title: Regulation of transcription by MLL2 complex and MLL complexes-associated protein AKAP95

status: Public on Jul 01 2013

city: Birmingham

first: Hao

last: Jiang

state: AL

address: 1825 University Blvd

department: Biochemistry and Molecular Genetics

institute: University of Alabama at Birmingham

summary: Although histone H3 lysine 4 (H3K4) methylation is widely associated with gene activation, direct evidence for its causal role in transcription, through specific MLL family members, is scarce. Here we have purified a human MLL2 (Kmt2b) complex that is highly active in H3K4 methylation and chromatin transcription in a cell-free system. This effect requires SAM and intact H3K4, establishing a direct and causal role for MLL2-mediated H3K4 methylation in transcription. We then show that human AKAP95, a chromatin-associated protein, is physically and functionally associated with the Dpy-30-MLL complexes  and directly enhances their methyltransferase activity. Ectopic AKAP95 stimulates expression of a chromosomal reporter in synergy with MLL1 or MLL2, whereas AKAP95 depletion impairs retinoic acid-mediated gene induction in embryonic stem cells. These results demonstrate an important role for AKAP95 in regulating histone methylation and gene expression, particularly during cell fate transitions.

overall_design:
Total RNAs from control or knockdown cells before and after RA-mediated differentiation were subjected to Illumina microarray analyses.
The complete dataset containing non_normalized, median-normalized and expression ratio (relative to Scramble shRNA, undifferentiated data) is linked below as a supplementary file [complete_data.txt].

first: H

first: R

middle: G

last: Roeder


title: Cardiomyocyte MR dependent DOC/salt-mediated gene regulation

status: Public on Jun 30 2013

city: Clayton

first: Morag

middle: J

last: Young

state: Victoria

address: Level 4 Block E 246 Clayton Rd

country: Australia

institute: Prince Henry's Institute of Medical Research

summary:
Genome wide gene expression analysis of mRNA siolated from whole heart tissue from wild type and cardiomyocyte selective MR null mice.
The role of mineralocorticoid receptors (MR) in specific cell types of the myocardium in cardiac remodeling remains unknown. We investigated MR in cardiomyocytes in DOC/salt-induced cardiac pathology. Cardiomyocyte MR-null mice (CM-MRKO) and control mice (WT) were given DOC/salt and cardiac responses were examined at 8 days and 8 weeks. Cardiac function in untreated mice wild type and CM-MRKO mice was determined by Langendorf and showed no differences. At 8 days CM-MRKO showed equivalent monocyte/macrophage recruitment to wild type mice in response to DOC/salt treatment. Profibrotic markers were significantly reduced in CM-MRKO hearts at base line and in response to DOC/salt. In contrast, at 8 weeks CM-MRKO mice showed no DOC/salt-induced increase in inflammatory cell infiltrate, fibrosis or systolic blood pressure (SBP). Similarly, DOC/salt-mediated increases in proinflammatory and profibrotic gene expression were not detected in CM-MRKO mice. Although mRNA levels for fibronectin and collagen III were similar for each genotype, this was not translated into protein expression. Interestingly, untreated CM-MRKO mice showed increased mRNA and protein for decorin and a further increase with DOC/salt. Together, these data suggest a direct role for cardiomyocyte MR in DOC/salt-induced tissue remodelling and SBP regulation. Moreover, a specific profibrotic pathway is dysregulated in CM-MRKO mice, suggesting a potential mechanism for the cardioprotective effects of selective MR deletion in cardiomyocytes.

overall_design: Pool mRNA (equal amounts) from whole heart from 8 animals per group.


title: Genome-wide expression profiling analysis of a Hmgn1, 3 and 5 mutant mouse model

status: Public on Jul 03 2013

city: Neuherberg

first: Martin

last: Irmler

state: Bayern

address: Ingolstaedter Landstrasse 1

department: Institute of Experimental Genetics

country: Germany

institute: Helmholtz Zentrum München GmbH

summary: Members of the HMGN protein family bind to nucleosomes and affect chromatin structure and functions as transcription, replication and DNA repair as well as epigenetic modifications. Overexpression of Hmgn1 may be linked to the etiology of Down syndrome while underexpression may be linked to some leukemias. Hmgn3 is highly expressed in eye and in brain and might influence behavioral phenotype. For Hmgn5 effects on transcription levels e.g. in liver are suggested.

overall_design: Total RNA obtained from four homozygote mutant and wildtype male mice were compared.

first: Johannes

last: Beckers

first: Marion

last: Horsch


title: S-adenosylmethionine modifies cocaine-induced DNA methylation and increases locomotor sensitization in mice

status: Public on Jun 27 2013

city: Tartu

first: Kaili

last: Anier

address: Ravila 19

country: Estonia

institute: University of Tartu

summary:
The aim of the study was to investigate whether environmental factors like S-adenosylmethionine (SAM) via affecting epigenome could alter cocaine-induced gene expression and locomotor sensitization in mice.
Using mouse nucleus accumbens (NAc) tissue, whole-genome gene expression profiling revealed that repeated SAM treatment affected a limited number of genes, but significantly modified cocaine-induced gene expression by blunting nonspecifically the cocaine response.
At the gene level, we discovered that SAM modulated cocaine-induced DNA methylation by inhibiting both promoter-associated CpG-island hyper- and hypomethylation in the NAc but not in the reference tissue cerebellum.

overall_design: Total RNA was extracted from the mouse nucleus accumbens (NAc) tissue. Two tissues were combined to a sample, 4 samples per group used. RNA quality and quantity were assessed using the Nano-Drop -1000 spectrophotometer and the Agilent 2100 Bioanalyzer.

first: Alexander

last: Zharkovsky

first: Anti

last: Kalda


title: The effect of aneuploidy on gene expression

status: Public on Jul 02 2013

city: Turku

first: Gunilla

last: Högnäs

address: Tykistökatu 6 B

department: Medical Biotechnology

country: Finland

institute: VTT

summary: Analysis of the gene expression changes observed in aneuploid b1 integrin YYFF MEFs generated as a result of repeated cytokinesis failure compared to tetraploid wild-type MEFs or tetraploid b1YYFF integrin MEFs. The results reveal aneuploidy-specific gene expression changes, both up-and downregulated genes uniquely detected in the aneuploid MEFs.

overall_design: Total RNA isolated from b1 integrin YYFF and B1 wildtype mouse embryonic fibroblasts that had been passaged on laminin 0, 4 or 8 times (L0, L4 or L8)

first: Johanna

last: Ivaska


title: Expression analysis of 3T3 cells that express Arabidopsis-derived Diaminopimelate Decarboxylase (DDC) in response to growth on meso-2,6-diaminopimelic acid (DAP) versus L-Lysine

city: New York

first: Nicholas

last: Gauthier

state: NY

address: 1275 York Avenue, Box #460

country: USA

institute: MSKCC

summary: This experiment aimed to investigate whether cells that express the L-Lysine-producing enzyme DDC exhibit any mRNA changes when grown on precursor DAP relative to L-Lysine.

overall_design: Total RNA obtained from DDC-expressing 3T3 cells after 3 days in culture with amino acid precursor DAP, L-Lysine, or starved of both.

middle: P

first: Boumediene

last: Soufi

first: William

middle: E

last: Walkowicz

first: Virginia

middle: A

last: Pedicord

first: Konstantinos

last: Mavrakis

first: Boris

last: Macek

first: David

middle: Y

last: Gin

first: Chris

last: Sander

middle: L

last: Miller


title: Gene Expression in Bone-marrow derived Dendritic Cells stimulated with H. pylori lysate vs. E. coli lysate

status: Public on Jun 14 2013

city: Baltimore

first: Jessica

last: Shiu

state: MD

address: 655 W Baltimore St

department: Pediatrics

institute: University of Maryland School of Medicine

summary: Gene Expression changes in BMDCs stimulated with H. pylori vs. E. coli. The hypothesis tested was that the gene expression profile in BMDCs stimulated with H. pylori lysate will be less inflammatory than BMDCs stimulated with E. coli.

overall_design: BMDCs were generated from bone marrow of wild type female C57BL/6 mice using 100ng/mL Flt3L. DCs were harvested at day 8 and stimulated with either media alone, H. pylori antigen lysate or E. coli lysate. At 24 hours, the cells were harvested and RNA was isolated for microarray analysis.

first: Thomas

last: Blanchard

first: Yezhou

last: Sun


title: Growth factor stimulation of cardiomyocytes induces changes in the transcriptional contents of secreted exosomes

status: Public on Jun 20 2013

city: Umeå

first: Nina

last: Gennebäck

address: NUS 6M

department: Public health and clinical medicin/medicin

country: Sweden

institute: Umeå University

summary: To study if the transcriptional content in exosomes derived from unntreated and growth factor treated cultured cardiomyocytes (HL-1)  differ and if so, can this difference be explained.This is results for the cells.The exosome reults can be find at GSE40503.

overall_design: 4 control untreated samples, 4 TFG-beta2 cardiomyocyte treated samples and 4 PDGF BB cardiomyocyte were studied., this reults are from the corresponding cells (that released the exosomes), used for data filtering of the exsomedata. The exosome reults can be find at GSE40503.

first: Urban

last: Hellman

first: Linus

last: Malm

first: Göran

last: Larsson

first: Gunnat

last: Ronquist

first: Anders

last: Waldenström

first: Stellan

last: Mörner


title: Study of transcriptional content in exosomes derived from untreated and growth factor-treated cultured cardiomyocytes (HL-1)

summary:
Introduction: Exosomes are nano-sized extracellular vesicles, released from various cells, which can stimulate or repress responses in target cells. We have recently shown that cultured cardiomyocytes release exosomes and that they, in turn, are involved in facilitating events in target cells by alteration of gene expression. We investigated whether external stimuli of the cardiomyocyte might influence the released exosome characteristics.

Material and Methods: Exosomes were isolated from media collected from cultured cardiomyocyte (HL-1) cells with or without growth factor treatment (TGF-beta2 and PDGF-BB), with a series of differential centrifugations. The exosomes were characterized with dynamic light scattering (DLS) and Western blot and analysed with Illumina whole genome microarray gene expression.

Results: An average size of 50-80 nm in diameter with no difference between treatment groups was found. Analysis of the mRNA content revealed 623 transcripts in the control group, 691 in the TGF-beta2-treated group and 362 in the PDGF-BB-treated group. 235 transcripts were common for all three groups.

