title: The YfgL lipoprotein is required for cell adhesion and invasion, type I fimbriae expression and virulence of Klebsiella pneomoniae infecion

status: Public on May 25 2016

city: Taipei

first: Pei-Fang

last: Hsieh

address: 1, Sec 1, Jen-Ai Rd.

department: Department of Microbiology

institute: National Taiwan University College of Medicine

type: Expression profiling by genome tiling array

summary:
To address and clarify the regulatory function of YfgL in K. pneumoniae, the transcriptome analyses of the yfgL mutant and the wild-type strain were compared. K. pneumoniae strain deleted for yfgL exhibited reduced adherence and invasion to host cells. A previous study has demonstrated that the YfgL lipoprotein is essential for type III secretion system expression of Salmonella enterica serovar Enteritidis. Several putative secretion systems, but not type III secretion system, were already identified of the genome of the NTUH-K2044. Transcription of type 1 fimbriae was more highly induced in the wild-type than in the yfgL mutant strain. In addition to the fim gene cluster, genes encoding some amino acid metabolism, peptidoglycan synthesis and putative phosphoenopyruvate:carbohydrate phosphotransferase system (PTS), including the tdc gene cluster, yraM and the kp0760-kp0763 (pts) gene cluster, were also up-regulated by YfgL.
Among a total 2,848 cloned sequences covering 99.9% of the entire genome sequence of NTUH-K2044, the expression of 9 cloned sequences was up-regulated and 3 cloned sequences were down-regulated at a cut-off value of 2.

overall_design: Total RNA was purified with the RNeasy Mini Kit (Qiagen) from log-phase cultures of the NTUH-K2044 wild-type and yfgL mutant K. pneumoniae strains in LB medium. Total RNA (40 μg) labeling, microarray hybridization, colorimetric detection and densitometry were performed and analyzed. Expression level of 23S rRNA on each membrane was used as an internal standard for normalization.

first: Jin-Town

last: Wang


title: Chronic p53-independent p21 expression deregulates replication licensing, leading to genomic instability II

status: Public on May 24 2016

city: New York

first: Prokopios Alexandros

last: Polyzos

address: 413 E 69th St

country: USA

institute: Weill Cornell Medicine

type: Genome variation profiling by genome tiling array

summary: The cyclin-dependent kinase inhibitor p21WAF1/Cip1 (p21) is a cell-cycle checkpoint effector and inducer of senescence, regulated by p53. Yet, evidence suggests that, through a so-far obscure mechanism, p21 could also be oncogenic. We report that a subset of atypical cancerous cells strongly expressing p21 showed proliferation features. This occurred predominantly in p53-mutant human cancers suggesting p53-independent upregulation of p21 selectively in more aggressive tumour cells. Multifaceted phenotypic and genomic analyses of p21-inducible, p53-null, cancerous and near-normal cellular models showed that after an initial senescence-like phase, a subpopulation of p21-expressing proliferating cells emerged, featuring increased genomic instability, aggressiveness and chemo-resistance. Mechanistically, sustained p21-accumulation inhibited mainly the CRL4CDT2 ubiquitin-ligase, leading to deregulated origin licensing and replication stress. Collectively, our data reveal tumour-promoting ability of p21 through deregulation of DNA replication licensing machinery, an unorthodox role to be considered in cancer treatment, since p21 responds to various stimuli including some chemotherapy drugs.

overall_design: We compare the genomic instability between Escape and OFF Li-Fraumeni and Saos2 p21WAF1/Cip1 Tet-ON

first: A

first: K

last: Vougas

first: V

last: Gorgoulis


title: Chronic p53-independent p21 expression deregulates replication licensing, leading to genomic instability I


title: Development of miRNA expression signatures for induction of histone deacetylase inhibitor (part 1)

status: Public on Jun 01 2016

city: Nagoya

first: Keisuke

last: Katsushima

address: 1 Kawasumi, Mizuho-cho, Mizuho-ku

department: Department of Epigenomics

country: Japan

institute: Nagoya City University Graduate School of Medical Sciences

summary: To clarify the relationship between histone acetylation and miRNA expression, we performed miRNA arrays to detect histone deacetylase inhibitor (OBP-801) induced miRNA regulating AR expression in LNCaP and VCaP.

overall_design: Agilent-041686 Unrestricted Human miRNA Microarray (Agilent Technologies, Santa Clara, California) was used according to the manufacturer’s protocols.

first: Shinya

last: Sato

first: Keiko

last: Shinjo

first: Akira

last: Hatanaka

first: Fumiharu

last: Ohka

first: Satoru

last: Takahashi

first: Yutaka

last: Kondo


title: Response of Tempranillo grapes to immersion in a concentrated NaCl solution

