title: ARID-DNA interactions are required for promoter occupancy by SWI/SNF

status: Public on Jan 15 2012

city: Chapel Hill

first: Jonathan

last: Schisler

address: MBRB, Rm 2340C

department: McAllister Heart Institute

institute: The University of North Carolina at Chapel Hill

summary: Every known SWI/SNF chromatin-remodeling complex incorporates an ARID DNA binding domain-containing subunit.  Despite being a ubiquitous component of the complex, physiological roles for this domain remain undefined.  Here we show that disruption of ARID1a-DNA binding in mice results in embryonic lethality, with mutant embryos manifesting prominent defects in the heart and extraembryonic vasculature.  The DNA binding defective mutant ARID1a subunit is stably expressed and capable of assembling into a SWI/SNF complex with chromatin remodeling activity, but promoter occupancy by ARID1a-containing, SWI/SNF complexes (BAF-A) is impaired.  Depletion of ARID domain-dependent, BAF-A associations at THROMBOSPONDIN 1 (THBS1) led to the concomitant upregulation of this anti-angiogenic protein.  Using a THBS1 promoter-reporter gene, we further show that BAF-A directly regulates THBS1 promoter activity in an ARID domain-dependent manner.  Our data not only demonstrate that ARID-DNA interactions are physiologically relevant in higher eukaryotes, but also indicate these interactions can facilitate SWI/SNF binding to target sites in vivo.  These findings support the model wherein cooperative interactions among intrinsic subunit-chromatin interaction domains and sequence-specific transcription factors drive SWI/SNF recruitment.

overall_design: Four-condition experiment, wild-type vs Baf250a/Arid1a^V1068G/V1068G yolk sacs isolated at E8.5 and E9.5. Biological replicates: 3 per condition.

first: Ron

last: Chandler

first: Cam

last: Patterson

first: Terry

last: Magnusun


title: Molecular signatures associated with Mx1-mediated resistance to highly pathogenic influenza virus infection: mechanisms of survival

status: Public on Feb 20 2012

city: Seattle

first: Michael

last: Katze

state: WA

address: Rosen Building 960 Republican St.

department: Microbiology

country: USA

institute: University of Washington

summary: Understanding the role of host factors during lethal influenza virus infection is critical to deciphering the events that will determine the fate of the host. One such factor is encoded by the Mx1 gene, which confers resistance to influenza virus infection. Here, we compared pathology and global gene expression profiles in lung tissue from BALB/c (Mx1(-)) and BALB•A2G-Mx1 mice (Mx1(+/+)) infected with the fully reconstructed 1918 pandemic influenza virus with an without interferon-alpha pretreatment. Mx1(+/+) mice showed less tissue damage than Mx(-) animals, and pathology and mortality were further reduced by treating the mice with interferon prior to infection. The goal of the global transcriptional profiling was to identify distinct molecular signatures associated with partial protection, complete protection, and the contribution of interferon to the host response.

overall_design: BALB/c mice carrying a defective allele of the Mx1 resistance gene or congenic Balb.A2G-Mx1 mice carrying the functional Mx1 allele. Half of the animals in each group were intranasally treated with 10,000 units of recombinant human IFN-α A/D (R&D Systems, Minneapolis, MN). Animals were anesthetized by IP injection and inoculated intranasally with 3.2 × 10^5 PFU (One hundred times 50% lethal dose (LD50)) of the reconstructed 1918 infectious virus diluted in 50 μl phosphate-buffered saline (PBS) or mock infected with PBS.  To assess gene expression in response to r1918 virus with and without IFN treatment, lungs were harvested at 12hr, 24hr, and 72hr post-innoculation (n=3 per group at each time point). To assess gene expression in the context of IFN treatment only, lungs were harvested at 8h and 24hr post-treatment (n=3 per group at each time point). To assess gene expression without IFN or virus infection, lungs were harvested from mock-infected animals at 12h, 24h and 72hr from both Balb/c (n=2 per at each time point) and Mx1+/+ (n=3 at each time point).

first: Cristian

last: Cilloniz

first: Mary

middle: J

last: Pantin-Jackwood

first: Chester

last: Ni

first: Victoria

middle: S

last: Carter

first: Marcus

last: Korth

first: David

middle: E

last: Swayne

first: Terrence

middle: M

last: Tumpey

middle: G


title: Gene expression analysis of ER-stressed growth plate chondrocytes in two mouse models of Schmid chondrodysplasia

status: Public on Jan 01 2012

city: Parkville

first: Trevor

middle: L

last: Cameron

address: Royal Children's Hospital, Flemington Road

country: Australia

institute: Murdoch Childrens Research Institute

summary: We set out to generate transcriptional maps of chondrocyte UPR gene networks in vivo using two mouse models (Schmid and Cog) of Schmid chondrodysplasia, in order to define the consequences of UPR activation for the adaptation, differentiation, and survival of chondrocytes experiencing ER stress during hypertrophy, thus providing insights into ER stress signaling and its impact on cartilage pathophysiology. Our data demonstrate that both models displayed similar unfolded protein responses (UPRs), involving activation of ER stress sensors Ire1 and Atf6 and upregulation of their downstream targets, including molecular chaperones, foldases, and ER-associated degradation machinery. Also upregulated were the emerging UPR regulators Wfs1 and Syvn1, recently identified UPR components including Armet and Creld2, and genes not previously implicated in ER stress such as Steap1 and Fgf21. Moreover, we transcriptionally profiled the expression of wildtype growth plate zone gene signatures in the mutant hypertrophic zones, in order to define the differentiation status of ER-stressed chondrocytes in the mutant hypertrophic zones. Hypertrophic zone gene upregulation and proliferative zone gene downregulation were both inhibited in Schmid hypertrophic zones, resulting in the persistence of a proliferative chondrocyte-like expression profile in ER-stressed Schmid chondrocytes.

overall_design: For the mutant hypertrophic zone gene expression profiling, the hypertrophic zone from one tibia from each of three two week old Schmid, wildtype (Schmid background), Cog, and wildtype (Cog background) mice was microdissected. In all cases, total RNA was extracted and amplified through two rounds of linear amplification, labelled with Cy3, and interrogated by microarray analysis using the Agilent 44K, mouse whole genome platform.

first: Katrina

last: Bell

first: Liliana

last: Tatarczuch

first: Eleanor

last: Mackie

first: M

middle: H

last: Rajpar

first: Ben

middle: T

last: McDermott

first: Raymond

middle: P

last: Boot-Handford

first: John

middle: F

last: Bateman


title: Response to Influenza infection in the pre-CC

status: Public on Dec 13 2011

city: Portland

first: Daniel

last: Bottomly

address: 3181 Sam Jackson Park Rd.

institute: OHSU

summary: Using the distribution of Influenza-infected phenotypes (immunohistochemical (IHC) staining for viral protein and weight loss at 4 days post infection) in 99 Influenza-infected pre-Collaborative Cross (CC) lines, we have categorized the extreme phenotypes with regard to host response:  severe (“high”) response to infection (N=26, IHC score: 4 or 5, % Weight loss > 15%) and mild (“low”) response to infection (N=18, IHC score: 0 or 1, % Weight loss < 5%). Global transcriptome profiling identified 2,671 transcripts that were significantly differentially expressed (DE; q-value < .05 and > 1.5 fold change either direction) due to differences in the host response phenotype. Using these DE transcripts, e-QTL mapping was performed to identify putative regulatory regions potentially controlling the expression of the transcripts. 21 significant e-QTLs (based on Bonferroni adjustment) were identified allowing direct examination of genes associated with regulation of host response. This is the first systems genetics study of influenza in a complex mouse model (where the level of genetic diversity approximates that seen in human populations), providing a framework for identification of causal variants and elucidation of the underlying biological sub-networks involved in response to infectious disease.

overall_design: 44 samples each derived from a different CC line with expression measured from lung tissue at day 4 post infection.  Infection was with the mouse adapted influenza A strain A/PR/8/34 (H1N1)

first: Shannon

middle: K

last: McWeeney


status: Public on Dec 08 2011

city: Gwangju

first: Darren

middle: Reece

last: Williams

address: 1 Oryong-dong

department: School of Life Sciences

country: South Korea

institute: Gwangju Institute of Science and Technology

summary:
In urodele amphibians, limb regeneration involves the dedifferentiation of muscle myotubes into single cells that may acquire pluripotent potential. We have employed small molecules (myoseverin and BIO) to attempt to reproduce this behavior in mammalian muscle culture. C2C12 myotubes derived from the C2C12 myoblast cell line were induced to undergo cellularization by myoseverin treatment, which destabilizes tubulin filaments. The GSK-3 inhibitor, BIO, was then used to induce dedifferentiation. Induce neuron formation; the cells were incubated with 250 nM reversine for 48 h, and neural induction media (DMEM/F12 supplemented with N2 (Invitrogen)) and 1.5  uM all-trans retinoic acid for 7 days.
C2C12 murine myoblast cell line and 48 h 10  uM BIO treated C2C12 cellulate (derived by 20 M myoseverin treatment for 48 h)

overall_design: C2C12 myoblasts were differentiated into myotubes with 2%horse serum in DMEM for 8 days (from 2-4 d, 10 uM AraC treatment was also used to kill any remaining myoblasts). Next, myotubes were cellularized by 20  uM myoseverin treatment for 48 h. 24 h after myoseverin treatment, myotubes were treated with 10  uM BIO for 2d.

middle: R

first: Woong-hee

last: Kim


title: Conditional keratinocyte-specific ADAM17 knockout in mice alters skin homeostasis

status: Public on Jun 21 2012

city: Freiburg

first: Claus-Werner

last: Franzke

address: Hauptstr. 7

department: Dermatology

country: Germany

institute: University of Freiburg

summary: This study investigates the role of ADAM17 (a disintegrin and metalloproteinase 17) in skin homeostasis. Here, we show that mice lacking ADAM17 in keratinocytes have a normal epidermal barrier and skin architecture at birth, but develop pronounced defects in epidermal barrier integrity soon after birth and chronic dermatitis as adults. The dysregulated expression of epidermal differentiation proteins becomes evident 2 days after birth, followed by transepidermal water loss and inflammatory immune cell infiltration. Our results identify a previously unappreciated critical role of the ADAM17/EGFR signaling axis in maintaining the homeostasis of the postnatal epidermal barrier.

overall_design: The genome-wide effects of ADAM17 deficiency were analyzed using Agilent Whole Mouse Genome microarrays. Conditional keratinocyte-specific ADAM17 knockout mice were generated by crossing Adam17flox/flox mice with keratin-14-Cre (Krt14-Cre) transgenic mice. Adam17flox/+Krt14-Cre mice were mated with Adam17flox/flox mice to generate pups of Adam17flox/flox Krt14-Cre positive (cKO) and Krt14-Cre negative (wild-type) control littermates. The genetic background was a mix of 129Sv and C57BL/6. As material, back skin tissue biopsies (postnatal day 10) from n = 2 wild-type skin and n = 2 ADAM17 epidermal KO skin (matched WT-cKO pairs from two different litters) were used in this study.