Conclusion: We conclude that there is a difference in mRNA content between exosomes derived from cultured cardiomyocytes stimulated with growth factors. We also conclude that all exosomes contain a basic package consisting of ribosomal transcripts and mRNAs coding for proteins with functions within the energy supply system.

overall_design: To study if the transcriptional content in exosomes derived from untreated and growth factor-treated cultured cardiomyocytes (HL-1) differ, and if so, can this difference be explained, 4 control (untreated) exosome samples, 4 TFG-beta2-treated cardiomyocyte-derived exosome samples and 4 PDGF-BB-treated cardiomyocyte-derived exosomes were studied.


title: Fine Time-Course Expression Analysis of Mammalian Sex Determination in 129S1/SvImJ and C57BL/6J XX and XY mice

status: Public on Jun 11 2013

city: Durham

first: Anirudh

last: Natarajan

state: NC

address: 4034 GSRBII Building, Research Drive

institute: Duke University Medical Center

summary: We analyzed the differentiation of the bipotential gonad into a testis or an ovary in 2 strains of mice - 129S1/SvImJ (129S1) and C57BL/6J (B6). Our results provide a high resolution view of the initiation and canalization of the differentiation of the gonad. It also reveals global differences in the transcriptome between 129S1 and B6 mice.

overall_design: Total RNA was obtained from XX and XY embryonic mouse gonads at 6 equally spaced time points between embryonic day (E) 11.0 and E12.0 from 129S1 and B6 mice. Mice were staged using tail somite numbers

first: Blanche

last: Capel


title: Genome-wide analysis of gene expression of livers of wild type and IL-4/IL-13-/- mice after carbon tetrachloride-induced injury

status: Public on Jun 05 2013

city: San Francisco

first: Sharon

last: Goh

state: California

address: 555 Mission Bay Blvd South

institute: UCSF

summary: Global analysis of differentially expressed genes of livers of wild type and IL-4/IL-13-/- two days after carbon tetrachloride treatment.

overall_design: Total RNA obtained from isolated livers from vehicle and carbon tetrachloride administered wild type and IL-4/IL-13-/- mice.

first: Ajay

last: Chawla


title: Toll-like Receptor 2-independent Host Innate Immune Response Against an Epidemic Strain of Streptococcus suis that Causes a Toxic Shock-Like Syndrome in Humans

status: Public on Jun 01 2013

city: Mississauga

first: Claude

last: Lachance

state: Ontario

address: 1329 Meyerside Drive

country: Canada

institute: Bio-Rad

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

overall_design: Refer to individual Series


title: Genome wide analysis of C57BL/6 mice and C57BL/6 TLR2-KO mice infected with European strain (P1/7) of Streptococcus suis

summary: Streptococcus suis is an emerging zoonotic agent causing meningitis and septicemia. Outbreaks in humans in China with atypical cases of streptococcal toxic shock-like syndrome have been described to be caused by a clonal epidemic S. suis strain characterized as sequence type (ST) 7 by multilocus sequence typing, different from the classical ST1 usually isolated in Europe. Previous in vitro studies showed that Toll-like receptor (TLR) 2 plays a major role in S. suis ST1 interactions with host cells. In the present study, the in vivo role of TLR2 in systemic infections caused by S. suis ST1 or ST7 strains using TLR2 deficient (TLR2-/-) mice was evaluated. TLR2-mediated recognition significantly contributes to the acute disease caused by the highly virulent S. suis ST1 strain, since the TLR2-/- mice remained unaffected when compared to wild type (WT) mice. The lack of mortality could not be associated with a lower bacterial burden; however, a significant decrease in the induction of pro-inflammatory mediators, as evaluated by microarray, real-time PCR and protein assays, was observed. On the other hand, TLR2-/- mice infected with the epidemic ST7 strain presented no significant differences regarding survival and expression of pro-inflammatory mediators when compared to the WT mice. Together, these results show a TLR2-independent host innate immune response to S. suis that depends on the strain.

overall_design: Total RNA obtained from spleen of C57BL/6 mice or C57BL/6 TLR2-KO mice infected with Streptococcus suis strain P1/7. Four replicates in both groups.

first: Mariela

last: Segura

first: Pehuén

last: Gerber

first: Jianguo

last: Xu

first: Marcelo

last: Gottschalk


title: Genome wide analysis of C57BL-6 mice and C57BL/6 TLR2-KO mice infected with Chinese strain (SC84) of Streptococcus suis

overall_design: Total RNA obtained from spleen of C57BL/6 mice or C57BL/6 TLR2-KO mice infected with Streptococcus suis strain SC84. Four replicates in both groups.


title: An epigenetic signature of developmental potential in neural stem cells and early neurons [expression]

status: Public on Jun 09 2013

city: London

first: Matt

last: Burney

address: 125 Coldharbour Lane

country: United Kingdom

institute: King's College London

summary: A cardinal property of neural stem cells (NSCs) is their ability to adopt multiple fates upon differentiation. The epigenome is widely seen as a read-out of cellular potential and a manifestation of this can be seen in embryonic stem cells (ESCs), where promoters of many lineage-specific regulators are marked by a bivalent epigenetic signature comprising trimethylation of both lysine 4 and lysine 27 of histone H3 (H3K4me3 and H3K27me3, respectively). Bivalency has subsequently emerged as a powerful epigenetic indicator of stem cell potential. Here, we have interrogated the epigenome during differentiation of ESC-derived NSCs to immature GABAergic interneurons. We show that developmental transitions are accompanied by loss of bivalency at many promoters in line with their increasing developmental restriction from pluripotent ESC through multipotent NSC to committed GABAergic interneuron. At the NSC stage, the promoters of genes encoding many transcriptional regulators required for differentiation of multiple neuronal subtypes and neural crest appear to be bivalent, consistent with the broad developmental potential of NSCs. Upon differentiation to GABAergic neurons, all non-GABAergic promoters resolve to H3K27me3 monovalency, whereas GABAergic promoters resolve to H3K4me3 monovalency or retain bivalency. Importantly, many of these epigenetic changes occur prior to any corresponding changes in gene expression. Intriguingly, another group of gene promoters gain bivalency as NSCs differentiate toward neurons, the majority of which are associated with functions connected with maturation and establishment and maintenance of connectivity. These data show that bivalency provides a dynamic epigenetic signature of developmental potential in both NSCs and in early neurons.

overall_design: Illumina Expresson BeadChip arrays (MouseRef-8v2.0) were used to assess gene expression changes in neural stem cells (n=5; derived from mouse embryonic stem cells) and their differentiated neuronal progeny (n=3; FACS-purified based on Tau-RedStar expression).

first: Matthew

first: Caroline

last: Johnson

first: Kee-Yew

last: Wong

first: Siaw-Wei

last: Teng

first: Vassilios

last: Beglopoulos

first: Lawrence

middle: W

last: Stanton

first: Brenda

last: Williams

first: Angela

last: Bithell

first: Noel

last: Buckley


title: Collagen Dynamics and Transcriptional Profiling in Bleomycin-induced Pulmonary Fibrosis

status: Public on May 26 2013

city: Zeist

first: Lars

last: Verschuren

address: Utrechtseweg 48

department: Microbiology and Systems Biology

country: Netherlands

institute: TNO

summary:
Collagen deposition is a key process during idiopathic pulmonary fibrosis (IPF); however, little is known about the dynamics of collagen formation during disease development. Tissue samples of early stages of human disease are not readily available and it is difficult to identify changes in collagen content, since standard collagen analysis does not distinguish between 'old' and 'new' collagen. Therefore, the current study aimed to (i) investigate the dynamics of new collagen formation in mice using bleomycin-induced lung fibrosis in which newly synthesized collagen was labelled with deuterated water and (ii) use this information to identify genes and processes correlated to new collagen formation from gene expression analysis.
Lung fibrosis was induced in female C57BL/6 mice by bleomycin instillation and sacrificed. Animals were sacrificed at 1 to 5 weeks after fibrosis induction. Collagen synthesized during the week before sacrifice was labelled with deuterium by providing mice with deuterated drinking water. After sacrifice, lung tissue was collected for microarray analysis, determination of new collagen formation, and histology. Deuterated water labelling showed a strong increase in new collagen formation already during the first week after fibrosis induction and a complete return to baseline at five weeks. Correlation of new collagen formation data with gene expression data revealed fibrosis specific processes, of which proliferation was an unexpected one. This was confirmed by measuring cell proliferation and collagen synthesis simultaneously using deuterated water incorporation. Furthermore, new collagen formation strongly correlated with gene expression of e.g. elastin, tenascin C, MMP-14, lysyl oxidase, and type V collagen. These data demonstrate, using a novel combination of technologies, that proliferation and extracellular matrix production are correlated to the core process of fibrosis, i.e. the formation of new collagen. In addition, it identified genes directly correlated to fibrosis, thus providing more insight into the aetiology of IPF.

overall_design: Total RNA was obtained from mouse lungs at timepoint 0 as a control (n = 7) or timepoints 1 (n = 7), 2 (n = 6), 3 (n = 6), 4 (n = 6) or 5 (n = 6) weeks after bleomycin-instillation to induce lung fibrosis.

first: Marjolein

last: Blaauboer

first: Claire

last: Emson

first: Marjan

last: van Erk

first: Scott

last: Turner

first: Vincent

last: Everts

first: Roeland

last: Hanemaaijer

first: Reinout

last: Stoop


title: Ethanol effect on myoblast differentiation

status: Public on Apr 30 2013

city: Boston

first: Michelle

last: Arya

address: 15 Kneeland Street

institute: MCRI

summary: Expression profiling of C2C12 myoblast cells treated with ethanol during differentiation. Ethanol inhibits C2C12 differentiation. Results provide insight into signaling pathways altered by ethanol during differentiation.

overall_design: When C2C12 cells reached 70% confluence in growth medium containing 20% FBS, culture medium was changed to differentiation medium containing 2% horse serum with and without 100mM ethanol. Samples were harvested from day zero (just prior to differentiation) as well as days 1, 2 and 3 following onset of differentiation with and without alcohol treatment. RNA was isolated using the Qiagen RNA mini-kit.

first: Albert

middle: K

last: Tai

first: Eric

middle: C

last: Wooten

first: Christopher

middle: D

last: Parkin

first: Elena

last: Kudryavtseva

first: Gordon

middle: S

last: Huggins


title: Response to catration in PTEN null and PTEN null ERG expressing mouse prostates

status: Public on Apr 25 2013

first: Yu

last: Chen

address: 1275 York Ave, Box 20

department: Human Oncology and Pathogenesis Program

institute: Memorial Sloan Kettering Cancer Center

summary: We performed expression mouse profiling of prostates of 3 month PTEN f/f and Pten f/f;R26(ERG) mice and assessed the response to 3 days of castration.

overall_design: Mice are in the C57B6 background. Two mice in each group were castrated. Three days after castration, the prostate were harvested and RNA isolated by standard protocols and analyzed by expression profiling.

first: Charles

last: Sawyers


title: The innate and adaptive immune response to BCG stimulation in splenocytes taken from C57BL/6 mice

city: Oxford

first: leanne

last: marsay

address: roosevelt drive

department: Nuffield department

institute: University of Oxford

summary: The aim of this experiment was to investigate differential gene expression in splenocytes stimulated with BCG from naïve and BCG vaccinated mice. The differences between naïve and BCG vaccinated mice might indicate the mechanisms by which BCG vaccination confers an enhanced ability of splenocytes from BCG vaccinated mice to inhibit growth of BCG in splenocyte cultures as compared with splenocytes from naive animals.

overall_design: Splenocytes from 4 naïve and 4 BCG vaccinated female C57bl/6 mice were cultured for 12 hours with BCG (MOI 1:1) or without (unstimulated control). Each animal had a stimulated and an unstimulated sample hybridised to a beadchip.

first: Leanne

last: Marsay

first: Helen

last: Fletcher

first: Magali

last: Kostov

last: McShane


title: Expression data from adult mouse testis exposed to cigarette smoke in utero

status: Public on Oct 23 2013

city: Newcastle

first: Alexander

middle: Peter

last: Sobinoff

state: NSW

address: University Drive

department: Science and IT

institute: University of Newcastle Australia

summary: In the context of male reproductive health, epidemiological studies have observed reduced testis size and abnormal sperm counts and morphology in adult men exposed in utero, although these findings are not always repeated. The ambiguity of these reports is confounded by a lack of controlled animal studies investigating the effects of maternal cigarette smoke exposure on male offspring reproductive health. In this study we examined the effects of cigarette induced reproductive toxicity on male offspring exposed during the gestational and weaning period using our novel direct nasal exposure mouse model of cigarette smoke-induced chronic obstructive pulmonary disease and female subfertility. This was done too gain a better understanding of the adverse effects of gestational maternal smoking on male offspring fertility.

