect. To examine how they affect topsoil microbial community, we conducted a study GeoChip techniques in a semiarid grassland of Inner Mongolia, China. We found that microbial communities were significantly (P<0.039) altered and most of microbial functional genes associated with carbon, nitrogen, phosphorus and potassium cycling were decreased or remained unaltered in relative abundance by both erosion and deposition, which might be attributed to acceleration of organic matter mineralization by the breakdown of aggregates during dust transport and deposition. As a result, there were strong correlations between microbial carbon and nitrogen cycling genes. amyA genes encoding alpha-amylases were significantly (P=0.01) increased by soil deposition, reflecting changes of carbon profiles. Consistently, plant abundance, total nitrogen and total organic carbon were correlated with functional gene composition, revealing the importance of environmental nutrients to soil microbial function potentials. Collectively, our results identified microbial indicator species and functional genes of aeolian soil transfer, and demonstrated that functional genes had higher susceptibility to environmental nutrients than taxonomy. Given the ecological importance of aeolian soil transfer, knowledge gained here are crucial for assessing microbe-mediated nutrient cyclings and human health hazard.

platform_organism: Bacteria Archaea Eukaryota Viruses

overall_design: The experimental sites comprised of three treatments of control, soil erosion and deposition, with 5 replicates of each treatment.

first: Xingyu


title: caArray_EXP-485: TCGA Analysis of Gene Expression for Ovarian Serous Cystadenocarcinoma Using Affymetrix HT_HG-U133A

status: Public on May 08 2015

first: Mervi

last: Heiskanen

overall_design:
EXP-485
Assay Type: Gene Expression
Provider: Affymetrix
Array Designs: HT_HG-U133A
Organism: Homo sapiens (ncbitax)
Material Types: Cell, solid_tumor, whole_organism, normal_tissue

first: Matthew

last: Meyerson

first: Stacey

last: Gabriel


title: Genome-Wide Gene Expression Profiles in the Pancreatic Lymph Nodes of non-obese diabetic (NOD) mice

status: Public on Mar 09 2015

city: Stanford

first: Keiichi

last: Kodama

state: CA

address: 269 Campus Drive, Room 2225

department: Department of Medicine, Division of Immunology & Rheumatology

institute: Stanford Univeristy School of Medicine

summary: Type 1 diabetes (T1D) is a polygenic autoimmune disorder caused by autoreactive T cells that recognize pancreatic islet antigens and subsequently destroy insulin-producing β-cells. Pancreatic lymph nodes (PLN) are an essential site for the development of T1D, where tolerance to pancreatic self-antigens is first broken and the autoimmune responses are amplified. The purpose of this study was to identify candidate genes and pathways in the PLN that may contribute to the pathogenesis of T1D using a mouse model of T1D.

overall_design: Genome-wide gene expression was measured in individual NOD PLN at 10 days (n=6), 4 weeks (n=6) or 12 weeks of age (n=5), against a pooled sample of age-matched NOD.B10 PLN as the control (n≥6), using Agilent Whole Mouse Genome Microarrays.

first: Linda

last: Yip

first: Rebecca

last: Fuhlbrigge

first: C

last: Fathman


title: Generation of Cloned Mice from Adult Neurons by Direct Nuclear Transfer

status: Public on Feb 03 2015

first: Kimiko

last: Inoue

summary: Whereas cloning mammals by direct somatic cell nuclear transfer has been successful using a wide range of donor cell types, neurons from adult brain remain “unclonable” for unknown reasons. Here we examined whether neurons from adult mice could be cloned, using a combination of two epigenetic approaches. First, we used a specific antibody to discover cell types with reduced amounts of a repressive histone mark - dimethylated histone H3 lysine 9 (H3K9me2) - and identified CA1 pyramidal cells in the hippocampus and Purkinje cells in the cerebellum as candidates. Second, reconstructed embryos were treated with trichostatin A (TSA), a potent histone deacetylase inhibitor. Using CA1 cells, cloned offspring were obtained at high rates, reaching 10.2% and 4.6% (per embryos transferred) for male and female donors, respectively. Cerebellar Purkinje cell nuclei were too large to maintain their genetic integrity during nuclear transfer, leading to developmental arrest of embryos. However, gene expression analysis using cloned blastocysts corroborated a high rate of genomic reprogrammability of CA1 pyramidal and Purkinje cells. Neurons from the hippocampal dentate gyrus and cerebral cortex, which had higher amounts of H3K9me2, could also be used for producing cloned offspring, but the efficiencies were low. A more thorough analysis revealed that TSA treatment was essential for cloning adult neuronal cells. This study demonstrated for the first time that adult neurons could be cloned by nuclear transfer. Furthermore, our data imply that reduced amounts of H3K9me2 and increased histone acetylation appear to act synergistically to improve the development of cloned embryos.

overall_design: Comparative gene expression analyses using blastocysts of cloned embryos were performed by microarray. Cloned embryos were produced with three different types of donor cells (neonatal Sertoli cells, CA1 pyramidal cells and Purkinje cells) and all cloned embryos were treated with Trichostatin A (TSA). Each embryos were cultured for 96 h and blastocysts derived from each donor cell types were subjected to gene expression microarray. For comparison of gene expression, the data sets of control sex- and genotype-matched embryos produced by in vitro fertilization and SCNT-derived blastocysts from cumulus cells treated with TSA from our previous paper (Inoue K. et al. Science 2010) were also used.