status: Public on May 22 2016

city: Logrono

first: Pablo

last: Carbonell-Bejerano

state: La Rioja

address: Madre de Dios, 51

department: Instituto de las Ciencias de la Vid y del Vino

country: Spain

institute: CSIC

summary:
The interplay between environmental and genetic factors conditions the fruit ripening program in plants. Transcriptome analysis of grapevine fruits can help understanding these interactions to consciously cope with conditions leading to detrimental effects for viticultural purposes. However, considering the grapevine characteristic ripening asynchrony, which can be intensified by contrasting conditions, accurate grape sampling may be essential for molecular comparisons. In this study, berry density sorting according to floatability in NaCl solutions was assessed as a grape ripening staging strategy. Total sugar content was more correlated with berry density than with other non-invasive ripening parameters. The transcriptome was compared between three density classes collected near commercial maturity using grapevine whole-genome NimbleGen microarrays. Expression profiles clearly related with ripening progression were detected in a density series simultaneously collected from a vineyard of Albariño. By contrast, considerable differences were detected when the same density series was sampled on two different dates from the same vineyard of Tempranillo. Functional analysis indicated that environmental differences between both sampling moments determined most of these expression differences. Ripening degree-dependent responses to the environment were also detected. Finally, the effect of the sorting procedures on the grape transcriptome showed negligible when it was directly tested. Altogether, these findings evidence the convenience of homogenizing the developmental stage and the sampling time conditions for transcriptome comparisons. Berry density sorting proved useful to this end, although this method could be limited when the berry sugar concentration is not determined by the ripening developmental program.
The potential berry transcriptional response to the high concentrated salt solutions used for berry density-sorting may involve a concern on the suitability of this method for transcriptomic studies. This possibility was directly tested by comparing the expression of berries immersed in a highly concentrated NaCl solution (170 g•L-1) during a relatively long time lapse (1 h) with that in berries kept at room air. This experiment was carried out using Tempranillo grapes at mid-véraison to standardize the ripening state by selecting berries with the same proportion of coloured skin surface (50%, corresponding to TSS of 9.9 ±0.3 ºBrix). Berries grown under watering (W) and no-watering (NW) conditions were analysed to test for possible irrigation-NaCl solution interactions affecting berry gene expression. No significant DEG was identified when the effect of the NaCl solution was analysed separately for berries collected from W or NW blocks (≥2-fold change and B-H adjusted P≤0.05 in 2-class limma). When W and NW samples were used together to analyse the effect of the NaCl immersion irrespectively of the irrigation treatment, 15 genes were detected with a B-H adjusted P≤0.05 and only 13 of these showed ≥2-fold change, confirming the slight effect. In summary, the effect of the NaCl immersion on the berry transcriptome is negligible and does not seem to interact with the transcriptomic response to other environmental cues.

overall_design: Berries grown under watering (W) and no-watering (NW) conditions were analysed to test for possible irrigation-NaCl solution interactions affecting berry gene expression. Three independent W and NW vineyard blocks were successively sampled and submitted to the treatment. NaCl-treated berries (NaCl) were immersed in a highly concentrated NaCl solution (170 g•L-1) during a relatively long time lapse (1 h) simulating the density sorting procedure. Control berries (C) were kept at room air 1 h prior to sample freezing. This experiment was carried out using Tempranillo grapes at mid-véraison to standardize the ripening state by selecting berries with the same proportion of coloured skin surface (50%, corresponding to TSS of 9.9 ±0.3 ºBrix). RNA from five NaCl-treated and six control samples were finally hybridized to grapevine whole-genome NimbleGen microarrays.

first: José

middle: M

last: Martínez-Zapater


title: Genome-wide DNA methylation and mRNA and the microRNA transcriptome profiling between oxidative and glycolytic skeletal muscles [array]

city: Chengdu

first: Linyuan

last: Shen

state: Sichuan

address: 211# Huiming Road

department: College of Animal Science and Technology

country: China

institute: Sichuan Agricultural University

summary: The physiological, biochemical and functional difference of oxidative and glycolytic muscles play important roles in human metabolic health as well as in meat quality of animal. To explore this aspect, we firstly provided a genome-wide landscape of DNA methylomes and their relationship with mRNA and miRNA transcriptome for PMM (psoas major muscle; oxidative) and LDM (longissimus dorsi muscle; glycotic) in this study. We observed hypomethylation of subtelomeric regions and high mitochondria content contributed to fast replicative senescence in PMM. The DMRs in promoter (478) and gene bodies (5718) were main enriched in GTPase regulator activity and signaling cascade mediated pathway. Integration analysis revealed methylation status within gene promoter (or gene body) and miRNA promoter have significant negative correlation with mRNA and miRNA expression, respectively. Which included numerous genes were closely related to distinct phenotypic traits between LDM and PMM. For instance, the hypermethylation and down-expression of HK-2 and PFKFB4 decreased the glycolytic potential in PMM. In addition, we validated the promoter hypomethylation and up-expression of miR-378 results in silencing the target gene expression and inducing promoted capillaries biosynthesis in PMM. Together, these results provide a thorough understanding of muscle metabolism and development from an genomic and epigenetic perspective.

overall_design: The aim of our study is to identify mRNAs that play essential roles in the phenotypic variations in oxidative and glycolytic skeletal muscles, and integrate miRNA profiling and methylation data to explore the underlying molecular mechanisms.

first: Zhendong

last: Tan

first: Shunhua

last: Zhang

first: Li

last: Zhu


title: Response to PI3K/mTOR dual inhibition in Glioma initiating cells

status: Public on May 20 2016

city: Houston

first: Dimpy

last: Koul

state: TX

address: 1515 Holcombe Ave

department: Neuro-Oncology

institute: The University of Texas MD Anderson Cancer Center

summary: The PI3K/mammalian target of rapamycin (mTOR) pathway is dysregulated in over 50% of human GBM but remains a challenging clinical target. Inhibitors against PI3K/mTOR mediators have limited clinical efficacy as single agents. Gene expression profiling after PI3K/mTOR inhibition treatment was analyzed by Affymetrix microarrays.

overall_design: Four Glioma Initiating cells (GIC) were treated with PI3K/mTOR dual inhibitors BEZ235 or DS7423 at 100nM for 24 hours. RNA was extracted and analyzed by Affymetrix U133.


title: Whole-genome expression profiling of embryonic and monocyte-derived Kupffer cells

