title: Identification of differentially regulated genes in flcn-1 mutant C. elegans

status: Public on Dec 31 2012

city: Koeln

first: Roman-Ulrich

last: Mueller

address: Kerpener Str. 62

institute: University Hospital Cologne

summary:
Birt-Hogg-Dubé syndrome is an autosomal dominantly inherited disorder that is characterized by the clinical triad of benign skin tumors - so-called fibrofolliculomas, recurrent pneumothoraces due to pulmonary cysts and the formation of kidney tumors. The molecular function of Folliculin (FLCN), the protein product of the BHD gene mutated in this syndrome, has remained elusive to a large extent. Animal models such as mouse, rat and canine models have been used to elucidate parts of the pathway in which FLCN plays a role showing it to interfere with AMP-kinase and mTOR signaling. Caenorhabditis elegans provides - due to its simple genetic amenability and large brood size - the perfect tool to study signal transduction pathways in detail. Thus, we decided to examine F22D3.2 (flcn-1) - a putative orthologue of FLCN in the nematode. We established the first gene expression profiles of a strain harboring a mutation in flcn-1 compared to WTN2 allowing for a first insight into the function of this gene in C. elegans.
This study examines the transcriptome of the flcn-1 mutant strain RB1035 in comparison to WTN2 in order to identify differentially regulated genes.

overall_design: RNA was prepared from pre-reproductive adults in both WTN2 and RB1035 (harboring a flcn-1 mutant allele, mutant worms had been backcrossed wo WTN2 8 times) using biological triplicates. RNA was labeled and hybridized to Agilent C. elegans whole genome microarrays and scanned using a Agilent Technologies Scanner G2505C US22502540.

first: Hakam

last: Gharbi

first: Francesca

last: Fabretti

first: Puneet

last: Bharill

first: Peter

last: Frommolt


title: Mycobacterium tuberculosis Requires Phosphate-Responsive Gene Regulation to Resist Host Immunity

status: Public on Jan 01 2013

city: Aurora

first: Martin

middle: I

last: Voskuil

state: CO

department: Microbiology

country: USA

institute: University of Colorado Denver

summary: Mycobacterium tuberculosis persists in the lungs of mammalian hosts despite inducing an immune response dominated by the macrophage-activating cytokine interferon-gamma (IFN-gamma).  We identified the M. tuberculosis phosphate uptake system component PstA1 as a factor required to resist IFN-gamma dependent immunity.  A ∆pstA1 mutant was fully virulent in IFN-gamma-/- mice but was attenuated in mice lacking the IFN-gamma-inducible nitric oxide synthase (NOS2).  This phenotype suggests that ∆pstA1 bacteria are hypersensitive to an IFN-gamma-dependent immune mechanism(s) other than NOS2.  In other species, the Pst system participates in phosphate-responsive gene regulation by interacting with a two-component signal transduction system.  We identified genes that exhibited dysregulated expression in the ∆pstA1 mutant and showed that aberrant gene expression was dependent on the two-component system response regulator RegX3.  Deletion of regX3 suppressed the replication and virulence defects of ∆pstA1 bacteria in NOS2-/- mice, suggesting that the ∆pstA1 mutant is attenuated, in part, due to aberrant RegX3-dependent gene expression.  Our data imply that phosphate is an important signal controlling M. tuberculosis gene expression during replication in the lung.

sample_organism: Mycobacterium tuberculosis str. Erdman = ATCC 35801

platform_organism:
Mycobacterium tuberculosis CDC1551
Mycobacterium tuberculosis H37Rv

overall_design: Aerobically growing logarithmic phase Wt or pstA1/regX3/pstA1regX3 mutant strains were grown in phosphate replete media and analyzed after several hours. Experiments were repeated in triplicate (pstA1 mutant) or quadruplicate (regX3/pstA1regX3 mutant).

first: Anna

middle: D

last: Tischler

first: Rachel

middle: L

last: Leistikow

first: Meghan

middle: A

last: Kirksey

first: John

last: Mckinney


title: Transcriptional immune response of PRRSV-infected porcine dendritic cells and monocytes to Streptococcus suis infection

status: Public on Jun 01 2016

city: Mississauga

first: Claude

last: Lachance

state: Ontario

address: 1329 Meyerside Drive

country: Canada

institute: Bio-Rad

summary: We investigated for the first time the in vitro response of PRRSV-infected porcine DCs and monocytes to S. suis. We first assessed the effect of PRRSV infection on the phagocytosis and intracellular survival of S. suis by these two cell populations. We then used a genomic approach to compare the gene expression profiles of both type of cells infected with S. suis, with or without a previous infection with PRRSV.