first: Thorsten

last: Kurz

first: Carl

last: Blobel


title: HSF1 drives a transcriptional program distinct from heat shock to support highly malignant human cancers [gene expression]

status: Public on Aug 07 2012

city: Cambridge

first: Marc

last: Mendillo

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

summary: Heat-Shock Factor 1 (HSF1), master regulator of the heat-shock response, facilitates malignant transformation, cancer cell survival and proliferation in model systems. The common assumption is that these effects are mediated through regulation of heat-shock protein (HSP) expression. However, the transcriptional network that HSF1 coordinates directly in malignancy and its relationship to the heat-shock response have never been defined. By comparing cells with high and low malignant potential alongside their non-transformed counterparts, we identify an HSF1-regulated transcriptional program specific to highly malignant cells and distinct from heat shock. Cancer-specific genes in this program support oncogenic processes: cell-cycle regulation, signaling, metabolism, adhesion and translation. HSP genes are integral to this program, however, even these genes are uniquely regulated in malignancy. This HSF1 cancer program is active in breast, colon and lung tumors isolated directly from human patients and is strongly associated with metastasis and death.  Thus, HSF1 rewires the transcriptome in tumorigenesis, with prognostic and therapeutic implications.

overall_design: We used microarrays to examine affect of HSF1 depletion on gene expression in cancer cell lines.  Three cancer cell lines (BPLER, HMLER & MCF7) were transduced with either control shRNAi (Scramble or GFP) or an shRNAi that targets and depletes HSF1 (hA6).  Another BPLER sample was subjected to a 1H, 42˚ C heat shock.  Two biological replicates for all samples.

first: Sandro

last: Santagata

first: Martina

last: Koeva

first: George

middle: W

first: Rong

last: Hu

first: Rulla

last: Tamimi

first: Ernest

last: Fraenkel

first: Tan

middle: I

last: Ince

first: Luke

last: Whitesell

first: Susan

last: Lindquist


title: Whole esophagi of WT, Nrf2-/- and Keap1-/- mice on C57BL background at E11.5, E15.5, P0 and P7,  and esophageal epithelium of adult (8 weeks old) mice

status: Public on Dec 09 2011

city: Camden

first: Xiaoxin

middle: Luke

last: Chen

state: NJ

address: 403 Haddon Avenue

institute: Coriell Institute for Medical Research

summary: Transcriptional profiling of mouse esophageal development. Goal was to globally profile critical genes and signaling pathways during the development of mouse esophagus and determine how Nrf2/Keap1 pathway regulates the morphogenesis of the esophageal epithelium.

overall_design: Mutiple-comparison. WT-E11.5 vs. WT-E15.5 vs. WT-P0 vs. WT-P7; WT-P7 vs. WT-adult; WT-adult vs. Nrf2-/--adult; WT-P7 vs. Nrf2-/--P7 vs. Keap1-/--P7 vs. Nrf2-/-Keap1-/--P7. Biological replicates: 3 replicates for each group.

first: Hao


title: Gene Expression from diabetic ischemic limbs in WT and p75KO mice

status: Public on Dec 24 2011

city: Vienna

first: Klemens

last: Vierlinger

address: Giefinggasse 4

department: HMD

country: Austria

institute: AIT

summary: Transcriptome analysis was carried out to characterise the different responses of diabetic and non-diabetic WT and p75KO mice to ischemia

overall_design: C57BL/6J-p75NTR-/- (p75KO) and p75NTR+/+ (WT) littermates were bred starting from breeding pairs.  Six to seven week old male p75KO and WT mice were made diabetic using streptozotocin (STZ, 40 mg/kg in 0.1mol/l citrate buffer pH4.5 i.p. per day for 5 days or left normoglycemic by STZ buffer injections. One or three months after diabetes induction, anesthetized mice underwent unilateral hindlimb ischemia by permanent ligation and electro-coagulation of the proximal end of femoral arteries. At the same time, full thickness wounds were created in the thigh dorsal skin of both legs using a sterile 5-mm-wide biopsy punch. Samples for  gene expression analysis were taken from the wounds three days later.

first: Costanza

last: Emanueli


title: Gene expression profiling of mouse prostate stem cells

status: Public on Dec 06 2011

city: South San Francisco

first: Yuting

last: Sun

state: CA

address: 1 DNA way

department: Research Oncology

institute: Genentech

summary:
The mouse prostate tissue exhibits strong power of regeneration, indicating the exisistence of prostate stem cells. Previously we showed that a single mouse prostate cells defined by Lin-CD44+CD133+Sca-1+CD117+ phenotype can generate a prostate after transplantation in vivo.
In this study, we compared gene expression profiles of mouse prostate stem cells ( Lin-CD44+CD133+Sca-1+CD117+) and prostate non-stem cells (Lin-CD44-CD133-Sca-1-CD117-).

overall_design: Primary mouse prostate cells were isolated from BL6 mice. Lin-CD44+CD133+Sca-1+CD117+ and Lin-CD44-CD133-Sca-1-CD117- cells were sorted via FACS, and microarray was performed to compare gene expressions between the two groups of cells.

first: Wei-Qiang

last: Gao

first: Jeffrey

last: Settleman

first: Leisa

last: Johnson


title: Early Peroxisome proliferator-activated receptor gamma regulated genes involved in expansion of pancreatic beta cell mass

status: Public on Jan 16 2012

city: Valencia

first: Francisco

middle: García

last: García

address: Eduardo Primo Yúfera, 3

department: Bionformatics & Biostatistics Unit

country: Spain

institute: CIPF

summary:
The progression towards type 2 diabetes depends on the success of the allostatic response of the pancreatic beta cells to synthesise and secrete enough insulin to compensate for insulin resistance. The endocrine pancreas is a plastic tissue able to expand or regress in response to the requirements imposed by physio and pathological states such as pregnancy, obesity or ageing. The mechanisms, mediating beta cell mass expansion in these scenarios are not well defined. We have recently showed that beta cell mass failed to expand in ob/ob mice with genetic ablation of PPARγ2, a mouse model known as the POKO mouse.
This phenotype contrasted with the appropriate expansion of the beta cell mass observed in their obese littermate ob/ob mice. Here we investigate PPAR gamma dependent transcriptional responses occurring during early stages of the adaptation of beta cells to insulin resistance. As it could be expected we have identified genes known to regulate proliferation and survival signals of the beta cells. Moreover we have also identified new pathways induced in ob/ob islets that fail to do so in POKO islets. Our data suggest that the expansion of beta cell mass observed in ob/ob islets is associated with activation of immune response and is missing in POKO islets. Other PPARγ dependent differentially regulated pathways include cholesterol biosynthesis, apoptosis through TGF-β signaling and decreased oxidative phosphorylation.

overall_design: In this study, we used gene expression arrays  to investigate differences between four experimental classes by pairs

first: Y

last: Vivas

first: C

last: Martínez-García

first: A

last: Izquierdo

first: F

last: García-García

first: S

last: Callejas

first: I

last: Velasco

first: M

last: Campbell

last: Ros

last: Dopazo

first: J

last: Vidal-Puig

first: G

last: Medina-Gomez


title: Gene Expression Analysis of Host Innate Immune Responses in the Brain and Spinal cord following Lethal CVS-11 Infection in Mice

status: Public on Dec 01 2011

city: Shinjuku-ku

first: Naoko

last: Sugiura

state: Tokyo

address: Toyama 1-23-1

country: Japan

institute: National Institute of Infectious Diseases

summary: The microarray and advanced pathway analysis of mice caused a paralysis in a fatal infection of a highly pathogenic CVS-11 was performed for the understanding of the detail gene networks and biological functions of inflammatory response and the related genes of innate immunity and apoptosis.

overall_design:
Brain Samples: Six female C57BL/6J mice aged six weeks old were inoculated 1E+7 focus-forming units (FFU) of CVS-11 propagated in MNA cells into the left hind limb, intramuscularly. On the other hand, MEM was inoculated into 6 negative control mice in a similar way. Each mice were sacrificed to collect their brains at days 7 postinoculation (dpi). Six mice were used for the analysis of microarray. The six of mock mice were also sacrificed at 7 dpi for the microarray analysis.
Spinalcord Samples: Six female C57BL/6J mice aged six weeks old were inoculated 1E+7 focus-forming units (FFU) of CVS-11 propagated in MNA cells into the left hind limb, intramuscularly. On the other hand, MEM was inoculated into 6 negative control mice in a similar way. Each mice were sacrificed to collect their spinal cords at days 7 postinoculation (dpi). Six mice were used for the analysis of microarray. The six of mock mice were also sacrificed at 7 dpi for the microarray analysis.

first: N

last: Inoue

last: Uda

first: D

last: Kojima

last: Kaku

last: Okutani

last: Noguti

last: Park

last: Yamada


title: A single N66S mutation in the PB1-F2 protein of influenza A virus increases virulence by inhibiting the early interferon response in vivo

first: Michael

last: Katze

summary: This study used virological, histological, and global gene expression from an experimental murine model of influenza infection to study the contribution of a specific mutation in the PB1-F2 protein (PB1-F2 N66S) of influenza A to viral pathogenesis.

overall_design: 6-8 week old, wild-type, female, C57Bl/6 mice were inoculated individually with 30 μl (10^4 PFU) of virus (recombinant influenza A/WSN/33 carrying the PB1 gene segment from A/Hong Kong/156/97 (H5N1) or a PB1 mutant recombinant virus resulting in an amino acid change at position 66 in the PB1-F2 protein [N66S]) in phosphate-buffered saline (PBS) containing penicillin-streptomycin and bovine serum albumin (PBS-BA-PS). A total of 10^4 PFU of virus was given in all inoculations. Control mice were given PBS-BA-PS.  Lung samples were taken for microarray analysis at 12h, 1d, 3d, and 5d post-infection (n=3 animals per group at each time point for virus infected animals; n=2 animals per time point for mock-infected animals).

first: Gina

last: Conenello

first: Jennifer

last: Tisoncik

first: Elizabeth

last: Rosenzweig

first: Zsuzsanna

last: Varga

first: Peter

last: Palese


title: WT vs Hypomethylated DRG Gene Expression

city: Nara

first: Masakazu

last: Namihira

address: 8916-5 Takayama, Ikoma

department: Graduate School of Biological Sciences

institute: NAIST

summary: Although DNA methylation plays a critical role in the development and function of mammalian central nervous system (CNS), its role in peripheral neurons has not been elucidated. To address this issue, we produced conditional knockout mice (CKO) specifically deleting the gene for maintenance DNA methyltransferase 1 (Dnmt1) during the development of neural crest cells. Despite global hypomethylation in the embryonic dorsal root ganglion (DRG) of the CKO mice, the number of sensory neurons was relatively unaffected.  However, expression of many genes required for sensory neuron development was altered in embryonic mutant DRG, including down-regulation of Runx1 and TrkA genes as well as up-regulation of Id1 and Dtx1, two negative regulators for neurogenesis. Accompanied with the downregulation of an NGF receptor TrkA, the peripheral axonal projection and the branching of sensory neurons were impaired. Furthermore, the expression of the neuropeptide Galanin and several vanilloid receptors such as TrpV1 and TrpM8 were not detected in the DRG of the CKO mice during late embryonic and neonatal stages, suggesting that DNA methylation regulates the differentiation program for a subset of nociceptive sensory neurons.  Taken together, our findings suggest that through transcriptional regulation of key developmental genes in sensory neurons, DNA methylation play a key role in the control of the axonal projection and fate specification of peripheral sensory neurons.

overall_design: We compared gene expression patterns in Wildtype and DNA methylation deficient (Wnt1-cre; Dnmt1 mutant) mouse dorsal cortex. We performed 4 replicates using different each individual mouse strain. The Sample GSM565172 table is the average log ratio for the 4 replicatesArrays were performed.

first: Norihisa

last: Masuyama

middle: J

last: Clark

first: Guoping

last: Fan


title: Murine bone marrow-derived mast cells (BMMCs) transduced with pAPM lentiviruses overexpressing miR-221 vs control overexpressing miR-221m.