first: Eiji

last: Mizutani

first: Mami

last: Oikawa

first: Hidetoshi

last: Kassai

first: Hirosuke

last: Shiura

first: Ryutaro

last: Hirasawa

first: Satoshi

last: Kamimura

first: Shogo

last: Matoba

first: Narumi

last: Ogonuki

first: Hiroaki

last: Nagatomo

first: Kuniya

last: Abe

first: Teruhiko

last: Wakayama

first: Atsu

last: Aiba

first: Atsuo

last: Ogura


title: Gene expression profile of ATF6a and ATF6b knockout mice with dextran sulfate sodium (DSS)-induced colitis

status: Public on Feb 08 2015

city: Tokushima

first: Seiichi

last: Oyadomari

state: Tokushima

address: 3-18-15 Kuramoto

department: Division of Molecular Biology

institute: Institute for Genome Research

summary: To understand the role of ATF6a and ATF6b in non-canonical endoplasmic reticulum stress response pathway, we have employed whole genome  microarray expression profiling to identify the genes regulated by ATF6s. WIild type or, ER stress mediators,ATF6a or ATF6b-knockout mice were treated with 3% DSS for 3days. Genes responsible for DSS in each mediator-dependent manner were extracted and categorized by Gene Ontology. Among them, expression of three cell structure-related genes (Muc2, Muc3, Muc4) was quantified in the RNA samples from another mice treated with DSS by real-time PCR.

overall_design: Colitis was induced with 3% DSS, 36,000-50,000 M.W. (MP Biomedicals,) in the drinking water for 3 days. Genes responsible for DSS treatment in each mediator-dependent manner were extracted and categorized by Gene Ontology in GeneRanker program of Genomatix platform.

first: Kazuna

last: Takahara

first: Taiji

last: Ito

first: Akitoshi

last: Nomura

first: Kiyoe

last: Kurahashi

first: Ryousuke

last: Sato

first: Tomoko

last: Mori

first: Kazue

last: Tsugawa

first: Robert

last: Zeng

first: Mari

last: Funahashi

first: Chinobu

last: Miyamoto

first: Naoko

last: Miura

first: Seiko

last: Kagawa

first: Masato

last: Miyake

first: Miho

last: Tanaka

first: Kazutoshi


title: Gene expression analysis in differentiated day 3 cells from mouse ESC under the treatment of DMSO and histone deacetylase inhibitors (TSA) [expression array]

status: Public on Feb 19 2015

city: shanghai

first: Naihe

last: Jing

address: 320 Yue Yang Road

institute: institute of biochemistry and cell biology

summary: Based on the cDNA microarrays performed with the RNAs prepared from the differentiated cells at day 3 with or without 24 hrs TSA treatment initiated at day 2, we reveal that the upregulated gene sets were highly enriched for biological functions related to mesoderm development, mesoderm morphogenesis and others.

overall_design: Three independent experiments were performed at each treatment (DMSO or TSA).

first: Pingyu

last: Liu


title: Reciprocal interaction of Wnt and RXR-α pathways in hepatocyte development and hepatocellular carcinoma

status: Public on Jan 17 2015

city: Stony Brook

first: Jinyu

last: Li

state: NY

address: 101 Nicolls Rd

department: Cancer Center

institute: Stony Brook University

summary: Genomic analysis of human hepatocellular carcinoma (HCC) is potentially confounded by the differentiation state of the hepatic cell-of-origin.   Here we integrated genomic analysis of mouse HCC (with defined cell-of-origin) along with normal liver development.  We found a major shift in expression of Wnt and RXR-α pathway genes (up and down, respectively) coincident with the transition from hepatoblasts to hepatocytes. A combined Wnt and RXR-α gene signature categorized HCCs into two subtypes (high Wnt, low RXR-α and low Wnt, high RXR-α), which matched cell-of-origin in mouse models and the differentiation state of human HCC.    Suppression of RXR-α levels in hepatocytes increased Wnt signaling and enhanced tumorigenicity, whereas ligand activation of RXR-α achieved the opposite.   These results corroborate that there are two main HCC subtypes that correspond to the degree of hepatocyte differentation and that RXR-α, in part via Wnt signaling, plays a key functional role in the hepatocyte-like subtype and potentially could serve as a selective therapeutic target.

overall_design: Total RNA from whole livers taken at different developmental timepoints (embryonic day 14, embryonic day 18, post-natal day 5 and post-natal day 56) along with hepatoblasts isolated from E14 livers and immature hepatocytes isolated from E18 livers was extracted and purified using the Qiagen RNeasy Mini Kit.   RNA purity and integrity were assayed by the Bioanalyser 2100 (Agilent Technologies).   For each sample, 2 µg of total RNA was reverse transcribed and amplified by using an RNA amplification kit from Ambion.  Fifteen micrograms of amplified RNA were labeled by direct chemical coupling to the Cy5 NHS ester (Amersham Biosciences). Normal adult mouse liver (Agilent) was used as control and Cy3 labeled. Labeled RNAs were purified, fragmented, and used as probes to hybridize microarrays. Gene expression profiling was done with the 4x44k mouse Agilent platform.  Expression profiling of the 23 human HCC samples was previously described

