title: Primary Mammary Epithelial Cells: Control vs 1023-Treated

city: Salt Lake City

first: Bryan

last: Welm

state: UT

address: 2000 Circle of Hope Drive

department: Oncological Science

institute: University of Utah, Huntsman Cancer Institute

summary: Gene expression profiling of primary mammary epithelial cells treated for 72 hours with compound 1023 compared to DMSO.  Goal was to determine genes differntially regulated by treatment with the novel compound, 1023.

overall_design: Two-condition experiment, DMSO vs. 1023. Biological replicates: 2 control replicates, 2 1023 replicates.

first: Kaitlin

last: Basham

first: Collin

last: Kieffer

first: Dawne

last: Shelton

first: Christoper

last: Leonard

first: Vasudev

middle: R

last: Bhonde

first: Hariprasad

last: Vankayalapati

first: Brett

last: Milash

first: David

last: Bearss

first: Ryan

last: Looper


title: Effect of Exportin-5 expression on Mouse fibroblasts in cell cycle re-entry phase

status: Public on Jan 01 2013

city: Freiburg

first: Yoko

middle: Fukuda

last: Yuzawa

address: Stübeweg 51

country: Germany

institute: Max-Planck Institute of Immunobiology

summary: To analyze the effect of Exportin-5 expression on the MEF cells in cell cycle re-entry phase, we have employed whole genome microarray expression profiling on the MEF cells in cell cycle re-entry phase with and without down regulation of Exportin-5 gene.

overall_design: Mouse MEF cells were transfected with 60nM of siRNA targeting either Exportin-5 or negative control, and incubated for 12 hours. After incubation, cells were starved with DMEM containing 0.2% FCS for 48 hours and re-fed with DMEM containing 20%FCS for 24 hours, along with second siRNA transfection. Two independant expreiments were preformed.

first: Taro

last: Fukao

first: Yuka

last: Watanabe


title: Transcriptome Analysis of Renal Ischemia/Reperfusion Injury and its Modulation by Ischemic Pre-Conditioning or Hemin treatment

status: Public on Dec 10 2012

city: São Paulo

first: Hatylas

last: Azevedo

state: Sao Paulo

address: Doutor Arnaldo Avenue, 455

department: Pediatrics

country: Brazil

institute: University of São Paulo

summary: We examined, through an oligonucleotide microarray protocol, the renal differential transcriptome profiles of mices submitted to IRI, IPC and Hemin treatment. After identifying the profiles of differentially expressed genes observed for each comparison, we carried out functional enrichment analysis to reveal transcripts putatively involved in potential relevant biological processes and signaling pathways. The most relevant enriched biological processes found in these comparisons were stress, inflammation, apoptosis, pathways in cancer, differentiation, angiogenesis, focal adhesion, ECM-receptor interaction, ion transport, angiogenesis, mitosis and cell cycle, inflammatory response, olfactory transduction and regulation of actin cytoskeleton. In addition, the most important overrepresented pathways were MAPK, ErbB, JAK/STAT, Toll and Nod like receptors, Angiotensin II, Arachidonic acid metabolism, Wnt and coagulation cascade. Also, new insights were gained about the underlying protection mechanisms against renal IRI promoted by IPC and Hemin treatment. Venn diagram analysis allowed us to uncover common and exclusively differentially expressed genes between these two protective maneuvers, underscoring potential common and exclusive biological functions regulated in each case. In summary, IPC exclusively regulated the expression of genes belonging to stress, protein modification and apoptosis, highlighting the role of IPC in controlling exacerbated stress response. Treatment with the Hmox1 inducer Hemin, in turn, exclusively regulated the expression of genes associated with cell differentiation, metabolic pathways, cell cycle, mitosis, development, regulation of actin cytoskeleton and arachidonic acid metabolism, suggesting a pleiotropic effect for Hemin.

overall_design: According to surgery and treatment procedures, mices were divided into five groups: Control, Ischemia-reperfusion injury (IRI), animals pre-treated with Hemin followed by IRI (Hemin + IRI), animals only treated with Hemin (Hemin) and animals pre-conditioned and submitted to IRI (IPC+IRI). To identify the consequences of IRI, Hemin treatment or IPC in gene expression profiles, the following statistical comparisons were made between the groups: IRI vs Control, IPC+IRI vs Control, IPC+IRI vs IRI, IRI+Hemin vs IRI and Hemin vs Control.

first: Matheus

last: Correa-Costa

first: Hátylas

first: Mariane

middle: T

last: Amano

first: Giselle

middle: M

last: Gonçalves

first: Meire

middle: I

last: Hyane

first: Marcos

middle: A

last: Cenedeze

first: Guilherme

last: Renesto

first: Alvaro

middle: P

last: Silva Filho

first: Carlos

last: Moreira-Filho

first: Niels

middle: O

last: Camara


title: Transcriptional signatures of thymic epithelial cells with distinct Meis1 expression levels

status: Public on Nov 30 2012

city: Noda-shi

first: Ryo

last: Goitsuka

state: Chiba

address: 2669 Yamazaki

department: Division of Development & Aging

country: Japan

institute: Research Institute for Biological Sciences

summary: Analysis of thymic epithelial cells with distinct Meis1 gene expression levels using Meis1-EGFP reporter mice. Meis1 is a TALE class homeodomain transcription factor that critically regulates numerous embryonic developmental processes. Results provide insight into the role of Meis1 in the maintenance of postnatal thymic epithelial cells.

overall_design: Gene expression in CD45- EpCAM+ thymic epithelial cells with distinct Meis1 expression levels (Meis1high, Meis1low and Meis1-) was measured by using Meis1-EGFP BAC-transgenic reporter mice. Two independent experiments (pools of 6 mice; 2 pools per genotype) were performed.

first: Takehiro

last: Hirayama


title: Meis1 deficiency effect on thymic epithelial cells

summary: Analysis of thymic epithelial cells lacking Meis1 gene using K14-CreERT2 Meis1fl/fl mice. Meis1 is a TALE class homeodomain transcription factor that critically regulates numerous embryonic developmental processes. Results provide insight into the role of Meis1 in the maintenance of postnatal thymic epithelial cells.

overall_design: Meis1-regulated gene expression in CD45- EpCAM+ mouse thymic epithelial cells was measured at 4 days after the induction of Meis1 deletion.  Two independent experiments (pools of 6 mice; 2 pools per genotype) were performed.


title: Biomarkers of residual disease, disseminated tumor cells, and metastases in the MMTV-PyMT breast cancer model

status: Public on Jan 18 2013

city: South San Francisco

first: Zhaoshi

last: Jiang

state: CA

address: 1 DNA Way

department: Bioinformatics

country: USA

institute: Genentech, Inc

summary: Gene expression profiling of disseminated tumor cells in lung, lung metastatses and residual tumor cells in the MMTV-PyMT breast cancer model.

overall_design: Profiling gene expression change between disseminated tumor cells, lung metastases and residual tumor cells from the MMTV-PyMT breast cancer model.

first: Hosein

last: Kouros-Mehr

first: Erica

last: Jackson

first: Zora

last: Modrusan


title: The role of Meis1 in the maintenance of postnatal thymic epithelial cells

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

overall_design: Refer to individual Series


title: Comparison of microarray platforms for measuring differential microRNA expression (Agilent data)

status: Public on Nov 26 2012

city: Milan

first: Loris

last: De Cecco

address: via Venezian 1

country: Italy

institute: IRCSS Istituto Nazionale Tumori

summary:
Microarray technology applied to miRNA profiling is a promising tool in many research fields. At present, only few studies have addressed intra- and inter-platform reproducibility by using tissues/cell-lines of different origin to maximize differences in miRNA content. Although the approach might provide an useful system to address technical issues since, for sure, a huge modulation can be evaluated, it  does not reflect the common experimental practice in laboratory. As a matter of fact, from all these studies it is not know how concordant can be expected the results obtained by different platforms starting from biological meaningful specimens.  We investigated the issue of inter-platform reproducibility using four miRNA microarray platforms and nine paired tumor/normal colon tissues.
The tumor and the normal counter-part samples were prospectively collected from 9 patients who underwent surgical resection at the INT-MI. Neoplastic samples were obtained from the central area of the neoplasia, avoiding to select necrotic material or transition zones with healthy mucosa. Samples of colonic healthy mucosa were resected at least 20 centimeters far from the neoplasia and distant from the surgical resection margins. Tissue samples were stored in liquid nitrogen until RNA extraction. Total RNA was extracted from 10–20 mg of tumor samples and from 30–40 mg of normal samples.

overall_design: Nine paired tumor/normal colon tissues on Agilent human miRNA Microarray.

first: Maurizio

last: Callari


title: Hepatic transcriptome in wild-type and LXR-deficient mice

status: Public on Nov 07 2012

city: Villenave d'Ornon

first: Pascal

middle: GP

last: Martin

address: 71 avenue Edouard Bourlaux

department: UMR1332 BFP

country: France

institute: INRAE

summary: LXR is a transcription factor. Two isoforms exist in mice (alpha and beta). They are both expressed in the liver. We examined the role of LXR by obtaining gene expression profiles from the livers of wild-type and LXR-/- mice from the same genetic background.

overall_design: Liver gene expression was measured from male mice (5 mice/group) of genotypes wild-type and LXR-/- on a mixed Sv129/C57Bl6J background (Repa et al. , 2000, Science, 289(5484):1524-9; Cummins et al., 2006, J Clin Invest,116(7):1902-12) fed for 7 weeks a normal diet (ND) or a Western diet (WD).

first: Simon

last: Ducheix

first: Normand

last: Podechard

first: Arnaud

last: Polizzi

first: Aurélien

last: Pommier

first: Jean-Marc

last: Lobaccaro

middle: G

first: Hervé

last: Guillou


title: Differential microRNA expression profiles in Retinoblastoma serum

status: Public on Oct 31 2012

city: Bangalore

first: madavan

last: vasudevan

state: Karnataka

address: Kasturi Nagar

country: India

institute: Theomics International Private Limited

summary: Retinoblastoma (RB) is a malignant intraocular neoplasm occurs mostly in children. The malignancy caused due to altered miRNA expression in cancer tumors and circulating body fluids has been reported in several cancers. The aberrantly expressed microRNAs are useful for diagnosis and prognosticating the tumors. Circulating miRNAs have been identified as potential markers in neoplastic and non -neoplastic diseases. The aim of the study involves identifying microRNA signatures of serum of Retinoblastoma and possible use of differential miRNA as unique biomarker for RB.

overall_design: Agilent Single Color Whole miRNA microarray: 14 advanced stage Retinoblastoma Serum (pooled) Vs 14 Non-Retinoblastoma Serum (pooled) samples

first: Madhu

last: Beta

first: Nalini

last: Venkatesan

first: Vikas

last: Khetan

first: Madavan

last: Vasudevan

first: Krishnakumar

last: Subramanian


title: The small RNA PsrR1 affects oligomerization of photosystem I by post-transcriptional repression of psaL in Synechocystis sp. PCC6803

status: Public on Oct 10 2012

first: Jens

last: Georg

address: Schänzlestr. 1

institute: University of Freiburg

summary: Comparison of gene expression of WT Synechocystis cells with cells overexpressing the sRNA PsrR1 in order to detect direct targets of the sRNA PsrR1.

overall_design: We monitored gene expression of an Synechocystis PCC6083 overexpressor strain (psrR1+) (Mitschke et al., 2011) harboring a self-replicating plasmid from which PsrR1 is transcribed under control of the copper responsive PpetJ promoter and a control strain (WT) harboring an empty plasmid 0h and 24 h after copper depletion. For the timepoint (0h) we sampled biological replicates and for timepoint (24h) we sampled biological triplicates.