overall_design: C57BL/6 5 week-old female mice were exposed via the nose-only to cigarette smoke [twelve 3R4F reference cigarettes (University of Kentucky, USA) twice/day, five times per week, for 12-18 weeks]. Each exposure lasted 60 minutes. Control mice received room air. In total, 27 mice underwent cigarette smoke exposure. Eleven week-old female mice exposed to cigarette smoke for 6 weeks were separated into groups of three and housed with a single control stud male aged 7-8 weeks with proven fertility for a maximum of 12 weeks. Females were monitored every second day for post-coital plugs and pregnancy. Pregnant females were separated into single cages and litter sizes/pup weights recorded. Smoke exposure via dams continued throughout mating/pregnancy/lactation until weaning of pups at 21days post birth. The testis of exposed offspring were then collected for RNA extraction and hybridization on an Illumina Sentrix Mouse ref-8 v2 Beadchip

first: Eileen

last: McLaughlin


title: Sox7 and Sox17

status: Public on Apr 23 2013

city: Lyon

first: Irene

last: Aksoy

address: 18 avenue du Doyen Lepine

country: France

institute: Stem Cell and Brain Research Institute


title: Gene expression analysis of V5 tagged Sox17 expressing ES cells

summary: Analysis of the expression of KH2 embryonic stem cells inducibly expressing V5 tagged Sox17 protein. Results provide information on the endodermal gene expression program activated after Sox17 expression in ES cells.

overall_design: Total RNA extracted from 48 hours doxycycline induced compaired to non-induced Sox17-V5 expressing ES cells

first: Larry

last: stanton


title: Genome-wide expression profiling analysis of a SMC6 mutant mouse model

status: Public on Apr 22 2013

first: Martin

last: Irmler

summary: The function of the SMC5-6 complex is less clear, but it has an important role in a variety of different DNA repair processes and in resolving recombination structures. Interestingly mutation at a highly conserved residue (Ser994) in the ATP hydrolysis motif in the SMC6 C-terminal domain, resulted in mice with a mild phenotype.

overall_design: Total RNA obtained from homozygote 4 male mutant mice was compared to 2-4 wild type or 2 heterozygote controls.

first: Johannes

last: Beckers

first: Marion

last: Horsch


title: Genome-wide analysis of the effects of propranolol on angiosarcoma tumor cells

city: El Paso

first: Brad

middle: Allen

last: Bryan

state: Texas

address: 5001 El Paso Drive

department: Biomedical Sciences

institute: Texas Tech University Health Sciences Center

summary: Analysis of the effects of 4 hr and 24 hr propranolol treatment on gene expression of SVR mouse angiosarcoma cells. The hypothesis tested in the present study was that inhibiton of beta adrenergic receptor signaling could ablate the oncogenic properties of angiosarcoma cells. Results provide important information of the response of angiosarcoma cells to ablated beta adrenergic receptor signaling.

overall_design: The total RNA was obtained from mouse angiosarcoma cells cultured in monolayer at 0, 4, and 24 hrs of 50 micromolar propranolol treatment.  Illumina microarrays were performed to determine the whole genome expression changes following treatment.

first: Dianne

last: Mitchell


title: Small RNA expression signatures of gastrointestinal stromal tumors: associations to imatinib resistance and patient outcome

status: Public on Apr 10 2013

city: Stockholm

first: Pinar

last: Akcakaya

address: CCK R8:04

department: Oncology-Pathology

institute: Karolinska Institutet

summary: We performed miRNA expression profiling in  a series of fresh-frozen neoadjuvantly imatinib treated gastrointestinal stromal tumors (GIST), using a microarray approach. Significant differentially expressed miRNAs among imatinib-resistant and imatinib-sensitive groups were identified using SAM analysis.

overall_design: Agilent microarray platform with probes matching 903 human miRNAs was used to determine miRNA expression profiles in 17 GISTs (imatinib-sensitive and 7 imatinib-resistant). To validate the microarray platform, the expression levels of selected miRNAs were evaluated using qRT-PCR.

last: Akçakaya

first: Stefano

last: Caramuta

first: Jan

last: Åhlen

first: Mehran

last: Ghaderi

first: Erik

last: Berglund

first: Arne

last: Östman

first: Robert

last: Bränström

first: Catharina

last: Larsson

first: Weng-Onn

last: Lui


title: Genome-wide analysis of gene expression in liver after insulin receptor antagonist S961 treatment

status: Public on Apr 02 2013

city: Cambridge

first: Peng

last: Yi

state: MA

address: 7 Divinity Ave.

department: SCRB

institute: Harvard University

summary: Insulin receptor antagonist S961 induces pancreatic beta cell replication. Microarray anaysis was performed in liver to find genes that may mediate beta cell replication.

overall_design: Mice were treated with either vehicle (PBS) or S961 (10nMol/week) for a week, the total RNA from liver was isolated and then subjected to illumina microarray analysis.

first: Douglas

last: Melton


title: Type 2 innate signals regulate functionality of fibro/adipogenic progenitors to facilitate muscle regeneration

status: Public on Apr 11 2013

city: SAN FRANCISCO

first: Rahul

last: Deo

state: CA

address: 555 Mission Bay Blvd. South

department: Cardiovascular Research Institute

institute: University of California San Francisco

summary: In vertebrates, activation of innate immunity is an early response to injury, implicating it in the regenerative process. However, the mechanisms by which innate signals might regulate stem cell functionality are unknown. Here we demonstrate that type 2 innate immunity is required for regeneration of skeletal muscle after injury. Muscle damage results in rapid recruitment of eosinophils, which secrete IL-4 to activate the regenerative actions of muscle resident fibro/adipocyte progenitors (FAPs). In FAPs, IL-4/IL-13 signaling serves as a key switch to control their fate and functions. Activation of IL-4/IL-13 signaling promotes proliferation of FAPs to support myogenesis, while inhibiting their differentiation into adipocytes. Surprisingly, type 2 cytokine signaling is also required in FAPs, but not myeloid cells, for rapid clearance of necrotic debris, a process that is necessary for timely and complete regeneration of tissues.

overall_design: Fibroadipocyte progenitors were isolated from wild-type and IL-4Ra knockout (IL-4Ra -/-) mice and were treated with vehicle or IL4 stimulation in culture prior to microarray analysis.  4 biological replicates of each condition were performed.

first: Jose

last: Heredia

first: Lata

last: Mukundan

first: Francis

middle: M

last: Chen

first: Alisa

last: Mueller

first: Richard

last: Locksley

first: Thomas

last: Rando

first: Ajay

last: Chawla


title: Mast cell expression data from murine aryl hydrocarbon receptor (AhR) null, AhR_d and normal control mice

status: Public on Apr 01 2013

first: Alan

middle: E.

last: Berger

address: 5501 Hopkins Bayview Circle Room 3B.74C

department: School of Medicine

institute: Johns Hopkins University

summary: We found that AhR, a unique chemical sensor, is critical in controlling mast cell differentiation, growth and function in vitro and in vivo. This study seeks to further the understanding of the mechanisms of how AhR control mast cell homeostasis.

overall_design: Three different batches of bone marrow derived mast cells (BMMCs) from AhR null, AhR_d and normal control mice were cultured in 30% WEHI-3-conditioned medium. BMMCs were purified by negative selection with MicroBeads (Miltenyi Biotec) after 4 weeks in culture. 99% BMMCs were FcεRI+ c-kit+ CD49b- by flow cytometry analysis. The cells were further rested in cytokine free medium for 4h. Subsequently, total RNA was collected. Gene expression profiling was performed on total RNA from mast cells using Illumina Sentrix® Murine Ref8_v2_R3 BeadChips. Details of the design and the gene signatures found are given in the paper associated with this GEO Series: Yufeng Zhou, Hui-Ying Tung, Ying-Ming Tsai, Shih-Chang Hsu, Hui-Wen Chang, Hirokazu Kawasaki, Hsiao-Chun Tseng, Beverly Plunkett, Peisong Gao, Chih-Hsin Hung, Becky M. Vonakis, and Shau-Ku Huang. “Aryl hydrocarbon receptor controls murine mast cell homeostasis”, Blood 2013 Mar 5 [Epub ahead of print]

first: Yufeng

last: Zhou

first: Hui-Ying

last: Tung

first: Ying-Ming

last: Tsai

first: Shih-Chang

last: Hsu

first: Hui-Wen

last: Chang

first: Hirokazu

last: Kawasaki

first: Hsiao-Chun

last: Tseng

first: Beverly

last: Plunkett

first: Peisong

last: Gao

first: Chih-Hsin

last: Hung

first: Becky

last: Vonakis

first: Shau-Ku

last: Huang


title: Generation of organized anterior foregut epithelia from pluripotent stem cells using small molecules

status: Public on Apr 15 2013

city: Munich

first: Michael

middle: Johannes

last: Ziller

address: Kraepelinstrasse 2-10

department: Translational Psychiatry

institute: Max Planck Institute of Psychiatry

summary: Anterior foregut endoderm (AFE) gives rise to many tissue types of interest for therapeutic research including the esophagus, salivary glands, lung, thymus, parathyroid and thyroid. Despite its importance, only few reports describe the generation of AFE from pluripotent stem cells (PSCs) by directed differentiation. Here, we describe a novel protocol to derive a subdomain of AFE, identified by expression of Pax9, from PSCs using small molecules and chemically defined conditions. Generation of a reporter PSC line allows isolation and characterization of Pax9+ AFE cells. When transplanted in vivo, Pax9+ AFE can form several distinct types of complex anterior foregut epithelia including mucosal glands and stratified squamous epithelium. Finally, we show that the directed differentiation protocol can be used to generate AFE from DiGeorge Syndrome patient-specific human induced PSCs, thus creating a platform to produce anterior foregut derivatives for therapy and to enable the study of disorders of the AFE.

overall_design: Total RNA obtained from FACS purified from in vitro dervied mouse definitive endoderm, anterior foregut and ES cells. AFE cells were derived from a 129X1/SvJ background, DE cells from 129X1/SvJ x 129S1/SV-+p+Tyr- cKitlSl-J/+ (R1 ES cells) and non reporter ES cells from a 129P2/OlaHsd background.

first: Rene

last: Maehr


title: Total Gene expression analysis of H3f3b null and WT MEFs

city: Sacramento

first: Paul

last: Knoepfler

address: 2425 Stockton Blvd

department: Cell Biology and Human Anatomy

institute: UC Davis

summary: Total gene expression analysis was performed on constitutive H3f3b KO E12.5 MEFs relative to WT littermates. Intent was to analyze the role of H3f3b in overall gene expression.

overall_design: Constitutive KO mice were obtained by mating H3f3b Fl/Fl mice to Zp3Cre mice. Heterozygous offspring were time mated and embryos were isolated 12.5 days after. MEFs were cultured transduced with a stable pBabe puro vector and total RNA was isolated from H3f3b KO and WT MEFs.