first: Maia

last: Chanrion

first: Eric

last: Sawey

first: Tim

last: Wang

first: Edward

last: Chow

first: Aaron

last: Tward

first: Yi

last: Su

first: Wen

last: Xue

last: Lucito

first: Lars

last: Zender

first: Scott

last: Lowe

first: J

last: Bishop

last: Powers


title: Gene expression profiling of HepG2 cells exposed to Endosulfan

status: Public on Jan 20 2015

city: Nagpur

first: Dr. saravana

last: devi

state: Maharashtra

department: Environmental Health Division

country: India

institute: CSIR-National Environmental Engineering Research Institute

summary: HepG2  cells grown in DMEM media were treated with 15µM endosulfan and total RNA was isolated from cells after 24 hour exposure

overall_design: Cells grown in  75mm2 flask. two replicates for control and two for treatment

first: Deepa

last: Gandhi

first: Saravana

last: Devi

first: K

last: Krishnamurthi


title: Transcriptional changes in skeletal muscle in response to 4 weeks of exercise training

status: Public on Feb 01 2015

city: Nuthetal

first: Timo

last: Kanzleiter

address: Arthur-Scheunert-Alle 114

department: Experimental Diabetology

country: Germany

institute: DIfE

summary: Consequence of physical exercise in skeletal muscle was investigated in C57BL/6 mice after 4 weeks of exercise training and compared to sedentary controls.

overall_design: Exercised mice received four 4 weeks of regular exercise training on a motorized treadmill and were compared to sedentary controls.  6 mice of each Treatment were used to extract RNA from the quadriceps muscle three hours after the last training bout

first: Annette

last: Schuermann


title: RNA-Seq Versus Oligonucleotide Array Assessment of Dose-Dependent TCDD-elicited Hepatic Gene Expression in Mice [Array]

status: Public on Feb 10 2015

city: East Lansing

first: Rance

last: Nault

state: United States

address: 1355 Bogue St. B403

department: Department of Pharmacology and Toxicology

institute: Michigan State University

summary: Dose-dependent hepatic gene expression was examined following repeated exposure (every 4 days for 28 days) to 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). These data were used to examine the effect of repeated TCDD exposure as well as compare the performance of RNA-Seq and Agilent oligonucleotide microarrays for detection and identificatioin of differentially expressed genes.

overall_design:
Three biological replicates for each dose (0.01, 0.03, 0.1, 0.3, 1, 3, 10, 30) of TCDD and sesame oil vehicle
This submission represents the Agilent microarrays component of study.

first: Kelly

last: Fader

first: Timothy

last: Zacharewski


title: Self-renewal of hepatoblasts under chemically defined conditions by reiterative growth factor and chemical screening

status: Public on Dec 29 2014

city: Shanghai

first: Wenlin

last: Li

address: 800 Xiangyin Road

institute: Second Military Medical University

summary: Throught an reiterative growth factor and chemical screening, we defined a small molecule and growth factor cocktail, including EGF, glycogen synthase kinase 3 inhibitor (CHIR99021), transforming growth factor β receptor inhibitor (e.g. E-616452), lysophosphatidic acid and sphingosine 1-phosphate, that can sustain long-term self-renewal of murine hepatoblasts under chemically defined conditions. The expandable hepatoblasts (eHBs) by this small molecule and growth factor cocktail expressed a set of genes typical of liver progenitor cells and liver development, and retained the ability to respond to liver developmental cues and produce functional hepatocytes and form bile duct-like structures. Moreover, both early- and late-passage eHBs demonstrated a similar transcriptome profile. Microarray analysis also confirmed that the gene expression of cultured cells resembled hepatoblasts.

overall_design: Expandable hepatoblasts (eHBs) were routinely cultured in basal medium (DMEM/F12 medium supplemented with insulin-transferrin-sodium selenite, 5 mM nicotinamide, 30 μg/ml 2-phospho-L-ascorbic acid and 50 μg/ml bovine serum albumin human recombinant albumin and 1% penicillin/streptomycin including 10 ng/ml EGF, 3 μM CHIR99021, 2 μM E-616452, 5 μM LPA and 0.5 μM S1P, on Matrigel or laminin-coated surface. The culture was split 1:6 using Accutase. Total RNA was prepared from passage 5 and passage 20 of eHBs (passage 5 and passage 20 of eHBs were derived from two independent experiments) using the RNeasy Plus Mini Kit.


title: Analysis of the lung transcriptome in Mycobacterium tuberculosis-infected mice reveals major differences in immune response pathways between TB-susceptible and resistant hosts.

status: Public on Dec 16 2014

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

institute: HCI - Helmholtz Centre for Infection Research

summary: Using whole genome microarrays, we compared changes in gene expression patterns in the lungs of TB-resistant A/Sn and TB-susceptible I/St mice at day 14 following infection with Mycobacterium tuberculosis  H37Rv. Analyses of differentially expressed genes for representation of gene ontology terms and activation of regulatory pathways revealed interstrain differences in antigen presentation, NK, T and B cell activation pathways. In general, resistant A/Sn mice exhibited a more complex pattern and stronger activation of host defense pathways compared to the TB-susceptible I/St mouse strain. In addition, in I/St mice elevated activation of  genes involved in neutrophil response was observed and confirmed by quantitative RT-PCR and histopathology. Furthermore, a specific post infection upregulation of cysteine protease inhibitors was found in  susceptible I/St mice.