first: Dennis

last: Dienst

first: Nils

last: Schürgers

first: Ekaterina

last: Kuchmina

first: Thomas

last: Wallner

first: Heiko

last: Lokstein

first: Wolfgang

last: Hess

first: Annegret

last: Wilde


title: SM015 - Infection with SARS MA15 of C57BL/6J mice and Tnfrsf1a/1b knockouts

status: Public on Sep 13 2012

city: Seattle

first: Michael

last: Katze

state: WA

address: Rosen Building 960 Republican St.

department: Microbiology

institute: University of Washington

summary: Comparing the host response of C57BL/6J mice to Tnfrsf1a/1b knockouts in the same strain of mice.

overall_design: Groups of 10-week-old C57BL/6 mice or Tnfrsf1a/1b knockout mice were infected with SARS MA15 at a dose of 10^5 PFU or mock infected. Mice were euthanized on days 4 and 7 post-infection to measure virus load and isolate samples for measurement of virus load, lung pathology, transcriptional analysis and proteomics analysis. Mock-infected animals were also harvested at each time point. Mice were weighed every 24 hours to measure general disease progression and any mouse approaching 30% weight loss was euthanized.

first: Ralph

last: Baric

first: Lisa

last: Gralinski

first: Lynn

last: Law

first: Jean

last: Chang


title: Gene expression profiling of the whole mouse brain using transcriptome tomography

status: Public on Sep 21 2012

city: Wako-shi

first: Yuko

last: Okamura-Oho

state: Saitama

address: 2-1, Hirosawa

institute: RIKEN

summary: We developed a novel framework to assess comprehensive endogenous gene expression maps in a broad and isotropic 3D-anatomical context using a relatively small number of original data points: transcriptome tomography. Using this method, we produced a dataset of gene expression maps of the whole mouse brain, computationally reconstructed from fraction data.

overall_design: A total of 61 fraction samples obtained with body axes-based slicing preparation conjugated with anatomical image acquisition were analysed. There are two sets of body axes-based preparation series: the S series, composed of 9 fractions/ C of 13 fractions/ H of 6 fractions , and the So series, composed of 10 fractions/ Co of 16 fractions/ Ho of 7 fractions.

first: Hideo

last: Yokota


title: Expression profiling of ovarian cancer cell lines

status: Public on Oct 12 2012

city: London

first: Ed

last: Curry

address: Hammersmith Hospital, Du Cane Road

country: United Kingdom

institute: Imperial College London

summary: Paired platinum-sensitive & platinum-resistant cell lines PEO1 and PEO4 (respectively) were derived from the same patient. Cell line cultures were profiled with the HT-HGU133a GeneChip to investigate chemotherapy resistance related expression of genes marked with different histone modifications in a primary ovarian tumour (clinical data for the primary ovarian tumour is available as Series supplementary file).

overall_design: 4 replicates of each of the PEO1 and PEO4 cell line were profiled using the HT-HGU133a GeneChip

first: Edward

middle: W

first: Euan

last: Stronach


title: SM020 - Infection with SARS MA15 of C57BL/6J mice and KEPI (ppp1r14c) knockouts

summary: Comparing the host response of C57BL/6J mice to KEPI (ppp1r14c) knockouts in the same strain of mice.

overall_design: Groups of 10-week-old C57BL/6 mice or KEPI (ppp1r14c) knockout mice were infected with SARS MA15 at a dose of 10^5 PFU or mock infected. Mice were euthanized on days 4 and 7 post-infection to measure virus load and isolate samples for measurement of virus load, lung pathology, transcriptional analysis and proteomics analysis. Mock-infected animals were also harvested at each time point. Mice were weighed every 24 hours to measure general disease progression and any mouse approaching 30% weight loss was euthanized.


title: Runx1 is a tumor suppressor gene in the mouse gastrointestinal tract

city: Amsterdam

first: Daoud

last: Sie

address: De Boelelaan 1117

department: Pathology

country: Netherlands

institute: Vrije Universiteit Medical Center

summary: The Runx1 transcription factor plays an important role in tissue homeostasis through its effects on stem/progenitor cell populations and differentiation. The effect of Runx1 on epithelial differentiation of the secretory cell lineage of the colon was recently demonstrated. This study aimed to examine the role of Runx1 in tumor development in epithelial cells of the gastrointestinal tract. Conditional knockout mice were generated that lacked Runx1 expression in epithelial cells of the GI tract. These mice were crossed onto the ApcMin background, sacrificed, and their intestinal tumor phenotypes were compared with ApcMin Runx1 wildtype control mice. Apc-wildtype Runx1-mutant mice were also examined for tumor development. Colons from Runx1 knockout and wildtype mice were used for genome-wide mRNA expression analyses followed by gene-specific quantitative RT-PCR of whole colon and colon epithelium, to identify Runx1 target genes. Runx1 deficiency in intestinal epithelial cells significantly enhanced tumorigenesis in ApcMin mice. Notably, epithelial Runx1 deficiency in Apc-wildtype mice was sufficient to cause tumor development. Absence of Runx1 was associated with global changes in expression of genes involved in inflammation and intestinal metabolism, and with gene sets indicative of metastatic phenotype and poor prognosis. Gene-specific analysis of Runx1 deficient colon epithelium revealed increased expression of genes linked to an expansion of the stem/progenitor cell population. These results identify Runx1 as a novel tumor suppressor gene for gastrointestinal tumors and support a role for Runx1 in maintaining the balance between the intestinal stem/progenitor cell population and epithelial differentiation of the GI tract.

overall_design: A total of 8 colon tissue RNA samples were analyzed, comprising 4 colon samples from wild-type mice (Villin-Cre negative / Runx1-floxed) and 4 colon samples from mice that lack epithelial expression of Runx1 (Villin-Cre positive/Runx1-floxed).

first: Remond

middle: J

last: Fijneman

first: Rebecca

last: Anderson

first: Ethan

last: Richards

first: Jieming

last: Liu

first: Marianne

last: Tijssen

first: Gerrit

last: Meijer

first: Annette

last: Rod

last: O’Sullivan

first: Patricia

last: Scott

first: Robert

last: Cormier


title: SM019 - Infection with SARS MA15 of C57BL/6J mice and Tnfrsf1b knockout mice

first: Michael

last: Katze

summary: Comparing the host response of C57BL/6J mice to Tnfrsf1b knockouts in the same strain of mice.

overall_design: Groups of 10-week-old C57BL/6 mice or Tnfrsf1b knockout mice were infected with SARS MA15 at a dose of 10^5 PFU or mock infected. Mice were euthanized on days 4 and 7 post-infection to measure virus load and isolate samples for measurement of virus load, lung pathology, transcriptional analysis and proteomics analysis. Mock-infected animals were also harvested at each time point. Mice were weighed every 24 hours to measure general disease progression and any mouse approaching 30% weight loss was euthanized.

first: Ralph

last: Baric

first: Lisa

last: Gralinski

first: Lynn

last: Law


title: MMTV tumor and host cells

status: Public on Aug 31 2012

first: Suchit

last: Jhunjhunwala

institute: Genentech

summary:
MMTV Wnt-1 and MMTV-Her2 tumors are transplanted onto GFP transgenic mice. Separate GFP+ cells and GFP- cells by FACS sorting to see the oncogene dependent gene expression changes in both tumor cell compartment (GFP- cells).
Wnt Fzd 6hrs group: Wnt inhibitor (Fzd8-CRD) treated tumor RNA which will give some clue for direct Wnt target genes only in tumor cells.

overall_design: GFP- Tumor cells (4 biological replicates) and Wnt-inhibitor treated cells (5 biological replicates)

first: Chie

last: Sakanaka

last: Soriano


title: Murine CD8+ T cells: in vitro-derived vs. thymocytes

status: Public on Sep 05 2012

city: Toronto

first: Dzana

middle: Dzenetdina

last: Dervovic

state: Ontario

address: 2075 Bayview Av.

department: Molecular and Cellular Biology

country: Canada

institute: Sunnybrook Research Institute

summary: Transcriptional profiling of mouse in-vitro derived CD8+ cells (obtained after culturing BM-HSCs isolated from B6 mice) with OP9-DL1 cells for 35 days were compared to CD8+ thymocytes isolated from 4-5 weeks old B6 mice.  Our goal was to determine similarities and differences in gene expression profile between in vitro-derived CD8+ cells and CD8+ cells isolated from the thymus. The procedure of in vitro differentiation of HSC using OP9-DL1 cocultures was previously described by: Schmitt, T. M., and J. C. Zuniga-Pflucker. 2002. Induction of T cell development from hematopoietic progenitor cells by delta-like-1 in vitro. Immunity 17:749-756 and Holmes, R., and J. C. Zuniga-Pflucker. 2009. The OP9-DL1 system: generation of T-lymphocytes from embryonic or hematopoietic stem cells in vitro. Cold Spring Harb Protoc 2009:pdb prot5156.

overall_design: Biological replicates: 2 different samples of in vitro-derived CD8+ T cells from day 35  were compared to 2 different samples of thymic CD8+ cells.

first: Juan

middle: C

last: Zuniga-Pflucker

first: Korosh

last: Kianizad


title: Expression data of lungs of mice infected with two highly pathogenic avian influenza viruses

status: Public on Sep 25 2012

city: yangzhou

first: Jiao

last: Hu

address: E. Wenhui Road 12

country: China

institute: yangzhou university

summary:
We isolated two highly pathogenic H5N1 avian influenza viruses (AIVs) (CK10 and GS10) with similar genetic background but greatly differ in pathogencity in mice. CK10 is highly pathogenic in mice, whereas GS10 is nonpathogenic. However, the host mechanism of this differecne in pathogenicity is unclear.
We used microarray analysis to evaluate the global transcriptional response in the lung of mice infected with CK10 or GS10.

overall_design:
Six-week-old female BALB/c mice were inoculated with CK10 or GS10 or mock-infected. At day 1 post infection, lungs were isolated from three mice per group for RNA extraction and hybridization on Agilent microarrays. Samples were named as follows:
CK10 (CK10_1_NS,CK10_2_NS,CK10_3_NS)
GS10 (GS10_1_NS,GS10_2_NS, GS10_3_NS)
control (C1_NS, C2_NS, C3_NS).

first: Zenglei


title: Epstein-Barr virus LMP1 and LMP2A transgenic B lymphocytes and lymphoma cells

status: Public on Sep 01 2012

city: Pittsburgh

first: Kathy

last: Shair

state: PA

address: 5117 Centre Avenue

department: UPMC Hillman Cancer Center

institute: University of Pittsburgh

summary:
Gene expression profile of splenic B cells (CD19+) from transgenic mice expressing the Epstein-Barr virus (EBV) latent membrane proteins (LMP) 1 and/or LMP2A.
Freshly harvested primary B cells were profiled.  B lymphocytes from transgenic LMP1, LMP2A, LMP1/2A mice and negative littermates were profiled from 6 month old adult mice; lymphoma cells were passaged in SCID mice and profiled for three LMP1 positive lymphomas and one negative lymphoma.

overall_design: 12 total samples.  4 transgenic B lymphocyte samples pooled from multiple biological replicates were hybridized to duplicate microarrays: LMP1 (pooled from 2 replicates), LMP2A (pooled from 3 replicates); LMP1/2A (pooled from 5 replicates), negative littermates (pooled from 4 replicates).  3 biological replicates of LMP1 lymphomas expressing high, medium and low levels of LMP1 and; 1 negative lymphoma was hybridized to 1 microarray chip.  The reference sample consisted of 4 biological replicates of splenic B cells (CD19+) pooled from 4-7 month old non-transgenic Balb/c mice.  The same reference was used for all hybridizations.