status: Public on Nov 23 2011

city: Bellinzona

first: Silvia

last: Monticelli

address: Via Vincenzo Vela, 6

country: Switzerland

institute: Institute for Research in Biomedicine

summary: Bone marrow-derived mast cells were derived from three different female C57Bl/6 mice of similar age. Cells were transduced with pAPM lentiviruses either overexpressing microRNA-221 or a non functional microRNA-221 mutant, termed miR-221m, where four point-mutations were introduced in the seed sequence of miR-221. The samples overexpressing miR-221m were used as references for the corresponding miR-221 overexpressing BMMCs from the same mouse (mouse matched reference). The experiment was performed in order to gain more insights about the molecular mechanisms underlying miR-221 effects in mast cells.

overall_design: Two-condition experiment, BMMC overexpressing miR-221 vs BMMC overexpressing miR-221m. Biological replicates: 3 replicates overexpressing miR-221, 3 control replicates overexpressing miR-221m.

first: Ramon

last: Mayoral


title: A key role for Mbd3 in 5-hydroxymethylcytosine-dependent gene regulation in embryonic stem cells

city: Worcester

first: Thomas

middle: G.

last: Fazzio

address: LRB 519, 364 Plantation Street

department: Program in Gene Function and Expression

institute: University of Massachusetts Medical School

summary: To identify functional interactions among six chromatin regulators with key roles in embryonic stem cells, we examined gene expression changes in mouse ES cells with single and pair-wise combinations of knockdowns for those factors, along with control (EGFP) KDs.

overall_design: Effects on gene expression of RNAi-mediated knockdown of combinations of chromatin regulators. KDs were performed in duplicate for each combination for 48 hours.


title: Gene expression profile of calcium mediated prevention of colorectal cancer in a mouse model

city: Shanghai

first: Jing-Yuan

last: Fang

state: Shanghai

address: 145 Middle Shandong Rd

department: Division of Gastroenterology

country: China

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

summary: To further elucidate the mechanism of calcium 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 high calcium 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 high calcium group were received high calcium diet(calcium concentration,3%) 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 high calcium group mice with tumors, and 3 from high calcium group mice without tumors) were used for the microarray analysis.

overall_design: The differentially expressed genes were indentified between high calcium group and DMH group,as long as differentially expressed pathways and gene ontology terms.

first: Ji-Lin

last: Wang

first: Yan-Wei

last: Lin


title: RNAi-mediated knockdown of Xist can rescue the impaired postimplantation development of cloned mouse embryo

status: Public on Nov 17 2011

city: Tsukuba

first: Kimiko

last: Inoue

state: Ibaraki

address: 3-1-1 Koyadai

department: Bioresource Engineering Division

institute: BRC, RIKEN

summary: Cloning mammals by somatic cell nuclear transfer (SCNT) is highly inefficient. Most SCNT-generated embryos die after implantation because of unidentified, complex epigenetic errors in the process of postimplantation embryonic development. Here, we identified the most upstream level of dysfunction leading to impaired development of clones by using RNA interference (RNAi) against  Xist, a gene responsible for X chromosome inactivation (XCI). A prior injection of Xist-specific short interfering (si)RNA into reconstructed oocytes efficiently corrected the SCNT-specific aberrant Xist expression at the morula stage, but failed to do so thereafter at the blastocyst stage. However, we found that shortly after implantation this aberrant XCI status in cloned embryos had been corrected autonomously in both embryonic and extraembryonic tissues, probably through a newly established XCI control for postimplantation embryos. Embryo transfer experiments revealed that the siRNA-treated embryos showed 10 times higher survival than controls as early as embryonic day 5.5 and this high survival persisted until term, resulting in a remarkable improvement in cloning efficiency (12% vs. 1% in controls).  Importantly, unlike control clones, these Xist-siRNA clones at birth showed only a limited dysregulation of their gene expression, indicating that correction of  Xist expression in preimplantation embryos had a long-term effect on their postnatal normality. Thus, contrary to the general assumption, our results suggest that the fate of cloned embryos is determined almost exclusively before implantation by their XCI status. Furthermore, our strategy provides a promising breakthrough for mammalian SCNT cloning because RNAi treatment of oocytes is readily applicable to most mammal species.

overall_design: Gene expression were measured in mouse in vitro fertilized and somatic cell cloned embryos. Four biological replicates were performed in each group of Xist- or Control-siRNA.

first: Shogo

last: Matoba

first: Takashi

last: Kohda

first: Michihiko

last: Sugimoto

first: Eiji

last: Mizutani

first: Narumi

last: Ogonuki

first: Toshinobu

last: Nakamura

first: Kuniya

last: Abe

first: Toru

last: Nakano

first: Fumitoshi

last: Ishono

first: Atsuo

last: Ogura


title: Expression data from MCF7 tumor xenografts treated with either single agent BMS754807, or Tamoxifen or Letrozole alone; or Tamoxifen or Letrozole in combination with BMS754807 for 28 days

status: Public on Nov 02 2011

city: Princeton

first: Fei

last: Huang

institute: Bristol-Myers Squibb Co

summary:
breast cancer. Combined IGF and estrogen-targeted therapy may improve the benefit of hormonal therapy alone. We employed a postmenopausal model of estrogen-dependent breast cancer in vitro and in vivo using the aromatase-expressing MCF-7/AC-1cells. Using this model, we investigated the anti-tumor effects of the dual IGF-1R/InsR tyrosine kinase inhibitor, BMS-754807 alone and in combination with letrozole or tamoxifen in vivo.
We used microarrays to compare gene expression changes of MCF7 breast xenograft treated with either BMS754807, or Tamoxifen or Letrozole alone; or Tamoxifen or Letrozole in combination with BMS754807 for 28 days

overall_design: Breast xenograft  MCF7 bearing mice treated with either BMS754807, or Tamoxifen or Letrozole alone; or  Tamoxifen or Letrozole in combination with BMS754807 for 28 days. RNA were extracted from tumors and hybridizedon Affymetrix microarrays to compare gene expression changes

first: Xiaonan

last: Hou

first: Luciana

last: Macedo

first: Sean

middle: C

last: Harrington

first: Karen

middle: A

last: Reeves

first: Ann

last: Greer

first: Friedrich

last: Finckenstein

first: Angela

last: Brodie

first: Marco

last: Gottardis

first: Joan

last: Carboni

first: Paul

last: Haluska


title: Mouse lung tumor tissue: Dnmt3a KO vs. Dnmt3a WT

status: Public on Oct 26 2011

first: Qing

last: Gao

institute: Whitehead Institute

summary: Transcriptional profiling of mouse lung tumors comparing Dnmt3a KO/K-ras G12D mutant with Dnmt3a WT/K-ras G12D mutant. The goal is to search for the difference of mRNA abundance between Dnmt3a KO and WT tumors.

overall_design: Two-condition experiment, KO vs. WT tissure. Biological replicates: 12.


title: The induction of integrin beta3 signaling in hematopoietic stem cells (HSCs)

status: Public on Nov 16 2011

city: Shinjuku-Ku

first: Terumasa

last: Umemoto

address: 8-1, Kawada-Cho

institute: Tokyo women's medical university

summary: To determine the molecules involved in beta3 integrin signaling in HSCs, we carried out DNA microarray analyses using HSCs stimulated with ligand-mimic antibody for intetegrin beta3 in the presence of stem cell factor(SCF) and/or thrombopoietin (TPO). All experiments were performed in duplicate or triplicate using sorted cells that were independently prepared in separate experiments.

overall_design: After CD34-KSL HSCs were cultured with 2C9.G2 or control IgG for 5 days in S-Clone SF-03 medium supplemented with 50 ng/ml SCF and/or 50 ng/ml TPO, gene expression profiles were examimed using 5,000 sorted CD48-KSL cells from each sample.

first: Masayuki

last: Yamato

first: Koji

last: Eto

first: Okano

last: Teruo


title: Clinical Relevance of Multidrug Resistance Gene Expression in Ovarian Serous Carcinoma Effusions

city: Namur

first: jean-pierre

last: gillet

address: 61 Rue de Bruxelles

department: URPhyM

country: Belgium

institute: University of Namur

summary:
The presence of tumor cells in effusions within serosal cavities is a clinical manifestation of advanced-stage cancer and is generally associated with poor survival.
Identifying molecular targets may help to design efficient treatments to eradicate these aggressive cancer cells and improve patient survival.
Using a state-of-the-art Taqman-based qRT-PCR assay, we investigated the multidrug resistance (MDR) transcriptome of 32 unpaired ovarian serous carcinoma effusion samples obtained
at diagnosis or at disease recurrence following chemotherapy. MDR genes were selected a priori based on an extensive curation of the literature published during the last three decades.
We found three gene signatures with a statistically significant correlation with overall survival (OS), response to treatment (complete response - CR vs. other), and progression free survival (PFS).
The median log-rank p-values for the signatures were 0.023, 0.034, and 0.008, respectively. No correlation was found with residual tumor status after cytoreductive surgery, treatment
(with or without chemotherapy) and stage defined according to the International Federation of Gynecology and Obstetrics. Further analyses demonstrated that gene expression alone can
effectively predict the survival outcome of women with ovarian serous carcinoma (OS: log-rank p=0.0000 and PFS: log-rank p=0.002). Interestingly, the signature for overall survival
is the same in patients at first presentation and those who had chemotherapy and relapsed. This pilot study highlights two new gene signatures that may help in optimizing the treatment
for ovarian carcinoma patients with effusions.

overall_design:
In the study presented here, effusion samples were obtained from 32 patients diagnosed with serous ovarian carcinoma (n=25), primary peritoneal serous carcinoma (n=6) or tubal serous carcinoma (n=1).
They were accrued at the Division of Pathology in the Norwegian Radium Hospital from 2000-2006. RNA was used to study the expression profile of 381 multidrug resistant-related genes.

first: Jean-Pierre

last: Gillet

first: Junbai

last: Wang

first: Anna-Maria

last: Calcagno

first: Lisa

last: Green

first: Sudhir

last: Varma

first: Mar-Bunkholt

last: Elstrand

first: Claes

middle: G

last: Trope

first: Suresh

middle: V

last: Ambudkar

first: Ben

last: Davidson

first: Michael

middle: M

last: Gottesman


title: Gene expression in Rspo2 and/or Wnt3a treated C57MG mouse mammary epithelial cells

status: Public on Oct 05 2011

city: Bethesda

first: Jeffrey

middle: S

last: Rubin

state: MD

address: 37 Convent Drive

department: CCR

institute: NIH/NCI

summary: R-spondins (Rspos) comprise a family of four secreted proteins that have important roles in cell proliferation, cell fate determination and organogenesis.  Rspos typically exert their effects by potentiating the Wnt/β-catenin signaling pathway. To systematically investigate the impact of Rspo/Wnt on gene expression, we performed a microarray analysis using C57MG mouse mammary epithelial cells treated with recombinant Rspo2 and/or Wnt3a.

overall_design: This study compares gene expression in C57MG cells after 24h treatment with recombinant Rspo2 and recombinant Wnt3a alone or in combination versus BSA treatment. Control cells were treated with BSA, since it was used as carrier for the recombinant proteins. Each treatment was done in biological triplicate.