city: Innsbruck

first: Piotr

last: Tymoszuk

state: Tirol

address: Anichstrasse 35

department: University Clinic of Internal Medicine VI

country: Austria

institute: Medical University of Innsbruck

summary:
Iron is an essential component of the erythrocyte protein hemoglobin and is crucial to oxygen transport in vertebrates. In the steady state, erythrocyte production is in equilibrium with erythrocyte removal1. In various pathophysiological conditions, erythrocyte life span is severely compromised, which threatens the organism with anemia and iron toxicity 2,3. Here we identify anon-demand mechanism specific to the liver that clears erythrocytes and recycles iron. We showthat Ly-6Chigh monocytes ingest stressed and senescent erythrocytes, accumulate in the liver, and differentiate to ferroportin 1 (FPN1)-expressing macrophages that can deliver iron to hepatocytes. Monocyte-derived FPN1+ Tim-4neg macrophages are transient, reside alongside embryonically-derived Tim-4high Kuppfer cells, and depend on Csf1 and Nrf2. The spleenlikewise recruits iron-loaded Ly-6Chigh monocytes, but they do not differentiate into ironrecycling macrophages due to the suppressive action of Csf2, and are instead shuttled to the livervia coordinated chemotactic cues. Inhibiting this mechanism by preventing monocyte recruitment to the liver leads to kidney failure and liver damage. These observations identify the liver as the primary organ supporting emergency erythrocyte removal and iron recycling, and uncover a mechanism by which the body adapts to fluctuations in erythrocyte integrity.
Pregnant CX3CR1-CreERT+/+ Stopfl/fl tdTomato mice were injected subcutaneously with tamoxifen (8 mg/animal in 400 µl corn oil s.c.) on days 13.5and 15.5 p.c to induce tdTomato expression in embryonic monocytes/macrophages. At the age of 3 months, the progeny was transplanted with GFP bone marrow after busulfan pre-conditioning. After establishment of stable chimerism among blood leukocytes (3 weeks), mice were transfused with stressed red blood cells (sRBC). Embryonic (eKCs, CD45+ CD11b- F4/80+ GFP- tdTomato+) and monocyte-derived Kupffer cells (mKCs, CD45+ CD11b- F4/80+ GFP+ tdTomato-) of the liver were FACS-sorted 7 days after sRBC treatment and subjected to whole-genome expression profiling

overall_design: Paired eKCs and mKCs samples were derived from 3 separate sRBC-treated  CX3CR1-CreERT+/+ Stopfl/fl tdTomato mice and their total RNA amplified, labeled and subjected to hybridisation with Affymetrix Mouse Gene 2.0 ST Arrays.

first: Igor

last: Theurl


title: Expression profiling of Natural killer B cells

status: Public on May 17 2016

city: Beijing

first: Pengyan

last: Xia

state: Beijing

address: 15, Datun Road, Chaoyang district

department: The CAS key Laboratory of Infection and Immunity, Institute of Biophysics

institute: Institute of biophysics, Chinese Academy of Sciences

summary: Investigation of global gene expression levels between B cells, Natural killer cells and Natural killer B cells

overall_design: Gene expression profiling using sorted B cells, Natural killer cells and Natural killer B cells from WT mouse spleen. Total RNA extracted from WT cells were quantified by the NanoDrop ND-1000 and RNA integrity was assessed by standard denaturing agarose gel electrophoresis. The sample preparation and microarray hybridization were performed based on the NimbleGen’s standard protocols.

first: Shuo

last: Wang

first: Zusen

last: Fan


title: Nonpathogenic SIV and Pathogenic HIV Infections Associate with Disparate Innate Cytokine Signatures in Response to M. bovis BCG

status: Public on May 27 2016

city: Seattle

first: Donald

last: Sodora

state: WA

address: 307 Westlake Ave N Ste. 500

institute: Center for Infectious Disease Research

summary: Infections with mycobacteria, including Mycobacterium tuberculosis (Mtb) and Mycobacterium bovis (M. bovis) BCG, are a leading cause of morbidity and mortality for HIV-infected persons.  In contrast to HIV, SIV infection of sooty mangabeys is nonpathogenic, characterized by a lack of clinical disease including an absence of opportunistic infections. The goal of this study was to identify innate immune responses to M. bovis BCG maintained during nonpathogenic lentiviral infections, through a comparison of functional responses during pathogenic HIV or nonpathogenic SIV infections. Monocytes were evaluated for their ability to express key anti-mycobacterial cytokines TNF-α and IL-12 following a six-hour ex vivo BCG exposure. While HIV-infection was associated with a decreased percentage of IL-12-producing monocytes, nonpathogenic SIV-infection was associated with an increased percentage of monocytes producing both cytokines.  Gene expression analysis of PBMC following ex vivo BCG exposure identified differential expression of NK cell-related genes and several cytokines, including IFN-γ and IL-23, between HIV-infected and control subjects.   In contrast, SIV-infected and uninfected-control mangabeys exhibited no significant differences in gene expression after BCG exposure. Finally, differential gene expression patterns were identified between species, with mangabeys exhibiting lower IL-6 and higher IL-17 in response to BCG when compared to humans.  Overall, this comparison of immune responses to M. bovis BCG identified unique immune signatures (involving cytokines IL-12, TNF-α, IL-23, IL-17, and IL-6) that are altered during HIV, but maintained or increased during nonpathogenic SIV infections. These unique cytokine and transcriptome signatures provide insight into the differential immune responses to Mycobacteria during pathogenic HIV-infection of humans or nonpathogenic SIV-infection of mangabeys.

sample_organism:
Cercocebus atys
Homo sapiens

platform_organism:
Macaca mulatta
Homo sapiens

overall_design: Seven HIVneg and 7 HIV+ human samples and four SIVneg and 4 SIV+ samples were used here.

middle: L

first: Melanie

middle: A

last: Gasper


title: Live Attenuated Tetravalent Dengue Vaccination in Non-Human Primates

status: Public on May 10 2016

city: Stanford

first: Fiona

last: Strouts

state: CA

address: Campus Drive

institute: Stanford

summary: We measured genome-wide transcript abundance patterns in 246 whole blood samples collected from 35 cynomolgus macaques before and after vaccination with a live attenuated tetravalent dengue vaccine (TDV) or PBS (placebo). Animal work was conducted at the Charmany Instructional Facility of the School of Veterinary Medicine, University of Wisconsin-Madison, and all animal procedures were approved by the University of Wisconsin-Madison's Animal Care and Use Committee. Thirty-five adult male, DENV-seronegative cynomolgus macaques from Vietnam were placed in quarantine for 30 days prior to the start of the study. Five groups of animals (n=6 animals per group) received TDV either subcutaneously (SC) in 0.5 mL inocula or intradermally (ID) in 0.1 mL inocula using a needle-free injector (PharmaJet' device) or needle and syringe (N&S). Animals received two doses (same route) of TDV either on the same day (Day 0) or sixty days apart. One group (n=5) received PBS by ID route and needle-free injector. On day 90 after primary vaccination, 3 animals from each group were challenged with 105 PFU wt DENV-2 (New Guinea C strain) or 105 PFU wt DENV-4 (Dominica/81 strain) by SC route using N&S. Whole blood samples were collected for transcriptional profiling from all animals on days -11, -2, 1, 3, 5, and 7 before and after immunization, and for placebo animals on days 88, 91, 93, 95, and 97 before and after wt DENV challenge. Blood samples were drawn into PAXgene Blood RNA tubes and stored at -80'C prior to RNA extraction and processing.