overall_design: To monitor the global transcriptome patterns in the two mouse strains, gene expression was assessed using Agilent 4 x44K whole genome microarrays. Genes that changed their expression level at least two-fold compared to non-infected controls with a p-value of  0.1 were considered as differentially expressed genes (DEG).

first: E

last: Wilk

first: R


title: Gene expression profiling of side population cells of mouse thyroid before and after partial thyroidectomy

status: Public on Jan 01 2015

city: Bethesda

first: Tsutomu

last: Matsubara

address: 9000 Rockville Pike

institute: NCI

summary: Side population (SP) cells are enriched with genes involved in stem cell activity and/or lineage specifications. Stem cell marker genes are upregulated after partial thyroidectomy.

overall_design: Four-condition experiment: control side population (CSP) vs. control main population (CMP) vs. thyroidectomized side population (TSP) vs. thyroidectomized main population (TMP). Biological replicates: 6 CSP, 3 CMP, 6 TSP, and 3 TMP samples.

first: Yoshihito

last: Sasaki

first: Daekwan

last: Seo

first: Shioko

last: Kimura


title: DosS Is Required for the Complete Virulence of Mycobacterium  tuberculosis in Mice with Classical Granulomatous Lesions

status: Public on Dec 11 2014

city: San Antonio

first: Deepak

last: Kaushal

state: TX

address: 8715 W Military Dr

department: HPI

institute: Texas Biomedical Research Institute

summary: Here we are including replicate mouse microarray data from Kramnik mice infected over the course of different time points with M. tuberculosis H37Rv and its isogenic mutants in dosR, dosS and dosT genes.

overall_design: Mice from day 1 infection universally served as controls and RNA derived from these was always labeled with Cy3. RNA derived from mice at 4, 8 and 16 weeks was labeled with Cy5

first: Smriti

last: Mehra


title: Gene regulated by Srebp1 and c-Myc during reprogramming

status: Public on Nov 29 2014

city: Guangzhou

first: Yi

last: Wu

address: 190 Kai Yuan Avenue, Science Park

institute: Guangzhou Institutes of Biomedicine and Health

summary: To identify genes regulated by Srebp1 and c-Myc during reprogramming, we performed genome-wide transcriptome profiling in mouse embryonic fibroblasts infected with SKO, SKOM or SKOM plus Srebp1.

overall_design: Gene expression of mouse embryonic fibroblasts infected with SKO, SKO, SKOM or SKOM plus Srebp1 was measured at day 5.

first: Keshi

last: Chen


title: Deregulation of the endogenous C/EBPβ LIP isoform predisposes to tumorigenesis

city: Berlin

first: Valerie

last: Begay

address: Robert-Rössle-Str. 10

institute: Max Delbrück Center

summary:
Two long and one truncated isoforms (termed LAP*, LAP,
and LIP, respectively) of the transcription factor CCAAT
enhancer binding protein beta (C/EBPβ) are expressed
from a single intronless Cebpb gene by alternative translation
initiation. Isoform expression is sensitive to mammalian
target of rapamycin (mTOR)-mediated activation of
the translation initiation machinery and relayed through an
upstream open reading frame (uORF) on the C/EBPβ
mRNA. The truncated C/EBPβ LIP, initiated by high
mTOR activity, has been implied in neoplasia, but it was
never shown whether endogenous C/EBPβ LIP may function
as an oncogene. In this study, we examined spontaneous
tumor formation in C/EBPβ knockin mice that constitutively
express only the C/EBPβ LIP isoform from its
own locus. Our data show that deregulated C/EBPβ LIP
predisposes to oncogenesis in many tissues. Gene expression
profiling suggests that C/EBPβ LIP supports a protumorigenic
microenvironment, resistance to apoptosis,
and alteration of cytokine/chemokine expression. The results
imply that enhanced translation reinitiation of C/
EBPβ LIP promotes tumorigenesis. Accordingly, pharmacological
restriction of mTOR function might be a therapeutic
option in tumorigenesis that involves enhanced expression
of the truncated C/EBPβ LIP isoform.

overall_design: A cohort of  C/EBPb LIP heterozygous (+/L) and wild type (+/+) mice were kept over 25 months and animals showing palpable lymphoma were sacrificed. The lymphoma developed spontaneously.  For each genotype, 5 lymphoma were used for RNA preparation and gene expression profiling analysis.

first: Jeske

last: Smink

first: Christoph

last: Loddenkemper

first: Karin

last: Zimmermann

first: Cornelia

last: Rudolph

first: Marina

last: Scheller

first: Doris

last: Steinemann

first: Ulf

last: Leser

first: Brigitte

last: Schlegelberger

first: Harald

last: Stein

first: Achim

last: Leutz


title: Mutations in G protein beta subunits promote transformation and kinase inhibitor resistance.