first: Bolormaa

last: Baljinnyam

first: Robert

last: Callahan


title: Class IA PI3Kinase regulatory subunit p85α regulates mast cell growth and survival related genes

status: Public on Sep 28 2011

city: Indianapolis

first: Raghuveer

last: Mali

state: Indiana

address: 1044 W Walnut St., R4 169

department: Pediatrics

institute: Indiana University School of Medicine

summary: Stem cell factor (SCF) mediated KIT receptor activation plays a pivotal role in mast cell growth, maturation and survival. However, the signaling events downstream from KIT are poorly understood. Mast cells express multiple regulatory subunits of class 1A PI3Kinase (PI3K) including p85α, p85β, p50α, and p55α. While it is known that PI3K plays an essential role in mast cells; the precise mechanism by which these regulatory subunits impact specific mast cell functions including growth, survival and cycling are not known. We show that loss of p85α impairs the growth, survival and cycling of mast cell progenitors (MCp). To delineate the molecular mechanism (s) by which p85α regulates mast cell growth, survival and cycling, we performed microarray analyses to compare the gene expression profile of MCps derived from WT and p85α-deficient mice in response to SCF stimulation. We identified 151 unique genes exhibiting altered expression in p85α-deficient cells in response to SCF stimulation compared to WT cells. Functional categorization based on DAVID bioinformatics tool and Ingenuity Pathway Analysis (IPA) software relates the altered genes due to lack of p85α to transcription, cell cycle, cell survival, cell adhesion, cell differentiation, and signal transduction. Our results suggest that p85α is involved in mast cell development through regulation of expression of growth, survival and cell cycle related genes.

overall_design: Two-condition experiment,  wildtype vs. p85α-deficient mast cell progenitors stimulated with SCF. Biological replicates: 3 wildtype replicates, 3 p85α-deficient replicates.

first: Subha

last: Krishnan

first: Reuben

last: Kapur


title: Gene expression in mouse Lhx2 knock out embryo (E16.5) vs FVB controls

status: Public on Oct 04 2011

city: Bradford

first: Andrei

last: Mardaryev

address: Richmond Road

country: United Kingdom

institute: University of Bradford

summary: The Lhx2 transcription factor plays essential roles in morphogenesis and patterning of ectodermal derivatives, as well as in controlling stem cell activity. Lhx2 is expressed in the hair follicle (HF) buds, while in postnatal telogen HFs Lhx2+ cells reside in the stem cell-enriched epithelial compartments (bulge, secondary hair germ) and co-express selected stem cell markers (Sox9, Tcf4 and Lgr5). Lhx2+ cells represent the vast majority of cells in the bulge and secondary hair germ that proliferate in response to skin injury. This is functionally important, since the wound re-epithelialization is significantly retarded in heterozygous Lhx2 knockout (+/-) mice, while anagen onset in the HFs located closely to the wound is accelerated compared to wild-type mice. Cell proliferation in the bulge and the number of Sox9+ and Tcf4+ cells in the HFs closely adjacent to the wound in Lhx2+/- mice are decreased in comparison to wild-type controls, while expression of Lgr5 and cell proliferation in the secondary hair germ are increased. Furthermore, acceleration of wound-induced anagen development in Lhx2+/- mice is inhibited by administration of Lgr5 siRNA. In addition, Chip-on-chip/ChIP-qPCR and reporter assay analyses reveal Sox9, Tcf4 and Lgr5 as direct Lhx2 targets in keratinocytes. These data strongly suggest that Lhx2 positively regulates Sox9 and Tcf4 in the bulge cells and promotes wound re-epithelization, while it simultaneously negatively regulates Lgr5 in the secondary hair germ and inhibits HF cycling. Thus, Lhx2 operates as a regulator of epithelial stem cell activity during skin response to injury.

overall_design: Total RNA derived from Lhx2KO and WT embryos was subjected to a dual-color microarray analysis, in which the RNA from Lhx2KO embryo was labelled with Cy3 and that of WT embryo with Cy5 respectivly

middle: N

first: Vladimir

last: Botchkarev


title: Expression data from treatment of actinomycin D and triptolide on MCF7 cells

status: Public on Oct 18 2011

city: Cambridge

first: Guo

last: Wei

address: 7 Cambridge Center

institute: Broad Institute or MIT and Harvard

summary:
Expression data from treatment of actinomycin D (2.5uM) and triptolide (500 nM) on MCF7 cells for 2, 4 and 6 hours.
We used microarrays to explore the mechanism of triptolide action.

overall_design: MCF7 cells were treated with actinomycin D or triptolide for 2, 4 and 6 hours, RNA was extracted and hybridization on Affymetrix microarrays. Data were normalized by RMA.

first: Todd

last: Golub


title: Uniform, integration-free iPS cells with a safeguard system using human artificial chromosome vectors

status: Public on Oct 16 2011

city: Yonago

first: Masaharu

last: Hiratsuka

state: Tottori

address: Nishicho 86

department: Molecular and Cellular Biology

institute: Tottori university, Faculty of Medicine

summary: Human artificial chromosomes (HACs) have unique characteristics as gene-delivery vector, e.g., episomal transmission and transfer of multiple, large transgenes. Here, we demonstrate the advantages of HAC vectors for reprogramming mouse embryonic fibroblasts (MEFs) to induced pluripotent stem (iPS) cells. Two HAC vectors (iHAC1 and iHAC2) were constructed. Both carried four reprogramming factors, and iHAC2 also encoded a p53-knockdown construct (see Kazuki et al 2011). The iHAC1 partially reprogrammed MEFs, and the iHAC2 efficiently reprogrammed MEFs. Global gene expression showed that the iHACs, unlike other vectors, generated relatively uniform iPS cells. We established iHAC-free iPS cells by isolating cells that spontaneously lost the iHAC2. Analyses of pluripotent markers, teratomas, and chimeras confirmed that these iHAC-free iPS cells were pluripotent. Moreover, iHAC-free iPS cells with a re-introduced HAC encoding Herpes Simplex Virus Thymidine Kinase were eliminated by Ganciclovir treatment; therefore, the HAC safeguard system functioned in iPS cells. Thus, the HAC vector could generate uniform, integration-free iPS cells with a safeguard system.

overall_design: Total RNA from mouse embryonic fibroblasts, two control ES cells (TT2 and B6ES), retrovirus vector-derived iPS cells (20D17), and twelve HAC-derived iPS clones were hybridized to the Agilent Whole Mouse Genome microarrays.

first: Mitsuo

last: Oshimura


title: Hippocampal gene network analysis to determine the effects of coral calcium hydride in an experimental model of accelerated senescence

status: Public on Sep 23 2011

city: Toyohashi

first: Toshio

last: Kojima

address: 1-1 Hibarigaoka Tenpaku-cho

department: Health Care Center

institute: Toyohashi University of Technology

summary: Recent studies strongly support the hypothesis that antioxidant diet inhibits the pathological aging process as shown in senescence-accelerated mouse prone 8 (SAM/P-8). In our previous study, we reported that a diet rich in antioxidants inhibits the pathological aging process, as shown coral calcium hydride (CCH) increased the endogenous antioxidant ability and contributed to prolonging the life-span of SAM/P-8.  In order to test the hypothesis that antioxidant CCH supplementation to SAM/P-8 mice would change the gene expression and understand how CCH reverses the acceleration of aging in SAM/P-8 mice, in the current study, we used a DNA array to compare the expression levels in the hippocampus of the brains from 16-week-old SAM/P-8 mice treated or not treated with CCH. The most significant up regulated changes in the gene network of SAM/P-8 mice were free radical scavenging and molecular transport, and genes associated with cell death, cancer, and cell cycle were downregulated. Our findings about changes in these mRNA might be associated with  that inhibition of the acceleration of aging is observed in SAM/P-8 mice fed a CCH-diet.

overall_design: Eight-week-old male SAM/P-8 and SAM/R-1 mice were assigned to two groups: the CCH-fed group (fed with CCH for 8 weeks with CE-2 (rodent diet, Clea Japan, Inc., Tokyo, Japan) containing 0.1% CCH) and the control group (fed with CE-2 for 8 weeks).

first: Yuto

last: Ueda

first: Taneaki

last: Oikawa


title: Identification of Hoxa1 downstream targets

status: Public on Sep 03 2011

city: Salt Lake city

first: Nadja

last: Makki

address: 15 North ,2030 East

institute: University of Utah

summary: To better understand the role of Hoxa1 during embryogenesis and gain insight to the transcriptional network controlled by this gene, we carried out a large-scale screening for Hoxa1 downstream targets by performing microarray analysis.  Tissue from the rhombomere 3-5 region of wildtype and Hoxa1 null embryos, including neuroectoderm, mesoderm and otic ectoderm was microdissected at the peak of Hoxa1 expression.  RNA from wildtype and Hoxa1Δ/Δ samples was hybridized to the Agilent mouse whole genome array.

overall_design: Tissue from the rhombomere 3-5 region of wildtype and Hoxa1 null embryos, including neuroectoderm, mesoderm and otic ectoderm was microdissected at the peak of Hoxa1 expression (1-6 somite stage).

first: Mario

last: Capecchi


title: Role of Eif4g3 and Deaf1 in Lymph node

status: Public on Sep 01 2011

city: Stanford

first: Linda

last: Yip

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

department: Medicine

institute: Stanford University

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

overall_design: Refer to individual Series


title: Differential gene expression in the Pancreatic lymph node of Deaf1 knockout mice vs. wild type littermate controls

summary: Gene expression in the the pancreatic lymph node of 4, 12, and 30 week old Deaf1-knockout (KO) mice compared to BALB/c littermate controls.

overall_design: Gene expression was measured in the pancreatic lymph nodes of 4 wk old Deaf1 KO mice (2 replicates), 12 wk old Deaf1-KO mice (3 replicates), and 30 wk old Deaf1-KO mice (3 replicates).


title: ECAT15-2/Dppa2 deficient ESCs

status: Public on Oct 17 2011

city: Kyoto

first: Shinya

last: Yamanaka

address: 53 Kawahara-machi, Shogoin, Sakyo-ku

institute: Center for iPS Cell Research and Applicaton (CiRA), Kyoto University

summary: Many transcription factors and DNA binding proteins play essential roles in the development of organs in which they are highly and/or specifically expressed. Embryonic stem cell (ESC) associated transcript (ECAT) 15-1 and ECAT15-2, also known as developmental pluripotency-associated (Dppa) 4 and Dppa2, are enriched in mouse ESCs and pre-implantation embryos, and encode homologous proteins with a common DNA binding domain known as the SAP motif. Previously, ECAT15-1 was shown to be important in the lung development, while it is dispensable in early development. In this study, we generated ECAT15-2 single and ECAT15-1/15-2 double knockout mice and found that almost all mutants, like ECAT15-1 mutants, died around birth with respiratory defects. Paradoxically, the expression of neither ECAT15-1 nor ECAT15-2 was detected in lung organogenesis. Several genes, such as Nkx2-5, Gata4, and Pitx2 were down-regulated in the ECAT15-2-null lung. On the other hand, genomic DNA of these genes showed inactive chromatin statuses in ECAT15-2-null ESCs, but not in wild-type ESCs. Chromatin immuno-precipitation (ChIP) assay revealed that ECAT15-2 binds to the regulatory region of Nkx2-5 in ESCs. These data suggest that ECAT15-2 have important roles in lung development where it is no longer expressed, by leaving epigenetic marks from earlier developmental stage.

overall_design: ESCs were established from E3.5 blasotcysts of 15-1+/CT, 15-2+/- intercross (CT allele; conditional targeted allele). They were harvested on gelation coated dish with ES medium containing 15% FCS and LIF for three days. The total RNA from two wild type and two ECAT15-2 deficient ESCs (15-1CT/CT, 15-2-/-) was labeled with Cy3. Samples were hybridized with Whole Mouse Genome Microarray 4 x 44K (G4122F, Agilent), with the one color protocol. Data was analyzed by using GeneSpring GX11 software (Agilent).

first: Nakamura

last: Tomonori

first: Narita

last: Megumi


title: Lymph node stromal cells: Control siRNA treated vs. Eif4g3 siRNA treated

summary:
Gene expression in the top, light and heavy polysome fractions of Eif4g3 siRNA treated lymph node stromal cells (LNSCs) compared to control-sIRNA treated samples
This study was performed to examine whether the expression of certain genes in LNSCs is regulated by the translation factor, eukaryotic translation initiation factor 4 gamma 3 (Eif4g3).