overall_design: Total RNA obtained from porcine monocytes and dendritic cells infected with S. suis, PRRSV, or S. suis & PRRSV. Four replicates in all groups.

first: Gaël

last: Auray

first: Yingchao

last: Wang

first: Carl

last: Gagnon

first: Mariela

last: Segura

first: Marcelo

last: Gottschalk


title: IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray

status: Public on Dec 04 2012

city: Irvine

first: Carolina

last: Lessa Aquino

address: 302 MedSurge II

institute: University of California Irvine

summary: Leptospirosis is the most widespread zoonotic disease in the world. The lack of an adequate laboratory test is a major barrier for the diagnosis, especially during the early stages of illness, when antibiotic therapy is most effective. Therefore, there is a critical need for an efficient diagnostic test for this life threatening disease. In order to identify new targets that could be used as diagnostic makers for leptopirosis, we constructed a protein microarray chip comprising 61% of Leptospira interrogans proteome and investigated the IgG response against leptospiral antigens from 274 individuals, including 80 acute-, 80 convalescent-phase patients and 114 healthy control subjects from regions with endemic, high endemic and no endemic transmission of leptospirosis. A nitrocellulose line blot assay was performed to validate the accuracy of the protein microarray results. We found 16 antigens that can discriminate between acute cases and healthy individuals from a region with high endemic transmission of leptospirosis, and 18 antigens that distinguish convalescent cases. Some of the antigens identified in this study, such as LipL32, the non-identical domains of the Lig proteins, GroEL and Loa22 are already known to be recognized by sera from human patients, thus serving as a proof-of-concept for the serodiagnostic antigen discovery approach. Several novel antigens were identified, including the hypothetical protein LIC10215 which showed good sensitivity and specificity rates for both acute- and convalescent-phase patients. Our study is the first large-scale evaluation of immunodominant antigens associated with naturally acquired leptospiral infection and novel as well as known serodiagnostic leptospiral antigens that are recognized by antibodies in the sera of leptospirosis cases were identified. The novel antigens identified here may have potential use in both the development of new tests and the improvement of currently available assays for diagnosing this neglected tropical disease. Further research is needed to assess the accuracy of these antigens in more appropriate diagnostic platforms.

overall_design: Antibody profiling was peformed on sera  from infected and non-infected subjects to investigate the IgG response against leptospiral antigens. These samples comprised 80 acute-, 80 convalescent-phase patients and 114 healthy control subjects, including 29 subjects from United States (non-endemic area), 35 blood donors from Salvador/Brazil (endemic area) and 50 healthy individuals from region with high endemicity of leptospirosis.

last: Lessa-Aquino

first: Jozelyn

last: Pablo

first: Rie

last: Sasaki

first: Algis

last: Jasinskas

first: Li

last: Liang

first: Elsio

last: Wunder

first: Guilherme

middle: S

last: Ribeiro

first: Adam

last: Vigil

first: Ricardo

last: Galler

first: Douglas

last: Molina

first: Xiaowu

first: Mitermayer

middle: G

last: Reis

first: Albert

last: Ko

first: Marco

last: Medeiros

first: Philip

last: Felgner


title: IL-7 and IL-15 instruct the generation of human memory stem T cells from naïve precursors

status: Public on Nov 16 2012

city: Padova

first: Silvio

last: Bicciato

address: via U. Bassi 59/b

department: Molecular Medicine

country: Italy

institute: University of Padova

summary:
The identification of the most appropriate T-cell subset to ensure optimal persistence and anti-tumor activity is a major goal of cancer immunotherapy. We identified a novel post-mitotic CD45RA+CD62L+ T cell subpopulation (TTN), generated in vitro upon activation of naïve T (TN) cells with beads conjugated to anti-CD3 and anti-CD28 antibodies. This cell population is highly proliferative, produces low levels of IFNg and cytotoxic molecules, and requires IL-7 and IL-15 for in vitro expansion.
To investigate whether this cell population represents a novel T-cell subset, we compared the transcriptomic profile of  TTN with that of other T-cell subsets, namely naturally occurring TN and central memory (TCM) and manipulated cells of TCM origin (TTCM).