middle: H

first: Nancy

last: Raab-Traub


title: ECM-dependent gene expression in normal and tumor-derived mammary organoids

status: Public on Aug 16 2012

city: Baltimore

first: Kevin

last: Cheung

state: MD

address: 855 N. Wolfe St, Rangos 452, Center for Cell Dynamics, Johns Hopkins School of Medicine

department: Cell Biology

institute: Center for Cell Dynamics

summary: A critical step in metastasis is cancer cell dissemination. Dissemination and metastasis are associated with specific genetic changes and changes in extracellular matrix (ECM), but how these changes interact to enable dissemination remains unclear.  Here we tested the importance of ECM to dissemination in both normal and malignant mammary epithelium.  By time-lapse imaging, we observed collective invasion and dissemination directly in 3D culture.  Our results reveal that the pattern of epithelial migration and local dissemination are constrained by the local ECM microenvironment.  To identify RNA expression changes that could regulate these changes in cell behavior, we conducted whole genome RNA expression profiling from normal and malignant mammary epithelium in 3D culture.  We collected RNA from normal and malignant epithelium during active growth at 4 days in culture in either Matrigel or collagen I. We hybridized the resulting RNA to Agilent single color microarrays with a minimum of three biologically independent microarray replicates per condition.  We observed significant gene expression differences between normal and malignant epithelium, even when cultured in the same ECM.  In contrast, the ECM microenvironment had a relatively small impact on RNA expression, despite its large effects on migratory strategy and local dissemination.

overall_design: Gene expression was measured in normal and malignant mammary epithelial fragments cultured in one of two 3D matrices (laminin-rich basement membrane gel or collagen I) and collected at day 4, which we observed to have peak invasion and dissemination.  At least three independent experiments were performed at each time using different mice for each experiment.

first: Andrew

last: Ewald

first: Zena

last: Werb


title: Comparative transcriptomic analysis of acute host responses during 2009 pandemic H1N1 influenza infection in mouse, macaque, and swine (mouse dataset)

status: Public on Aug 14 2012

summary:
Background: The 2009 pandemic H1N1 influenza virus emerged in swine and quickly became a major global health threat. In mouse, non-human primate, and swine infection models, the pH1N1 virus efficiently replicates in the lung and induces pro-inflammatory host responses; however, whether similar or different cellular pathways were impacted by pH1N1 virus across independent infection models remains to be further defined. To address this, we have performed a comparative transcriptomic analysis of acute host responses to a single pH1N1 influenza virus, A/California/04/2009 (CA04), in the lung of mice, macaques and swine.

Results: Despite similarities in the clinical course, we observed differences in inflammatory molecules elicited, and the kinetics of their gene expression changes across all three species. The retinoid X receptor (RXR) signaling pathway controlling pro-inflammatory and metabolic processes was differentially regulated during infection in each species, though the heterodimeric RXR partner, pathway associated signaling molecules, and gene expression patterns differed in each species.

Conclusions: By comparing transcriptional changes in the context of clinical and virological measures, we identified differences in the host transcriptional response to pH1N1 virus across independent models of acute infection. Antiviral resistance and the emergence of new influenza viruses have placed more focus on developing drugs that target the immune system. Underlying overt clinical disease are molecular events that suggest therapeutic targets identified in one host may not be appropriate in another.

overall_design: The goal of this experiment was to use global gene expression profiling to understand mouse lung cellular responses to pandemic H1N1 influenza A/Californica/04/2009 virus infection. Six- to eight-week-old female BALB/c mice were anesthetized and inoculated with either 50 μl of phosphate-buffered saline (PBS; Mock) or with 10^6 pfu of pandemic H1N1 influenza A/California/04/2009 virus in a 50 μl volume, and whole lungs were collected at days 1, 3 and 5 post-inoculation. Lung samples from 9 animals for the infection group were used for array analysis, three animals per time point. Lung samples from 8 animals for the mock group were used for array analysis, three animals for the day 1 and 3 time points and 2 animals for the day 5 time point.

first: Jennifer

last: Tisoncik Go

first: Sarah

middle: E

last: Belisle

first: Nicolas

last: Tchitchek

first: Terrence

last: Tumpey

first: Wenjun

last: Ma

first: Juergen

last: Richt

first: Heinz

last: Feldmann


title: Transcriptional profiling of IRF4 -/- vs IRF4 +/- T-cells under Th17 polarizing conditions

first: Smita

last: Agrawal

department: Immunology

institute: Genentech Inc.

summary: Transcriptional profiling of T-cells isolated from spleen of IRF4 -/- mice and cultured under Th17 polarizing conditions for 42 hrs compared to cells similarly isolated and cultured from spleen of IRF4 +/- mice. The aim of the study was to identify global misexpression of genes in IRF4 -/- cells and hence identify key pathways regulated by IRF4 during Th17 differentiation.

overall_design: Two-condition experiment, IRF4 -/- vs IRF4 +/- Th17 cells at 42hrs. Biological replicates: 3 for each condition

first: Harinder

last: Singh


title: Targeting PyMT oncogene to diverse mammary cell populations enhances tumor heterogeneity and generates rare breast cancer subtypes

status: Public on Aug 10 2012

first: Bryan

last: Welm

address: 2000 Circle of Hope Drive

institute: University of Utah, Huntsman Cancer Institute

summary: We are generating a new mouse model for breast cancer heterogenaity using lentiviral infection to integrate the sporatically transforming EF1α-PyMT10C or Muc-PyMT10C lentivirus into mouse mammary epithelial cell genomes. We then transplant those cells into cleared mammary fat pads of recipient mice, allowing tumors to develop from luminal , myoepithelial, stem and progenitor cell lineages. We developed a wide variety of tumors including rare histologies such as squamous, tubular, spindloid and lipid rich. We used microarray analysis to compare our mouse model with a microarray analysis of 9 established mouse models (Herschkowitz, J.I. et al. Genome Biology, 2007). Heirarchal clustering was used to establish the molecular subtype of tumors developed through the lentiviral-PyMT mouse model. In addition, micrarray analysis was used in conjunction with GeneSifter and GO ontology to identify unique pathways for each of the rare tumor types.

overall_design:
43 total microarrays were generated from lentiviral-PyMT tumors, MMTV-PyMT transgenic tumors, and embryonic samples . Nine samples were two color arrays run at UNC microarray facility, while 34 were one color arrays run at Huntsman Cancer Instutite. The two color arrays were treated as one color arrays, we used the Cy5 intensity data for analysis. These data were merged and normalized (quantile and combat) with previously published arrays from UNC. Data were filtered on an intrinsic gene set developed in 2007 (Herschkowitz, J.I. et al. Genome Biology, 2007) and clustered using euclidian distance metrics

This GEO submission consists of the 34 one color arrays run at Huntsman Cancer Instutite. The nine two color arrays run at UNC microarray facility are not included.

first: Brittni

last: Smith

first: Dawne

last: Shelton

first: Collin

last: Keiffer

first: Brett

last: Milash

first: Chuck

last: Perou

first: Phil

last: Bernard


title: Inference of pathways, non-coding RNAs and regulatory elements during iron deprivation of Synechocystis based on comprehensive expression profiling

status: Public on Aug 01 2012

first: Jens

last: Georg

summary: Iron is an essential cofactor in many metabolic reactions. Mechanisms controlling iron homeostasis need to respond to changes in extracellular conditions, but must also keep the concentration of intracellular iron under strict control, as free ferrous iron (Fe2+) can lead to the generation of reactive oxygen species. Due to its role as redox carrier in photosynthesis, the iron quota in cyanobacteria is about 10 times higher than in model enterobacteria, but the molecular details how such high quota is tightly regulated have remained obscure. Here, we measured time-resolved gene expression changes after iron depletion in the cyanobacterium Synechocystis sp. PCC 6803 using a comprehensive microarray platform monitoring both protein-coding and non-coding transcripts. In total, 644 protein-coding genes were differentially expressed during the first 72h. Many of these proteins are associated with iron transport, photosynthesis or ATP synthesis. Comparing our data with three previous studies, we identified a core set of 28 genes involved in the iron stress response. Among them were genes encoding proteins important for assimilation of inorganic carbon, suggesting a previously unknown link between the carbon and iron regulatory networks. Nine of the 28 genes are of unknown function and constitute key targets for detailed functional analysis. Applying identical statistical and clustering criteria as for the protein-coding fraction, we also identified 10 small RNAs, 62 anti-sense RNAs, four 5’UTRs and 7 intergenic elements as likely to be involved in the iron regulatory network. Hence, our genome-wide profiling results indicate an unprecedented complexity in the iron-related regulatory network of cyanobacteria.

overall_design: We monitored iron limitation stress induced gene expression changes in the cyanobacterial model organism Synechocystis sp. PCC 6803. We included a control sample without iron-stress (0h) and 5 samples from timepoints after stress induction (3h, 12h, 24h, 48h, 72h). Each timepoint was sampled from two independent biological replicates.

first: Miguel

last: Hernández-Prieto

first: Verena

last: Schön

first: Luísa

last: Barreira

first: João

last: Varela

first: Wolfgang

last: Hess

first: Matthias

last: Futschik


title: Gene expression data on lungs of wild-type and Rora (Retinoic acid related orphan receptor) mutant mice exposed to room air and smoke

status: Public on Jul 23 2012

first: Kusum

middle: Vijay

last: Pandit

address: 200, Lothrop street, W1200-25A Biomedical Science Tower

department: Medicine-PACCM

summary: Gene expression data on wild-type and Rora mutant mice exposed to room air and smoke. The results provide a general insight into the relationship of Rora to known DNA damage response pathways and its role in cigarette smoke-induced airspace enlargement.

overall_design: This dataset includes 4 wild-type mice exposed to room air, 4 wild-type mice exposed to cigarette smoke and 4 Rora mutant mice exposed to cigarette smoke.

middle: V

first: Danielle

last: Morse

first: Naftali

last: Kaminski


title: Pulmonary innate immune response to ozone and TLR2 agonist Pam3CYS in C57BL/6 mice

city: Aurora

first: David

last: Schwartz

state: CO

address: Anschutz Medical Campus

department: Medicine

institute: University of Colorado, Anschutz Medical Campus

summary: Rationale:  Previous work demonstrated that pre-exposure to ozone primes innate immunity and increases TLR4-mediated response to subsequent stimulation with lipopolysaccharide (LPS). To further explore the pulmonary innate immune response to ozone exposure, we investigated the effect of ozone in combination with Pam3CYS, a synthetic TLR2/TLR1 agonist.    Methods:  Bronchoalveolar lavage (BAL)  and lungs were harvested from C57Bl/6 mice after exposure to ozone or filtered air followed by saline or Pam3CYS 24 hours later.  Cells and cytokines in the BAL, surface expression of TLRs on macrophages, and lung RNA genomic expression profiles were examined.  Results:  We demonstrate an increased BAL cell influx, increased IL-6 and KC, and decreased MIP-1α and TNF-α in response to Pam3CYS as a result of ozone pre-exposure. We also observed increased cell surface expression of TLR4, TLR2 and TLR1 on macrophages as a result of ozone alone or in combination with Pam3CYS. Gene expression analysis of lung tissue revealed a significant increase in expression of genes related to injury repair and cell cycle as a result of ozone exposure.  When comparing Pam3CYS treated animals to saline treated animals with or without ozone, genes associated with inflammation were significantly increased.  Potentially novel ozone exposure candidate genes (CCK, RELM-α and β) were identified.     Conclusion: Our results extend previous findings with ozone/LPS to other TLRs PAMPs and suggest that ozone priming of innate immunity is a general mechanism. Gene expression profiling of lung tissue identified transcriptional networks and genes that contribute to the priming of innate immunity at the molecular level.

overall_design: Mice were exposed to either 2ppm ozone or filtered air (FA) for 3 hours.  24 hours following ozone exposure, mice from either the ozone or FA group were treated intratracheally with either 100ug of Pam3CYS in saline or saline alone. Animals were euthanized 4 or 24 hours post-Pam3CYS exposure.  RNA from whole lung tissue from 4 animals per group was profiled.