first: Stephen

last: Popper


title: Gene expression analysis of maternal zygotic ezh2 mutant zebrafish embryos vs wildtype at 0 and 3.3 hpf

status: Public on May 06 2016

city: Nijmegen

first: Leonie

last: Kamminga

address: Geert Grooteplein 28

department: Molecular Biology

country: Netherlands

institute: Radboud University

summary: Goal of the experiment was to assess the differences in gene expression between maternal zygotic ezh2 mutant zebrafish embryos and wildtype embryos at 0 and 3.3 hpf.

overall_design: Experiment with two conditions (wildtype and ezh2 mutant), two timepoints (0h and 3.3h) and two biological replicates.

first: Nadine

last: Wittkopp

first: Simon

middle: J

last: van Heeringen

first: Bilge

last: San

first: Naomi

middle: D

last: Chrispijn

first: Anne

middle: K

last: Lagendijk

first: Jeroen

last: Bakkers

first: René

middle: F

last: Ketting

first: Marco

last: Aben


title: Vibrio cholerae temperature shift microarray analysis

status: Public on May 09 2016

city: Chapel Hill

first: Loni

last: Townsley

state: NC

address: 250 Bell Tower Dr Genome Sciences Building #4144

department: Biology

institute: University of North Carolina

summary: Temperature is a crucial environmental signal that govers the occurrence of Vibrio cholerae and cholera outbreaks. To understand how temperature impacts the transcriptome of V. cholerae we performed whole-genome level transcriptional profiling using custom microarrays on cells grown at human body temperature (37 C)  then shifted to temperatures V. cholerae experience in the environment (15 C and 25 C).

overall_design: Wild-type V. cholerae  grown at 37 C were compared to those shifted to either 15 C or 25 C. Threee biological replicates were performed for each condition.  All reference RNA  was harvested from a wild-type strain grown at 30 C.

first: Marilou

middle: P

last: Sison-Mangus

first: Sanjin

last: Mehic

first: Fitnat

middle: H

last: Yildiz


title: Functional characterization of RNA-binding protein IMP2 in primary Glioma cell lines [array]

status: Public on May 12 2016

city: Basel

first: Tommy

middle: Beat

last: Schlumpf

state: Basel-Stadt

address: Mattenstrasse 26

department: D-BSSE

country: Switzerland

institute: ETH Zürich

summary: Cancer stem cells (CSC) dictate tumor cell heterogeneity in diverse cancer types and arise, in part, from microRNA (miRNA)-dependent alteration of gene expression. The let-7 miRNA family induces differentiation by silencing genes that maintain stemness and is repressed by the RNA-binding proteins LIN28A/B, which preserve stemness in normal embryonic and malignant cells. Here, we observed that LIN28A/B is undetectable in glioma stem cells (GSC) whereas let-7 and, paradoxically, their target genes are highly expressed. Using photoactivatable-ribonucloside-enchanced crosslinking and immunoprecipitation (PAR-CLIP), we show that insulin-like growth factor-2 mRNA-binding protein 2 (IMP2) protects let-7 target genes from silencing and provides a mechanistically distinct alternative to LIN28A/B toward both GSC and neural stem cell specification. Our observations define the RNA-binding repertoire of IMP2 and identify a mechanism by which it supports GSC maintenance.

overall_design: We characterized miRNA expression differences between glioma stem cells and their differentiated progeny using agilent miRNA microarrays in three different glioma cell lines and both cell states.

first: Nils

last: Degrauwe

middle: B

first: Renato

last: Paro

first: Ivan

last: Stamenkovic


title: Comparative high-throughput gene expression analysis between cultured and sand fly vector-derived Leishmania infantum promastigotes.

status: Public on May 05 2016

city: MADRID

first: PEDRO

middle: JOSÉ

last: ALCOLEA ALCOLEA

address: Ramiro de Maeztu, 9

department: CENTRO DE INVESTIGACIONES BIOLÓGICAS

institute: CONSEJO SUPERIOR DE INVESTIGACIONES CIENTÍFICAS

summary: Leishmania infantum (Kinetoplastida:Trypanosomatidae) is the etiological agent of zoonotic visceral leishmaniasis in the Mediterranean basin. The motile promastigote stage infects the hematophagous sand fly vector host and amastigotes survives and multiplies within phagocytes of the mammalian host. Promastigotes are routinely cultured in liquid undefined media and are considered to mimic the environment within the sand fly gut. We have put this to the test by high-throughput gene expression profiling by shotgun DNA microarrays generated in our laboratory. This has been possible thanks to RNA amplification.

overall_design:
Two condition experiment. Hybridization of cDNA with shotgun DNA genome microarrays of L. infantum. Total RNA was doubly amplified to get enough material from sand fly-derived promastigotes. This allowed cDNA synthesis and microarray hybridization. Normalization of fluorescence intensity values was performed by the LOWESS per pin algorithm. Student`s t-test was conducted for statistical inference, including FDR adjustment.