status: Public on Dec 07 2014

city: Boston

first: Andrew

last: Lane

address: 450 Brookline Ave

institute: Dana-Farber Cancer Institute

summary: Activating mutations of G protein alpha subunits (Ga) occur in 4-5% of all human cancers1 but oncogenic alterations in beta subunits (Gb) have not been defined.  Here we demonstrate that recurrent mutations in the Gb proteins GNB1 and GNB2 confer cytokine-independent growth and activate canonical G protein signaling.  Multiple mutations in GNB1 affect the protein interface that binds Ga subunits as well as downstream effectors, and disrupt Ga-Gbg interactions.  Different mutations in Gb proteins clustered to some extent based on lineage; for example, all eleven GNB1 K57 mutations were in myeloid neoplasms while 6 of 7 GNB1 I80 mutations were in B cell neoplasms.  Expression of patient-derived GNB1 alleles in Cdkn2a-deficient bone marrow followed by transplantation resulted in either myeloid or B cell malignancies.  In vivo treatment with the dual PI3K/mTOR inhibitor BEZ235 suppressed GNB1-induced signaling and markedly increased survival.  In several human tumors, GNB1 mutations co-occurred with oncogenic kinase alterations, including BCR/ABL, JAK2 V617F and BRAF V600K.  Co-expression of patient-derived GNB1 alleles with these mutant kinases resulted in inhibitor resistance in each context.  Thus, GNB1 and GNB2 mutations confer transformed and resistance phenotypes across a range of human tumors and may be targetable with inhibitors of G protein signaling.

overall_design: The GM-CSF dependent human cell line TF-1 was transduced with a retrovirus expressing GNB1 K89E or empty vector. RNA was extracted from cells 12 hours after withdrawal of GM-CSF and from cells maintained in GM-CSF. Biological triplicates of each condition were performed. Gene expression differences were calculated between the four conditions.

first: Akinori

last: Yoda

first: Bjoern

last: Chapuy


title: Adventitial tertiary lymphoid organs in AAA are a potential source of miRNAs as biomarkers

status: Public on Nov 21 2014

city: Lille

first: David

last: Hot

address: 1 rue du professeur Calmette

department: Center for Infection and Immunity of Lille

institute: Institut Pasteur de Lille

summary:
This study aims to identify and characterize miRNA expression inATLOs isolated by laser microdissection from human AAA biopsy samples.
The aim of this study was to profile (with microarray technology) miRNAs in ATLOs (Adventitial tertiary lymphoid organs), isolated by laser capture microdissection (LCM). Smooth muscle cells (SMCs) isolated from control non-aneurysmal aortas were the control group according to which data were normalized. ATLOs were microdissected (mean 13.5mm2)  from two different biopsy samples of human abdominal aortic aneurysm. An area enriched in smooth muscle cells was microdissected from two biopsy samples of non aneurysmal abdominal aortas. Each microdissected samples were analyzed independently on microarray.

overall_design: ATLOs located in human abdominal aneurysmal aortas were each analyzed in duplicate (each isolated from different human donors of abdominal aortic aneurysm). Data were normalized with smooth muscle cells isolated from human abdominal non aneurysmal aortas.

first: Rafaëlle

last: Spear

first: Renaud

last: Blervaque


title: Testis expression in Mus musculus domesticus x Mus musculus musculus hybrid zone mice

status: Public on Dec 04 2014

city: Ploen

first: Leslie

last: Turner

address: August-Thienemann Str 2

department: Evolutionary Genetics

institute: Max Planck Institute for Evolutionary Biology

summary: We collected whole genome testis expression data from hybrid zone mice. We integrated GWAS mapping of testis expression traits and low testis weight to gain insight into the genetic basis of hybrid male sterility.

sample_organism: Mus musculus musculus x M. m. domesticus

overall_design: Gene expression was measured in whole testis from males aged 62-86 days. Samples include 190 first generation lab-bred male offspring of wild-caught mice from the Mus musculus musculus - M. m. domesticus hybrid zone.


title: The expression pattern of microRNAs during the overexpression of cofilin1

city: Taipei

first: Liang-Ting

last: Lin

address: No.155, Sec.2, Li-Nong St., Beitou District

country: Taiwan

institute: National Yang-Ming University

summary: To screen who are the microRNAs that were regulated during the overexpression of actin cytoskeleton depolymerizing protein cofilin1, and we further examine whether the modulation of the key regulator would result in changes of cellular migration or invasion

overall_design: The tetracycline-induced overexpression of cofilin1 was conducted in HCOXP (H1299 cofilin overexpressed) cells and parental H1299 cells by doxycycline treament. The cells were treated with designated time intervals (2 and 7 days).

first: Cheng-Han

last: Tsai

first: Yi-Jang

last: Lee


title: Laser-microdissected tissue from Tg2576 and APPPS1 plaque-depositing mouse model of Alzheimer's disease

status: Public on Nov 04 2014

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

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

overall_design: Refer to individual Series


title: Expression profiling of laser-microdissected tissue from Tg2576 plaque-depositing mouse model of Alzheimer's disease

summary: Amyloid-ß (Aß) plaques are pathological hallmarks of Alzheimer disease. However, the precise neuropathological changes that occur in brain in response to amyloid deposition are largely unknown. To study the molecular mechanism(s) responsible for Aß-mediated neuropathology, we performed a gene expression analysis on laser-microdissected brain tissue of Tg2576 mice compared to their littermate controls.