first: Kelly

last: Bush

first: John

last: Riggs


title: IRF-3, IRF-5, and IRF-7 coordinately regulate the type I IFN response in myeloid dendritic cells downstream of MAVS signaling

city: Cleveland

first: Peter

last: Wilkinson

state: Ohio

address: 2103 Cornell Road

department: Pathology / Systems Biology & Bioinformatics

institute: Case Western Reserve University

summary: Myeloid dendritic cells from WT, Irf3-/-xIrf7-/-, Irf3-/-xIrf5-/-xIrf7-/-, Mavs-/- (IPS1-/-)and Ifnar-/- mice were infected with West Nile virus to assess the contributions of specific signaling and transcription factors in initiating the antiviral response

overall_design: RPMI + rmGM-CSF purified bone marrow derived myeloid DC (mDC), mock and WNV infected with insect derived virus and RNA isolated at 24 hours post infection . Each genotype has matched mock and infected samples. n=6 for WT mock, WT infected, IFNAR mock, IFNAR infected, IRF3x7 infected; n=5 IRF3x7 infected; n=3 IRF3x5x7 mock, IRF3x5x7 infected, MAVS mock, MAVS infected. RNA was prepared using the Illumina bead station assay and hybridized to Illumina RefSeq-8 V2 BeadChips. Note: MAVS=IPS1

first: Helen

last: Lazear

first: Alissa

last: Lancaster

first: Courtney

last: Wilkins

first: Mehul

last: Suthar

first: Albert

first: Sarah

last: Vick

first: Lisa

last: Clepper

first: Larissa

last: Thackray

first: Margaret

last: Brassil

first: Herbert

last: Virgin

first: Janko

last: Nikolich-Zugich

first: Ashlee

middle: V

last: Moses

last: GaleJr

first: Klaus

last: Fruh

last: Diamond


title: Genome wide analysis of C57BL-6 mice infected with European strain (P1/7) of Streptococcus suis

status: Public on Mar 27 2013

first: Claude

last: Lachance

summary: Streptococcus suis is a major swine pathogen that can be transmitted to humans causing severe symptoms. A large human outbreak was described in China, where approximately 25% out of 215 infected humans developed an unusual streptococcal toxic shock-like syndrome (STSLS). Albeit increased expression of inflammatory mediators following infection by the Chinese S. suis strain was suggested as responsible for STSLS case severity, the mechanisms involved are still poorly understood. In this study, we investigated the host innate immune response to infection by either one of 3 strains of S. suis: 89-1591 (Canadian, intermediate virulence), P1/7 (European, high virulence), and SC84 (Chinese, epidemic strain). Using Illumina microarray and validating those results with qPCR and Luminex assay, infected mice showed elevated expression of mainly pro-inflammatory chemokine and cytokine genes. Generally, pro-inflammatory genes were expressed at a higher level in mice infected with S. suis strain SC84 > P1/7 > 89-1591. Interestingly, IFNγ was expressed at much higher levels only in mice infected with the S. suis strain SC84, which could potentially explain some of the STSLS symptoms. IFNγ-KO mice infected with SC84 showed better survival than WT mice while no differences was seen in mice infected with highly virulent P1/7 strain. Overall, our results show an important role of IFNγ in S. suis infections and might explain in part the increased virulence of SC84 responsible for a recent outbreak in China.

overall_design: Total RNA obtained from spleen of C57BL/6 mice infected with Streptococcus suis strain P1/7 or mock-infected with THB. Four replicates in both groups.

first: Marcelo

last: Gottschalk

first: Pehuén

last: Gerber

first: Paul

last: Lemire

first: Jianguo

last: Xu

first: Mariela

last: Segura


title: Genome wide analysis of C57BL-6 mice infected with North-American strain (89-1591) of Streptococcus suis

overall_design: Total RNA obtained from spleen of C57BL/6 mice infected with Streptococcus suis strain 89-1591 or mock-infected with THB. Four replicates in both groups.


title: mRNA expression profiles in androgenetic, parthenogenetic and fertilized embryonic stem cells

status: Public on Apr 04 2013

city: Cheongju

first: Nam-Hyung

last: Kim

state: Chungbuk

address: Gaeshin-dong

country: South Korea

institute: Chungbuk National University

summary: In this study, mRNA expression profiles were examined by Illumina microarray in mouse embryonic stem cells (ESCs) derived from androgenetic (aESC), parthenogenetic (pESC) and fertilized (fESC) blastocysts. Results showed that 2394, 87 and 1788 mRNAs were differentially expressed in the aESCs vs. fESCs, pESCs vs. fESCs and aESCs vs. pESCs, respectively.

overall_design: Androgenetic, parthenogenetic and fertilized embryonic stem cell lines were established from androgenetic, parthenogenetically activated and fertilized blasotocyst. mRNA microarrays were repeated three times using passages 6, 7 and 8.

first: Xiang

last: Cui

first: Teruhiko

last: Wakayama

first: Nam

middle: H


title: mRNA and microRNA expression profiles in androgenetic, parthenogenetic and fertilized embryonic stem cells

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: Conversion of genomic imprinting by reprogramming and re-differentiation

status: Public on Mar 20 2013

city: Seoul

first: MIN JUNG

last: KIM

address: 605-21 YeokSamDong

institute: CHA University

summary:
We determined whether the changed imprinted genes are maintained or reverted to the parthenogenetic state when the reprogrammed cells are re-differentiated into specialized cell types. To address this question, we re-differentiated miPSCs into neural stem cells (miPS-NSCs) and compared them with biparental female NSCs (fNSCs) and parthenogenetic NSCs (pNSCs)
large-scale gene expression analysis of miPS-NSCs, fNSCs, and pNSCs, using the Illumina gene expression array

overall_design: Total RNA obtained from the three different NSC samples

first: Min-JUNG

first: JEONG-TAE

last: Do


title: Genome wide analysis of C57BL-6 mice infected with Chinese strain (SC84) of Streptococcus suis

address: 1329 Meyerside Drive

institute: Bio-Rad

overall_design: Total RNA obtained from spleen of C57BL/6 mice infected with Streptococcus suis strain SC84 or mock-infected with THB. Four replicates in both groups.

middle: P


title: Gene expression in brain and liver produced by three different regimens of alcohol consumption in mice: Comparison with immune activation

city: Austin

first: Elizabeth

last: Osterndorff-Kahanek

state: TX

address: 2500 Speedway

institute: University of Texas at Austin

summary:
We investigated the molecular mechanisms of chronic alcohol consumption or lipopolysaccharide insult by gene expression profiling in prefrontal cortex and liver of C57BL/6J mice.
We identified similar patterns of transcriptional changes in brain and liver among three different alcohol consumption tests and lipopolysaccharide injection.
We also demonstrated distinct genomic consequences of different types of alcohol consumption.

overall_design:
The microarray experiment was performed to compare gene expression changes induced by three separate paradigms of alcohol consumption and immune activation by lipopolysaccharide injection.
The three tests of alcohol consumption were the continuous chronic two bottle choice (Chronic), two bottle choice available every other day (Chronic Intermittent) and limited access to one bottle of ethanol (Drinking in the Dark).
All alcohol studies utilized 20% ethanol and each treatment group had it's own control group which received only water.
The immune activation test consisted of 2 lipopolysaccharide injections (1 mg/kg i.p.) spaced one week apart, with animals being sacrificed one week after the last injection. Control animals received saline injections.
All studies used female, adult mice.

first: Igor

last: Ponomarev

first: Yuri

last: Blednov

first: R

last: Harris


title: Depletion of Jak2V617F MPN-propagating stem cells by interferon-alpha in a murine model of polycythemia vera

status: Public on Mar 09 2013

city: Brisbane

first: Steven

last: Lane

address: 300 Herston Rd

institute: QIMR

summary: Interferon alpha (IFNa) is an effective treatment for patients with myeloproliferative neoplasms (MPN). In addition to inducing hematological responses in most MPN patients, IFNa reduces the JAK2V617F allelic burden and can render the JAK2V617F mutant clone undetectable in some patients. The precise mechanism underlying these responses is incompletely understood and whether the molecular responses that are seen occur due to the effects of IFNa on JAK2V617F mutant stem cells is debated. Using a murine model of Jak2V617F MPN, we investigated the effects of IFNa on Jak2V617F MPN-propagating stem cells in vivo. We report that IFNa treatment induces hematological responses in the model and causes depletion of Jak2V617F MPN-propagating cells over time, impairing disease transplantation. We demonstrate that IFNa treatment induces cell-cycle activation of Jak2V617F mutant long-term hematopoietic stem cells (LT-HSC) and promotes a predetermined erythroid-lineage differentiation program. These findings provide insights into the differential effects of IFNa on Jak2V617F mutant and normal hematopoiesis and suggest that IFNa achieves molecular remissions in MPN patients through its effects on MPN stem cells. Furthermore, these results support combinatorial therapeutic approaches in MPN, by concurrently depleting dormant JAK2V617F MPN-propagating stem cells with IFNa and targeting the proliferating downstream progeny with JAK2-inhibitors or cytotoxic chemotherapy.

overall_design: HSC-enriched population from WT (CD45.1) or Jak2VF knockin (CD45.2), after 4 weeks of interferon alpha or vehicle treatment. N=4 per condition

first: A

last: Mullally

first: C

last: Bruedigam

first: L

last: Poveromo

first: F

last: Heidel

last: Purdon

first: T

last: Vu

last: Austin

first: D

last: Heckl

middle: J

last: Breyfogle

last: Paine Kuhn

last: Kalaitzidis

first: S

last: Armstrong

last: Williams

first: G

middle: R

last: Hill

first: B

last: Ebert


title: Bmi-regulated miRNA expression pattern in head and neck cancers

status: Public on Feb 11 2013

city: Taipei

first: Muh-Hwa

last: Yang

address: No.155, Sec.2, Li-Nong Street

department: Institute of Clinical Medicine

country: Taiwan

institute: National Yang-Ming University

summary: The critical role of Bmi1 in promoting stem cell properties has been shown in different type of human cancers. Here, we established four stable clones to study Bmi-regulated miRNA expression patterns in head and neck caners.

overall_design: Bmi1-overexpressing cell lines (FaDu- Bmi1vs. FaDu-pcDNA3 cell line), and knock-down of Bmi1 cell lines (OECM1-sh-Bmi vs. OECM1-sh-Bmi1 cell lines) were established and used for analyzing miRNA expression patterms in Bmi-regulatory mechanism.

first: MuhHwa


title: Melanoma tissue samples from a clinical trial: no treatment vs. post-temsirolimus alone vs. post-combination temsirolimus and bevacizumab

status: Public on Mar 08 2013

city: Charlottesville

first: Aubrey

last: Wagenseller

state: Virginia

address: 345 Crispell Drive

department: Surgery

institute: University of Virginia

summary: To determine if treatment with a combined therapeutic regimen, which resulted in clinical benefit in a subset of patients in a clinical trial, alters miRNA expression in a way that may be used to guide treatment with these agents and to identify miRNAs that may be involved in the mechanism of action of this regimen

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus
Human alphaherpesvirus 1
Human alphaherpesvirus 2
Human betaherpesvirus 5
Murid betaherpesvirus 1
human gammaherpesvirus 4
JC polyomavirus
Human immunodeficiency virus 1
Murid gammaherpesvirus 4
Human gammaherpesvirus 8
Merkel cell polyomavirus
Mus musculus cytomegalovirus 2
Betapolyomavirus hominis
Betapolyomavirus macacae

overall_design: Three-condition experiment, untreated tissue, post-temsirolimus alone treatment, post combination-treatment tissue. 33 total samples, including 5 samples resubmitted for quality control.

first: Amber

last: Shada

middle: G

first: Cheryl

last: Murphy

first: Craig

last: Slingluff

first: Dandan

last: Sun

first: Anindya

last: Dutta

first: Kerrington

last: Molhoek

first: Jason

last: Papin

first: Kevin

last: D'Auria


title: The expression level of microRNA after knockdown of Twist1 or Bmi1

summary: To screen the microRNA regulated by Twist1 and Bmi1

overall_design: Establish stable transfectants of pSUPER-sh-Twist1 or pSUPER-sh-Bmi1 in OECM1 cells and analyze the miRNA expression level of  by microRNA microarray. OECM1 transfected with pSUPER-sh-scr was used as a control experiment.