Please note that the 'Pro-insect vs. Pro-culture' sample represents three replicates (3 raw data files; Pper_cultR*.txt) and averaged data across arrays (i.e. mean of normalized fold change data).

first: Pedro

last: Alcolea


title: Transcriptome differences among Albariño densimetrically-sorted berries

first: Pablo

last: Carbonell-Bejerano

summary: The interplay between environmental and genetic factors conditions the fruit ripening program in plants. Transcriptome analysis of grapevine fruits can help understanding these interactions to consciously cope with conditions leading to detrimental effects for viticultural purposes. However, considering the grapevine characteristic ripening asynchrony, which can be intensified by contrasting conditions, accurate grape sampling may be essential for molecular comparisons. In this study, berry density sorting according to floatability in NaCl solutions was assessed as a grape ripening staging strategy. Total sugar content was more correlated with berry density than with other non-invasive ripening parameters. The transcriptome was compared between three density classes collected near commercial maturity using grapevine whole-genome NimbleGen microarrays. Expression profiles clearly related with ripening progression were detected in a density series simultaneously collected from a vineyard of Albariño. By contrast, considerable differences were detected when the same density series was sampled on two different dates from the same vineyard of Tempranillo. Functional analysis indicated that environmental differences between both sampling moments determined most of these expression differences. Ripening degree-dependent responses to the environment were also detected. Finally, the effect of the sorting procedures on the grape transcriptome showed negligible when it was directly tested. Altogether, these findings evidence the convenience of homogenizing the developmental stage and the sampling time conditions for transcriptome comparisons. Berry density sorting proved useful to this end, although this method could be limited when the berry sugar concentration is not determined by the ripening developmental program.

overall_design: Vitis vinifera cv. Albariño plants grafted on Millardet et de Grasset 420 A rootstock at Finca Pé Redondo (Meis, Galicia, Spain) were used. This experimental vineyard was planted in 2003, presents East-West oriented rows and belongs to Bodegas Martín Códax winery. Twelve samples were independently analysed: samples from the north and the south side of the rows were processed in separate for three W and three NW blocks. On each sample, 20-22 bunches were randomly and simultaneously harvested at maturity on 22/09/2010, each from a different plant and all the berries were densimetrically-sorted. Berries of the three density ranges 120-140, 140-160 and 160-180g NaCl•L-1 (corresponding to under-ripe, ripe, and pre-ripe ripening degrees, respectively) from each replicate were immediately rinsed in distilled H2O, dried, frozen in liquid nitrogen and kept at -80ºC until further analysis. Sampling started at 8:00 am (solar time) and time lapse from bunch collection to berry freezing ranged between 3-5 h. Water supplied to W blocks throughout the season was 204 mm (from 23/06/2010 to 26/09/2010). RNA from twelve under-ripe berry class, twelve ripe berry class, and eight over-ripe berry class samples was obtained and hybridized to grapevine whole-genome NimbleGen microarrays.

first: José

last: Martínez-Zapater


title: Chronic p53-independent p21 expression deregulates replication licensing, leading to genomic instability

first: Prokopios Alexandros

last: Polyzos

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

overall_design: Refer to individual Series


title: Peripheral blood transcriptome profiles derived from parallel venipuncture (PAXgene and mononuclear cell; PBMC) and dried blood spot (DBS) samples.

status: Public on May 18 2016

city: Los Angeles

first: Steve

last: Cole

address: 11-934 Factor Bldg, UCLA

department: Medicine

institute: UCLA School of Medicine

summary: Comparison of transcript abundance estimates and bioinformatic inferences derived from DBS vs PAXgene vs peripheral blood mononuclear cell (PBMC) samples.

overall_design: Gene expression profiling was conducted using parallel collection and assay of venipuncture samples (PAXgene and PBMC) and DBS samples. Data come from 83 community dwelling adults recruited from the Chicago metropolitan area.  In addition to basic demographic characteristics (age, sex, race/ethnicity), participants were also assessed on health-related characteristics (body mass index/BMI; history of smoking or heavy alchol consumption), and educational attainment (z-score transformed).  Categorial variables were coded 0=no/absent and 1=yes/present.


title: Microarray analysis of CurDC versus BMDC

city: Changchun

first: Yinghua

last: Zhao

address: Dongminzhu street 519

institute: 1st hosptal of Jinli University

summary: We found that dendritic cells (DCs) activated by dectin-1 agonists Curdlan potently promoted naïve CD4+ T cells to differentiate into Th9 cells. To clarify the underlying mechanisms, we examine the gene expression profiles of Curdlan-activated DCs (CurDCs) and regular DCs matured by TNFalpha and IL1beta. We identified 42 upregulated genes of cytokines, chemokines and costimulatory molecules, especially the TNF/Receptor members. Subsequent studies proved that the TNF family members TNFSF15 and OX40L play a major role in mediating CurDC-induced Th9 differentiation.

overall_design: Immature DCs were generated from Balb/c mice and matured with TNF-α/IL-1β (BMDCs) or Curdlan (CurDCs) for 48 hours. DCs were collected and stored in Trizol reagent (Invitrogen) at -80℃. All samples were sent to OneArray (http://www.OneArray.com.cn/, Beijing, China) for transcription profiling via genome-wide microarrays, and the subsequent data analysis was also performed by OneArray.

first: Xiao

last: Chu

first: Jintong

last: Chen

first: Ying

last: Wang

first: Sujun

last: Gao

first: Yuxue

last: Jiang

first: Xiaoqing

last: Zhu

first: Guangyun

last: Tan

first: Wenjie

first: Huanfa

last: Yi

first: Honglin

last: Xu

first: Xingzhe

last: Ma

first: Yong

last: Lu

first: Qing

first: Siqing


title: Comparison of aged wt, krt18+/- and krt18-/- non-tumorous liver tissues

status: Public on May 04 2016

city: Graz

first: Vendula

last: Svendova

address: Auenbruggerplatz 2

institute: Medical University Graz

type:
Expression profiling by array
Genome variation profiling by array


title: DNA Microarray of Global Transcription Factor Mutant Reveals Membrane-Related Proteins Involved in n-Butanol Tolerance in Escherichia coli

city: Wuxi

first: Ye

last: Ni

state: Jiangsu

address: 1800 Lihu Road

department: School of Biotechnology

institute: Jiangnan University

summary: We successfully isolated an E. coli strain harboring rpoD mutant B8 with 2% (v/v) butanol tolerance using global transcriptional machinery engineering approach. DNA microarrays were employed to assess the transcriptome profile of n-butanol tolerance strain B8 and control strain E. coli JM109. The goal of this study is therefore to identify E. coli genes that are involved in n-butanol tolerance.