overall_design: 4 samples; 2 biological replicates of each condition = 2 transgenic versus 2 non-transgenic mice; double amplification of total RNA; only Cy3; no dye-swaps

first: Sandra

last: Pereson

first: Dieter

last: Deforce

first: Christine

last: Van Broeckhoven

first: Samir

last: Kumar-Singh


title: Expression profiling of laser-microdissected tissue from APPPS1 plaque-depositing mouse model of Alzheimer's disease

summary: Amyloid-ß (Aß) plaques are pathological hallmarks of Alzheimer disease. However, the precise neuropathological changes that occur in brain in response to amyloid deposition are largely unknown. To study the molecular mechanism(s) responsible for Aß-mediated neuropathology, we performed a gene expression analysis on frontal neocortical brain tissue of APPPS1 mice compared to their littermate controls.

overall_design: 4 samples; 2 biological replicates of each condition = 2 transgenic versus 2 non-transgenic mice; no amplification of total RNA; Cy3/Cy5 dye-swap design

first: Mathias

last: Jucker


title: Transcriptional analysis of follistatin influence on C2C12 mice myoblasts differentiation

status: Public on Oct 31 2014

city: Warsaw

first: Zofia

last: Wicik

state: mazovia

address: Pawinskiego 5

department: Department of Human Epigenetics

country: Poland

institute: Mossakowski Medical Research Center

summary:
Background: Follistatin (FS) is an activin-binding glycoprotein, known for its antagonistic action on the TGF-β super-family of cytokines. It has ability to prevent muscle atrophy and to stimulate muscle growth through binding of myostatin (GDF8). FS does not cause these changes only by inhibition of GDF8 but this mechanism is still not well elucidated. In order to identify GDF8-dependent and GDF8-independent action of FS, we performed comprehensive transcriptomic analysis of differentiating C2C12 mouse myoblasts.
Results: To evaluate influence of FS-288 (200ng/ml) on differentiating C2C12 myoblasts was used immunofluorescence analysis of MyHC protein expression in the culture and counting of the number and type of myotubes. Differentiating myoblasts treated with FS showed increase in number and size of myotubes. Microarray studies performed by us identified 30 genes oppositely regulated by FS and GDF8. Analyses of the transcriptomic profiles showed that FS has highly significant influence, associated with GDF8 binding, on the regulation of cell cycle, transport processes, cell communication, cell adhesion, cell motion, developmental processes and binding functions. The signalling pathways that may play a primary role in the myogenesis stimulation by FS are associated with TGF-β, Delta-Notch and Wnt signalling pathways, integrin and actin cytoskeleton signalling and adipogenesis regulation. Changes in expression of Hgf, Sort1, Trdn, Stmn2, Hdac1 genes, significantly involved in the process of myoblasts differentiation were validated with Real-Time PCR method.
Conclusions: Our results implicate which aspects of transcriptional regulation of myogenesis process by FS could have significant and protective influence. We have shown that FS activity is associated not only with GDF8 binding but also with inhibited expression of genes involved in TGF-β signalling and by regulating of genes associated with vesicle transport apoptosis signalling pathway, inflammatory pathways and adipogenesis expression. Our analysis showed that follistatin GDF8-independent on differentiating myotubes involves regulation of localization processes, cell-matrix adhesion, mRNA processing, apoptosis, fatty acid metabolic processes, SNAP receptor activity functions and partial regulation of transcription processes. These results give a new and complete image of the follistatin role in the muscle cell differentiation and indicate target genes for FS which in the future may be a good therapeutic approach.

overall_design: After scanning of hybridized microarrays, quantitation of slide images were performed using Feature Extraction Software 10.7.3.1 (Agilent) using default parameters. Normalized raw data was exported to GeneSpring GX 11.0.5 (Agilent, Santa Clara, CA). For identification of genes significantly altered in cells treated with FSl compared with untreated cells. T total detected entities were filtered by flags (present, marginal) and error (coefficient of variation: CV < 50.0 percent) to remove very low signal entities and to select reproducible signal values of entities among the replicated experiments, respectively. In statistical analysis, separated for experiment with myoblasts treated with FS(FS vs. CTRL 1-4) was used t-test unpaired (p < 0.05) with multiple testing correction: Benjamini-Hochberg <0.05, all significant changes over fold change 1.6 were selected. Analysis of GO, GSEA and signaling pathway was carried out using GeneSpring GX 12 (Agilent) and the DAVID, KEEG and PANTHER Classification System (p<0.01). In the analysis of signaling pathways using GeneSpring GX 12 (Agilent) and Ariadne Pathway Studio.

first: Michał

last: Jank

first: Tomasz

last: Motyl


title: Gene expression in whole mouse E9.0 embryos comparing wt with Arid3b-null embryos

status: Public on Oct 07 2014

city: Madrid

first: Juan Jose

last: Sanz-Ezquerro

address: Darwin, 3

department: Biologia Molecular y Celular

institute: Centro Nacional dde Biotecnologia

summary: We have analysed and compared mRNA expression between wt embryos and embryos deficient for Arid3b at E9.0 days of development, with the aim of identifying differentially expressed genes that could give us a clue to the functions of Arid3b during development.

overall_design: Four wild-type and four mutant samples, consisting of 3-4 embryos each, were used.