first: Wen-Hao


title: Hypoxia-induced Arterial Differentiation Requires Adrenomedullin and Notch Signaling

status: Public on Feb 08 2013

city: Singapore

first: Kian Leong

last: LEE

state: Singapore

address: #07-21, 8 College Road

department: Duke-NUS Medical School

country: Singapore

institute: National University of Singapore (NUS)

summary: Hypoxia (low oxygen) and Notch signaling are two important regulators of vascular development, but how they interact in controlling the choice between arterial and venous fates for endothelial cells during vasculogenesis is less well understood. In this report, we show that hypoxia and Notch signaling intersect in promotion of arterial differentiation. Hypoxia upregulated expression of the Notch ligand Dll4 and increases Notch signaling, in a process requiring the vasoactive hormone adrenomedullin but not endogenous VEGF. Notch signaling also upregulated Dll4 expression, leading to a positive feedback loop sustaining Dll4 expression and Notch signaling. In addition, functional Notch signaling was required for hypoxia to upregulate the arterial marker genes Depp, connexin40 (Gja5), Cxcr4 and Hey1. In conclusion, the data reveal an intricate interaction between hypoxia and Notch signaling in the control of endothelial cell differentiation, including a hypoxia/adrenomedullin/Dll4 axis that initiates Notch signaling and a requirement for Notch signaling to effectuate hypoxiamediated induction of the arterial differentiation program.

overall_design: 12 microarray samples consisting of >50,000 FACS sorted CD31+ cells purified from wild type mouse CCE ES cells that were differentiated into the endothelial lineages in 3 biological replicates. The ES cells were subjected to embryoid body formation over 4 days in hanging drop cultures, FACS sorted for Flk1 positive vascular progenitors cells and plated for a further 4 days in normoxia (21% oxygen) or hypoxia (1.5-2% oxygen) with or without 4 umol/l gamma-secretase inhibitor L-685.458.

first: Fredrik

last: Lanner

first: Kian

middle: L

last: Lee

first: Germán

last: Ortega

first: Marcus

last: Sohl

first: Xiujuan

last: Li

first: Shaobo

last: Jin

first: Emil

last: Hansson

first: Lena

last: Claesson-Welsh

first: Lorenz

last: Poellinger

first: Urban

last: Lendahl

first: Filip

last: Farnebo


title: Total Gene expression analysis of H3f3b conditional knockout MEFs

first: Paul

last: Knoepfler

summary: Total gene expression analysis was performed on CRE induced conditional knockout E12.5 MEFs relative to GFP infected control MEFs. Intent was to analyze the role of H3f3b in overall gene expression.

overall_design: For conditional KO, three lines of H3f3b FL/FL E12.5 MEFs (cKO1, cKO2 and pcKO1) were transduced with Cre retroviruses and compared to their respective lines of MEFs transduced solely with GFP vector (as control). Total RNA was isolated for gene analysis.

first: Kelly

last: Bush

first: John

middle: W

last: Riggs


title: Gene expression profiling of Nodal versus Activin-derived endoderm from mouse ES cells

status: Public on Jan 01 2013

first: Alice

middle: E

last: Chen

state: Ma

address: 7 Divinity Avenue

department: Stem Cell and Regenerative Biology

summary: To explore the molecular basis of functional differences observed between Nodal versus Activin-derived endoderm, we compared their respective gene expression profiles. Sox17-GFP mouse ES cells were differentiated in the presence of Nodal or Activin for 7 days, after which GFP(+) cells were purified by FACs. Undifferentiated ES cells were also included for comparison as a control. Results indicate that the two endoderm populations are nearly identical at the level of global transcription.  Subtle differences suggest a difference in the degree of endoderm progression.

overall_design:
Total RNA obtained from SOX17-GFP (+) mouse ES cells, Sox17-GFP treated with Nodal, Sox17-GFP treated with Activin.
Two replicates for each sample;  Sample data table contains average values of two replicates. The non_normalized.txt file contains individual signal values for each replicate.

first: Douglas

middle: A

last: Melton


title: Transcriptomic Analysis Comparing Tumor-Associated Neutrophils with Granulocytic Myeloid-Derived Suppressor Cells and Normal Neutrophils

status: Public on Jan 04 2013

city: Philadelphia

first: Louise

middle: C

last: Showe

state: PA

address: 3601 Spruce St

institute: The Wistar Institute

summary: The role of myeloid cells in supporting cancer growth is well established. Most work has focused on myeloid-derived suppressor cells (MDSC) that accumulate in tumor-bearing animals, but tumor-associated neutrophils (TAN) are also known to be capable of augmenting tumor growth. However, little is known about their evolution, phenotype, and relationship to naive neutrophils (NN) and to the granulocytic fraction of MDSC (G-MDSC). In the current study, a transcriptomics approach was used in mice to compare these cell types. Our data show that the three populations of neutrophils are significantly different in their mRNA profiles with NN and G-MDSC being more closely related to each other than to TAN. Structural genes and genes related to cell-cytotoxicity (i.e. respiratory burst) were significantly down-regulated in TAN. In contrast, many immune-related genes and pathways, including genes related to the antigen presenting complex (e.g. all six MHC-II complex genes), and cytokines (e.g. TNF-a, IL-1-a/b), were up-regulated in G-MDSC, and further up-regulated in TAN. Thirteen of the 25 chemokines tested were markedly up-regulated in TAN compared to NN, including striking up-regulation of chemoattractants for T/B-cells, neutrophils and macrophages. This study characterizes different populations of neutrophils related to cancer, pointing out the major differences between TAN and the other neutrophil populations.

overall_design:
Various types of myeloid cells have been shown to promote tumor progression by direct immune suppression and by production of angiogenic factors, matrix-degrading enzymes, or growth factors. In untreated tumors, neutrophils have been reported to produce angiogenic factors and matrix-degrading enzymes, support the acquisition of a metastatic phenotype, and suppress the anti-tumor immune response. Neutrophils, like all other leukocytes, move into tissues from the blood under the influence of specific chemokines (e.g. KC/CXCL-1, MIP-2a/CXCL-2 and GCP-2/CXCL-6), cytokines (e.g. TNFa and IFN-x), and cell adhesion molecules located on their own surface (e.g. CD11b) and on the surface of endothelial cells (e.g. selectins, ICAM-1 and PECAM-1). When they traffic into tumors, they are referred to as TAN. In mice, TAN can be defined by the specific surface markers CD11b and Ly6G with low expression of macrophage markers such as F4/80.

Myeloid-derived suppressor cells (MDSC) are a heterogeneous population of immune suppressive cells that are produced excessively in cancer. They comprise at least two subsets -granulocytic (Ly6G+, G-MDSC) and monocytic cells (Ly6C+, M-MDSC), potentially with different immunosuppressive properties. It has been previously shown that MDSC can enter tumors and differentiate to mature macrophages (TAM) or neutrophils (TAN). However, since no definitive markers have been established, it is unknown whether intratumoral N2 neutrophils (N2 TAN) are granulocytic MDSC from spleen that are attracted to the tumor or if they are typical blood-derived neutrophils that are then converted to an N2 phenotype by the tumor microenvironment, specifically by the high local concentrations of TGF-b.

The purpose of this study was to use a transcriptomics approach to gain further information about TANs by comparing the RNA profile of these cells to naive bone-marrow neutrophils (NN) and to the granulocytic fraction of myeloid derived suppressor cells (G-MDSC). We examined which pathways and gene-groups varied amongst these 3 populations of neutrophils and performed a detailed analysis on pathways related to the main functions of neutrophils, such as respiratory burst, granule proteins, phagocytosis, apoptosis, structural genes, antigen presentation and specific immune effects. Our data defines TAN as a unique population of neutrophils, quite distinct from both NN and G-MDSC.

first: Zvi

last: Fridlender

first: Jing

last: Sun

first: Inbal

last: Mishalian

first: Sunil

last: Singhal

first: Guanjun

last: Cheng

first: Veena

last: Kapoor

first: Wenhwai

last: Horng

first: Gil

first: Rachel

last: Bayuh

first: Scott

last: Worthen

first: Steven

last: Albelda


title: Systems biology analysis unravels complementary action of combined Rosuvastatin and Ezetimibe therapy

status: Public on Feb 27 2013

city: Zeist

first: Lars

last: Verschuren

address: Utrechtseweg 48

institute: TNO

summary: Transcriptomics analysis to understand both efficacy and side effects of a cholesterol lowering drug combination therapy based on biological pathways and molecular processes affected by each drug alone or in combination. We have treated ApoE*3Leiden mice, a humanized atherosclerosis model with a unique human-like response to cholesterol-lowering drugs, with RSV and EZE alone and in combination. We demonstrate that processes affected by monotherapy can be retained and enhanced by combination therapy. In addition, combination therapy also affects a number of processes which are not predictable on basis of monotherapy – at least when analysis is performed within the borders of statistical significance. Our data however provide clues for these “non-predictable” effects.

overall_design: Total RNA obtained from mouse liver from mice treated with High-Cholesterol (HC) diet as control (n=8) or HC+RSV (n=8) or HC+EZE (n=8) or HC+RSV+EZE (n=8).

first: Marijana

last: Radonjic

first: Peter

middle: Y

last: Wielinga

first: Thomas

last: Kelder

first: Teake

last: Kooistra

first: Ben

last: van Ommen

first: Robert

last: Kleemann


title: Genome-wide analysis of gene expression profile of Intestinal (COLON) Tumors from APCmin/+/VP16LXRa vs APCmin/+/VP16

status: Public on Feb 05 2013

city: Santa Maria Imbaro

first: Antonio

last: Moschetta

address: Via Nazionale 8A

country: Italy

institute: University of Bari & Consorzio Mario Negri Sud

summary: Changes in gene expression profile of intestinal (COLON) Tumors from APCmin/+/VP16LXRa vs APCmin/+/VP16.  The hypothesis tested in the present study was that LXRa overexpression influence cancer growth modulating lipid metabolism in cancer cells. Results provide the information that LXRa induces expression of genes encoding proteins able to regulate cholesterol efflux.

overall_design: Total RNA obtained from colonic tumors from APCmin/+/VP16LXRa mice was compared to total RNA extracted from APCmin/+/VP16 mice.

first: Fabiola

last: Bovenga

first: D'Orazio

last: Andria


title: Transcript levels in CCE WT and RARgamma knockout murine embryonic stem cells treated with either all-trans retinoic acid (8 and 24 hr) or with vehicle control

status: Public on Dec 31 2012

city: New York

first: Kristian

middle: Bruun

last: Laursen

address: 1300 York Avenue

department: Pharmacology

institute: Weill Cornell Medical College

summary:
Retinoic acid receptors (RARs) α, β, and γ heterodimerize with Retinoid X receptors (RXR) α, β, and γ and bind the cis-acting response elements known as RAREs to execute the biological functions of retinoic acid during mammalian development. RARγ mediates the anti-proliferative and apoptotic effects of retinoids in certain tissues and cancer cells, such as melanoma and neuroblastoma cells. Furthermore, ablation of RARγ enhanced the tumor incidence of Ras transformed keratinocytes and was associated with resistance to retinoid mediated growth arrest and apoptosis.
We used microarray analysis to identify genes, which upon 8 or 24 hr of treatment with all-trans retinoic acid display differential expression in RARγ knockout (RARγKO) murine embryonic stem cells relative to CCE WT cells. We demonstrate that following RA treatment the majority of inducible transcripts are present at lower levels in RARγKO ES cells compared to WT ES cells.