first: Judy

last: Oakes

first: Brian

last: O'Connor

first: Laura

last: Warg

first: Rachel

last: Burton

first: Ashley

last: Hock

first: Joan

last: Loader

first: Daniel

last: LaFlamme

first: Lesly

last: DeArras

first: Ivana

last: Yang


title: Lymph node stromal cells: Control siRNA treated vs. Eif4g3 siRNA treated - Total RNA and Heavy polysome fraction

status: Public on Jul 20 2012

city: Stanford

first: Linda

last: Yip

address: 269 Campus Drive West, CCSR Building Rm. 2240

institute: Stanford University

summary:
Gene expression in the total RNA and heavy polysome fractions of Eif4g3 siRNA treated lymph node stromal cells (LNSCs) compared to control-sIRNA treated samples
The objective of this study was to identify genes whose translation are reduced after silencing Eif4g3 (the gene which encodes the translation initiation factor eIF4GII).  Genes with reduced translation are expected to have lower expression in RNA samples isolated from heavy polysomes but not in RNA samples isolated from whole cell lysates.

overall_design: LNSCs were grown in 10 cm plates, allowed to reach ≥ 80% confluency and then transfected with 400 pmol of control or Eif4g3 siRNA using Lipofectamine 2000.  7 plates were transfected with control or Eif4g3 siRNA.  Total RNA was extracted from cells 48h after transfection.  To isolate RNA from the heavy polysome fractions, cells were pooled, lysed and fractionated on a 10% to 60% continuous sucrose gradient. Fractions containing the heavy polysome fractions were pooled. RNA was extracted from these samples and used for microarrays on the Agilent Whole Mouse Genome Microarray Kit, 4×44K 2-color arrays.


title: An overlapping protein-coding region in Influenza A Virus Segment 3 modulates the host response

status: Public on Jul 12 2012

first: kathie

last: walters

address: 401 Terry Ave N

institute: Institute for Systems Biology

summary: Segment 3 of influenza A virus contains a second open reading frame accessed via robosomal frameshifting.  The frameshift product, PA-Z, comprises the endonuclease domain of viral PA protein with  C-terminal demain encoded by the X-ORF and functions to repress cellular gene expression.  PA-X also modulates IAV virulence in a mouse infection model.

overall_design: The effect of PA-X deltions were examined using 2 separate mutant influenza viruses (1918-FS/1918-PCT1)  and the results compared to wild-type 1918 influenza virus.  Balb/c mice were infected and samples harvested at days 3, 5 and 8 days.  Four animals/condition were used. Gene expression levels from infected animals were compared to mock animals.

first: Kathie-Anne

last: Walters

first: Brett

last: Jagger

first: Paul

last: Digard


title: Gene expression analysis during reprogramming with sequential infecion of Oct4/Klf4/cMyc/Sox2

city: Guangzhou

first: Hui

last: Zheng

state: Guangdong

address: 190 Kaiyuan Ave. Science City

department: Stem Cell

institute: Guangzhou Institutes of Biomedicine and Health, Chinese Academic of Science

summary: To further understand the mechanism of reprogramming, the mouse embryonic fibroblast cells were infected with Oct4, Klf4, c-Myc and Sox2 with special sequence. 1) Oct4 and Klf4 containing retrovirus was delivered on day 0. 2) Oct4, Klf4 and c-Myc were delivered on Day 1.5. 3) c-Myc and Sox-2 were deivered on Day 3. 4) Sox2 were delivered on Day 4.5. 5) Vitamin C containging medium were used from Day 6. The gene expression of Day 0 (MEF), Day 1.5, Day 3, Day 4.5 and Day 6 were analyzed with micro array to indentify the possible underlying mechanism. Especially the factors related to MET/EMT, cell cycle and epigenetic were focused.

overall_design: MEF cells were subjected for reprogramming with special protoocl: 1) Oct4 and Klf4 containing retrovirus were delivered on day 0. 2) Oct4, Klf4 and c-Myc were delivered on Day 1.5. 3) c-Myc and Sox-2 were deivered on Day 3. 4) Sox2 were delivered on Day 4.5. 5) Vitamin C containging medium were used from Day 6. RNA on Day 0 (MEF), Day 1.5, Day 3, Day 4.5 and Day 6 were collected for analysis.

first: Xiaopeng

last: Liu


title: BMPER regulates cardiomyocyte size and vessel density in vivo

status: Public on Sep 20 2012

city: Chapel Hill

first: Jonathan

last: Schisler

state: NC

address: MBRB, Rm 2340C

department: McAllister Heart Institute

institute: The University of North Carolina at Chapel Hill

summary: Background:  BMPER, an orthologue of Drosophila melanogaster crossveinless-2, is a secreted factor that regulates BMP activity in endothelial cell precursors and during early cardiomyocyte differentiation.  Although previously described in the heart, the role of Bmper in cardiac development and function remained unknown.  Methods: BMPER deficient hearts were phenotyped histologically and functionally using echocardiography and Doppler analysis.  Since BMPER -/- mice die perinatally, BMPER +/- mice were then challenged to pressure overload induced cardiac hypertrophy and hind limb ischemia to determine changes in angiogensis and regulation of cardiomyocyte size. Results: We identified for the first time the cardiac phenotype associated with BMPER haploinsufficiency.  BMPER mRNA and protein are present in the heart during cardiac development through at least E14.5 but is lost by E18.5.  BMPER +/- ventricles are thinner and less compact than sibling wild-type hearts.  In the adult, BMPER +/- hearts present with decreased anterior and posterior wall thickness, decreased cardiomyocyte size, and an increase in cardiac vessel density. Despite these changes, BMPER +/- mice respond to pressure overload-induced cardiac hypertrophy challenge largely to the same extent as wild-type mice.  Conclusion: BMPER appears to play a role in regulating both vessel density and cardiac development in vivo; however, BMPER haploinsufficiency does not result in marked effects on cardiac function or adaptation to pressure overload hypertrophy.

overall_design: Unpaired, two-condition experiment, wild-type vs BMPER+/- adult hearts. Biological replicates: 4 per condition.

first: Eunice

last: Kang

first: Monte

middle: S

last: Willis

first: Cam

last: Patterson


title: The Role of the E2F1 transcription factor in the innate immune response to systemic LPS [mRNA]

status: Public on Jul 01 2012

first: David

last: Schwartz

summary: Our recent study of gene expression in mice treated with LPS systemically identified the E2F1 transcription factor as a novel regulator of innate immune response in lung, liver, and spleen tissue. Our follow up studies showed that RNAi-mediated inhibition or E2F1 gene deficiency lead to reduced inflammatory response to LPS in vitro and in vivo. Furthermore, a clear role for the role of miRNAs in the regulation of innate immune response to LPS has emerged.  In the current study, we further examined B6;129E2F1-/- and B6x126 F2 mice in the systemic LPS model and used gene expression profiling to identify a defect in the coagulation cascade that contributes to increased morbidity of B6;129E2F1-/- mice despite their reduced systemic inflammatory response. We also studied miRNA expression profiles identified miRNAs that are differentially expressed in B6;129E2F1-/- but not B6x129 F2 mice.

overall_design: 32 mice (4-6) per group, E2F+/+ or E2F-/- genotype, treated with saline or LPS, 6 or 20 hrs

first: Laura

last: Warg

first: Judy

last: Oakes

first: Rachel

last: Burton

first: Holly

middle: R

last: Rutledge

first: Steve

last: Groshong


title: Gene regulation in hematopoietic cells by Pcgf1 in a Runx1 null background

status: Public on Jun 18 2012

city: Dresden

first: Maciej

last: Paszkowski-Rogacz

address: Tatzberg 47/49

department: UCC / Medical Faculty and University Hospital Carl Gustav Carus

institute: Technische Universität Dresden

summary: The transcription factor Runx1 is essential for the establishment of definitive hematopoiesis during embryonic development. In adult blood homeostasis, Runx1 plays a pivotal role in the maturation of lymphocytes and megakaryocytes. Furthermore, Runx1 is required for the regulation of hematopoietic stem and progenitor cell (HSPC) pools. However, how Runx1 orchestrates self-renewal and lineage choices in combination with other factors is not well understood. Here we describe a genome-scale RNAi screen to detect genes that cooperate with Runx1 in regulating HSPCs. We identify the polycomb group protein Pcgf1 as an epigenetic regulator involved in hematopoietic cell differentiation. We show that simultaneous depletion of Runx1 and Pcgf1 allows sustained self-renewal while blocking differentiation of HSPCs in vitro. We find an upregulation of HoxA cluster genes upon Pcgf1 knockdown that possibly accounts for the increase in self-renewal. Further, our data suggest that cells lacking both Runx1 and Pcgf1 are blocked at an early progenitor stage, indicating that a concerted action of the transcription factor Runx1 together with the epigenetic repressor Pcgf1 is necessary for terminal differentiation. Thus, our work discovers a genetic link between transcriptional and epigenetic regulation that is required for hematopoietic differentiation.

overall_design: Hematopoietic stem and precursor cells freshly isolated from mice were transduced with an shRNA targeting Pcgf1 or a control shRNA. Cells were selected with puromycin for 36 h before total mRNA was isolated.

first: Anna

middle: K

last: Sedello

first: Julia

last: Jarrells

first: Katharina

last: Ross

first: Frank

last: Buchholz


title: Identification of Sox9-Regulated Pathways During the Secondary Transition Stage of Pancreas Development

status: Public on Aug 02 2012

city: La Jolla

first: Brandon

last: Taylor

address: Sanford Consortium for Regenerative Medicine, 2880 Torrey Pines Scenic Dr., Room 3101

department: Pediatrics and Cellular & Molecular Medicine

institute: University of California, San Diego

summary: Sox9 target genes were identified during the secondary transition stage of pancreas development by comparing gene expression in Sox9-ablated versus wild-type pancreata using microarray analysis.

overall_design: Sox9 was conditionally ablated during the secondary transition in the developing pancreas via recombination of a Sox9-flox allele (Kist et al., 2002) using the tamoxifen-inducible Rosa26-CreER allele (Vooijs et al., 2001). Dams were injected with 6 mg/40 g tamoxifen in corn oil at e12.5. Pancreata were manually microdissected at e15.5. Total RNA was isolated and pooled from pancreata of e15.5 Sox9fl/fl; Rosa26-CreER (mutant) versus Rosa26-CreER (wild-type) littermates for four biological replicates.

first: HungPing

last: Shih

first: Philip

last: Seymour

first: Maike

last: Sander


title: Microarray analysis of gene expression in ATM-deficient MEFs

status: Public on Jun 20 2012

city: Rokkasho

first: Takashi

last: Sugihara

state: Aomori

address: 2-121 Hacchazawa

department: Radiobiology

institute: Institute for Environmental Sciences

summary: The expression of interferon-related genes was more enhanced in irradiated ATM-deficient mouse embryonic fibroblasts (MEFs) than in irradiated ATM wild-type MEFs.

overall_design: Nonirradiated-ATM-WT vs Irradiated-ATM-WT vs  Nonirradaited-ATM-KO vs IrradiatedATM-KO


title: Murine Spermatogonial Stem Cells: Rapamycin- vs Vehicle-exposed in vivo (2-wk treatment)

status: Public on May 01 2012

city: Chicago

first: Christopher

middle: J.

last: Payne

address: 2430 N. Halsted St.

institute: Northwestern University Feinberg School of Medicine

summary: Male FVB strain mice aged 12-days-old through 26-days-old were administered daily intraperitoneal injections of rapamycin (4mg/kg body weight) or control vehicle (5% Tween-80, 5% PEG-400), beginning at postnatal day (P)12. Mice were euthanized at P26 and their testes were isolated for germ cell enrichment. Single cell suspensions of germ cells were prepared from isolated testes and subjected to magnetic-activated cell sorting (MACS). This procedure enriches the undifferentiated spermatogonia fraction, which represents the spermatogonial stem cell (SSC) population. Total RNA from cells double-positive for the SSC surface markers thymus cell antigen 1, theta (THY1) and glial cell line-derived neurotrophic factor family receptor alpha 1 (GFRA1) was isolated for gene expression microarray analysis.