overall_design: We collected RNA from unmanipulated purified T-cell subsets (TN and TCM) or from T-cell subsets that were in vitro activated and transduced (TTN and TTCM). In vitro generated subsets were kept in culture for 15 days after activation before harvesting. Samples were then processed for total RNA extraction and hybridization on Affymetrix microarrays. Three biological replicas (A, B, C) were used for each of the 4 conditions (1: TN; 2: TCM; 3: TTN; 4: TTCM) for a total of 12 samples.

first: Nicoletta

last: Cieri

first: Barbara

last: Camisa

first: Fabienne

last: Cocchiarella

first: Mattia

last: Forcato

first: Giacomo

last: Oliveira

first: Elena

last: Provasi

first: Attilio

last: Bondanza

first: Claudio

last: Bordignon

first: Jacopo

last: Peccatori

first: Fabio

last: Ciceri

first: Maria

middle: T

last: Lupo-Stanghellini

first: Fulvio

last: Mavilio

first: Anna

last: Mondino

first: Alessandra

last: Recchia

first: Chiara

last: Bonini


title: CENP-B cooperates with Set1 in bidirectional transcriptional silencing and genome organization of retrotransposons

status: Public on Oct 12 2012

city: Chestnut Hill

first: Hugh

middle: P

last: Cam

state: MA

address: Higgins Hall Room 355, 140 Commonwealth Avenue

department: Biology

institute: Boston College

summary:
Expression profiling of mutant cells compared to wild-type cells.
Expression profiling of S. pombe CENP-B homolog cbp1∆ (abp1/SPBC1105.04c) and histone deacetylase double mutant clr3∆ clr6-1 (SPBC800.03 SPBC36.05c) cells.

overall_design: Wildtype and mutant cDNA was reverse transcribed from total RNA using the Invitrogen SuperscriptIII Indirect labeling kit and the supplied anchored oligo-dT according to the manufacturer's instructions. cDNA from mutant and wildtype samples were labeled with Alexa Fluor 555 and 647 dyes, respectively. Biological duplicates were performed for each mutant and wildtype sample. An Agilent 44K in situ 60mer DNA microarray that tiles the entire Schizosaccharomyces pombe genome every 300 bp alternately on both strands was used to probe expression of transcripts in CENP-B homolog cbp1∆ (abp1/SPBC1105.04c) and histone deacetylase double mutants clr3∆ clr6-1 (SPBC800.03 SPBC36.05c) cells versus wildtype.

first: David

middle: R

last: Lorenz


title: RNAi triggered by specialized machinery silences developmental genes and retrotransposons (ChIP-chip)

status: Public on Nov 26 2012

city: Bethesda

first: Shiv

last: Grewal

state: MD

address: NCI bldg 37 Rm 6068 9000 Rockville Pike

department: LBMB

institute: NCI

type: Genome binding/occupancy profiling by array

summary: RNAi is a conserved mechanism in which small interfering RNAs (siRNAs) guide the degradation of cognate RNAs, but also promote heterochromatin assembly at repetitive DNA elements such as centromeric repeats. However, the full extent of RNAi functions and its endogenous targets have not been explored. Here we show that in the fission yeast Schizosaccharomyces pombe, RNAi and heterochromatin factors cooperate to silence diverse loci, including sexual differentiation genes, genes encoding transmembrane proteins, and retrotransposons that are also targeted by the exosome RNA degradation machinery. In the absence of the exosome, transcripts are processed preferentially by the RNAi machinery, revealing widespread occurrence of siRNA clusters and corresponding increase in heterochromatin modifications across large domains. We show that the generation of siRNAs and heterochromatin assembly by RNAi is triggered by a mechanism involving the canonical poly(A) polymerase Pla1 and an associated RNA surveillance factor Red1, which also activate the exosome. Remarkably, siRNA production and heterochromatin modifications at genes are regulated by environmental growth conditions, and by developmental signals that induce gene expression during sexual differentiation. Our analyses uncover interplay between RNAi and the exosome that is conserved in higher eukaryotes, and show that differentiation signals modulate RNAi silencing to regulate developmental genes.

overall_design: 8 ChIP samples

first: Soichiro

last: Yamanaka

first: Francisca

middle: E

last: Reyes-Turcu


title: Transcriptional consequences of aneuploidy

status: Public on Jun 29 2012

city: Seattle

first: Maitreya

middle: J.