platform_organism: Escherichia coli str. K-12 substr. MG1655

overall_design: E. coli strains harboring σ70 mutant B8 and WT were cultured overnight and inoculated (1%) into fresh medium. n-Butanol (0.8%, v/v) was added at 0.8 OD660 and further incubated for 1.5 h. Cells were harvested by centrifugation (5500 g, 4°C). Total RNA was extracted using Qiagen RNeasy kit (Hilden, Germany) following manufacturer’s instructions. Qualified total RNA was further purified by Qiagen RNeasy mini kit and RNase-Free DNase Set. Three biological replicates of RNA samples were used to further DNA microarrays analysis.

first: Hai-Ming

last: Si

first: Fa

last: Zhang

first: An-Ning

last: Wu

first: Rui-Zhi

last: Han

first: Guo-Chao


title: Investigation of MET copy number in various cancer cell lines

city: Thousand Oaks

first: Dan

last: Baker

address: 1 Amgen Center Drive

department: Molecular Sciences

institute: Amgen Inc.

summary: This experiment investigates In Vitro and In Vivo Activity of AMG 337, a Potent and Selective MET Kinase Inhibitor, in MET-Dependent Cancer Models.  The goal of this study was to examine the effects of AMG337 on proliferation in cancer cell lines with varying MET copy number, the hypothesis being that high-level focal MET amplification is required to confer MET oncogene addiction and AMG337 sensitivity.

overall_design: Each of 21 cancer cell lines hybridized competitively against a pooled human male reference genomic DNA to determine CNV through array CGH.

first: Paul

middle: E

last: Hughes

first: Karen

last: Rex

first: Sean

last: Caenepeel

first: Yajing

last: Yang

first: Yihong

first: Martin

last: Broome

first: Hue

middle: T

last: Kha

first: Terri

last: Burgess

first: Benny

last: Amore

first: Paula

last: Kaplan-Lefko

first: Jodi

last: Moriguchi

first: Jonathan

last: Werner

first: Michael

last: Damore

first: Daniel

first: Deborah

last: Choquette

first: Jean-Christophe

last: Harmange

first: Robert

last: Radinsky

first: Richard

last: Kendall

first: Isabelle

last: Dussault

first: Angela

last: Coxon


title: Comparison of wt, krt18+/- and krt18-/- non-tumorous liver tissues at the age of 12 and 18 months [aCGH]

first: Vendula

last: Svendova

summary: Analysis of the different genotypes of non-tumorous mouse livers in 3 different ages revealed more genetic alterations in Krt18-/- and Krt18+/- compared to wt livers. This speaks in favor of a higher genomic instability being causally related to K-deficiency and aging, even at a preneoplastic stage.

overall_design: Wild type healthy liver tissue vs. healthy krt18+/- / healthy krt18-/- at the age of 12 and 18 months

first: Anita

last: Mehta

first: Eva

last: Ladderer


title: Changes in miRNA profile induced by mutant IDH1

status: Public on Apr 30 2016

city: Chicago

first: Craig

last: Horbinski

state: IL

address: 303 E Chicago Avenue

department: Pathology and Neurosurgery

institute: Northwestern University

summary: Pilot study aimed at comparing miRNA profiles of human glioma cells with and without the R132H IDH1 mutation.

overall_design: Three cultures of U87MG cells expressing GFP-vector, and three cultures of U87MG cells expressing GFP-R132H IDH1

first: Chi

last: Wang


title: Pax6 targets in neural stem cells

status: Public on May 02 2016

city: Cambridge

first: Sudhir

last: Thakurela

address: 7 Divinity Avenue

institute: HSCRB

type: Genome binding/occupancy profiling by genome tiling array

summary: Pax6 is a highly conserved transcription factor among vertebrates and is important in various aspects of the central nervous system (CNS) development. However, the gene regulatory circuitry of Pax6 underlying these functions remains elusive. We find that, following expression in neural progenitor cells, Pax6 targets many promoters embedded in an active chromatin environment. Intriguingly, many of these sites are also bound by another progenitor factor, Sox2, which cooperates with Pax6 in gene regulation. A combinatorial analysis of Pax6 binding dataset with transcriptome changes in Pax6-deficient neural progenitors reveals a dual role for Pax6, in which it activates the neuronal (ectodermal) genes while concurrently represses the mesodermal and endodermal genes thereby ensuring the unidirectionality of lineage commitment towards glutamatergic neuronal differentiation. Furthermore, Pax6 is critical for inducing activity of transcription factors that elicit neurogenesis and repress others that promote non-neuronal lineages. In addition to many established downstream effectors, Pax6 directly binds and activates a number of genes that are specifically expressed in neural progenitors but have not been previously implicated in neurogenesis. The in utero knockdown of one such gene, Ift74, during brain development impairs polarity and migration of new-born neurons. These findings demonstrate new aspects of the gene regulatory circuitry of Pax6, revealing how it functions to control neuronal development at multiple levels to ensure unidirectionality and proper execution of the neurogenic program.

overall_design: Pax6 chip-chip was performed in neural stem cells to elucidate its genomic targets and down-stream gene regulatory network

first: Neha

last: Tiwari

first: Sandra

last: Schick

last: Garding

last: Ivanek

first: Benedikt

last: Berninger

first: Vijay


title: Detection of Alzheimer’s Disease at Mild Cognitive Impairment and Disease Progression Using Autoantibodies as Blood-based Biomarkers

status: Public on May 03 2016

city: Stratford

middle: G

last: Nagele

state: NJ

address: 2 Medical Center Drive

department: NJISA

institute: UMDNJ-SOM

summary: Human serum samples from Alzheimer's disease driven mild cognitive impairment and non-diseased controls were probed onto human protein microarrays in order to identify differentially expressed autoantibody biomarkers that could be used as diagnostic indicators.  Other neurodegenerative and non-neurodegenerative diseases were also used to help measure the specificity of the selected biomarkers.