first: Verónica

last: Uribe

first: Juan


title: Regulation of neuronal gene expression and survival by basal NMDA receptor activity: a role for Histone Deacetylase 4

status: Public on Oct 23 2014

city: South San Francisco

first: Josh

last: Kaminker

address: 1 DNA Way

department: Bioinformatics and Computational Biology

institute: Genentech

summary: Gene expression analysisis of NR2A and NR2B containing NMDA receptors after treatment with AP5, NVP-AAM077 and Ro25-6981

overall_design: 4 conditions, vehicle, AP5, Ro25, and NVP, 4-5 replicates of each sample

first: Joshua

first: Yelin

last: Chen

first: Morgan

last: Sheng

first: Yuanyuan

last: Wang

first: Modrusan

last: Zora


title: Epigenetic regulation of gene expression is instructed by promoter sequence and refined by developmental progression [expression]

status: Public on Aug 31 2014

city: Research Triangle Park

first: Deepak

last: Mav

state: NC

address: 2 Davis Drive

institute: Sciome LLC

summary: A large body of literature suggests that local features of chromatin are crucial in determining functional properties of underlying DNA.  The extent to which DNA sequence plays an active role in the establishment and maintenance of patterns of histone and DNA modification at promoters in cells and tissues in an adult animal remains poorly understood.  Likewise, whether passage through development is required for refinement of transcriptional states and chromatin marks characteristic of fully differentiated adult cells remains unclear.  Here we undertook analysis of gene expression along with the genomic distribution of DNA methylation and a set of histone marks in primary tissues derived from different primordial germ layers in adult mice.  We find that promoter CpG content correlated strongly with specific repressive mechanisms.  Likewise, RNA polymerase II occupancy and active histone marks were omnipresent on CpG rich promoters regardless of transcriptional output and of cell type.  However, these same chromatin features cleanly demarcate transcriptional activity on promoters with low CpG content.  While these observations imply an instructive role for DNA sequence in establishment and maintenance of epigenetic states, experimental evidence presented here also suggests an additional role for development in refining these features at individual promoters.

overall_design: Gene expression in B cells and liver was measured using Agilent Whole Mouse Genome 4x44 multiplex format oligo arrays.

first: Ruifang

last: Li

first: Paul

last: Wade

first: Ruchir

last: Shah


title: Identification of a novel biomarker serum miRNA from the patients with colorectal cancer (CRC).

status: Public on Oct 02 2014

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

summary: Serum microRNAs (miRNAs) have been shown to have a potential for cancer diagnosis lately. The main objective of this study is to identify a novel biomarker serum miRNA from the patients with colorectal cancer (CRC). Microarray analysis of miRNA expression was performed using paired pre- and post- operative serum from 10 CRC patients. Two miRNAs (let-7a, miR-199a-3p) decreased significantly in the post-operative serum when compared to pre-operative serum (P=0.015 and 0.029, respectively).

overall_design: Microarrays were performed for paired pre- and post- operative serum from 10 CRC patients.

first: Ryoji

last: Nonaka

first: Hirofumi

last: Yamamoto


title: Epigenetic regulation of gene expression is instructed by promoter sequence and refined by developmental progression.

type: Methylation profiling by genome tiling array

type: Genome binding/occupancy profiling by genome tiling array


title: Gene expression analysis in adoptive T cell immunotherapy (ACT)

status: Public on Aug 25 2014

city: Kisarazu

first: Osamu

last: Ohara

state: Chiba

address: 2-6-7 Kazusa-Kamatari

department: Technology Development

institute: Kazusa DNA Research Institute

summary: To understand the global effector immune responses in the tumor induced by ACT, we performed a gene chip analysis using B16 melanoma-pmel-1 TCR transgenic T cells model.

overall_design: Gene expression was measured in the tumor from untreated or ACT mice on day 1, 3, 5 and 7. Gene expression was also measured in the tumor on day 3, 5 and 7 from ACT mice with anti-IFNg or control Rat IgG antibodies treatment.

first: Kazuhiro

last: Kakimi

first: Hirokazu

last: Matsushita


title: Expression data from 786-O renal cell cancer cells treated with pentamidine

status: Public on Aug 05 2014

first: Manoj

last: Bhasin

address: 330 Brookline Avenue  RN 380E

institute: Beth Israel Deaconess Medical Center

summary:
While early stages of clear cell renal cell carcinoma (ccRCC) are curable, survival outcome for metastatic ccRCC remains poor. The purpose of the current study was to apply a new individualized bioinformatics analysis (IBA) strategy to these transcriptome data in conjunction with Gene Set Enrichment Analysis of the Connectivity Map (C-MAP) database to identify and reposition FDA-approved drugs for anti-cancer therapy. We demonstrated that one of the drugs predicted to revert the RCC gene signature towards normal kidney, pentamidine, is effective against RCC cells in culture and in a RCC xenograft model. Most importantly, pentamidine slows tumor growth in the 786-O human ccRCC xenograft mouse model. To determine which genes are regulated by pentamidine in a human RCC cell line, 786-O, we treated these cells with pentamidine and performed transcriptional profiling analysis.
We used microarrays to determine the set of genes regulated by pentamidine in 786-O renal cell cancer cells.

overall_design: Total RNA was isolated from 786-O cells treated with 25 μM pentamidine or vehicle control (DMSO) for 6 hours and hybridized to Affymetrix microarrays.