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.  Cells were pooled, lysed and fractionated on a 10% to 60% continuous sucrose gradient. Fractions were collected and pooled into the top, light and heavy polysome fractions.  RNA was extracted from these samples and used for microarrays on the Agilent Whole Mouse Genome Microarray Kit, 4×44K 2-color arrays.


title: Lung of ECAT15-2/Dppa2 deficient embryo at E18.5

overall_design: Embryos from 15-1+/Flox, 15-2+/- intercross at E18.5 were digested, and their lungs were removed. The whole lung RNA from three wild type and three ECAT15-2 deficient embryos (15-1Flox/Flox, 15-2-/-) was labeled with Cy3. Samples were hybridized with Whole Mouse Genome Microarray 4 x 44K (G4122F, Agilent), with the one color protocol. Data was analyzed by using GeneSpring GX11 software (Agilent).


title: ECAT15-2/Dppa2 transgenic rescue into ECAT15-2/Dppa2 deficient ESCs

overall_design: The ECAT15-2 mutant ESCs (15-1CT/CT, 15-2-/-) were established from E3.5 blasotcysts of 15-1+/CT, 15-2+/- intercross (CT allele; conditional targeted allele). Then the Flag-tagged ECAT15-2/Dppa2 transgenic vector based on piggyBac system were introduced. They were harvested on gelation coated dish with ES medium containing 15% FCS and LIF for three days. The total RNA from two wild type, two mock transduced ECAT15-2 deficient ESCs and two Flag-tagged ECAT15-2 transduced ECAT15-2 deficient ESCs were labeled with Cy3. Samples were hybridized with Whole Mouse Genome Microarray 4 x 44K (G4122F, Agilent), with the one color protocol. Data was analyzed by using GeneSpring GX11 software (Agilent).


title: Role of ECAT15-2/Dppa2 in lung development


title: Gene expression in astrocytes upon sustained GSK-3 inhibition by small molecule

city: Tokyo

first: francois

middle: frederic

last: renault-mihara

address: 35 Shinanomachi, Shinjuku-ku

department: Physiology

institute: Keio University School of Medicine

summary: In order to identify molecular targets that mediates the stimulation of astrocyte's migration upon sustained specific inhibition of GSK-3, we have employed whole genome microarray expression profiling. Murine cortical-striatal astrocytes grown in primary culture were treated in vitro for 48 h with either 1 micromolar Ro3303544, or control medium (final equivalent concentration of DMSO), or washed-out for 48h in control medium after an initial 48h treatment with 1 micromolar Ro3303544.

overall_design: The three different conditions: Ctrl, Ro and wash-out (each in duplicate) were compared.

first: Francois

last: Renault-Mihara

first: Hideyuki

last: Okano


title: High-fat dietary restriction in mice induces substrate efficiency and improves metabolic health

status: Public on Aug 24 2011

city: Wageningen

first: Evert

last: van Schothorst

address: Marijkeweg 40

department: Human and Animal Physiology

country: Netherlands

institute: Wageningen University

summary: High energy intake and, specifically, high dietary fat intake challenges the mammalian metabolism and correlates with many metabolic disorders, such as obesity and diabetes. Dietary restriction (DR) is, on the other hand, known to prevent the development of metabolic disorders. The current Western diets are highly enriched in fat and it is as yet unclear whether DR on a certain high-fat (HF) diet elicits similar beneficial effects on health. Here, we report that HF-DR improves metabolic health of mice, compared to mice receiving the same diet on an ad-libitum basis (HF-AL). Already after five weeks of restriction the serum levels of cholesterol and leptin were significantly decreased in HF-DR mice, while their glucose sensitivity and serum adiponectin levels were increased. The body weight and measured serum parameters remained stable in the following 7 weeks of restriction, implying metabolic adaptation. To understand the molecular events associated with this adaptation, we analysed gene expression in white adipose tissue (WAT) with whole genome microarrays. HF-DR strongly influenced gene expression in WAT; in total 8,643 genes were differentially expressed between both groups of mice, with a major role for genes involved in lipid metabolism and mitochondrial functioning. This was confirmed by qRT-PCR and substantiated by an increase in mitochondrial density in WAT of HF-DR mice. These results provide new insights in the metabolic flexibility of dietary restricted animals and suggest the development of substrate efficiency. Limiting food intake by decreasing portion sizes, while maintaining energy sufficiency, may similarly benefit metabolic health in humans.

overall_design: Epididymal white adipose tissue (epiWAT) samples were obtained from 36 C57BL/6J male adult mice. All mice started with a three week adaptation phase, in which they were fed a high-fat diet. 12 mice were sacrificed immediately after the adaptation phase (t=0). The other 24 mice remained on the same diet for 12 weeks. Half of the mice, however, received the diet on an ad-libitum basis (HF-AL), while the remaining 12 mice received the high-fat diet on a restricted basis (of 70 en%) (HF-DR). The diet that was used for dietary restriction was in ratio supplemented with a vitamin and mineral premix to guarantee the same level of intake as in the non-restricted group to prevent deficiencies.

first: Loes

middle: P

last: Duivenvoorde


title: Vitamin C Promotes Positive Selection of Mouse T Cells

city: Salt Lake City

first: Gerald

middle: J.

last: Spangrude

state: UT

department: Medicine/Hematology

summary:
We discovered that vitamin C (ascorbic acid) is required for differentiation of mouse bone marrow-derived progenitor cells in T cell cultures based on OP9-DL1 stromal cells.
This microarray dataset evaluates differential expression of genes in OP9-DL1 stromal cells as well as in lymphocytes developing in the cultures when a stabilized form of ascorbic acid (l-ascorbic acid 2-phosphate; pAsc) is added.
Cultures were maintained in the absence of pAsc for 13 days, at which time 800 micromolar pAsc was added. Cells were harvested after 24 and 72 hours (24 hours only in the case of OP9-DL1 cells) and solubilized in Trizol.

overall_design: Two-condition experiment, differentiating T lymphoid cells with or without pAsc, 2 timepoints, OP9-DL1 cells with or without pAsc, 1 timepoint, no technical replicates


title: A genome-wide expression profile of steroidogenic cells selectively isolated from adrenal glands of knockout mice lacking steroidogenic acute regulatory protein

status: Public on Aug 14 2011

first: Tomohiro

last: Ishii

institute: School of Medicine, Keio University

summary: Steroidogenic acute regulatory protein (Star) facilitates cholesterol transfer into the inner mitochondrial membrane in the acute and regulated production of steroid hormones. Mice lacking Star (Star-/-) share the phenotypes with patients with congenital lipoid adrenal hyperplasia such as compromised production of steroid hormones and florid accumulation of cholesterol esters in adrenal glands and gonads.    To define specific patterns of molecular changes with disruption of Star, we performed a transcriptome analysis of steroidogenic cells in adrenal glands. We harvested adrenal glands at E17.5 or 18.5 from seven wild-type (Star+/+) mice or four Star-/- mice having the transgene targeting enhanced green fluorescent protein (eGFP) under the control of regulatory sequences of mouse Star gene. Steroidogenic cells were selectively isolated by fluorescent-activated cell sorting. The gene expression profile of the fluorescence-positive cells was obtained with Agilent Whole Mouse Genome Microarray and was confirmed by quantitative real-time PCR.    We identified 961 and 622 genes that were significantly up-regulated and down-regulated, respectively, in Star-/- mice compared with Star+/+ mice (fold difference ≥2, p value of Student t test <0.05, and Benjamini-Hochberg false discovery rate of multiple comparison test <0.2). In Star-/- mice, expression levels of genes involved in cholesterol mobilization and efflux or immune response as antigen presenting cells were significantly increased, and transition from fetal to adult adrenocortical cells were significantly decreased, whereas those of genes related to steroid hormone biosynthesis or cholesterol biosynthesis and influx were not significantly changed. The trancriptome analysis revealed hitherto undescribed characteristic changes in adrenocortical cells and expanded our understanding of the pathophysiology of the steroidogenic cells with disruption of Star.

overall_design: Gene expression profiles of isolated adrenal steroidogenic cells were compared between seven wild-type mice and four knockout mice lacking steroidogenic acute regulatory protein at E17.5-18.5.

first: Toshikatsu

last: Mitsui

first: Sadafumi

last: Suzuki

first: Yumi

last: Matsuzaki

first: Keith

middle: L

last: Parker

first: Tomonobu

last: Hasegawa


title: AngII-regulated genes sensitive to CsA in Vascular Smooth muscle cells.

status: Public on Aug 11 2011

city: Madrid

first: Vanesa

last: Esteban

state: Madrid

address: Melchor Fernández Almagro, 3.

department: Department of Vascular Biology and Inflammation

institute: Centro Nacional de Investigaciones Cardiovasculares (CNIC)

summary: We have employed whole genome microarray expression profiling as a platform to identify  AngII -regulated genes sensitive to CsA.  VSMC were treated with AngII with or without CsA ( as an inhibitor of the CN/NFAT pathway).

overall_design: 4 independent VSMC cultures (4 replicates) from aortas of C57BL/6 mice were used for each condition (1uM AngII or 1uM AngII+200ng/ml CsA).

first: Juan

last: Redondo


title: Murine Myoblast C2C12 Cells: Control vs. Mybbp1a Knockdown

status: Public on Aug 10 2011

city: Kwei-San, Tao-Yuan

first: Bertrand

last: Tan

address: 259 Wen-Hwa 1st Road

department: Department of Biomedical Sciences

country: Taiwan

institute: Chang Gung University

summary: Transcriptional profiling of mouse myoblast cells comparing control vs. Mybbp1a knockdown. Stable clones of C2C12 cells harboring control or Mybbp1a-targeting shRNA were established and further pooled for analysis. Goal was to determine, based on the effects of Mybbp1a depletion on global gene expression, candidate downstream target genes of Mybbp1a, a putative transcriptional co-repressor.

overall_design: Two-condition experiment, control vs. Mybbp1a knockdown C2C12 cells (mixed stable clones). Biological replicates: 2.

first: Hsuan

last: Liu


title: Gene expression data from sorted and unsorted primary human acute myeloid leukemia (AML) samples

status: Public on Aug 28 2011

city: Toronto

first: Kolja

last: Eppert

state: Ontario

address: 101 College St., rm 8-301

country: Canada

institute: University Health Network

summary: Experiments using xenografts show that some solid tumours and leukemias are organized as cellular hierarchies sustained by cancer stem cells (CSC). Despite promise, the relevance of the CSC model to human disease remains uncertain. Here we show that acute myeloid leukemia (AML) follows a CSC model based on sorting multiple populations from each of 16 primary human AML samples and identifying which contain leukemia stem cells (LSC) using a sensitive xenograft assay. Analysis of gene expression from all functionally validated populations yielded an LSC-specific signature. Similarly, a hematopoietic stem cell (HSC) gene signature was established. Bioinformatic analysis identified a core transcriptional program shared by LSC and HSC, revealing the molecular machinery underlying stemness properties. Both stem cell programs were highly significant independent predictors of patient survival and also found in existing prognostic signatures. Thus, determinants of stemness influence clinical outcome of AML establishing that LSC are clinically relevant and not mere artifacts of xenotransplantation.