last: Dunham

state: WA

address: Foege Building, S403B, Box 355065

department: Genome Sciences

institute: University of Washington

summary: Aneuploidy, or an aberrant karyotype, results in developmental disabilities and has been implicated in tumorigenesis. However, the causes of aneuploidy-induced phenotypes and the consequences of aneuploidy on cell physiology remain poorly understood. We have performed a meta-analysis on gene expression data from aneuploid cells in diverse organisms, including yeast, plants, mice, and humans. We found highly-related gene expression patterns that are conserved between species: genes that were involved in the response to stress were consistently upregulated, while genes associated with the cell cycle and cell proliferation were downregulated in aneuploid cells. Within species, different aneuploidies induced similar changes in gene expression, independent of the specific chromosomal aberrations. Taken together, our results demonstrate that aneuploidies of different chromosomes and in different organisms impact similar cellular pathways and cause a stereotypical anti-proliferative response that must be overcome prior to transformation.

overall_design: These experiments are two-color hybridizations of RNA isolated from aneuploid samples vs matched wt cells, all grown to midlog phase.

first: Jason

middle: M

last: Sheltzer

first: Eduardo

last: Torres

middle: J

first: Angelika

last: Amon


title: Gene expression in the chronic ethanol-treated rat liver during liver regeneration

status: Public on Jul 24 2012

city: Philadelphia

first: Egle

last: Juskeviciute

state: PA

address: 1020 Locust st. JAH 527

department: Pathology

institute: Thomas Jefferson University

summary: In this study, we analyzed the effects of chronic alcohol consumption on liver repair and regeneration after partial hepatectomy (PHx). Rats were fed a liquid diet containing 36% of total calories derived from ethanol for 5 weeks; corresponding pair-fed calorie-matched controls were fed diets in which ethanol calories were replaced either by carbohydrate or by fat. After 5 weeks, rats were subjected to 70%  PHx and liver samples were collected at 1, 6 and 24h after the surgery. The excised liver samples at t=0 served as within-animal controls. We used Affymetrix Rat Gene 1.0 ST  arrays to obtain global gene expression data from each liver sample (n=4 replicate rats, 72 arrays total).

overall_design: Gene expression was profiled in the chronic ethanol-fed (EtOH) and carbohydrate control pair-fed (CHO) liver prior to (control) and 1 h, 6 h, 12 h, and 24 h after partial hepatectomy (PHx).

first: Rachael

last: Dippold

first: Rajanikanth

last: Vadigepalli

first: Jan

middle: B

last: Hoek


title: Digital gene expression tag profiling of M. grisea G11 and T146

status: Public on Feb 22 2012

city: hangzhou

first: liu

last: xiaoguang

address: yuhang road

country: China

institute: Zhejiang University

summary: The rice blast fungus Magnaporthe oryzae is a major constraint to the world food security. To study the intracellular mechanism involved in its pathogenic morphogenesis, digital gene expression tag profiling was used to compare a previously generated temperature sensitive mutant, T146, which stopped pathogenic morphogenesis at 33°C, with its related wide type, Guy11. 416 genes were detected as differential expressed genes, 26 of which were specifically expressed in Guy11 but stopped expression in the mutant. Functional analysis revealed the mutated morphology maybe caused by a defection in translational or mitochondrial related processes. The results and the protocol used will improve our knowledge on the formation of the ts mutant and promote the further study on M. oryzae pathogenesis.

overall_design: In our experiments, two samples are analyzed. There are no replicates included.

first: Wang

last: hongkai

first: Xu

last: fei


title: RNA elimination machinery targeting meiotic mRNAs promotes facultative heterochromatin formation

status: Public on Dec 01 2011

type: Genome binding/occupancy profiling by genome tiling array

summary: Occupancy profiling of lysine 9 dimethylated histone H3 in fission yeast.

overall_design: Agilent 60mer array was used to analyze DNA recovered by immunoprecipitation of lysine 9 dimethylated histone H3 from asynchronous culture of fission yeast.

first: Martin

last: Zofall

first: Ke

last: Zhang

first: Vanivalasini

last: Balachandran

first: Chanan

last: Rubin


title: An SRY homolog cooperates with a transposon-derived CENP-B protein to control sex-specific directed recombination

status: Public on Nov 21 2011

first: Shiv

last: Grewal

summary: Occupancy profiling of Myc tagged Mc protein in fission yeast.

overall_design: Agilent 60mer array was used to analyze DNA recovered by immunoprecipitation of  Mc-myc protein from culture of fission yeast.