overall_design:
In the study presented here, 50 Alzheimer's disease driven mild cognitive impairment samples and 50 control human serum samples were probed onto human protein microarrays in order to identify differentially expressed autoantibodies.  Microarray data was analyzed using several statistical significance algorithms, and autoantibodies that demonstrated significant differences in group prevelance were selected as potential biomarkers of disease.  Prediction classification analysis using Invitrogen's Prospector v5.2.1 and Random Forest tested the diagnostic efficacy of the identified biomarkers.  Differentiation of mild cognitive impairment samples from other neurodegenerative and non-neurodegenerative controls (Parkinson's disease, multiple sclerosis, and breast cancer) assessed the specificity of the selected biomarkers, while comparison with mild-moderate Alzheimer's disease samples assessed their utility for use in disease staging.
contributor: Alzheimer's Disease Neuroimagining Initiative

first: Cassandra

last: DeMarshall

first: Abhirup

last: Sarkar

first: Nimish

last: Acharya

first: George

last: Godsey

first: Eric

last: Goldwaser

first: Mary

last: Kosciuk

first: Umashanger

last: Thayasivam

first: Min

last: Han

first: Benjamin

last: Belinka


title: Emergence of undifferentiated colonies from mouse embryonic stem cells undergoing differentiation by retinoic acid treatment.

city: Baltimore

first: Minoru

last: Ko

state: MD

address: 251 Bayview Blvd, Suite 100, 10C

department: National Institute on Aging

institute: NIH

summary: Pluripotent mouse ES cells maintain their genomic stability via regular passage through the 2-cell-like state (2CLS) with a distinct pattern of gene expression. In a standard culture, only ~5% cells are in the 2CLS; thus, it is desirable to find conditions that facilitate cell transition through this state as a method for improving the quality of ES cells. Here we show that low concentration of retinoic acid (RA) in the presence of LIF increases the proportion of cells undergoing the 2CLS without causing differentiation. Colonies of undifferentiated cells with high contribution of 2CLS marker, Zscan4c, appear clearly by the day 7. These colonies consist of a mixture of three types of cells: (1) cells in the 2CLS, (2) regular pluripotent ES cells that express Pou5f1, Sox2, and Nanog, and (3) endodermal cells, which are located at the periphery of the colony. Cell tracking with LacZ-staining shows that descendants of 2CLS-cells represent the majority of cells in these colonies. Cells exposed to RA and then transferred to the regular medium retain pluripotency, judged by their high ALP staining, typical ES colony morphology, gene expression profile, and stable karyotype. These cells readily differentiate into derivatives of all 3 germ layers in embryoid bodies assay and yield a higher contribution to chimeras after the injection into blastocysts than regular ES cells. In  conclusion, transient culture of ES in low concentration of RA could increase the number of ES passaging through 2CLS and thus improve ES pluripotent phenotype and performance in chimera experiments.

overall_design:
MC1-ZE-3 control day3, MC1-ZE-3 atRA50 48h, and MC1-ZE-3 LY294002 48h are MC1 ES cells cultured in standard conditions. They were treated with 50nM retinoic acid (RA) or with PI3K inhibitor LY294002. RNA was extracted with  Trizol (TM) (Invitrogen) 48 h after treatment.
MC1-ZE3 day3 cells are cultured in standard conditions, RNA collected on day 3.
MC1-ZE16, RA50 day4 cells are treated with 50nM retinoic acid (RA), colonies of pluripotent cells were picked manually on day 4
ES MC1 Intact Lif+ RA cells are treated with 50nM retinoic acid (RA), colonies of pluripotent cells were picked manually on day 7.
MC1-ZE3 day3 2nd replication P10 day3 cells were initially treated with RA for 7 days (as in ES MC1 Intact Lif+ RA),and then cultured for 10 passages in standard conditions (without RA). RNA collected on day 3.

first: Lioudmila

middle: V

last: Sharova

first: Alexei

last: Sharov

first: Yulan

last: Piao

first: Carole

last: Stagg

first: Tomokazu

last: Amano

first: Yong

last: Qian

first: Dwaood

last: Dudekula

first: David

last: Schlessinger

middle: S


title: mRNA Expression profiles of parental Panc cell lines and Gemcitabine resistance Panc1cell lines

status: Public on Apr 26 2016

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

summary: Gemcitabine (GEM) is a key drug for treating PDAC, and it is commonly used for adjuvant chemotherapy. Although the majority of PDAC is sensitive to GEM at first, GEM cannot control PDAC for very long, suggesting that PDAC develops resistance to GEM after prolonged exposure. No reliable predictors of susceptibility to gemcitabine chemotherapy exist in pancreatic ductal adenocarcinoma. This study assesses gemcitabine resistant PDAC for its specific mRNA expression pattern. Gemcitabine resistant variants of Panc1, a human pancreatic adenocarcinoma cell line, were established. mRNA screening was investigated by microarray.

overall_design: GEM-resistant cells were generated by exposure to gradually increasing concentrations of the reagent for 2 months. Parental Panc1cells (Panc1-Pt) were exposed to GEM at an initial concentration of 2 ng/ml. When the cells adapted, the GEM concentration was increased. The final GEM concentration was 30 ng/ml. Limiting the dilution of the established cells allowed the cloning of the GEM-resistant Panc1cells, and the three independent clones (Panc1-GRs: Panc1-GR1, -GR3, and –GR4) were used in the present experiments. Total RNA was isolated from parental Panc1and gemcitabine resistance Panc1 cell lines using Trizol reagent (Invitrogen) according to the manufacturer’s instructions. cDNA and Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion#1753). CyeDye Coupling and fragmentation were performed as the protocol supplied by TORAY Industries, Inc.. Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc.. 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan). The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals.

first: S

last: Hasegawa

first: Mi

last: Mikamori

first: H

last: Eguchi


title: Discovering miRNA regulatory networks in Holt-Oram Syndrome using a Zebrafish model [array]

status: Public on Apr 24 2016

city: Pisa

first: Romina

last: D'Aurizio

state: PI

address: via Moruzzi 1

department: IIT

country: Italy

institute: CNR

summary: To investigate the complex regulatory networks disrupted in Holt-Oram Syndrome, we characterized genome-widely the miRNA and mRNA expression profiles in WT and Tbx5 depleted zebrafish embryos at two development time points, 24 and 48 hpf.