overall_design: Analysis of gene expression in FACS sorted AML fractions that were functionally determined to be enriched for LSC or not (25 and 29 respectively).

first: John

middle: E

last: Dick

first: Benjamin

last: Ebert


title: Effect of dietary cholesterol on gene expression in the liver of apoE-KO mice

status: Public on Aug 08 2011

first: Takashi

last: Obama

address: 1-5-8, Hatanodai

department: Biological Chemistry

institute: Showa University, School of Pharmacy

summary: Apolipoprotein E-knock out (apoE-KO) mouse is known as a model animal for atherosclerosis accompanied by spontaneous hypercholesterolemia. When apoE-KO mice were fed a chow supplemented with 1.25% cholesterol (high-Chol diet), cholesterol and bile acids were highly increased in the liver within a week. However, the amount of triacylglycerol (TG) in very low-density lipoprotein (VLDL), but not in the liver, was reduced by 78%. The epididymal adipose tissue was almost diminished in the long term. Cholesterol metabolism is  tightly regulated by both cholesterol and its metabolites in the mammalian liver, but the regulatory mechanism of TG synthesis remains to be elucidated. To evaluate the impact of high-Chol diet for 1 week on gene expression in the liver of apoE-KO mice, DNA microarray analysis was performed with comparison to apoE-KO mice fed a normal chow. We found that mRNA expression related to lipid metabolism was suppressed by the high-Chol diet in the liver of apoE-KO mice, which includes beta-oxidation and glycerol-3-phosphate (G3P) pathway for TG synthesis. In particular, the mRNA and protein expression of lipin-1 and lipin-2 was markedly decreased. PGC-1α, which up-regulates the transcription of lipin-1, was also suppressed. Lipin is reported to function as a coactivator of PGC-1α and is an inducible amplifier of PPARα, indicating that the suppression of genes involved in beta-oxidation could be induced by suppression of the lipins. These data using apoE-KO mice indicate that cholesterol and its metabolites are involved in regulating TG metabolism through a suppression of lipin-1 and lipin-2 in the liver. This research provides evidence for the mechanism of lipin expression in the liver.

overall_design: Apo E-KO mice at 10 weeks of age were fed normal chow (control) or high-Chol diet containing 1.25% cholesterol for 1 week. Three independent experiments were performed at each diet.

first: Sayaka

last: Nagaoka

first: Hiroyuki

last: Itabe


title: Gene expression arrays for different dendritic cell subset

city: Beijing

first: Xuebin

last: Qu

address: 5 Dongdansantiao

institute: Institute of Basic Medical Sciences & School of Basic Medicine

summary: To further distinguish the different subset of DCs, changes in gene expression were analyzed using Agilent mouse gene expression 4×44,000 microarrays. BALB/C mouse bone marrow–derived imDCs and maDCs were generated from bone marrow progenitors. Bone marrow hematopoietic progenitor cells cocultured with Sca-1+Lin-CD117- MSCs could differentiate into a novel IL-10-dependent regDC subset-sDCs. The gene expression differentiations of the four groups (imDCs, maDCs, sDCs and neutralizing antibody-IL-10-treated sDCs) were analyzed by GeneChip microarray.

overall_design: The formed four groups of cells (imDCs, maDCs, sDCs and neutralizing antibody-IL-10-treated sDCs) were purified respectively, and then gene expression in them was measured.

first: Xingxia


title: miRNA-29 regulation of gene expression in helper T cells

status: Public on Aug 01 2011

city: San FRANCISCO

first: David

last: Steiner

address: 513 Parnassus Ave UCSF Box 0414 HSE 201

department: Microbiology and Immunology

institute: UCSF

summary: The goal of this study was to identify genes regulated by miRNA-29 in helper T cells. We compared gene expression in miRNA-deficient helper T cells (DGCR8-deficient) transfected with miR-29b versus control miRNA.  We also compared gene expression in wildtype helper T cells transfected with miR-29 inhibitor to cells transfected with control inhibitor

overall_design: 3 biological replicates of each genotype (DGCR8-deficient or Wildtype C57BL/6 mice), with 2 conditions per genotype for 12 samples total. Cells from each DGCR8-deficient mouse were transfected with either miR-29b or control miRNA and cells from wildtype mice were transfected with either miR-29 inhibitors or control inhibitors

middle: F

first: K

last: Ansel


title: Replication Timing in Yeast: CGH microarrays:  S vs G1 cells in various stress conditions

status: Public on Sep 09 2011

city: Rehovot

first: Ariel

last: Gispan

address: P.O. Box 26

department: Molecular Genetics

country: Israel

institute: Weizmann Institute of Science

type: Genome variation profiling by genome tiling array

summary:
Replication timing in Saccharomyces cerevisiae in various replication stress conditions using CGH microarrays of S vs G1 cells.
Replication of the eukaryotic genomes follows a characteristic temporal program, with different regions replicating at different times in S phase. We describe a stochastic model of DNA replication that naturally explains the replication profiles of a dozen of S. cerevisiae mutants. Each profile is described by a single parameter that differ between the mutants: the ratio between the fork velocity and the typical initiation rate (the “replicon length”), while all other origin-specific parameters remain unchanged. We devise an analytical method to infer the replicon lengths from the available data, and predicted its value in different mutant backgrounds. Further experiments verified model’s predictions. Our study supports a stochastic model of DNA replication in S. cerevisiae and explains the apparent robustness of this profile to perturbations that extend S phase.

overall_design: DNA from FACS-sorted cells was extracted, labeled with Cy dyes, hybridized to the CGH microarray and scanned. 18 strains were used, with variable biological repeats number.

first: Miri

last: Carmi

first: Naama

last: Barkai


title: MiRNA expression analysis of cancer-associated fibroblasts (CAFs) and normal fibroblasts (NFs) in breast cancer

status: Public on Sep 28 2012

city: Chongqing

first: liuyang

last: zhao

address: 1#  Yixueyuan Road, Yuzhong District

institute: Chongqing Medical  University

summary: To identify miRNA differentially expressed in CAFs vs matched NFs and analyze the heterogeneity of miRNA expression profiles in the two kinds of cells, we established primary cultures of CAFs and paired NFs from six resected breast tumor tissue without any radiotherapy and chemotherapy treatment.

overall_design: Paired CAFs and NFs from six primary human breast carcinoma specimens were cultured,the third passage of primary cells was used in the experiments.

first: Manran

first: Liuyang

last: Zhao


title: Gene Expression Analysis of Transgenic Myc-Driven Liver Tumor Formation and Regression

status: Public on Jul 06 2011

city: San Francisco

first: Andrei

last: Goga

address: 513 Parnassus Ave

department: Cell & Tissue Biology

summary:
Gene expression changes were examined in transgenic MYC-driven liver cancers at different time points as tumors formed and upon early regression.  Time points evaluated include: Control (non-tumor bearing), Pre-tumor (mice were removed from doxyclycine in their diet to induce MYC oncogene expression for 4-5 weeks), Tumor (tumor nodules from mice that had been off of doxycycline for 8-9 weeks) and Early tumor regression (tumor-bearing mice were placed back on doxycycline for 72 hrs to inhibit MYC oncogene expresion).
MYC-Driven Mouse Tumor Models are described in Schahaf, et al., Nature, 2004 and Goga, et al., Nature Medicine, 2007.

overall_design: 11 Total Samples:  3 Control, 4 Pre-Tumor, 4 Tumor, 4 Early Tumor Regression.  Control =  LAP-tTA transgenic mice.  Others = TRE-MYC x LAP-tTA double transgenic mice (doxy off).

first: Asha

last: Balakrishnan


title: mRNA expression data from mice infected with H. pylori treated with estradiol, tamoxifen, or placebo

status: Public on Jun 30 2011

city: Cambridge

first: Alexander

last: Sheh

state: ma

address: 77 Massachusetts ave 16-828

department: Biological Engineering

institute: MIT

summary:
We are investigating the mRNA expression profiles of gastric tissue within H. pylori-infected mice treated with estradiol, tamoxifen, or placebo
We used microarrays to compare the global mRNA expression profiles in H. pylori infected mice in response to estradiol and tamoxifen

overall_design: Male mice were infected with H. pylori. After 16 weeks of H.pylori infection, mice were treated with 17beta-estradiol, Tamoxifen or placebo pellets implated subcutaneously for 12 weeks.  At that point, longitudinal strips of gastric tissue were snap-frozen.  Tissue was later weighed and RNA extracted using Trizol and purified with RNeasy kit including DNase treatment.  9 samples with 3 groups (n= 3 per group, except Tamoxifen (n=2)).  Placebo samples are controls and were compared to estradiol or Tamoxifen treated samples.

first: Zhongming

last: Ge

first: Nicola

last: Parry

first: Sureshkumar

last: Muthupalani

first: Julia

last: Rager

first: Arkadiusz

middle: R

last: Raczynski

first: Melissa

middle: W

last: Mobley

first: Amanda

last: McCabe

first: Rebecca

last: Fry

first: Timothy

last: Wang

first: James

last: Fox


title: Effect of Glis1, Dmrtb1, and Pitx2 on mouse iPS cell generation

status: Public on Jun 10 2011

first: Shinya

last: Yamanaka

summary:
Induced pluripotent stem cells (iPSC) are generated from somatic cells by the transgene expression of three transcription factors Oct3/4, Sox2, and Klf4 (OSK), albeit at a low efficiency. The protooncogene c-Myc enhances the efficiency of iPSC generation by OSK, but it also increases the tumorigenicity of the resulting iPSC.
In the current study, we found the Gli-like transcription factor Glis1, when expressed together with OSK, to markedly enhance the generation of iPSC from both mouse and human fibroblasts. Mouse iPSC generated by OSK and Glis1 can form germline-competent chimeras. Glis1 is enriched in unfertilized oocytes and one cell-stage embryos. DNA microarray analyses revealed that Glis1 promotes multiple pro-reprogramming pathways, including Myc, Nanog, Lin28, Wnt, mesenchymal-epithelial transition (MET), and Esrrb. These results therefore demonstrated that oocyte transcription factor Glis1 effectively promote direct reprogramming during iPSC generation.

overall_design: Mouse embryonic fibroblasts were transduced with OSKM, OSM+Glis1, OSM+Dmrtb1, and OSM+Pitx2 and were used for microarray analyses.

first: M

last: Maekawa

first: T

last: Nakamura

last: Nrita


title: Promotion of Direct Reprogramming by Glis1

overall_design: p53-null mouse embryonic fibroblasts were transduced with OSK and OSK+Glis1 and were used for microarray analyses.


title: Global gene expression analysis for mouse embryonic fibroblasts (MEFs), induced hepatocyte-like (iHep) cells and adult mouse hepatocytes.

status: Public on Jun 28 2011

city: Fukuoka

first: Atsushi

last: Suzuki

state: Fukuoka

address: 3-1-1 Maidashi, Higashi-ku

department: Division of Organogenesis and Regeneration

institute: Medical Institute of Bioreguration, Kyushu University

summary: In order to characterize iHep cells more precisely, we conducted global gene expression analyses using microarrays to compare among the gene expression profiles of MEFs, iHep cells and adult mouse hepatocytes.

overall_design: Three MEF samples that were individually prepared from 13.5 days post coitum (dpc) embryos, three types of iHep cells and hepatocytes obtained from the adult mouse liver were used.

first: Sayaka

last: Sekiya


title: Expression profile of WT and IKKb(EE)IEC epithelial cells (IEC)

status: Public on Jun 09 2011

city: la Jolla

first: monica

last: guma

address: 9500 Gilman Drive

institute: UCSD

summary: To investigate NF-kB-driven gene expression in IEC, we performed microarray analysis from enterocytes of mice that express a constitutively active form of IKKb in intestinal epithelial cells

overall_design: Total RNA  was prepared from enterocytes obtained from small intestines of IKKb(EE)IEC and WT littermates. Two biological replicates were performed for each experimental condition.