first: Emiko

last: Matsuda

first: Rie

last: Sugioka-Sugiyama

first: Takeshi

last: Mizuguchi

first: Sameet

last: Mehta

first: Bowen

last: Cui


title: Polysome-associated mRNA levels upon glucose repletion

status: Public on Sep 05 2011

city: Cambridge

first: Joshua

last: Arribere

address: 31 Ames St

institute: MIT

type:
Expression profiling by array
Other

summary: Cell survival in changing environments requires appropriate regulation of gene expression, including post-transcriptional gene regulatory mechanisms. Based on reporter gene studies in glucose-starved yeast, it was proposed that translationally silenced eukaryotic mRNAs accumulate in P-bodies and can return to active translation. We present evidence contradicting the notion that this model is a widespread and general phenomenon. First, genome-wide measurements of mRNA abundance, translation, and ribosome occupancy following glucose withdrawal show that most mRNAs are lost from the cell coincident with their loss from polysomes. Second, only a very limited sub-population of translationally repressed transcripts, comprising fewer than 400 genes, can be reactivated for translation upon glucose re-addition in the absence of new transcription. This highly selective post-transcriptional regulation could be a mechanism for cells to minimize the energetic costs of reversing gene-regulatory decisions in rapidly changing environments by transiently preserving a pool of transcripts whose translation is rate-limiting for growth.

overall_design: Sigma 1278b yeast were grown to OD600=1.0-1.1 in YPD in baffled flasks at 30C with vigorous shaking. Cells were treated with thiolutin to a final concentration of 3ug/mL, harvested by centrifugation, and resuspended in pre-warmed YPA medium lacking glucose. Cells were returned to 30C for shaking for 10 minutes. For the refed samples, glucose was added to a final concentration of 2% and samples were taken after 5 minutes. Polysome preparation and RNA isolation were as described in Experimental Procedues. A common RNA sample, polysomal RNA from cells grown in YPD, was used for one channel of each array.

first: Jennifer

last: Doudna

first: Wendy

middle: V

last: Gilbert


title: Reconsidering Movement of Eukaryotic mRNAs Between Polysomes and P-bodies

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

sample_organism:
Saccharomyces cerevisiae
Saccharomyces cerevisiae Sigma1278b

overall_design: Refer to individual Series


title: Zebrafish nephrogenic stem cells: lhx1a vs cdh17

status: Public on Nov 01 2011

city: SAN FRANCISCO

first: Rahul

middle: C

last: Deo

state: CA

address: 555 Mission Bay Blvd. South

department: Cardiovascular Research Institute

institute: University of California San Francisco

summary: Transcriptional profiling of zebrafish nephrogenic stem cells (lhx1a+) vs. zebrafish renal tubular cells (cdh17+): 2 color design, 3 biological replicates

overall_design: Two-condition experiment, renal tubule vs. nephrogenic stem cells. 3 biological replicates

first: Alan

last: Davidson


title: Roles of the Clr4 methyltransferase complex in nucleation, spreading and maintenance of heterochromatin

status: Public on Mar 16 2008

summary:
ChIP-chip analyses of ClrC components across the S. pombe genome.
Keywords: ChIP-chip

overall_design: Chromatin immunoprecipitated DNA recovered with antibody against FLAG-tagged protein from wild-type asynchronous growing fission yeast cells and whole cell extracts DNA were amplified by random priming and respectively labeled with Cy5 and Cy3. Labeled DNA samples were mixed and hybridized onto a 44k pombe Agilent oligo array. Data were processed using Agilent scanner and Feature Extraction software

first: Kerstin

last: Mosch

first: Wolfgang

last: Fischle


title: Life span-extending effects of royal jelly and its related substances on the nematode Caenorhabditis elegans