overall_design: Magnetic-activated cell sorting (MACS) was used to enrich undifferentiated spermatogonia from a pool of primary testicular cells isolated from 5 littermate rapamycin (RM)-treated male mice and from 5 littermate control vehicle (VEH)-treated male mice. With MACS-enriched cells from pool generating RNA, no technical replicates performed.

first: Margeaux

last: McGraw

first: Amber

last: Kofman


title: Expression data of pre-stasis cultured HMEC

status: Public on May 03 2012

city: Montreal

first: Francois

last: Pepin

state: Quebec

address: 1160 Pine Av W

institute: McGill University

summary: We have generated a large collection of normal human mammary epithelial cell strains from women aged 16 to 91 years, derived from primary tissues, to enable functional and molecular interrogation of aging. We demonstrate in finite-lifespan cultured and uncultured epithelial cells that aging is associated with reduction of myoepithelial cells and with increases in luminal cells expressing keratin 14 and integrin α6, traits that are expressed exclusively in myoepithelial cells in women under 30. We find that changes to the luminal lineage result from age-dependent expansion of multipotent progenitors that bear defects resulting in incompletely differentiated luminal cells. These findings were verified in vivo in normal breast tissues. Myoepithelial cells have been suggested to act as tumor suppressors, and progenitor cells are implicated as the etiological roots of mammary carcinomas. Thus with aging there is a shift in the balance of luminal/myoepithelial lineages, and changes in the functional spectrum of multipotent progenitors, which presages increased potential for malignant transformation.

overall_design: Finite lifespan pre-stasis HMEC from specimens from reduction mammoplasties of 7 patients of different age were collected. The expression data was queried for different biological replicates and at different passages. For strain 240, luminal and myoepithelial cells were collected using flow cytometry.

first: Mark

middle: A

last: LaBarge

first: James

last: Garbe

first: Martha

last: Stampfer


title: miR-1204 promotes tumor development in breast and ovarian cancer cell lines

city: Portland

first: Laura

middle: M.

last: Heiser

state: OR

address: 3181 SW Sam Jackson Park Rd.

institute: OHSU

summary: Introduction: Amplification at chromosome 8q24 is one of the most frequent genomic abnormalities in human cancers and is associated with reduced survival duration in breast and ovarian cancers. The minimal amplified region encodes c-MYC and the non-coding RNA, PVT1 including miR-1204 encoded in exon 1b. Here we analyzed the genomic changes at chromosome 8q24.21 in breast cancer and the functional roles of miR-1204  in breast and ovarian cancer progression.  Methods: The genomic changes at chromosome 8q24.21 were detected in 997 breast cancer tumors and 40 breast cancer cell lines. Expression of miR-1204 in breast and ovarian cancer cell lines was investigated by qRT-PCR method. The role of miR-1204 in the tumorigenesis of breast and ovarian cancer was explored using both knockdown and overexpression of miR-1204 in vitro. Candidate miR-1204 target genes from two independent expression microarray datasets and computational predict programs were identified and further validated by qRT-PCR and western blot methods. The role of inhibition of miR-1204 on tamoxifen sensitivity in breast cancer cells was also investigated.  Results: MiR-1204 is frequently co-amplified with MYC and expression of miR-1204 is strongly correlated with the expression and amplification of the noncoding PVT1 transcript and less so with MYC in human breast and ovarian cancer cells. Inhibition of miR-1204 decreases cell proliferation and increased apoptosis in breast and ovarian cancer cell lines with 8q24 amplification, but not in lines without amplification and so may be involved in Myc-induced apoptosis. Additionally, overexpression of miR-1204 enhances both breast and ovarian cancer cell growth and Myc-initiated Rat1A cell transformation. Computational and experimental analyses 30 promising candidate miR-1204 target genes.  mRNA levels for these genes were  assessed after over expression and knockdown of miR-1204 as were protein levels for 10 genes for which antibodies were available. These studies implicated VDR and ESR1 as miR-1204 targets. Inhibition of miR-1204 increased response to tamoxifen in Estrogen Receptor negative breast cancer cell lines.   Conclusions: We conclude that amplification of miR-1204 contributes to breast and ovarian pathophysiology at least in part, by increasing proliferation and down regulating apoptosis and by decreasing expression of VDR and ESR1.

overall_design: Seven cell line sample pairs, where samples are LNA transfected with antimiR-1204 or antimiR-1204 control

first: Jing

last: Huang

middle: M


title: The effect of alpha, beta, gamma interferon receptors on host reponse to influenza virus in mouse embryonic fibroblasts

status: Public on Apr 30 2012

city: Seattle

first: Michael

last: Katze

address: Rosen Building 960 Republican St.

institute: University of Washington

summary: The objective of this study was to examine the host transcriptional response to high and low pathogenecity viruses in mouse embryonic fibroblasts (MEFs) isolated from different mouse genetic backgrounds to further understand the contribution of interferon signaling pathways to host response to influenza.

overall_design: WT, IFNgR-/-, IFNabR-/-, or IFNabgR-/- MEFs were mock-infected or infected with the A/WSN/33 (WSN), reconstructed 1918 (r1918), or A/Vietnam/1203/2004 (VN1203) strains of influenza virus at an MOI of 2 PFU/cell.  At 24 h p.i., total RNA was isolated from the cells and used for microarray hybridization.  Experiments with VN1203 and r1918 were performed seperately (experiment a) from experiments with WSN (experiment b). Appropriate mock samples were harvested in each experiment. All gene expression profiles are compared to time-, experiment-, and genotype-matched mock-infected samples.

first: Alan

last: Goodman

first: Hui

last: Zeng

first: Sean

last: Proll

first: Xinxia

last: Peng

first: Cristian

last: Cilloniz

first: Victoria

last: Carter

first: Marcus

last: Korth

first: Terrence

last: Tumpey


title: IM004 - mouse infection with HA avirulent mutation in A/Vietnam/1203-CIP048_RG1/2004(H5N1)

status: Public on Apr 25 2012

summary: Determination of the host response (C57Bl6 mouse model) to the HA avirulent mutation in A/Vietnam/1203-CIP048_RG1/2004(H5N1) virus at 10^4PFU.

overall_design: Groups of 20 week old C57BL6 mice were infected with the HA avirulent mutation in A/Vietnam/1203-CIP048_RG1/2004(H5N1) virus at 10^4PFU or time-matched mock infected. Time points were 1, 2, 4 and 7 d.p.i.  There were 3-4 animals/dose/time point. Lung samples were collected for virus load, transcriptional and proteomics analysis. Weight loss and animal survival were also monitored.

first: Yoshihiro

last: Kawaoka

first: Chengjun

last: Li

first: Jean

last: Chang

first: Amie

last: Eisfeld

first: Lynn

last: Law


title: Primary murine embryonic fibroblasts (MEFs): Cdk7 wild type versus Cdk7 KO

status: Public on Apr 18 2012

city: Madrid

first: David

last: Santamaría

state: Madrid

address: Melchor Fernandez Almagro 3

department: Molecular Oncology

country: Spain

institute: CNIO

summary: Transcriptional profiling of primary Cdk7lox/lox MEFs comparing Adeno-Cre vs Adeno-GFP infected controls. Samples were obtained 7 days after the Adeno-Cre mediated elimination of Cdk7. Goal was to determine the effects of Cdk7 elimination on RNA polII-mediated transcription.

overall_design: Two-condition experiment, Adeno-Cre vs. Adeno-GFP infected Cdk7lox/lox MEFs. Biological replicates: 10 independent primary MEF preparations.

first: Miguel

last: Ganuza

first: Cristina

last: Saiz-Ladera

first: Marta

last: Cañamero

first: Gonzalo

last: Gomez-Lopez

first: Ralph

last: Schneider

first: Maria

last: Blasco

last: Pisano

first: Jesus

last: Paramio

last: Santamaria

first: Mariano

last: Barbacid


title: Transcription profile of primordium gut organs

status: Public on Jun 01 2012

city: Tsukuba

first: Takaaki

last: Noguchi-Suda

state: Ibaraki

address: Tennoudai 1-1-1

department: Graduate school of life and enviromental sciences

institute: University of Tsukuba

summary: The mechanisms of gastrointestinal morphogenesis in mammals are not well understood. This is partly due to the lack of organ specific gene expression pattern in the gastrointestinal tract during development. The initiation of organ bud formation occurs at E9.5-E11.5 in mice. These primordia for the digestive organs, including esophagus, stomach, and intestine,  protrude from a tube-like structured endoderm, and have their own distinct morphogenesis. Thus, using mouse embryos, we surveyed transcription of prospective these three regions at E11.5 during gastrointestinal morphogenesis. This early digestive organ specific transcription profile will be useful for understanding of the mechanisms of gastrointestinal development.

overall_design: Mouse gut organs morphogenesis begin at E9.5-E11.5. The primordium esophagus, stomach, and intestine at E11.5 were dissected and analysed transcription profile.

last: Noguchi


title: Gene expression profiling of CD4+CD25+Foxp3+ regulatory T cells and CD4+CD25-Foxp3- T cells in the course of Plasmodium yoelii infection of BALB/c mice

status: Public on Apr 16 2012

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

institute: HCI - Helmholtz Centre for Infection Research

summary: The objective of the present study was to characterize the phenotype of CD4+CD25+Foxp3+ regulatory T cells (Tregs) in the course of parasitic Plasmodium yoelii (P .yoelii) infection of BALB/c mice. Therefore we performed microarray expression analysis of CD4+CD25+Foxp3+ Tregs isolated by FACS from spleens of non-infected mice and from spleens of mice infected with P. yoelii 3 days and 5 days post infection. By comparing the gene expression profiles, we were able to identify molecules which were differentially expressed by Tregs during parasitic infection and thereby might be involved in their immune-suppressive function. Moreover, we included CD4+CD25-Foxp3- T cells from spleens of non-infected and P. yoelii-infected mice in our analysis. It was proposed that immune-suppressive CD4+CD25-Foxp3- T cells might be induced during Plasmodium infection of mice. Thus, detailed gene expression data of these cells in comparison to CD4+CD25+Foxp3+ Tregs would contribute a better understanding in the phenotype.

overall_design: FACS sorted CD4+CD25+Foxp3+ Tregs and CD4+CD25-Foxp3- T cells from pooled spleens of non-infected Foxp3/ eGFP mice (served as reference) and from pooled spleens of P. yoelii infected Foxp3/ eGFP mice 3 days and 5 days post infection were analyzed as single probes.

first: R

first: W

last: Hansen

first: S

last: Abel


title: Regulation of Monocyte Functional Heterogeneity by miR-146a

status: Public on Apr 06 2012

city: Boston

first: Martin

last: Etzrodt

state: MA

address: 185 Cambridge Street

department: Center for Systems Biology

institute: Massachusetts General Hospital

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

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

overall_design: Refer to individual Series

first: Virna

last: Cortez-Retamozo

first: Andita

last: Newton

first: Jimmy

last: Zhao

first: Aylwin

last: Ng

first: Moritz

last: Wildgruber

first: Pedro

last: Romero

first: Thomas

last: Wurdinger

first: Ramnik

last: Xavier

first: Frederic

last: Geissmann

first: Etienne

last: Meylan

first: Matthias

last: Nahrendorf

first: Filip

last: Swirski

last: Baltimore

last: Weissleder

first: Mikael

last: Pittet


title: CA04M001 - Virus Dose and Time Response

first: Michael

last: Katze

department: Microbiology

summary: Determination of the host response (C57Bl6 mouse model) to A/CA04/2009 virus infection at 4 doses and 4 time points post infection.