first: Towia

last: Libermann


title: Gene expression changes in mouse pancreatic cancer xenograft induced by exposure to enriched environment

city: Shanghai

first: Yu

last: Gan

address: 25/Ln. 2200 Xietu Road

institute: Shanghai Cancer Institute

summary: Previous studies reported that mice living in an enriched environment (EE) showed reduced growth of melanoma, colon and breast tumors. Our study extended the potential anti-tumor effect of EE exposure to pancreatic cancer, and firstly provided evidence demonstrating that EE exposure significantly inhibits tumor growth in a syngeneic murine model of pancreatic cancer. To further investigate the mechanisms underlying the EE-induced pancreatic tumor inhibition, we analyzed the gene expression changes in pancreatic tumor xenograft using an integrative transcriptomic and proteomic approach. Our results found that EE largely decreased the expression of genes associated with mitochondrial function at transcriptional level in pancreatic tumor, suggesting mitochondrial dysfunction in tumor cells may play a critical role in EE-induced anti-tumor phenotype.

overall_design: Three-week-old C57BL/6 mice were randomized to live in either enriched environment or standard environment conditions. Mice from both groups were given subcutaneous injection of Panc02 murine pancreatic cancer cells (6 × 105 cells per mouse) and lived in their respective homes for 5 additional weeks. Pooled RNA samples extracted from Panc02 tumors (6 mice for each group) were then subjected to Agilent-014868 Whole Mouse Genome 4☓44k Microarray analyses.

first: Hong

last: Tu

first: Guohua


title: Transcription profile of FBL-knock down ES cells

status: Public on Aug 01 2014

city: Tsukuba

first: Akira

last: Kurisaki

address: Tsukuba central 4, 1-1-1, Higashi

department: Research Center for Stem Cell Engineering

institute: National Institute of Advanced Industrial Science and Technology

summary: Pluripotent stem cells have been shown to have unique nuclear properties, e.g., hyperdynamic chromatin and large, condensed nucleoli. However, the contribution of the latter unique nucleolar character to pluripotency has not been well understood. Here, we show fibrillarin (FBL), a critical methyltransferase for ribosomal RNA (rRNA) processing in nucleoli, as one of the proteins highly expressed in pluripotent embryonic stem (ES) cells. Stable expression of FBL in ES cells prolonged the pluripotent state of mouse ES cells cultured in the absence of leukemia inhibitory factor (LIF). Analyses using deletion mutants and a point mutant revealed that the methyltransferase activity of FBL regulates stem cell pluripotency. Knock down of this gene led to significant delays in rRNA processing, growth inhibition, and apoptosis in mouse ES cells. Interestingly, both partial knock down of FBL and treatment with actinomycin D, an inhibitor for rRNA synthesis, induced the expression of differentiation markers in the presence of LIF and promoted stem cell differentiation into neuronal lineages. Moreover, we identified p53 signaling as the regulatory pathway for pluripotency and differentiation of ES cells. These results suggest that proper activity of rRNA production in nucleoli is a novel factor for the regulation of pluripotency and differentiation ability of ES cells.

overall_design: Tc-inducible FBL-knock down ES cells were cultured for 2 days with or without Tc in the presence of LIF. These 2 conditions were analysed transcription profile.

first: Kanako

last: Watanabe-Susaki

first: Kei

last: Enomoto

first: Kyoko

last: Miwata

first: Hiromu

last: Sugino

first: Makoto

last: Asashima


title: Identifying conserved and novel miRNAs in developing seeds of Brassica napus using deep sequencing [small RNA-seq]

city: Porto Alegre

first: Rogerio

last: Margis

state: RS

address: Av. Bento Goncalves 9500

department: Centro de Biotecnologia

institute: Universidade Federal do Rio Grande do Sul

type: Non-coding RNA profiling by high throughput sequencing

summary: MicroRNAs (miRNAs) are important post-transcriptional regulators of plant development and seed formation. In Brassica napus, an important edible oil crop, valuable lipids are synthesized and stored in specific seed tissues during embryogenesis. The miRNA transcriptome of B. napus is currently poorly characterized, especially at different seed developmental stages. This work aims to describe the miRNAome of developing seeds of B. napus by identifying plant-conserved and novel miRNAs and comparing miRNA abundance in mature versus developing seeds. A total of 62 miRNA families were detected through a computational analysis of a large number of reads obtained from deep sequencing two small RNA and two RNA-seq libraries of (i) pooled immature developing stages and (ii) mature B. napus seeds. Among these miRNA families, 17 families are currently known to exist in B. napus; additionally, 32 families not reported in B. napus but conserved in other plant species were identified by alignment with known plant mature miRNAs. The contigs from the assembled mRNA-seq data allowed for a search for putative new precursors and led to the identification of 13 novel miRNA families. Differential expression between the libraries was determined through a statistical analysis of normalized miRNA reads and revealed several miRNAs and isomiRNAs that were more abundant during the developing stages. The predicted miRNA target genes encode a broad range of proteins related to seed development and energy storage. This work presents a comprehensive study of the miRNA transcriptome of B. napus seeds and will provide a basis for future research on more targeted studies of individual miRNAs and their functions in embryogenesis, seed maturation and lipid accumulation in B. napus.

overall_design: microRNA profiles in 2 different seed libraries (mature seeds and a pool of developing seed stages) of Brassica napus by deep sequencing (Illumina HiSeq2000).

first: Ana

last: Körbes

first: Frank

middle: F

last: Guzman

first: Rogério