title: miRNA expression profile of unmutated and mutated CLL cells

city: Aviano

first: daniela

last: marconi

address: Via franco Gallini 2

country: Italy

institute: CRO AVIANO

summary: The aim is to identify the differential miRNA expression profile of  B-CLL stimulated with different type of stimulation CPG

overall_design: One color design, 36 samples, Two-condition experiment, CPG-stimulated B-CLL unmutated  and mutated vs. Unstimulated B-CLL unmutated and mutated. Biological replicates: 18 unstimulated replicates, 18 CPG-stimulated replicates.

first: Riccardo

last: Bomben

first: Daniela

last: Marconi

first: Dimitar

last: Efremov

first: Valter

last: Gattei


title: Effect of ECAT11 disruption in mouse ESCs

status: Public on May 27 2011

summary: The principal factors that lead to proliferation and pluripotency in embryonic stem cells (ESCs) have been vigorously investigated. However, the global network of factors and their full signaling cascade is still unclear. In this study, we found that ECAT11 (L1td1) is one of the ESC-associated transcripts harboring a truncated fragment of ORF-1, a component of the L1 retrotransposable element. We generated an ECAT11 knock-in mouse by replacing its coding region with green fluorescent protein. DNA microarray analyses revealed that ECAT11EGFP/EGFP ESCs showed similar global gene expression profiles as the wild type ESCs

overall_design: Samples from wild type ESCs and ECAT11EGFP/EGFP ESCs

first: Kumiko

last: Iwabuchi

first: Megumi

last: Kumazaki


title: Gene Expression Profiles of Jaw and Alveolar Bones Are Uniquely Different from Those of Trunk and Limb Bones

city: Shinagawa-ku

first: Tomohiro

last: Taguchi

address: 1-5-8 Hatanodai

department: School of Dentistry

institute: Showa University

summary: Certain bone graft materials are employed for alveolar bone regeneration, and autografts are commonly used. Alveolar and jaw bones are developmentally derived from neural crest cells, while most trunk and limb bones are derived from mesodermal mesenchymal cells. Consequently, the chosen bone graft material is likely to have a different developmental origin than the recipient bone. We hypothesized that there are differences in the gene expression profiles and bone healing capacities between bones with different developmental origins. Therefore, we investigated these properties in the maxilla, mandible, ilium and femur. DNA microarray data revealed close homology between the gene expression profiles of the ilium and femur. The gene expressions of Wnt-1, P75, SOX10, Nestin and Musashi-1 were significantly higher in the maxilla and mandible than in the ilium and femur. The frontal bone healed faster than the parietal bone. Parietal bone defects transplanted with maxillary and mandibular bone grafts exhibited closure. Thus, it is suggested that the maxilla and mandible have different gene expression profiles from the other bones examined, and exhibit neural crest cell properties with a marked healing ability in adults. The data further suggest that jaw bones are effective as both bone graft materials and graft beds.

overall_design:
Animals:
Twenty-five 5-week-old male C57BL/6J mice were randomly divided into five groups (n=5 each) based on the bone graft materials as follows: group 1, ilium group; group 2, femur group; group 3, maxilla group; group 4, mandible group; group 5, negative control group with no implanted material. All the mice were sacrificed after 4 weeks. All the animal procedures were approved by the Animal Research Committee of Showa University, Tokyo, Japan.

RNA Isolation:
Bones were extirpated from 5-week-old mice and the regenerated tissue in the bone graft areas were extirpated from 9-week-old mice that were grafted bones into bone defects. Total RNA was isolated from the bones and tissue using an RNeasy Lipid Tissue Midi Kit (Qiagen, Hilden, Germany) .

DNA Microarray:
A Whole Mouse Genome Oligo Microarray (Agilent Technologies Inc., Santa Clara, CA, USA), which contains more than 41,252 probe sets, was used to probe the comprehensive gene expression profiles of the maxilla, mandible, ilium and femur. The expression analysis file created from each sample was imported into GeneSpring 10.0.2 (Agilent Technologies Inc.).

Quantitative Real-Time PCR:
We performed quantitative real-time PCR of the maxilla, mandible, ilium and femur, as well as the regenerated tissue in the bone graft areas. An Omniscript Reverse Transcriptase Kit (Qiagen, Valencia, CA, USA) was used to create cDNAs. Real-time PCR was performed for 50 cycles of 95°C for 15 s and 60°C for 1 min, followed by 50°C for 2 min and 95°C for 10 min. We used primers for six genes (Wnt-1, P75, SOX10, Nestin, Musashi-1 and GAPDH). Wnt-1, P75 and SOX10 are neural crest cell markers (Stemple and Anderson, 1992; Kelsh, 2006; Yoshida et al., 2008), while Nestin and Musashi-1 are nerve stem cell markers (Sakakibara et al., 1996; Kawaguchi et al., 2001). The gene expression levels of these five genes were determined after normalization by the expression levels of the control gene GAPDH.

Graft Material Procedure:
All surgical procedures were performed under general anesthesia in sterile conditions. After inhalation of ethyl ether, general anesthesia was achieved with an intraperitoneal injection of pentobarbital sodium. Bones for the graft materials were removed and granulated. The amounts of graft materials transplanted in the four groups were approximately 0.2 g.

Surgical Procedure:
An incision was made in the head, and a full-thickness flap was created exposing the calvarial bone. A diamond bur was used to perforate an area of 2 mm in diameter on the mouse frontal bone and parietal bone, avoiding perforation of the dura mater (Figure 3A). Subsequently, one of the four materials was grafted into each frontal and parietal bone defect. The negative control group did not receive implantation of a graft material (Figure 3B). All of the graft materials were transplanted into the defects within 30 min after extirpation. The flap was repositioned and sutured tightly with non-absorbable sutures, covering the bone defect.

Micro-computed Tomography (µCT) Observations:
A µCT system (eXplore Locus CT System and MicroView; GE Healthcare, Tokyo, Japan) was used to observe new bone formation. Images were acquired immediately after surgery and after 4 weeks.

Histologic Procedures:
The animals were euthanized at 4 weeks after surgery with an overdose of ethyl ether. All of the defects in the groups were dissected together with the surrounding soft and hard tissues. Section blocks were fixed with 4% paraformaldehyde, decalcified for 2 days, neutralized with 5% anhydrous sodium sulfate and then embedded in paraffin. Sections were cut, deparaffinized and stained with hematoxylin and eosin.

Immunohistochemical Procedures:
Sections were cut, mounted on slides, deparaffinized and incubated with an anti-Wnt-1 antibody (AnaSpec Inc., San Jose, CA, USA) at appropriate dilutions.

first: Junichi

last: Watahiki

first: Tomoki

last: Nampo

first: Gou

last: Yamamoto

first: Akiko

last: Enomoto

first: Miki

last: Ono

first: Tarou

last: Irie

first: Tetsuhiko

last: Tachikawa

first: Koutaro

last: Maki


title: Atlas of Gene Expression at Microanatomical Resolution of the Submandibular Salivary Gland

status: Public on Jul 01 2011

city: Bethesda

first: Kurt

last: Musselmann

address: 30 Convent Dr, Room 426

department: Laboratory of Cell and Developmental Biology

institute: NIDCR

summary: The goal of this study was to generate a spatiotemporal atlas of gene expression in the developing salivary gland.  This will allow us to identify changes in gene expression that may result in the formation of the different domains of the salivary gland.

overall_design:
At least 4 microarrays per location per time point were collected.  The originating samples are rather small, so many clefts, ducts and buds had to be pooled to generate enough aRNA for hybridization.

Supplementary file: cluster heat map from anova 0.05 passing entities, E12.5 main bud vs E15 main bud (averaged readings)

first: Khin

last: Sone

first: Ian

last: Bothwell

first: Sarah

last: Johnson

first: Kenneth

last: Yamada


title: Gene profile of dystrophic cardiac progenitor cells

status: Public on Apr 19 2011

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

institute: VIB

summary:
Cardiac resident stem/progenitor cells are intensively studied as a potential therapeutic tool for cardiomyopathies. While surface marker expression and ability to generate cardiomyocytes have been characterized in some detail for several types of these progenitors, little is known on how their cardiac differentiation is regulated. Beta sarcoglycan null (bSG KO) mice are a model for limb girdle muscular dystrophy type 2E (LGMD2E), and are characterized by muscular dystrophy and progressive dilated cardiomyopathy. In the present study we isolated and characterized cardiac progenitors (mesoangioblasts) from the small vessels of neonatal hearts bSG KO mice and unexpectedly observed that they differentiate spontaneously into skeletal muscle fibers both in vitro and when transplanted in regenerating muscles and infarcted hearts. The micro array data showed that dystrophic cardiac progenitor  and myogenic cells (C2C12) share similar gene expression profile.

Keywords: Beta sarcoglycan null mice, muscular dystrophy, cardiac mesoangioblasts, myogenic differentiation

overall_design: Biological triplicates of cardiac wild-type  and  dystrophic mesoangioblasts isolated from different heart region (atrium, ventricle, aorta) were compared.  C2C12 cells were used as positive control for myogenic differentiation.

first: Stefania

last: Crippa

first: Maurilio

last: Sampaolesi


title: Rap1a GTPase mVSM Knockout vs. Rescue Expression

status: Public on Apr 13 2011

city: Columbus

first: Maqsood

last: Chotani

state: OH

address: 700 Children's Drive

department: Center for Cardiovascular and Pulmonary Research

institute: Nationwide Childrens 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


title: Development of gene expression signatures on immunity for bursal peptide BPP-II

city: Nanjing

first: Pu

middle: Yan

last: Chen

address: No. 1, Weigang

institute: Nanjing Agriculture University

summary: To further elucidate the mechanism of BPP-II on immunity on the broad molecular level, we have employed whole genome microarray expression profiling as a discovery platform to examine gene expression patterns during BPP-II treatment in a mouse derived hybridoma culture system. Hybridoma cell was treated ex vivo, and robust normalization of the data identified 2478 differentially expressed probe sets exhibiting minimum 1.5-fold changes that distinguished between BPP-II and control samples. Various pathwayswere significantly impacted by BPP-II treatment, and gene Ontology annotations show changes in the expression of molecules involved in immune and immunocyte related cellular processes. Expression of 8 genes (MS4A2，CD86，CD80， Fas，CDKN2A，CBLC, FGF21 and Fyn) from this signature was quantified in the RNA samples by QRT-PCR, confirming low variability between the predicted response patterns.

overall_design: BPP-II induced gene expression in hybridoma cell was measured at 4 hours after exposure to doses of 0ug/ml and 0.2ug/ml.  Two independent experiments were performed using different cells for each experiment.

middle: Y

first: Xiu

last: Feng


title: Dexamethasone and lenalidomide have distinct functional effects on erythropoiesis

status: Public on Apr 28 2011

first: Fatima

last: Al-Shahrour

address: 7 Cambridge Center

department: Cancer program

institute: Broad Institute of MIT and Harvard

summary: We explored the effects of dexamethasone and lenalidomide, individually and in combination, on the differentiation of primary human bone marrow progenitor cells in vitro.  Both agents promote erythropoiesis, increasing the absolute number of erythroid cells produced from normal CD34+ cells and from CD34+ cells with the types of ribosome dysfunction found in DBA and del(5q) MDS.  However, the drugs had distinct effects on the production of erythroid progenitor colonies; dexamethasone selectively increased the number burst-forming units-erythroid (BFU-E), while lenalidomide specifically increased colony-forming units-erythroid (CFU-E).  Use of the drugs in combination demonstrates that their effects are not redundant.