overall_design: Groups of 20 week old C57BL6 mice were infected with H1N1 A/CA/04/2009 at 4 doses:10^3, 10^4, 10^5 and 10^6 PFU and time-matched mock infection. Time points were 1, 2, 4 and 7 d.p.i.  There were 3-4 animals/dose/time point. Lung samples were collected for virus load, transcriptional and proteomics analysis. Weight loss and animal survival were also monitored.

first: Ralph

last: Baric

first: Jean

last: Chang

first: Lisa

last: Gralinski

first: Lynn

last: Law


title: Comparison of gene expression in Wild type and T cell-specific conditional Trim28 KO in TCR stimulated and un-stimulated naive CD4 positive and T regulatory cells

status: Public on Apr 29 2012

city: Kyoto

first: Tasuku

last: Honjo

address: Yoshida Konoe-cho, Sakyo-ku

department: Department of Immunology and Genomic Medicine

institute: Kyoto University

summary: A microarray study was performed in unstimulated and TCR-stimulated CD4 + T cells and Treg in wild type and conditional Trim28 KO mice to identify genes that are regulated by Trim28.  These experiments constitute a portion of the study described below:     Paper Abstract: Peripheral T cell activation and differentiation into specialized effectors are regulated by TCR- and cytokine-mediated signals that induce clonal expansion and unique transcriptional factors. These processes may include active chromatin modification by nuclear factors. In search of such molecules, we found Trim28, a component of large nuclear chromatin-regulatory complex is tightly controlled upon TCR stimulation at the level of phosphorylation, and examined global impact of Trim28 loss in especially CD4+ T cells, by generating T cell-specific conditional Trim28 KO mice (CKO). CD4+ T cells from CKO mice showed defective IL-2 production and T cell proliferation associated with defective upregulation of cell-cycle associated proteins. Accordingly, young CKO showed T-lymphopenia. Surprisingly, Trim28 CKO mice eventually accumulated auto-reactive memory-phenotype T cells that produced inflammatory IL-17. CKO mice are also susceptible to induced auto-inflammatory disease with TH-17 dominant immune response.  Loss of Trim28 showed aberrant accumulation of TH-17 and FoxP3+ T cells, two key T cells in inflammation vs. tolerance. We found CKO T cells showed a cell-extrinsic promotion of TH-17 and FoxP3+ T cell development by a mechanism involving overproduction of TGF-beta. Our study revealed unexpected roles of Trim28, a global chromatin regulator in both T cell activation and tolerance.

overall_design: Trim28 conditional KO mice and age-matched control mice were sacrificed, and neive CD4+ T cells (CD4+CD62+CD25-) and Treg (CD4+CD62+CD25+) were sorted. Stimulation of naive T cells was done with anti-CD3 and anti-CD28 for 13 hours.  We collected quadruplicates for each group.

first: Shunsuke

last: Chikuma

first: Naomasa

last: Suita

first: Il-mi

last: Okazaki

first: Shiro

last: Shibayama


title: Downstream targets of Fgfrl1 signaling

status: Public on Mar 16 2012

city: Bern

first: Beat

last: Trueb

address: Murtenstrasse 35

department: Dept. of Clinical Research

country: Switzerland

institute: University of Bern

summary: Comparison of the gene expression profiles between normal and Fgfrl1 deficient kidneys

overall_design: 3 individual RNA preparations from 6-9 pooled normal kidneys each vs. 3 individual RNA preparations from 6-9 Fgfrl1-/- kidneys each

first: Stefan

last: Wyder

first: Simon

middle: D

last: Gerber


title: STAT1 independent control of a neurotropic measles virus challenge in primary neurons and infected mice

status: Public on Mar 14 2012

city: Philadelphia

last: Slifker

address: 333 Cottman Ave.

institute: Fox Chase Cancer Center

summary: The objective of this study was to compare the ability of mice that lack STAT1 to resolve a neurotropic viral challenge, and to assess the ability of neurons obtained from these mice to be effectively cleared of virus by interferon gamma

overall_design: For the array, primary neurons were isolated from embryonic mice, grown as pure cultures, exposed to recombinant interferon gamma for 3, 6 or 24 hours and harvested for microarray analysis to identify and compare the gene profiles between wild type and STAT1 knockout neurons.

first: Glenn

last: Rall


title: A unique role of Cohesin-SA1 in gene regulation and development [Expression]

status: Public on Mar 15 2012

first: Silvia

last: Remeseiro

address: Calle Melchor Fernandez Almagro 3

institute: Spanish National Cancer Research Centre (CNIO)

summary: Vertebrates have two cohesin complexes that consist of Smc1, Smc3, Rad21/Scc1 and either SA1 or SA2, but their functional specificity is unclear. Mouse embryos lacking SA1 show developmental delay and die before birth. Comparison of the genome wide distribution of cohesin in wild-type and SA1-null cells reveals that SA1 is largely responsible for cohesin accumulation at promoters and at sites bound by the insulator protein CTCF. As a consequence, ablation of SA1 alters transcription of genes involved in biological processes related to Cornelia de Lange syndrome (CdLS), a genetic disorder linked to dysfunction of cohesin. We show that the presence of cohesin-SA1 at the promoter of myc and of protocadherin genes positively regulates their expression, a task that cannot be assumed by cohesin-SA2. Cohesin binding pattern along some gene clusters is also affected by the lack of SA1, leading to dysregulation of the genes within. We hypothesize that impaired cohesin-SA1 function in gene expression underlies the molecular etiology of CdLS.

overall_design: Two-condition experiment, SA1 KO vs. WT cells. 3 Biological replicates.

first: Ana

last: Cuadrado

first: Gonzalo

last: Gomez-Lopez

first: David

middle: G

last: Pisano

last: Losada


title: Translational control in early adipogenesis

status: Public on Mar 29 2012

city: Göttingen

last: von der Heyde

address: Humboldtalle 32

department: Medical Statistics

institute: University Medical Center Göttingen

summary: In obesity, adipose tissue expands by increasing the volume of existing adipocytes (hypertrophy), increasing the number of small adipocytes (hyperplasia) or both. Much is known about transcriptional control during adipogenesis, including early events. However, translational control plays a pivotal role in many dynamic processes and we presume that it is also important for the control of adipogenesis, especially in the first hours after hormonal induction. By use of ribosome profiling we identified 43 genes that are up-regulated and 2 genes that are down-regulated during the first six hours of adipogenesis in 3T3-L1 cells. Interestingly, we found Ghrelin to be down-regulated. Up-regulated genes comprise factors that are nucleic acid binding (Cdkn1c, eIF4b, Hsf1, Irf6, Myc, Plekhn1, Polr2a, Rpl18, Rpl27a, Rpl6, Rpl7a, Rps18, Rpsa, Sema3g, Tbc1d22a, Tsc22d3), form part of ribosomes (L6, L7a, L18, L27a, Sa, S18, S15a pseudogene), act on the regulation of translation (eIF4b) or transcription (Hsf1, Irf6, Myc, Tsc22d3). Others act as chaperones (Bag3, Hspa8/Hsc70, Hsp90ab1) or in other metabolic or signals transducing processes. We conclude that a moderate reorganisation of the functionality of the ribosomal machinery is a very important step for the growth and expression control at the beginning of adipogenesis.

overall_design: 12 samples: 4 (0h, non-polysomal fraction; 0h, polysomal fraction; 6h, non-polysomal fraction; 6h, polysomal fraction) x3 replicates

first: Carolin

last: Fromm-Dornieden

first: Olexandr

last: Lytovchenko

first: Gabriela

last: Salinas-Riester

first: Lennart

last: Opitz

first: Tim

last: Beissbarth

first: Bertram

last: Brenig

first: Bernhard

last: Baumgartner


title: The response of murine primary airway epithelial cells to Influenza infection and the importance of Interferon type I signaling in this response [mAEC].

status: Public on Mar 12 2012

city: COLUMBUS

first: IOANNIS

last: IOANNIDIS

state: OH

address: 700 CHILDRENS DRIVE

department: VACCINES AND IMMUNITY

institute: NATIONWIDE CHILDRENS HOSPITAL

summary: To investigate how murine airway epithelial cells respond to Influenza infection and how important interferon type I signaling is for this response, we harvested airway epithelial cells from the tracheas of wild type, interferon type I knockout(IFNaR-/-) and STAT1 knockout (STAT1-/-) mice and cultured them as previously described (Pickles et al,1998) in polarized airway epithelial cell cultures (mAECs). Triplicate mAECs from each type of mouse (wt,IFNaR-/-,STAT1-/-) were infected with 2X105 PFUs Influenza A (WSN) for 2h or mock inoculated and harvested 24h after infection.

overall_design: Triplicate murine polarized airway epithelial cell cultures from wild type, IFNaR-/- or STAT1-/- mice were mock treated or infected with 2x10^5 PFUs of Influenza A (WSN) for 2h and harvested 24 h post infection.

first: Ioannis

last: Ioannidis

first: Beth

last: McNally

first: Meredith

last: Willette

first: Emilio

last: Flano


title: Glucosylceramide fed mice skin before SDS treatment (0d), after SDS treatment (2d)

status: Public on Apr 01 2012

city: Yokohama

first: Ritsuro

last: Ideta

address: 2-12-1 Fukuura, Kanazawa-ku

department: Functional Food Research & Development Center

institute: Shiseido Research Center

summary: Dietary glucosylceramide (GC) improves skin barrier function. To elucidate the molecular mechanisms involved, we used a microarray system to analyze mRNA expression in SDS-treated dorsal skin of hairless mouse. Transepidermal water loss of mouse skin was increased by SDS treatment and the increase was significantly reduced by prior oral administration of glucosylceramides. Microarray-evaluated mRNA expression ratios showed statistically significant increase of expression of genes related to cornified envelope and tight junction formation versus all genes in glucosylceramide-fed/SDS-treated mouse skin. We then examined the contribution of glucosylceramide metabolites to tight junction formation of cultured keratinocytes. SDS treatment of cultured keratinocytes significantly decreased the transepidermal electrical resistance, and the decrease was significantly ameliorated in the presence of sphingosine or phytosphingosine, the major metabolites of glucosylceramide. These results suggest that oral administration of glucosylceramide improves skin barrier function by upregulating genes associated with both cornified envelope and tight junction formation.

overall_design: Two-condition experiment, effect of oral intake of GC on mice skin before SDS treatment (0d), and after SDS treatment(2d), Biological replicates: 3 replicates for 0d, 4 replicates for 2d.

first: Tomohiro

last: Sakuta

first: Yusuke

last: Nakano

first: Taro

last: Uchiyama


title: Identification of a new pathway for Th1 cell development induced by cooperative stimulation with IL-4 and TGFbeta [Agilent]

status: Public on Mar 17 2012

city: Kisarazu

first: Soichi

last: Tofukuji

address: 2-6-7 Kazusa-kamatari

department: Human Genome Research

institute: Kazusa DNA Research Institute

summary: IL-4 plays an important role in the induction of Th2 and Th9 cells as well as in the inhibition of Th1 cell generation.  We herein show that a combination of IL-4 and TGFbeta augment the development of Th1 cells that express CD103 (CD103+ Th1 cells) if IFNgamma is present.  The T-box containing transcription factor, eomesodermin (Eomes) is preferentially expressed in CD103+ Th1 cells, and is involved in IFNgamma production.  The induction of T-bet during early T cell activation is essential for the formation of the active chromatin at both the Eomes and IFNgamma gene loci.  TGFbeta is required for the induction of Eomes and CD103, as well as the inhibition of Th2 cytokine expression.  In addition, IL-4 induces Eomes transcription through activation of the Stat6 signaling pathway.  IFNgamma-producing CD103+ Th1 cells are detected in the IEL of normal mice, and their numbers significantly decrease in Tbet- and Stat6-deficient mice.  These results represent the first molecular mechanism of IL-4/TGFbeta-dependent augmentation of Th1 cell generation, and raise the possibility that IL-4 and TGFbeta may simultaneously enhance the Th1 cell-mediated immune responses under certain cytokine conditions.