overall_design: Murine embryonic stem cells (WT and RARγKO) were treated with either all-trans retinoic acid (up to 24 hr) or with vehicle control (EtOH).

middle: B

first: Lorraine

last: Gudas


title: Notch signaling/MyoD double deficient embryonic muscle progenitors

city: Berlin

first: Dominique

last: Bröhl

state: Berlin

address: Robert-Rössle-Str. 10

department: Research Program Function and Dysfunction of the Nervous System

institute: Max-Delbrück-Center for Molecular Medicine

summary: Skeletal muscle growth and regeneration rely on myogenic progenitor and satellite cells, the stem cells of postnatal muscle. Elimination of Notch signals during mouse development results in premature differentiation of myogenic progenitors and formation of very small muscle groups. Here we show that this drastic effect is rescued by mutation of the muscle differentiation factor MyoD. However, rescued myogenic progenitors do not assume a satellite cell position and contribute poorly to myofiber growth. The disrupted homing is due to a deficit in basal lamina assembly around emerging satellite cells and to their impaired adhesion to myofibers. On a molecular level, emerging satellite deregulate the expression of basal lamina components and adhesion molecules like integrin a7, collagen XVIIIa1, Megf10 and Mcam. We conclude that Notch signals control homing of satellite cells, stimulating them to contribute to their own microenvironment and to adhere to myofibers.

overall_design: Gene expression analysis using total RNA from FACS-isolated Vcam-1+/CD31-/CD45-/Sca1-  embryonic muscle progenitor cells from E17.5 back muscle tissue of MyoD-/-, Pax3cre/+;Rbpjflox/flox;MyoD-/- and Pax3cre/+;DnMamlflox/flox;MyoD-/- mice.

first: Elena

last: Vasyutina

first: Maciej

middle: T

last: Czajkowski

first: Joscha

last: Griger

first: Claudia

last: Rassek

first: Hans-Peter

last: Rahn

first: Bettina

last: Purfürst

first: Hagen

last: Wende

first: Carmen

last: Birchmeier


title: Genome-wide analysis of gene expression profile of Intestinal (ILEUM) Tumors from APCmin/+/VP16LXRa vs APCmin/+/VP16

summary: Changes in gene expression profile of intestinal (ILEUM) Tumors from APCmin/+/VP16LXRa vs APCmin/+/VP16. The hypothesis tested in the present study was that LXRa overexpression influence cancer growth modulating lipid metabolism in cancer cells. Results provide the information that LXRa induces genes encoding proteins able to regulate cholesterol efflux.

overall_design: Total RNA obtained from Ileum tumors from APCmin/+/VP16LXRa mice was compared to total RNA extracted from APCmin/+/VP16 mice.


title: Expression data from adult mouse ovaries exposed to cigarette smoke in vivo

status: Public on Dec 13 2012

city: Newcastle

first: Alexander

middle: Peter

last: Sobinoff

address: University Drive

institute: University of Newcastle Australia

summary: Mammalian females are born with a finite number of non-renewing primordial follicles, the majority of which remain in a quiescent state for many years. Due to their non-renewing nature, these “resting” oocytes are particularly vulnerable to xenobiotic insult, resulting in premature ovarian senescence and the formation of dysfunctional oocytes.  In this study we characterised the mechanisms behind cigarette smoke induced ovotoxicity, which is characterised by primordial follicle depletion. C57BL/6 5 week old female mice were exposed to cigarette smoke five times per week, for 12-18 weeks using a custom-designed and purpose-built nose-only, directed flow inhalation and smoke-exposure system. This was done in the hopes of gaining a better understanding of the mechanisms underpinning cigarette smoke induced ovotoxicity.

overall_design: C57BL/6 5 week old female mice were exposed to cigarette smoke (twelve 3R4F reference cigarettes (University of Kentucky, USA) twice/day, 2.7 mg particulate matter) five times per week, for 12-18 weeks using a custom-designed and purpose-built nose-only, directed flow inhalation and smoke-exposure system. Their ovaries were then collected for RNA extraction and hybridization on an Illumina Sentrix Mouse ref-8 v2 Beadchip

first: Eileen

last: McLaughlin


title: Genome-wide analysis of gene expression in murine breast fibroblasts from normal tissue, hyperplasia, adenoma and carcinoma (MMTV-PyMT model)

status: Public on Mar 19 2013

city: London

first: Fernando

last: Calvo

address: 44 Lincoln's Inn Fields

department: London Research Institute

institute: Cancer Research UK

summary: Analysis of differences at gene expression level of hpvE6 immortalized fibroblasts isolated from normal mammary glands and from hyperplasia, adenoma and carcinoma stages using the MMTV-PyMT model (FVB/N background). Analysis demonstrated the activation of specific transcriptional programs in fibroblasts from later stages.

overall_design: Total RNA obtained from isolated hpvE6 immortalized fibroblasts from normal mammary gland (NF) and from different stages of tumour development using the MMTV-PyMT murine breast cancer model. Stages were hyperplasia (HpAF), adenoma (AdAF) and carcinoma (CAF). Fibroblasts were seeded in a deformable Matrigel:collagen I matrix and total RNA isolated 72h later.

first: Erik

last: Sahai


title: Comparison of RelB-/- and RelB+/- thymi

status: Public on Dec 27 2012

first: Brendan

middle: John

last: O'Sullivan

state: Queensland

address: Level 6, 37 Kent Street Woolloongabba

institute: The University of Queensland Diamantina Institute Translational Research Institute

summary: Thymic medullary epithelial cell (mTEC) expression of the autoimmune regulator AIRE, and of tissue-specific antigens, is controlled by members of the non-canonical NF-kB signalling pathway, including RelB and NF-kB2. Of the genes in this pathway, RelB-/- mice develop a particularly severe multi-organ autoimmune syndrome, resembling Foxp3-deficiency. RelB-/- mice have medullary atrophy and few mTECs but the mechanism is unknown. We show that RelB is required for expression of medullary chemokines and mTEC AIRE, selection of a diverse peripheral T cell repertoire, and for peripheral Foxp3+ Treg function. Vβ families of T cells infiltrating diseased peripheral organs and thymic Treg were similarly skewed. Surprisingly, medullary atrophy results from intra-thymic granulocyte infiltration, consequent upon the Th2-mediated autoimmune disease. Dominant tolerance corrects thymic inflammatory disease and loss of thymic function. We demonstrate a reversible RelB-dependent inflammatory mechanism for loss of central tolerance associated with medullary atrophy.

overall_design: Thymi from 4 RelB+/- mice and 3 RelB-/- mice were profiled by microarays


title: Transcriptional Reprogramming of Mature CD4 T helper Cells generates distinct MHC class II restricted Cytotoxic T Lymphocytes

status: Public on Dec 10 2012

first: Bernardo

last: Reis

state: NY

address: 1234 York Avenue

institute: Rockefeller University

summary: We show here that the T helper-fate is not fixed and that mature antigen-stimulated CD4 T cells can switch off Thpok expression and reactivate CD8- lineage genes. This unexpected plasticity results in the post-thymic termination of the T helper- program and the functional differentiation of distinct MHC class II restricted CD4 cytotoxic T lymphocytes

overall_design: Small intestine CD4 intraepithelial T lymphocytes from ThPOK-GFP reposter mice were isolated and sorted (FACS Aria) based on ThPOK and CD8aa expression. Cell were isolated either from non-experimental ThPOK-GFP reporter mice (WT) or after transfering CD4 naive T cells from ThPOK-GFP reporter mice to RAG-/-recipient animals (TR) as an experimental colitis model. Experimet was done in duplicate.

first: Daniel

last: Mucida

middle: S


title: Comparison of gene expression in Dnmt1+/+ MEFs treated with 5-aza-2'-deoxycytidine or vector control

status: Public on Feb 12 2013

city: Heidelberg

first: James

last: Reddington

address: Meyerhofstrasse 1

institute: EMBL

summary: DNA methylation and the Polycomb Repression System are epigenetic mechanisms that play important roles in maintaining transcriptional repression. Recent evidence suggests that DNA methylation can attenuate the binding of Polycomb protein components to chromatin and thus plays a role in determining their genomic targeting. However, whether this role of DNA methylation is important in the context of transcriptional regulation is unclear. By genome-wide mapping of the Polycomb Repressive Complex 2 (PRC2)-signature histone mark, H3K27me3, in severely DNA hypomethylated mouse somatic cells, we show that hypomethylation leads to widespread H3K27me3 redistribution, in a manner that reflects the local DNA methylation status in wild-type cells. Unexpectedly, we observe striking loss of H3K27me3 and PRC2 from Polycomb-target gene promoters in DNA hypomethylated cells, including Hox gene clusters. Importantly, we show that many of these genes become ectopically expressed in DNA hypomethylated cells, consistent with loss of Polycomb-mediated repression. An intact DNA methylome is required for appropriate Polycomb-mediated gene repression by constraining PRC2 targeting. These observations identify a previously unappreciated role for DNA methylation in gene regulation and therefore influence our understanding of how this epigenetic mechanism contributes to normal development and disease.

overall_design: Two biological replicates are compared, each consisting of two technical replicates

first: Richard

last: Meehan


title: Disruption of sorting nexin 5 causes respiratory failure associated with undifferentiated alveolar epithelial type I cells in mice

city: Mainz

first: Hyobin

last: Jeong

state: Germany

address: Richard shirrmann Str 12.

institute: IMB

summary: Deletion of Snx5 leads to respiratory failure in neonatal mice. Here we analyzed the effect of depleted SNX5 in a lung. We used expression microarray to compare between  wild lungs and mutant lungs at E18.5 and  E18.5 after air-breathing test.

overall_design: Total RNA were extracted from embryonic 18.5 day (E18.5) wild and mutant mice lung. Also other total RNA samples were extracted after air-breathing test at E18.5.

first: Young-Yun

last: Kong

first: Daehee

last: Hwang

first: Kyoung-Tai

last: Kim

first: Machiko

last: Ikegami

first: Sun-Kyoung

last: Im

first: HyoBin

first: Hyun-woo


title: Transcriptomic and metabolomic analysis of autosomal dominant polycystic kidney disease identifies HNF4α as a disease modifier

status: Public on Nov 29 2012

city: Bethesda

first: Luis Fernando

last: Menezes

state: MD

address: Room 8D12A, Building 10, 10 Center Dr

department: NIDDK

institute: National Institutes of Health

summary: Autosomal Dominant Polycystic Kidney Disease (ADPKD; MIM ID’s 173900, 601313, 613095) leads to end stage kidney disease, caused by mutations in PKD1 or PKD2. Inactivation of Pkd1 before or after P13 in mice results in distinct early- or late-onset disease. Using a mouse model of ADPKD carrying floxed Pkd1 alleles disrupted using a tamoxifen-inducible Cre recombinase, transcriptomics and metabolomics were applied to follow disease progression in animals induced before P10. Network analysis suggests that Pkd1-cystogenesis does not cause developmental arrest and occurs in the context of gene networks similar to those that regulate/maintain normal kidney morphology/function. These analyses also predict metabolic pathways, notably those controlled by HNF4α, are key elements in postnatal kidney maturation and early steps of cyst formation. To test this hypothesis, metabolic networks were altered by inactivating Hnf4a and Pkd1. The Pkd1/Hnf4a double knock-out have significantly more cystic kidneys thus indicating that modulating metabolic pathways might be an effective therapeutic approach.

overall_design:
We crossed fifth-generation C57/BL6 Pkd1cond mice to fifth-generation C57/BL6 tamoxifen-Cre (B6.Cg-Tg(Cre/Esr1)5Amc/J mice (stock 004682), Jackson Laboratories) and C57/BL6 congenic B6.129S4-Gt(ROSA)26Sortm1Sor/J (stock 003474, Jackson Laboratories) to produce Pkd1 conditional mice with TamCre (mutant) or without TamCre (control). We induced Cre recombinase activity in mice < 10 days of age by intraperitoneally injecting nursing mothers with tamoxifen (10 mg/40 g) , and harvested kidney samples of control and mutant (34 and 36 animals, respectively) between the ages of 11 and 24 days.