status: Public on Jul 22 2011

city: Toyohashi

first: Toshio

last: Kojima

address: 1-1 Hibarigaoka Tenpaku-cho

department: Health Care Center

country: Japan

institute: Toyohashi University of Technology

summary: One of the most important issues in the study of aging is to discover compounds with longevity-promoting activity and to unravel their underlying mechanisms. Queen honey bees are continuously fed royal jelly (RJ), and they live more than 10 times longer than hive workers, derived from the same diploid genome, which are fed it only for a short period of time during their larval stages. Therefore, RJ is likely to contain longevity-promoting agents for queens. RJ has been reported to possess diverse pharmacological properties. Furthermore, protease-treated RJ (pRJ) has additional beneficial activities. How RJ and pRJ exert these effects and which components in them play a critical role is largely unknown. The evolutionally conserved mechanisms that control lifespan have been indicated. The nematode Caenorhabditis elegans has been widely used for study of aging and longevity, due to its relatively short lifespan and well-established genetic pathways. The purpose of the present study was to elucidate whether RJ and its related substances contain the life span-extending activity in C. elegans and to obtain some insight into the active agents and their mechanisms. We found that both RJ and pRJ extended the lifespan of C. elegans. The life span-extending activity of pRJ was enriched by ODS column chromatography (pRJ-Fraction 5). pRJ-Fr. 5 extended the life span partly by acting through the FOXO transcription factor DAF-16, the activation of which is known to promote longevity in C. elegans by reducing insulin/IGF-1 signaling (IIS). pRJ-Fr. 5 induced changes in the expression of 3 genes encoding insulin-like peptides. Moreover, pRJ-Fr. 5 and reduced IIS shared some common features in terms of their effect on gene expression, such as up-regulation of dod-3 and down-regulation of dod-19, dao-4 and fkb-4. The dod-19 is a previously identified life span determinant in C. elegans, and the fkb-4 encodes a homologue of the mammalian FK506-binding protein. 10-Hydroxy-2-decenoic acid (10-HDA), which was present in high concentration in pRJ-Fr. 5, increased the lifespan independently of DAF-16 activity.These results demonstrate that RJ and its related substances extended the life span in C. elegans, suggesting that RJ may contain longevity-promoting factors common to diverse species across phyla. pRJ-Fr. 5 had higher life span-extending activity than either RJ or pRJ and extended the life span in part through the IIS-DAF-16 pathway. We provide the first evidence that 10-HDA, a defined natural product in RJ, extended organismal lifespan. It is noteworthy that 10-HDA performed its lifespan-extending function through a mechanism totally different from the IIS-DAF-16 pathway. Further search and characterization of the lifespan-extending agents in RJ and pRJ may broaden our understanding of the gene network of longevity regulation in diverse species and provide the possibility for nutraceutical interventions in the aging process.

overall_design: C. elegans N2 hermaphrodites were untreated or treated with pRJ-Fr. 5 (25mg/ml) for 24 h starting at the larval 4 (L4) stage.

first: Akira

last: Sato

first: Yoko

last: Honda

first: Yasunori

last: Fujita

first: Hiroe

last: Maruyama

last: Araki

first: Kenji

last: Ichihara

first: Masashi

last: Tanaka

first: Yoshinori

last: Nozawa

first: Masafumi

last: Ito

first: Shuji


title: MicroRNA expression profiling predicts clinical outcome of chronic hepatitis C by interferon administration

status: Public on Dec 30 2010

city: Sinjuku-ku

first: Masami

state: Tokyo

address: Sinjuku 6-1-1

institute: Tokyo Medical University

summary: We attempt to catalog the microRNA (miRNA) expression profile according to the response of combination therapy in order to predict the outcome of drug-response before administration and clarify the relationship between aberrant expression of miRNAs and chronic liver disease.

overall_design: We quantified expression profile of 474 mature miRNAs by microarray in the liver biopsy specimen from 105 CH patients without history of anti-viral therapy.

first: Yoshiki

last: Murakami

first: Hidenori

last: Toyoda

first: Katsuyuki

last: Hayashi

first: Atsushi

last: Tajima

first: Takashi

last: Kumada

first: Fumihiko

last: Matsuda

first: Kenichi

last: Matsubara

first: Kunitada

last: Shimotohno


title: Human lupus netting neutrophils induce endothelial damage, infiltrate tissues and expose immunostimulatory molecules

status: Public on Jun 22 2011

city: Ann Arbor

first: Celine

last: Berthier

state: MI

address: 1150 W. Medical Center Dr, MSRB2

institute: University of Michigan

summary:
Our group has proposed that low-density granulocytes (LDGs) play an important role in lupus pathogenesis, as they can damage endothelial cells and synthesize increased levels of proinflammatory cytokines and type I interferons. LDGs have a heightened capacity to synthesize neutrophil extracellular traps (NETs).  NETs from LDGs display increased levels of bactericidal and immunostimulatory proteins, such as the cathelicidin LL37 and externalize double-stranded DNA (dsDNA). Lupus netting LDGs have increased capacity to kill endothelial cells and expose IL-17.  Through NETosis, lupus neutrophils stimulate plasmacytoid DCs to synthesize IFN-α. Our results further expand the potential pathogenic role of aberrant lupus neutrophils through a NET-mediated effect.
We used microarrays to analyze the gene expression of neutrophils in healthy and lupus patients, and of low-density granulocytes in lupus patients.