overall_design: Th9+IFNgamma and Th9 cells are profiled for mRNA expression

first: Makoto

last: Kuwahara

first: Junpei

last: Suzuki

first: Osamu

last: Ohara

first: Toshinori

last: Nakayama

first: Masakatsu

last: Yamashita


title: Microarray analysis to identify genes that are differentially expressed in resting and in LPS-activated splenic B cells of Ebf1+/fl-RERTCre and Ebf1fl/fl-RERTCre mice

status: Public on Apr 03 2012

city: Freiburg

first: Soeren

last: Boller

address: Stuebeweg 51

department: Cellular & Molecular Immunology

institute: Max Planck Institute of Immunobiology and Epigenetics

summary:
Using resting and LPS-stimulated B cells from mice carrying two Ebf1 alleles flanked with loxP sites and an inducible Cre recombinase, target genes of Ebf 1 and the effect of Ebf1 deletion on the cells was analyzed.
Target genes of Ebf 1 and the effect of Ebf1 deletion on the cells was analyzed.

overall_design:
Ebf1 fl/fl mice and heterozygote control animals carrying an ER-Cre fusion protein were treated with  Tamoxifen-Citrate  and were  sacrificed for analysis. Resting B cells were sorted and were either left untreated or were stimulated with LPS,  followed by RNA extraction for expression analysis.
See related Series GSE35915.

first: Ildiko

last: Györy

first: Rudolf

last: Grosschedl


title: CDK8 and MED12 knockdown in R1 mouse ES cells

status: Public on Mar 05 2012

city: South San Francisco

first: Adam

last: Adler

state: CA

address: 1 DNA Way

institute: Genentech

summary: Transcriptional profiling of R1 mouse ES cells infected with non-targeting control (NTC) shRNA and two different shRNA sequences against Cdk8 (shCdk8-1 and shCdk-2) and Med12 (shMed12-1 and shMed12-2).

overall_design: Multi-condition experiment comparing shNTC versus shCdk8-1 and shCdk8-2 after 8 days (3 biological replicates each) and shNTC versus shCdk8-1, shCdk8-2, shMed12-1, and shMed12-2 after 13 days (3 biological replicates each); in total 24 samples profiled.

first: Zora

last: Modrusan


title: IM002, IM009 - Implication of inflammatory macrophages, nuclear receptors and interferon regulatory factors in increased virulence of pandemic 2009 H1N1 influenza A virus after host adaptation

status: Public on Mar 08 2012

first: Michael

last: Katze

summary: While pandemic 2009 H1N1 influenza A viruses were responsible for numerous severe infections in humans, these viruses do not typically cause corresponding severe disease in mammalian models. However, the generation of a virulent 2009 H1N1 virus following serial lung passage in mice has allowed for the modeling of human lung pathology in this species. Genetic determinants of mouse-adapted 2009 H1N1 viral pathogenicity have been identified, but the molecular and signaling characteristics of the host response following infection with this adapted virus have not been described. Here, we compared the gene-expression response following infection of mice with A/CA/04/2009 (CA/04) or the virulent mouse-adapted strain (MA-CA/04). Microarray analysis revealed that increased pathogenicity of MA-CA/04 was associated with: (1) early and sustained inflammatory and interferon response that could be driven in part by interferon regulatory factors (IRFs) and increased NF-kappaB activation, as well as inhibition of the negative regulator TRIM24, (2) early and persistent infiltration of immune cells, including inflammatory macrophages, and (3) the absence of activation of lipid metabolism later in infection, that may be mediated by nuclear receptors inhibition, including PPARG, HNF1A and 4A, with pro-inflammatory consequences. Further investigation of these signatures in the host response to other H1N1 viruses of varied pathogenicity confirmed their general relevance for virulence of influenza virus and suggested that lung response to MA-CA/04 virus was similar to that following lethal H1N1 r1918 influenza virus. This study links for the first time differential activation of IRFs, nuclear receptors, and macrophage infiltration with influenza virulence in vivo.

overall_design: Six-to-eight-week-old female BALB/c mice were anesthetized and inoculated with 50 ul of phosphate-buffered saline (PBS; Mock) or with 10^6 pfu of virus in a 50 ul volume. Nine animals per condition group were used for tarray analysis, two or three animals per time point. There were seven condition groups: A/California/04/2009, MA1-A/California/04/2009, A/Mexico/4482/09, A/Brisbane/59/07, A/New Jersey/8/76, the reconstructed 1918 virus and time–matched mocks.

first: Laurence

last: Josset

first: Jessica

last: Belser

first: Jean

last: Chang

first: David

last: Swayne

first: Sarah

last: Belisle

first: Mary

last: Pantin-Jackwood

first: Stewart

first: Terrence

last: Tumpey


title: Expression analysis of pre-phenotype dt27J mouse dorsal root ganglia

status: Public on Feb 23 2012

city: Ottawa

first: Scott

last: Ryan

state: ON

address: 501 Smyth Rd

department: Regenerative Medicine

institute: Ottawa Hospital Research Institute

summary: Loss of function of dystonin cytoskeletal linker proteins causes neurodegeneration in the sensory ataxia, dystonia musculorum (dt).  While much investigation has focused on understanding dt pathology, divergent functions of dystonin isoforms are still unknown.  Here, we highlight a novel function of the dystonin-a2 isoform in mediating microtubule (MT) stability, golgi organization and flux through the secretory pathway.  Using dystonin-null mice combined with isoform-specific loss of function analysis, we find dystonin-a2 is bound to MAP1B in the area surrounding the centrosome, where it maintains MT acetylation. In dt, the absence of the MAP1B-dystonin-A2 interaction results in a loss of MAP1B perinuclear localization, leading to MT deacetylation and instability.  Deacetylated MTs lead to golgi fragmentation and prevent anterograde trafficking of motor proteins.  Maintenance of MT acetylation through TSA administration or MAP1B overexperssion in vitro, mitigates the observed defect.  These aberrations are apparent in pre-phenotype dorsal root ganglia (DRG) and primary sensory neurons, suggesting they are causal in the dt disorder.

overall_design: P4 dorsal root ganglia (DRG) tissue from 3 WT and 3 dt27J animals from 2 separate litters was subjected to RNA extraction and analyzed.

first: Alphonse

last: Chu

first: Alexandre

last: Blais

first: Rashmi

last: Kothary


title: Murine blood monocyte subsets

first: Martin

last: Etzrodt

summary: Monocytes and their lineage descendants serve as a central defense system against infection and injury but if uncontrolled can also promote an excessive pathological inflammatory response. Therefore a current research goal is to understand how the organism controls the number and function of monocytes and how these variables can be tailored in therapy. Considering the evidence that monocytes are heterogeneous and exist in at least two subsets committed to divergent functions, we investigated whether distinct factors regulate the balance between monocyte subset responses in vivo. Here we investigate the differential expression of mRNA among murine steady-state monocyte subsets.

overall_design: Blood was drawn from healthy C57BL/6 donors. For each biological replicate 1000 monocytes of the Ly-6Chi and Ly-6Clo phenotype were isolated from the blood sample through fluorescence activated cell sorting.


title: Comparison of Hepatocyte nuclear factor 4 alpha developmental and temporal knockout mice

status: Public on Feb 21 2012

city: Bethesda

last: Bonzo

address: 9000 Rockville Pike, Building 37, Rm3112

department: CCR

institute: NCI/NIH

summary: The goal of this experiment was to distinguish those genes regulated following acute HNF4alpha depletion compared to a developmental knockout model where gene compensation may comfound results. Expression profile of livers from 8 week old male Hnf4alpha Flox mice that express either albumin cre or the tamoxifen inducible ErT2-albumin cre for liver-specific deletion. Mice were fed a control diet or tamoxifen diet in the case of the ErT2-albumin cre to induce recombination.

overall_design: Six-condition experiment, H4N  vs H4T vs H4EN vs H4ET vs H4CN vs H4CP. Biological replicates: 4 samples each group.

first: Tsutomu

last: Matsubara

first: Frank

last: Gonzalez


title: GSK-3A and GSK-3B knockdown in AML cell lines

status: Public on Feb 27 2012

first: Kimberly

last: Stegmaier

address: Harvard Medical School

department: Department of Pediatric Oncology

institute: Dana-Farber Cancer Institute and Children’s Hospital Boston

summary:
Gene expression data from AML cell lines, MOLM-14, U937, THP-1 and HL-60, that were infected with a scrambled control hairpin (shControl), two shRNAs directed against GSK-3B (shGSK3B_1 and shGSK3B_2), or two shRNAs directed against GSK-3A (shGSK3A_5 and shGSK3A_6).
Acute myeloid leukemia (AML) is the most common form of acute leukemia in adults. Long-term survival of patients with AML has changed little over the past decade, necessitating the identification and validation of new AML targets. Integration of genomic approaches with small-molecule and genetic-based high-throughput screening holds the promise of improved discovery of candidate targets for cancer therapy. Here, we identified a role for glycogen synthase kinase 3A (GSK-3A) in AML by performing two independent small-molecule library screens and an shRNA screen for perturbations that induced a differentiation expression signature in AML cells. GSK-3 is a serine-threonine kinase involved in diverse cellular processes including differentiation, signal transduction, cell cycle regulation, and proliferation. We demonstrated that specific loss of GSK-3A induced differentiation in AML by multiple measurements, including induction of gene expression signatures, morphological changes, and cell surface markers consistent with myeloid maturation. GSK-3A–specific suppression also led to impaired growth and proliferation in vitro, induction of apoptosis, loss of colony formation in methylcellulose, and anti-AML activity in vivo. Although the role of GSK-3B has been well studied in cancer development, these studies support a role for GSK-3A in AML.

overall_design: The AML cell lines, MOLM-14, U937, THP-1 and HL-60, were infected with a scrambled control hairpin (shControl), two shRNAs directed against GSK-3B (shGSK3B_1 and shGSK3B_2), and two shRNAs directed against GSK-3A (shGSK3A_5 and shGSK3A_6).

first: Versha

last: Banerji

first: Stacey

last: Frumm

first: Kenneth

middle: N

last: Ross


title: How cyanobacteria pose new problems to old methods: Challenges in microarray time series analysis

status: Public on Apr 02 2013

city: Berlin

first: Robert

last: Lehmann

address: Invalidenstrasse 43

department: Institute for Theoretical Biology

institute: Humboldt University Berlin

summary: Quantification of circadian gene expression in WT Synechocystis sp. PCC 6803 cells

overall_design: We quantified circadian gene expression of the wild type Synechocystis PCC6083 strain. Over a 24 h time course, 6 samples for RNA isolation were taken at the following time points: 30 minutes before and after light is switched off (sample 1 - CT 11.5 and sample 2 - CT 12.5), 30 minutes before midnight (sample 3 - CT 17.5), 348 30 minutes before and after light onset (sample 4 - CT 23.5 and sample 5 - CT 0.5) and 30 minutes before noon (sample 6 - CT 5.5).

first: Rainer

last: Machne

first: Jens

last: Georg

first: Manuela

last: Benary

first: Stefanie

last: Hertel

first: Anne

last: Rediger

first: Christian

last: Beck

first: Anika

last: Wiegard

first: Ilka

last: Axmann

first: Ralf

last: Steuer


title: IM010 - Infection with A/Vietnam/1203/04 H5N1 influenza virus of C57BL/6J mice, IDO1 KO mice or TNFRSF1B KO mice

status: Public on Sep 12 2012

city: Seattle

first: Michael

last: Katze

state: WA

address: Rosen Building 960 Republican St.

institute: University of Washington

summary: Comparison of the host response to VN1203 infection in three different strains of mice: Wild-type C57BL/6J mice, IDO1 KO mice and TNFRSF1B KO.