overall_design: Human CD34+ cells were cultured for 48 hours in the erythroid differentiation media described above with the addition of 40 ng/mL of FMS-like tyrosine kinase 3 (flt-3; Miltenyi Biotech) and 15 ng/mL of Granulocyte colony-stimulating factor (G-CSF; Amgen). Cells were cultured in the presence of the drugs of interest for 24 hours. RNA was purified using Trizol (Invitrogen). RNA was amplified and labeled by in vitro transcription and hybridized to the Affymetrix HT Human Genome U133A Array. Three replicates per condition.

first: Anupama

last: Narla

first: Shilpee

last: Dutt

first: J

last: McAuley

first: Slater

last: Hurst

first: Marie

last: McConkey

first: Benjamin

last: Ebert


title: Effect of pressure overload on cardiac gene expression in wild-type and CHIP(-/-) mice

status: Public on May 01 2011

city: Chapel Hill

first: Jonathan

middle: C

last: Schisler

state: NC

address: MBRB, Rm 2340C

department: McAllister Heart Institute

institute: The University of North Carolina at Chapel Hill

summary: Wild-type mice or mice lacking the expression of CHIP (Stub1) were subjected to either sham surgery (Sham) or trans-aortic banding (TAB).  After one week, RNA was extracted from heart and run on the Agilent 4x44K gene expression array to look at differences in the cardiac transcriptional response to pressure overload-induced hypertrophy in the absence of CHIP.

overall_design: Four-condition experiment: WT vs. CHIP(-/-) with SHAM or TAB surgery. Biological replicates: 4 per condition.

first: Chunlian

last: Zhang

first: Cam

last: Patterson


title: Development of gene expression signatures on immunity for bursal peptide BSP-II

status: Public on Feb 17 2011

summary: To further elucidate the mechanism of BSP-II on immunity on the broad molecular level, we have employed whole genome microarray expression profiling as a discovery platform to examine gene expression patterns during BSP-II treatment in a mouse derived hybridoma culture system. Hybridoma cell was treated ex vivo, and robust normalization of the data identified 1279 differentially expressed probe sets exhibiting minimum 1.5-fold changes that distinguished between BSP-II and control samples. Various pathwayswere significantly impacted by BSP-II treatment, and gene Ontology annotations show changes in the expression of molecules involved in immune and immunocyte related cellular processes. Expression of nine genes (MS4A2, CD3D, FGF21, CD80, PTPRC, NFATC4, IL2RB, Fas and LAT) from this signature was quantified in the RNA samples by QRT-PCR, confirming low variability between the predicted response patterns.

overall_design: BSP-II induced gene expression in hybridoma cell was measured at 4 hours after exposure to doses of 0ug/ml and 5ug/ml.  Two independent experiments were performed using different cells for each experiment.


title: Expression profiling of Endothelial (EC) and Non-endothelial Cells

status: Public on Apr 04 2011

city: Boston

first: Manoj

last: Bhasin

address: 330 Brookline Avenue  RN 380E

institute: Beth Israel Deaconess Medical Center

summary: Gene expression profiling of HUVEC (human umbilical vein EC cell; Lonza), HAEC (human aortic EC cells), HCAEC (human coronary artery EC cells), HPAEC (human pulmonary artery EC cells), HMVEC (human microvascular (dermal) , HASMC ( Human Aortic Smooth Muscle Cells), T cells and Bcells.

overall_design: Gene expression profiling of Endothelial cells and Non-endothelial cells in order to identify the genes with preferntial expression to endothelial cells.  The experiments are performed in duplicate on both the HT Human Genome U133A and U133B arrays.

first: Peter

middle: J

last: Oettgen


title: Transcriptional profiling of ATP-competitive mTOR inhibitors reveals mTORC1 and mTORC2 specific regulatory networks

status: Public on Mar 15 2011

first: Beatrice

last: Wang

address: 600 16th Street MC 2280

institute: Univeristy of California, San Francisco

summary: The mammalian target of rapamycin (mTOR) is a central regulator of cell growth and proliferation in response to growth factor and nutrient signaling.  Consequently, this kinase is implicated in metabolic diseases including cancer and diabetes so there is great interest in understanding mTOR regulatory networks.  mTOR exists in two functionally distinct complexes, mTORC1 and mTORC2, and whereas the natural product rapamycin only inhibits a subset of mTORC1 functions, recently developed ATP-competitive mTOR inhibitors have revealed new roles for both complexes.  To examine the complete spectrum of mTOR responsive cellular processes, we compared the transcriptional profiles of mammalian cells treated with rapamycin versus the ATP-competitive inhibitor PP242.  Our analysis provides a genome-wide view of the transcriptional outputs of mTOR signaling that are insensitive to rapamycin.

overall_design: Gene expression in mouse NIH3T3 cells was measured after 18 hour treatment with DMSO (control), 50 nM rapamycin, or 2 uM PP242.  Four independent experiments were performed for each condition.

middle: T

first: Gregory

last: Ducker

first: Andrea

last: Barczak

first: Rebecca

last: Barbeau

first: David

last: Erle

first: Kevan

last: Shokat


title: Expression data from tumor and normal epithelium derived from BRCA1-mutation carriers

status: Public on Feb 04 2011

first: Charlotte

last: Kuperwasser

address: 750 Washington St. Box 5609

institute: Tufts University School of Medicine

summary: Microarrays were used to determine relative global gene expression changes in WT and BRCA1-mutation carrier breast epithelium as well as tumors created from WT and BRCA1-mutation carrier breast epithelial cells.

overall_design: Total RNA was isolated from freshly dissociated mammary epithelilal cells obtained from disease-free prophylactic masectomy tissues of 4 different BRCA1-mutation carriers or 4 different reduction mammoplasty tissues from non-mutation carriers.  Total RNA was also isolated from fresh tumor tissues derived from in vivo transformed human mammary epithelial cells created from cells obtained from WT or BRCA1-muation carrires. Dissociated mammary epithelial cells were transduced with lentiviruses encoding mutant p53, mutant ras, mutant PI3K and cyclin D1 and injected into in humanized glands. There were four tumor tissues isolated for each genetic background.

first: Piyush

middle: B

last: Gupta

first: Theresa

middle: A

last: Proia

first: Patricia

last: Keller

first: Eric

last: Lander


title: Altered gene expression in the mouse heart after 2-day fasting

status: Public on Apr 29 2011

city: Shinjuku

first: Isao

last: Ishii

address: 35 Shinanomachi

department: Biochemistry

institute: Keio Univ School of Medicine

summary: To obtain insight into the effect of starvation on heart ischemia/reperfusion injury, gene expression patterns in the hearts of satiated and fasted mice were examined.

overall_design: Gene expression was examined in the hearts of satiated (n=4) and 2-day-fasted C57BL/6J male mice.

first: Shintaro

last: Nakano


title: De novo DNA methylation by Dnmt3a and Dnmt3b is dispensable for nuclear reprogramming of somatic cells to a pluripotent state

status: Public on May 16 2011

first: Mathias

last: Pawlak

address: 9 Cambridge Center

institute: Whitehead Institute

summary: Induced pluripotent stem cells (iPSCs) are generated from somatic cells by the transduction of defined transcription factors and involves dynamic changes in DNA methylation. While the reprogramming of somatic cells is accompanied by de-methylation of pluripotency genes, the functional importance of de novo DNA methylation has not been clarified. Here, using loss-of-function studies, we generated iPSCs from fibroblasts that were deficient in de novo DNA methylation mediated by Dnmt3a and Dnmt3b. These iPSCs reactivated pluripotency genes, underwent self-renewal and showed restricted developmental potential which was rescued upon re-introduction of Dnmt3a and Dnmt3b.  We conclude that de novo DNA methylation by Dnmt3a and Dnmt3b is dispensable for nuclear reprogramming of somatic cells.

overall_design: RNA levels of Dnmt3ab deficient iPSC cell lines were compared to control iPSC cell lines

first: Rudolf

last: Jaenisch


title: Reference maps of human ES and iPS cell variation enable high-throughput characterization of pluripotent cell lines

status: Public on Feb 03 2011

city: Vienna

first: Christoph

last: Bock

address: Lazarettgasse 14

institute: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences

summary:
The developmental potential of human pluripotent stem cells suggests that they can produce disease-relevant cell types for biomedical research. However, substantial variation has been reported among pluripotent cell lines, which could affect their utility and clinical safety. Such cell-line specific differences must be better understood before one can confidently use embryonic stem (ES) or induced pluripotent stem (iPS) cells in translational research. Towards this goal we have established genome-wide reference maps of DNA methylation and gene expression for 20 previously derived human ES lines and 12 human iPS cell lines, and we have measured the in vitro differentiation propensity of these cell lines. This resource enabled us to assess the epigenetic and transcriptional similarity of ES and iPS cells and to predict the differentiation efficiency of individual cell lines. The combination of assays yields a scorecard for quick and comprehensive characterization of pluripotent cell lines.
We used microarrays to compare the gene expression profiles between human ES cell lines, iPS cell lines, fibroblasts and embryoid bodies, and to identify cell-line specific outlier genes.

overall_design: 20 human ES cell lines (HUES1, HUES3, HUES6, HUES8, HUES9, HUES13, HUES28, HUES44, HUES45, HUES48, HUES49, HUES53, HUES62, HUES63, HUES64, HUES65, HUES66, H1, H7, H9), 12 human iPS cell lines (hiPS 11a, hiPS 11b, hiPS 11c, hiPS 15b, hiPS 17a, hiPS 17b, hiPS 18a, hiPS 18b, hiPS 18c, hiPS 20b, hiPS 27b, hiPS 27e), 6 fibroblast cell lines (hFib 11, hFib 15, hFib 17, hFib 18, hFib 20, hFib 27), 5 embryoid bodies (hEB16d HUES1, hEB16d HUES3, hEB16d HUES6, hEB16d HUES45, hEB16d H1)

first: Evangelos

last: Kiskinis

first: Griet

last: Verstappen

first: Kevin

last: Eggan

first: Alexander

last: Meissner


title: Rap1a GTPase mVSM Knockout vs. Rescue mRNA Expression

first: Maqsood

last: Chotani

summary: Transcriptional profiling of mouse tail artery explanted microvascular smooth muscle (mVSM) cells comparing Rap1a -/- mVSM cells transduced with vector backbone (control) with Rap1a -/- mVSM cells transduced with a Rap1 CA 'rescue' plasmid.  The experiment will compare mRNA expression in Rap1A -/- mVSMs and 'rescued'with Rap1A CA.

overall_design: Two-condition experiment, mVSM Rap1a -/- (vector control) vs. mVSM-RapCA. Biological replicates: 4 control replicates, 4 transduced replicates.

first: Selvi

last: Jeyaraj


title: Gene expression in wild type and mENT1 knock out mice

status: Public on Apr 27 2011

city: Edmonton

first: Kathryn

last: Graham

state: Alberta

address: 11560 University Ave

department: Oncology

institute: University of Alberta

summary: To investigate the functional importance of a nucleoside transporter, the mENT1 (Slc29a1) was knocked out in mice. The gene expression profile was compared between wildtype and mENT1 knock out mice in two tissues.

overall_design: RNA was isolated from heart and kidney from 3 mENT1 knockout and 3 wildtype (FVB/N) mice.Gene expression profiles were compared between the knockout and wild type tissues.

first: Carol

last: Cass