overall_design: Human neutrophils and LDGs were isolated from PBMCs. RNA from healthy neutrophils, lupus neutrophils and lupus LDGs was extracted and processed for hybridization on Affymetrix microarrays.

first: Eneida

last: Villanueva

first: Srilakshmi

last: Yalavarthi

first: Jeffrey

last: Hodgin

first: Ritika

last: Khandpur

first: Andrew

last: Lin

first: Cory

last: Rubin

first: Wenpu

last: Zhao

first: Stephen

middle: H

last: Olsen

first: Matthew

last: Klinker

first: David

last: Shealy

first: Michael

middle: F

last: Denny

first: Joel

last: Plumas

first: Laurence

last: Chaperot

first: Matthias

last: Kretzler

first: Allen

last: Bruce

first: Mariana

last: Kaplan


title: Expression data from BMDCs treated with BI2536 or vehicle control and stimulated with LPS or poly(I:C)

status: Public on Apr 12 2011

first: Nicolas

last: Chevrier

state: Massachusetts

address: 415 Main Street

institute: Broad Institute of Harvard and MIT

summary: We used microarrays to detail the global programme of gene expression underlying Polo-like kinase inhibition with BI 2536 compound in mouse bone marrow-derived dendritic cells (BMDCs) stimulated with Toll-like receptor agonists LPS and poly(I:C).

overall_design: CD11c+ BMDCs were treated for 1 hour with BI 2536 (1µM) or vehicle control (DMSO) prior to stimulation with LPS or poly(I:C) for 4 h. Total RNA was extracted and prepared for hybridization on Affymetrix microarrays.


title: Identification of Aneuploidy-Tolerating Mutations

status: Public on Feb 25 2010

first: Maitreya

last: Dunham

type:
Expression profiling by array
Genome variation profiling by array

summary:
Aneuploidy causes a proliferative disadvantage in all normal cells analyzed to date, yet this condition is associated with a disease characterized by unabated proliferative potential, cancer. The mechanisms that allow cancer cells to tolerate the adverse effects of aneuploidy are not known. To probe this question, we identified aneuploid yeast strains with improved proliferative abilities. Their molecular characterization revealed strain-specific genetic alterations as well as mutations shared between different aneuploid strains. Among the latter, a loss-of-function mutation in the gene encoding the deubiquitinating enzyme Ubp6 improves growth rates in four different aneuploid yeast strains by attenuating the changes in intracellular protein composition caused by aneuploidy. Our results demonstrate the existence of aneuploidy-tolerating mutations that improve the
fitness of multiple different aneuploidies and highlight the importance of ubiquitin-proteasomal degradation in suppressing the adverse effects of aneuploidy.

overall_design:
This dataset contains both expression analysis and CGH of yeast strains bearing extra chromosomes.  In all cases, the wt euploid strain grown under the same conditions was used as the reference sample.  Reference nucleic acid was generally labeled with Cy3, though some were labeled with Cy5 as indicated in the associated annotations for each array.  No replicate arrays are included.

Expression Samples: GSM513249-GSM513277
CGH Samples: GSM513278-GSM513369

first: Eduardo

last: Torres

first: Noah

last: Dephoure

first: Amudha

last: Panneerselvam

first: Cheryl

last: Tucker

first: Charles

last: Whittaker

first: Steven

last: Gygi

first: Angelika

last: Amon


title: Microgravity effect on C. elegans N2/VC (CERISE, 8days)

status: Public on Jun 30 2012

city: Tsukuba

first: Akira

last: Higashibata

state: Ibaraki

department: Department of Space Biology and Microgravity Sciences

institute: Japan Aerospace Exploration Agency

summary: Microgravity effect on C. elegans gene expression was analysed by whole genome microarray. The worms were cultivated under microgravity for 8days in the Japanese Module of the International Space Station.

overall_design:
The samples of this study were divided three experimental groups:
1. microgravity for 8days
2. artificial 1G control for 8days on orbit
3. ground 1G control for 8days
This study was repeated with three biological and two technical replicates.

first: Toko

last: Hashizume