overall_design: Groups of 6-week-old mice were infected with A/Vietnam/1203/04 H5N1 influenza virus at a dose of 10^3 PFU or mock infected. Mice were euthanized on days 2 and 6 post-infection to measure virus load and isolate samples for measurement of virus load, lung pathology, transcriptional analysis and proteomics analysis. Mock-infected animals were also harvested at each time point. Mice were weighed every 24 hours to measure general disease progression and any mouse approaching 30% weight loss was euthanized.

first: Yoshi

last: Kawaoka

first: Amie

last: Eisfeld

first: Lynn

last: Law

first: Jean

last: Chang

first: Chengjun

last: Li


title: Functional genomics of central nervous system and liver following herpes simplex virus corneal infection.

summary:
The overall goal of the study was to use in vivo data combined with functional genomics to define gene expression signatures representative of a spectrum of HSV CNS infections.
Innate immune deficiencies result in a spectrum of severe clinical outcomes following infection. In particular, there is a strong association between loss of the signal transducer and activator of transcription (Stat) pathway, breach of the blood-brain barrier (BBB), and virus-induced neuropathology. The gene signatures that characterize resistance, disease, and mortality in the virus-infected nervous system have not been defined. Herpes simplex virus type 1 (HSV-1) is commonly associated with encephalitis in humans, and humans and mice lacking Stat1 display increased susceptibility to HSV central nervous system (CNS) infections. In this study, two HSV-1 strains were used, KOS (wild type [WT]), and Δvhs, an avirulent recombinant lacking the virion host shutoff (vhs) function. In addition, two mouse strains were used: strain 129 (control) and a Stat1-deficient (Stat1(-/-)) strain. Using combinations of these virus and mouse strains, we established a model of infection resulting in three different outcomes: viral clearance without neurological disease (Δvhs infection of control mice), neurological disease followed by viral clearance (Δvhs infection of Stat1(-/-) mice and WT infection of control mice), or neurological disease followed by death (WT infection of Stat1(-/-) mice). Through the use of functional genomics on the infected brain stem and liver, we determined gene signatures that were representative of the three infection outcomes.

overall_design: Gender matched, 6- to 8- week old immunocompetent, control 129S6 and 129S6 Stat1 knockout mice were infected corneally with 2x10^6 PFU of either wild type HSV-1, a vhs-null HSV virus, or mock-infected. Brain stems and liver of individual mice were isolated at days 1, 3, 5 and 7 post-inoculation for microarray analysis. For microarray analysis, samples were collected from n=2 animals (1 male, 1 female) per mouse strain and virus strain for each time point. Equal masses of tissue were pooled from two mock-infected mice per time point and run on microarray.

first: Tracy

middle: J

last: Pasieka

first: Cristian

last: Cilloniz

first: Victoria

last: Carter

first: Pamela

last: Rosato

first: David

last: Leib


title: Effect of obestatin, its N-terminal fragment and fragment analog Nt8U on mice epididymal tissue

status: Public on Feb 08 2012

city: Mysore

first: Uma

middle: Venkateswaran

last: Manjappara

state: Karnataka

address: Cheluvamba Mansion

department: Protein Chemistry and Technology

institute: Central Food Technological Research Institute

summary: mRNA profiling of epididymal tissue of mice treated with obestatin, its N-terminal fragment residues 1-13 and a N-terminal fragment analog Nt8U

overall_design: Four groups of six mice each were placed in individual metabolic cages and acclamatised to fasting from 6AM to 6PM and ad libitum water. The mice were administered 80ng/kg of the respective peptides intraperitoneally for 8 days and the epididymal tissue was subjected to mRNA extraction and microarray analysis.

first: Shreeranga

last: Nagaraj

first: Sudha

last: Rao


title: Death Receptors DR6 and TROY Regulate Brain Vascular Development

status: Public on Feb 15 2012

first: Josh

last: Kaminker

department: Bioinformatics and Computational Biology

summary: Signaling events that regulate central nervous system (CNS) angiogenesis and blood-brain barrier (BBB) formation are only beginning to be elucidated. By evaluating the gene expression profile of mouse vasculature, we identified DR6/TNFRSF21 and TROY/TNFRSF19 as regulators of CNS-specific angiogenesis in both zebrafish and mice. Furthermore, these two death receptors interact both genetically and physically and are required for vascular endothelial growth factor (VEGF)-mediated JNK activation and subsequent human brain endothelial sprouting in vitro. Increasing beta-catenin levels in brain endothelium upregulate DR6 and TROY, indicating that these death receptors are downstream target genes of Wnt/beta-catenin signaling, which has been shown to be required for BBB development. These findings define a role for death receptors DR6 and TROY in CNS-specific vascular development.

overall_design: 5 replicates of 3 time points for either brain or liver/lung facs sorted vascaulture.  One adult liver/lung replicate was not used as it failed QC

first: Stephen

last: Tam

middle: L

last: Richmond

first: Joshua

first: Zora

last: Modrusan

first: Baby

last: Martin-McNulty

first: Tim

middle: C

last: Cao

first: Robby

last: Weimer

first: Richard

last: Carano

first: Nick

last: van Bruggen

first: Ryan

last: Watts


title: Inferring rules of lineage commitment in haematopoiesis

status: Public on Feb 14 2012

city: London

first: Shamit

last: Soneji

address: 72 Huntley Street

institute: UCL

summary: Fractionation of EML cells isolated based on surface expression of immunophenotypic markers reveals the existence of a subpopulation that has undergone spontaneous commitment to an erythroid fate. Uncommitted fractions were compared to committed cells, derived from both spontaneous (EryCP) and cytokine-driven (Ediff) commitment.

overall_design: EML cells were separated by flow cytometry based on their expression of the markers Sca1, CD34 and cKit as described.

first: Tariq

last: Enver


title: Transcriptional profiling of disease progression in bovine tuberculosis and the identification of potential diagnostic biomarkers

status: Public on Jan 31 2012

city: ADDLESTON

first: ELIHU

last: Aranday-Cortes

state: SURREY

address: Woodham Lane, New Haw

department: SEB 4

institute: Central Veterinary Laboratories Agency-Weybridge

summary: The definition of biomarkers correlating with disease progression could have impact on the rational design of novel diagnostic approaches for bovine tuberculosis in cattle. We have used the advantages of the murine model to identify promising candidates in the host transcriptome post-infection. RNA from BALB/c splenocytes and lung cells after aerogenic Mycobacterium bovis infection were with high-density microarrays to defining biomarkers of disease progression. In antigen-stimulated splenocytes we found statically significant modulation of 1109 genes early after infection and 1134 at later time-point post-infection. 618 of these genes were modulated at both time points. In the lung 282 genes were significantly modulated post-infection. Amongst the most strongly up-regulated genes were granzyme A in spleen, and cxcl9, granzyme B, interleukin-22, interluekin-17A receptor, and ccr6 in lungs. The expression of 20 of the most up-regulated genes identified in the murine studies were evaluated using PBMC from uninfected and naturally infected cattle. We could show that the expression of cxcl9, granzyme A and interleukin-22 following in vitro stimulation with PPD was significantly increased in infected cows compared to naïve animals. Thus, we have demonstrated that murine transcriptome analysis can be used to predict responses in cattle. In addition, we have prioritised CXCL9, GnzA and IL-22 as potential additional readout systems for the ante-mortem diagnosis of bovine tuberculosis.

overall_design: Two groups of 5 BALB/c mice each were infecetd with approx 600 CFU M. bovis via the intranasal route. At days 3 and 14 post challenge five mice per group were euthanized and spleens and lungs harvested. One group of 5 mice were used as a control. Their splenocytes and lung cells were stimulated in vitro for 3 days with M7 protein pool. Antigen cell culture stimulations in mice were performed using an equal pool of seven secreted, immunogenic recombinant mycobacterial proteins (Rv1886c, Rv3019c, Rv3763, Rv3804c, Rv0251, Rv0287 and Rv0288) common to M. bovis and BCG, referred here as M7 protein cocktail. Each protein was used at final concentration of 2μg/ml in 3-day culture.

first: Elihu

first: Philip

last: Hogarth

first: Daryan

last: Kaveh

first: Martin

last: Vordermeier


title: Suppressor of cytokine signaling-1 influences bacterial clearance and pathology during the infection with Mycobacterium tuberculosis

status: Public on Jan 18 2012

city: Braunschweig

first: Sabin

last: Bhuju

address: Salzdhalumerstr

institute: Lionex

summary:
Tuberculosis results from an interaction between a chronically persistent pathogen counteracted by IFN-g-mediated immune responses. Modulation of IFN-g signaling could therefore constitute a major immune evasion mechanism for M. tuberculosis. SOCS1 plays a major role in the inhibition of IFN-g-mediated responses. We found that M. tuberculosis infection stimulates SOCS1 expression in mouse and human myeloid cells. Significantly higher levels of SOCS1 were induced after in vitro or in vivo infection with virulent M. tuberculosis-than with attenuated M. bovis BCG. Different innate and adaptive immune mechanisms participated in infection-induced SOCS1 expression. SOCS1 hampered M. tuberculosis clearance both in macrophages and during murine infection in vivo. On the other hand, SOCS1 protected the host from an infection-induced inflammation.  Despite SOCS1 expression, mycobacteria-infected macrophages were not tolerant to IFN-g. Instead, an impaired IFN-g secretion by macrophages, associated to lower responses to IL-12, accounted for the increased mycobacterial intracellular growth in presence of SOCS1. SOCS1 attenuated the expression of the majority of genes modulated by infection of macrophages (6,1% of the transcriptome), indicating the relevance of the molecule in the outcome of infection with M. tuberculosis.  We suggest that SOCS1 is expressed during M. tuberculosis infection to establish a successful chronic infection, and dampen inflammatory damage.
Difference in genotype and TB infection comparison

overall_design: Relative gene expressions were determined by normalized intensity values. GeneSpring analysis was performed using the Treg transcriptome data with following comparisons: no GvHD d90 versus no GvHD d150, no GvHD d90 versus acute GvHD, no GvHD d150 versus chronic GvHD, acute GvHD versus chronic GvHD, acute GvHD versus GvHD d90 and chronic GvHD versus GvHD d150 (Figure 2). Cut-off was a transcript fold change of +2 or -2 in at least one comparison. Student´s t-test was used to identify significant expression changes.

first: Xiang-qun

last: Ye

first: Berit

last: Carow

first: Dolores

last: Gavier-Widén

first: Wulf

last: Oehlmann

first: Mahavir

last: Singh

first: Hans

last: Wigzell

middle: E

last: Rottenberg


title: Gene expression profile of butyrate mediated prevention of coloractal cancer in a mouse model

status: Public on Dec 31 2011

city: Shanghai

first: Jing-Yuan

last: Fang

state: Shanghai

address: 145 Middle Shandong Rd

department: Division of Gastroenterology

institute: Shanghai Jiao-Tong University School of Medicine Ren-Ji Hospital

summary: To further elucidate the mechanism of butyrate mediated chemoprevention of colorectal cancer,we have employed whole genome microarray expression profiling as a discovery platform to identify genes that differentially expressed in mice from Butyrate group compared those from DMH group. The mice of DMH group were received normal diet (calcium concentration,1.24%) and subcutaneous injection of 1,2-Dimethylhydrazine at a dose of 20 mg/kg once weekly for 20 weeks; the mice of Butyrate group were received high calcium diet (calcium concentration,3%) with 1.5% Butyrate and subcutaneous injection of 1,2-Dimethylhydrazine at a dose of 20 mg/kg once weekly for 20 weeks. The mice were sarcrificed at 24 week. Nine normal colonic mucosa (3 from DMH group, 3 from Butyrate group mice with tumors, and 3 from Butyrate group mice without tumors) were used for the microarray analysis.

overall_design: The differentially expressed genes were identified between butyrate group and DMH group,as long as differentially expressed pathways and gene ontology terms.

first: Hui-min

last: Chen

first: Yan-Wei

last: Lin

first: Ji-Lin

last: Wang