Postprocessed files (expression p value<0.05; quantile normalized; merged and corrected for batch-effect using COMBAT) linked below as supplementary files.

first: Luis

middle: F

first: Gregory

last: Germino


title: Genome-wide expression profiling analysis of a Sphingomyelin Synthase 1 mutant mouse model

city: Neuherberg

first: Martin

last: Irmler

state: Bayern

address: Ingolstaedter Landstrasse 1

department: Institute of Experimental Genetics

institute: Helmholtz Zentrum München GmbH

summary: Lysosomal storage diseases are congenital lipid metabolism disorders, often accompaning by male infertility. Sms1, the enzyme, that generates sphingomyelin from ceramides seems to be involved in spermatogeneis and spermiogenesis. Therefore, testis but also muscle and brain of a mouse line carrying an insertional mutation in Sms1 were analysed.

overall_design: Total RNA obtained from 4 male mutant mice was compared to four wild type controls.

first: Johannes

last: Beckers

first: Marion

last: Horsch

first: Thomas

last: Floss

first: Anke

last: Wittmann


title: Effect of small molecules on activated BV2 microglia cell line

status: Public on Nov 03 2012

city: Münster

first: Susanne

last: Höing

address: Röntgenstraße 20

department: Cell and Developmental Biology

institute: Max Planck Institute for Molecular Biomedicine

summary:
We have developed an assay to test the neuroprotective properties of compounds using stem cell–derived motor neurons and astrocytes, together with activated microglia as a stress paradigm.
Hit compounds were discovered and the transcriptional response on activated BV2 cells was tested.

overall_design: The BV2 cell line was activated with LPS and IFN-γ and treated with hit compound for 4 hr.


title: Effect of small molecules on activated astrocytes

summary:
We have developed an assay to test the neuroprotective properties of compounds using stem cell–derived motor neurons and astrocytes, together with activated microglia as a stress paradigm.
Hit compounds were discovered and the transcriptional response on activated astrocytes cells was tested.

overall_design: Neural stem cell (NSC)-derived astrocytes (AC) were activated with LPS and IFN-γ and treated with hit compound for 4 hr.


title: Identification of global alteration of translational regulation in glioma in vivo

first: Karim

last: Helmy

address: 1275 York Avenue

institute: Memorial Sloan-Kettering Cancer Center

summary: Post-transcriptional regulation of gene expression contributes to the protein output of a cell, however, methods for measuring translational regulation in complex in vivo systems are lacking. Here, we describe a sensitive method for measuring translational regulation in defined cell populations from heterogeneous tissue in vivo. We adapted the translating ribosome affinity purification (TRAP) methodology to measure the relative occupancy of individual mRNA transcripts in translating ribosomes in the Olig2-positive tumor cell population in a genetically engineered mouse model (GEM) of glioma. Global measurement of paired ribosome-bound and total cellular mRNA populations from tumor cells in vivo identified a broad distribution of relative ribosome occupancies amongst mRNA species that was highly reproducible across biological samples. Comparison of the translation state of glioma cells to non-transformed oligodendrocyte progenitor cells in normal brain identified global alteration of translation in tumor, and specifically of genes involved in cell division and synthetic metabolism. Furthermore, investigation of alteration in steady state translational efficiencies upon loss of PTEN, one of the most frequently mutated and deleted tumor suppressors in glioma, identified differential translation of proteins involved in cellular respiration, canonically regulated by PI3K/Akt signaling, and cellular glycosylation profiles, deregulation of which is known to be associated with tumor progression. Application of the translation efficiency profiling method described here to other biological contexts and conditions would extend our knowledge of the scope and impact of this important mode of gene regulation in complex in vivo systems.

overall_design: Total RNA and ribosome-bound RNA from Olig2+ cells in normal mouse brain and a mouse model of glioma was collected, microarray and compared.

first: John

last: Halliday

first: Elena

last: Fomchenko

first: Manu

last: Setty

first: Christof

last: Hafemeister

first: Eric

last: Holland


title: Neutrophils play a key role in schistosome-induced hepatic granuloma formation

status: Public on Nov 01 2012

first: Geoffrey

last: Gobert

address: 300 Herston Rd

institute: QIMR

summary: The severity of schistosome egg-induced hepatic granulomatous pathology depends markedly on the nature of the mammalian host immune response. The local cellular and molecular mechanisms that co-ordinate hepatic granuloma formation during schistosome infection are still poorly understood. We used a combination of laser microdissection microscopy and microarray analysis to further our understanding of fibrogenesis and granuloma formation in C57BL/6 mice infected with Schistosoma japonicum. We compared hepatic gene expression profiles in histologically distinct zones both within, and directly proximal to, granulomas during the course of their development.

overall_design: Defined zones of granulomas develop in the murine liver infected by Schistosoma japonicum over a period of 4, 6 and 7 weeks post infection were microdissected, and subjected to total RNA isolation and gene expression analysis. Microarray analysis of this study was performed using samples derived from 2 individual mice per group/time-point.

first: Candy

last: Chuah

first: Malcolm

middle: K

last: Jones

middle: N


title: Androgen-Responsive microRNAs in mouse Sertoli Cells

status: Public on Dec 21 2012

city: San Antonio

first: Yidong

last: Chen

address: 8403 Floyd Curl Drive, MSC 7784

department: Population Health Sciences

institute: UT Health Science Center at San Antonio

summary: Although decades of research have established that androgen is essential for spermatogenesis, androgen’s mechanism of action remains elusive. This is in part because only a few androgen-responsive genes have been definitively identified in the testis. Here, we report that microRNAs—small, noncoding RNAs—are one class of androgen-regulated trans-acting factors in the testis. Specifically, by using androgen suppression and androgen replacement in mice, we show that androgen regulates the expression of several microRNAs in Sertoli cells. Our results reveal that several of these microRNAs are preferentially expressed in the testis and regulate genes that are highly expressed in Sertoli cells. Because androgen receptor–mediated signaling is essential for the pre- and postmeiotic germ cell development, we propose that androgen controls these events by regulating Sertoli/germ cell–specific gene expression in a microRNA-dependent manner.

overall_design: Control, Treated, Rescued (3 groups)

first: Rao

last: Manjeet

first: Panneerdoss

last: Subbarayalu

first: Kalyan

last: Buddavarapu

first: Hung-I

middle: H


title: The role of FGF21 in aging and aging-related diseases

status: Public on Oct 18 2012

city: La Jolla

first: Ruth

last: Yu

address: 10010 N Torrey Pines Rd

department: Gene Expression Lab

institute: Salk Institute

summary: Aging and aging-related diseases represent an increasing burden on modern society.  Thus, drugs that retard the aging process are highly desirable.  Fibroblast growth factor-21 (FGF21) is a hormone secreted by the liver during fasting that elicits diverse aspects of the adaptive starvation response.  Among its effects, FGF21 induces hepatic fatty acid oxidation and ketogenesis, increases insulin sensitivity and blocks somatic growth.  Here we show that transgenic overexpression of FGF21 markedly extends lifespan in mice without reducing food intake or affecting AMP kinase or mTOR signaling or NAD metabolism.  Transcriptomic analysis suggests that FGF21 acts primarily by blunting the growth hormone/insulin-like growth factor-1 signaling pathway in liver.   These findings raise the possibility that FGF21 can be used as a hormone therapy to extend lifespan.

overall_design: Liver, epididymal fat and gastrocnemius muscle RNA expression profiles were compared between C57Bl/6J ad libitum, fasted, and calorically restricted mice, as well as between FGF-21 transgenic and their wild-type C57Bl/6J controls.

first: Yuan

last: Zhang

first: Steven

last: Kliewer


title: Interaction of c-Myb with p300 is required for the induction of acute myeloid leukemia (AML) by human AML oncogenes

city: Brisbane

first: Konstantin

last: Shakhbazov

address: Ipswich Road

institute: UQDI

summary: The MYB oncogene is widely expressed in acute leukemias and is important for the continued proliferation of leukemia cells, raising the possibility that MYB may be a therapeutic target.  However realization of this potential requires (i) a significant therapeutic window for MYB inhibition, given its essential role in normal hematopoiesis; and (ii) an approach for developing an effective therapeutic. We previously showed that the interaction of Myb with the coactivator CBP/p300 is essential for its transforming activity. Here we use hematopoietic cells from the Booreana mouse strain, which carries a mutation in Myb that prevents interaction with CBP/p300, to examine the requirement for this interaction in myeloid transformation and leukemogenesis. Using this strain and a strain (plt6) carrying a “complementary” mutation in p300, we show that the Myb-p300 interaction is essential for in vitro transformation by the myeloid leukemia oncogenes AML1-ETO, AML1-ETO9a, MLL-ENL, and MLL-AF9. We further show that unlike cells from wild-type (WT) mice, Booreana cells fail to induce leukemia upon transplantation into irradiated recipients following transduction with an AML1-ETO9a retrovirus. These data highlight disruption of the Myb-p300 interaction as a potential therapeutic strategy for AML and suggest that such a strategy would have a useable therapeutic index since Booreana mice, unlike Myb null mice, are viable. Finally we have begun to explore the molecular basis of the these observations by gene expression profiling; this highlighted several genes previously implicated in myeloid leukemogenesis as being differentially expressed between WT and Booreana cells transduced with AML1-ETO9a.

overall_design: Total RNA was obtained from FACS sorted GFP+;c-Kit+ primary bone marrow cells from WT and Booreana mouse strains which had been cultured for 48 hours post-transduction with Control or AML1-ETO9a retroviruses. RNA was extracted from each of 4 samples per group and used to probe Illumina mouse Beadchips array.

first: Diwakar

middle: R

last: Patabiraman

first: Thomas

middle: J

last: Gonda


title: Inflammatory mediators alter astrocyte genomic profiles and G-protein receptor evoked calcium signaling

city: Los Angeles

first: Giovanni

last: Coppola

address: 1524 Gonda, 695 Charles Young Drive South

department: Psychiatry and Neurology

institute: UCLA

summary: Inflammation features in diverse central nervous system disorders such as stroke, trauma, neurodegeneration, infection and autoimmunity. To better understand how inflammatory mediators may alter astrocyte functions, we examined the effects of transforming growth factor-β1 (TGF-β1), lipopolysaccharide (LPS) and interferon-gamma (IFNγ) on purified, murine, primary cortical astrocyte cultures. We used microarrays to conduct whole genome expression profiling, and measured calcium signaling, which is implicated in mediating dynamic astrocyte functions. Combinatorial exposure to TGF-β1, LPS and IFNγ significantly modulated astrocyte expression of over 6,800 genes and resulted in both additive and synergistic changes compared with individual stimuli alone. Bioinformatic analysis revealed that combinatorial treatment significantly and markedly up regulated molecular networks and pathways associated with immune signaling and with regulation of cell compromise, death, growth and proliferation. These findings provide databases of astrocyte transcriptome changes elicited by the inflammatory stimuli, TGF-β1, LPS and IFNγ alone and in combination, and show that these stimuli up regulate astrocyte molecular networks associated with immune- and injury-related functions and significantly alter astrocyte calcium signaling evoked by multiple GPCR.

overall_design: We used microarrays to examine the effects of transforming growth factor-β1 (TGF-β1), lipopolysaccharide (LPS) and interferon-gamma (IFNγ) on purified, murine, primary cortical astrocyte cultures.

first: Mary

last: Hamby

first: Daniel

last: Geschwind

first: Baljit

last: Khakh

first: Michael

middle: V

last: Sofroniew


title: Differentiation stage-specific donor memory in induced pluripotent stem cells (iPSC) generated from hepatic lineage cells

status: Public on Oct 02 2012

first: Daekwan

last: Seo

address: 37 Convent Dr. Rm 4140

department: NCI

institute: NIH

summary: Recent studies suggested that embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs) may represent different pluripotent states as defined by gene expression profiles and differentiation potential.  Here we addressed a contribution of a lineage stage-specific donor cell memory in modulating the functional properties of iPSCs. iPSCs were generated from hepatic lineage cells at an early (hepatoblast-derived, HB-iPSCs) and end stage (adult hepatocyte, AH-iPSCs) of hepatocyte differentiation as well as from mouse fetal fibroblasts (MEF-iPSCs) using a lentiviral vector encoding four pluripotency-inducing factors Oct4, Sox2, Klf4, and c-Myc.  All resulting iPS cell lines acquired iPSCs phenotype as judged by the accepted criteria including morphology, expression of pluripotency markers, silencing of transducing factors, capacity of multilineage differentiation in teratoma assay and normal diploid karyotype. However, hepatoblasts were more susceptible to reprogramming than either AH or MEF, and HB-iPSCs were more efficient in directed differentiation towards hepatocytic lineage as compared to AH-iPSCs, MEF-iPSCs or mESCs. Extensive comparative transcriptome analyses of the early passage iPSCs, donor cells and mESCs revealed that despite global similarities in gene expression patterns between generated iPSCs and mESCs, HB-iPSCs retained a transcriptional memory (7 up- and 20 down-regulated genes) typical of the original cells. Continuous passaging of HB-iPSCs abolished most of these differences including a superior capacity of hepatic re-differentiation. These results suggest that retention of lineage stage-specific donor memory in iPSCs may facilitate differentiation into donor cell type. The identified gene set may be helpful to improve hepatic differentiation for therapeutic application in liver disease modeling.

overall_design: A total of 200 ng RNA from four independent biological replicates of MACS-sorted mESC and iPSC were linearly amplified according to manufactures’ specification (Ambion, Austin, Tx,). For in vitro transcription (IVT), reactions were incubated for 16 h at 37ºC. The efficiency of the single round amplification was measured by NanoDrop (ND1000, Thermo Scientific). Hybridization, washing, detection (Cy3-streptavidin, Amersham Biosciences, GE Healthcare), and scanning were performed on an illumina iScan system (Illumina) using reagents and following protocols supplied by the manufacturer. The biotinylated cRNA (750 ng/sample) was hybridized on Sentrix beadchips human Ref-8v3 for 18 h at 58ºC while rocking (5 rpm).

first: Seung-Bum

last: Lee

first: Dongho

last: Choi

first: Jens

middle: U

last: Marquardt

first: Snorri

last: Thorgeirsson


title: Genome-wide studies of murine ovarian follicle maturation in vitro

status: Public on Dec 08 2012

city: Chicago

first: and

last: PhD

state: Illinois

address: 5841 South Maryland Avenue, MC 5032 Room AB540

department: Department of Surgery

institute: University of Chicago

summary: A microarray study to compare gene expression during ovarian follicle development to better understand transcriptional changes during follicular growth.  Multi-layered secondary follicles (150-180 µm in diameter) were mechanically isolated from ovaries of 16-day old CD-1 mice and individually encapsulated in 0.5% alginate. Follicles were culture for up to 8 days. Day 0 samples correspond to follicles that were isolated and immediately frozen.

overall_design: Samples were collected after 0, 2, 4, 5, 6 and 8 days in culture in triplicate and day 0 was collected 5 times.

first: Beatriz

middle: P

last: Bernabe

first: Eugene

last: Galdones

first: Robin

middle: M

last: Skory

first: Lonnie

middle: D

last: Shea

first: Linda

last: Broadbelt

first: Teresa

last: Woodruff


title: Gene expression analysis of cardiac left-ventricle tissue from hybrid mice harboring the Scn5a-1798insD/+ mutation

status: Public on Dec 01 2012

city: Msida

first: Brendon

last: Scicluna

address: Msida campus

country: Malta

institute: University of Malta

summary: Prolonged electrocardiographic indices reflecting myocardial impulse conduction and repolarization are risk factors for sudden cardiac death and drug-induced arrhythmia. The PR-interval, QRS-duration and QT-interval are heritable traits influenced by multiple genetic and environmental factors. The genetic underpinnings of these traits are still largely unknown. In this study, we leveraged the variability in cardiac gene expression and the variation in PR-, QRS- and QT-intervals among F2 mice harboring the cardiac sodium ion-channel mutation Scn5a-1798insD/+ derived from the 129P2-Scn5a1798insD/+ and FVB/NJ-Scn5a1798insD/+ cross, to isolate novel genes and biological pathways impacting on cardiac conduction and repolarization.

overall_design: Cardiac left-ventricle total RNA from 120 F2-(129P2xFVBN/J)-Scn5a-1798insD/+ mice at 12 to 14 weeks old.

first: Connie

last: Bezzina


title: Functional modulation of dendritic cells (DCs) by photo-switchable generation of intracellular ROS

status: Public on Nov 24 2012

city: Seoul

first: Taek-Chin

last: Cheong

address: Daehakro 103

institute: Seoul National University

summary: This experiment was performed to estimate the difference between DCs stimulated with intracellular ROS or LPS.

overall_design: Total RNA obtainded from DCs stimulated with intracellular ROS or LPS was analyzed for transcriptome

first: Nam-hyuk

last: Cho

first: Taek-chin


title: Control vs. PGISp spine samples

status: Public on Nov 15 2012

city: Woolloongabba

first: Gethin

last: Thomas

state: QLD

address: Princess Alexandra Hospital

institute: University of Queensland Diamantina Institute

summary:
OBJECTIVES: Ankylosing spondylitis (AS) is unique in its pathology where inflammation commences at the entheses before progressing to an osteoproliferative phenotype generating excessive bone formation that can result in joint fusion. The underlying mechanisms of this progression are poorly understood. Using the proteoglycan-induced spondylitis mouse (PGISp) model which displays spondylitis and eventual joint fusion following an initial inflammatory stimulus, we have characterised the structural and molecular changes that underlie disease progression
METHODS: PGISp mice were characterised 12 weeks after initiation of inflammation using expression profiling.
RESULTS: Microarray profiling showed genes involved in inflammation and immune-regulation were altered. Further, a number of genes specifically involved in bone regulation including other members of the Wnt pathway were also dysregulated.
CONCLUSION:  This study implicates the Wnt pathway as a likely mediator of the mechanism by which inflammation induces bony ankylosis in spondyloarthritis, raising the potential that therapies targeting this pathway may be effective in preventing this process.

overall_design: 4 unaffected spines vs. 4 spines from PGISp-affected mice


title: High-fat diet induced gene expression changes in mouse retina may be prevented by introducing bilberries in diet

status: Public on Sep 08 2012

city: Kuopio

first: Otto

middle: Taavetti

last: Mykkänen

address: Yliopistonranta 1

department: Public Health and Clinical Nutrition

institute: University of Eastern Finland

summary:
Obesity and diabetes associated visual impairment and vascular dysfunctions are increasing reasons for vision loss. The detailed mechanisms in these diseases are still largely unknown, but mice models have been useful to study these mechanisms and explore the detailed effects of potential compounds. Such compounds usually have antioxidant and anti-inflammatory properties.
These properties are found in anthocyanins and a major source of dietary anthocyanins in Nordic diet is bilberries (European wild blueberries, Vaccinium myrtillus). In this explorative study we show results with differentially expressed genes in retina using a high-fat diet (HFD) mouse model.  Our findings displayed differential regulation of genes in pathways for apoptosis, inflammation and oxidative stress, especially systemic lupus erythematosus (SLE), mitogen activated protein kinase (MAPK) and glutathione metabolism. Mice fed with HFD had increased retinal gene expression of several crystallins, which was reduced in the retina of mice fed with bilberries.  Bilberries seem to reduce the expression of genes in MAPK and to increase the expression of genes in glutathione metabolism pathway. All together despite minor effects in the mouse phenotype, a diet rich in bilberries may prevent the retinal gene expression changes in the early stages of obesity.

overall_design:
Mice were fed ad libitum with normal control diet (NCD, 10% kcal fat), high-fat diet (HFD, 45% kcal fat), 5% (w/w) freeze-dried biberries (Vaccinium myrtillus) in NCD (NCD+BB) or HFD (HFD+BB) for 12 weeks. Diets were prepared in Research Diets Inc. Feed consumption and weight gain were measured during the feeding trial, and blood pressure and serum markers of obesity at the end.
Retinas were collected and RNA extracted from all 24 mice samples, and pooled retinas from 4 mice per group were hybridized with standard Illumina protocols. The expression in retinas was analyzed using R, Pathvisio and DAVID to screen for differences between high-fat and berry induced changes to control diets and further bilberry induced changes to HFD up- or downregulated transcripts.
diet: NCD, HFD, NCD+BB, HFD+BB

first: Michiel

last: Adriaens

first: Giedrius

last: Kalesnykas

first: Chris

last: Evelo

first: Riitta

last: Törrönen

first: Kai

last: Kaarniranta


title: Dual knockdown of Esrrb and Sox2 in mouse embryonic stem cells

status: Public on Nov 22 2012

city: Shenzhen

first: Andrew

last: Hutchins

address: 1088 Xueyuan Rd

department: Bioinformatics

country: China

institute: Southern University of Science and Technology

summary:
Esrrb, Sox2 or Esrrb and Sox2 were knocked down in mouse ES cells using shRNA plasmid pSUPER.puro containing shRNAs from the publications Feng et al., 2009 and Rodda et al., 2005.
Knockdown was transfected into mouse ES cells using lipofectamine and then cells were selected for knockdown using puromycin.
RNA was harvested after 2 days of knockdown.

overall_design: Esrrb and Sox2 were knocked down in mouse ES cells either individually or together, cells were selected with puromycin and RNA harvested and subjected to microarray after 2 days.

first: Paul

last: Robson


title: The effect of pertussis toxin on lung airway gene expression during B. pertussis infection in mice

status: Public on Aug 31 2012

city: Baltimore

first: Nicholas

last: Carbonetti

address: 685 W. Baltimore St. HSF I-380

department: Microbiology and Immunology

institute: University of Maryland Baltimore

summary: Genome-wide expression analysis of mouse lung responses to Bordetella pertussis infection and the effects of pertussis toxin

overall_design: Total lung RNA from wild-type and pertussis toxin-defficient B. pertussis-infected mice at two and four days post inoculation compared to control, mock-infected mice.  Seven-week old female BALB/c mice were intranasally inoculated with 1 x 106 CFU WT B. pertussis (Tohama I), 1 x 106 CFU ΔPT (WT carrying a PT deletion), or 30 x 106 CFU of the ΔPT strain.  Whole lung tissue was collected from mice sacrificed at 2 and 4 days post inoculation (n = 3 per group per time point).  Control mice were inoculated with PBS and sacrificed 2 days post inoculation (n = 2).

first: Carey

middle: E

last: Connelly

first: Yezhou

last: Sun