overall_design: The zebrafish gene Tbx5a was silenced with antisense morpholino oligonucleotide MO-Tbx5a against the TSS of the gene. A MO-CT was used in CT samples. 1,5ng morpholinos were injected into the yolk of 1-cell stage embryos and total RNA extracted from 50 embryos collected at 24 and 48hpf.The Zebrafish  wild-type AB strain line was used.

first: Letizia

last: Pitto

first: Elena

last: Chiavacci

first: Mara

last: D'Onofrio

first: Ivan

last: Arisi


title: miRNA profiling during fracture repair

status: Public on Apr 05 2016

city: Old Westbury

first: Michael

last: Hadjiargyrou

state: New York

address: New York Institute of Technology

department: Department of Life Sciences

institute: New York Institute of Technology

summary: To further understand the molecular complexity of fracture repair, we investigated miRNA profiling during the first 14 days post fracture.

overall_design: miRNA expression was investigated at post-fracture days 1, 3, 5, 7, 11, 14 as well as in intact (unfractured bone).

first: Jizu

last: Zhi

last: Komatsu


title: The target spectrum of SdsR small RNA in Salmonella

status: Public on Jan 25 2016

city: Würzburg

first: Kai

last: Papenfort

state: Würzburg

address: Josef-Schneider Str.2/BAU D15

department: RNA Biology

country: Germany

institute: IMIB Würzburg

summary: Enteric model bacteria such as Escherichia coli and Salmonella enterica express hundreds of small non-coding RNAs (sRNAs), targets for most of which are yet unknown. Some of these sRNAs are remarkably well-conserved, indicating that that they serve cellular functions that go beyond the necessities of a single organism. One of these “core sRNA” of largely unknown functions is the abundant ~100-nucleotide SdsR sRNA which accumulates in stationary phase after transcription by the general stress σ-factor, σS. In Salmonella, SdsR was known to inhibit the synthesis of the species-specific porin, OmpD. However, the sdsR gene is present in almost all enterobacterial genomes, suggesting additional, more conserved targets of this sRNA must exist. Here, we have combined SdsR pulse-expression with whole genome transcriptomics to discover 18 previously unknown targets of SdsR. These new targets include mRNAs coding for physiologically important regulators such as the carbon regulator, Crp, the nucleoid-associated chaperone, StpA and the antibiotic resistance transporter, TolC. SdsR is processed by RNase E giving rise to two independent SdsR variants with distinct target spectra. While the overall physiological role of this orphan core sRNA remains to be fully understood, the here presented catalog of new SdsR targets contains valuable leads to understand sRNA functions in resting bacteria.

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

overall_design: To determine the targets of the small regulatory RNA SdsR in S. Typhimurium, we looked at the effect of a short pulse of SdsR over-expression on the Salmonella transcriptome. To achieve over-expression, the sdsR gene was cloned in the pBAD plasmid and induced with 0.2% L-arabinose for 10 min. We then extracted the total RNA for transcriptional profiling. A strain carrying the pBAD plasmid w/o insert was used as negative control (also induced by L-arabinose). 3 biological replicates were performed. This sRNA target identification strategy has been described in Papenfort et al; Molecular Microbiology (2006) 62(6), 1674–1688.

first: Kathrin

last: Fröhlich

first: Katharina

last: Haneke

first: Jörg

last: Vogel


title: Human hematopoietic leukemic k562 cells: control Vs CXCR4 constitutively active mutant cells

status: Public on Feb 29 2016

city: Delhi

first: Gurudutta

middle: U

last: Gangenahalli

state: Delhi

address: Brig. S. K. Mazumdar Marg, Timarpur

department: Stem Cell Research Division

country: India

institute: Institute of Nuclear Medicine & Allied Sciences

summary: The low homing and engraftment efficiency especially in context of low availability of donor CD34+ HSPCs is a major challenge, which limits the clinical applications of HSC therapies. SDF-1/CXCR4 axis plays a principle role in the homing and engraftment of hematopoietic stem/progenitor cells. Activation of CXCR4 induces cell trafficking and homing to the marrow microenvironment, where it retains hematopoietic stem cells in close contact with marrow stromal cells. The aim of our study is to understand the mechanisms of other molecules acting along with CXCR4 to provide new insights in the regulation of cell phenotypes. This data shows the transcriptional profiling of human hematopoetic leukemic k562 cells comparing control, wild type and two different mutant cells where mutant cells have constitutively activated CXCR4 gene expression where mutant 1 and 2 have different aminoacid substituions.

overall_design: biological replicates: three control, three wild type,  three mutant 1, three mutant 2

first: Menka

last: Sharma

first: Richpreet

last: Kaur


title: Response of Cupriavidus metallidurans CH34 to different Pt-species

status: Public on Feb 27 2016

city: Halle/Saale

first: Cornelia

last: Große

department: Faculty of Biology/Microbiology

summary: Response of Cupriavidus metallidurans CH34 to cisplatin, Pt(IV)chloride and Au-NP

overall_design: In this study 7 different treatments were performed (first 2 as 3 replicates) to acquire expression profiles of the total genome of Cupriavidus metallidurans

last: Grosse

first: Dietrich

last: Nies


title: Gene expression profiling of human c-Kit mutant D816V

summary: To decipher molecular targets responsible for c-Kit mutant D816V mediated hematopoietic malignancy, we employed whole genome microarray expression profiling as a discovery platform to identify important gene targets downstream of c-Kit mutant D816V expressing cells compared to wild-type c-Kit.

overall_design: Agilent one-color experiment, Organism: Human, Agilent-Custom Whole Genome Human 8x60k designed by Genotypic Technology Pvt. Ltd. (AMADID: 27114), Labeling kit: Agilent Quick-Amp labeling Kit (p/n:5190-0444).

first: GU

last: Gurudutta

first: Shilpa


title: Clusterin knockdown sensitizes prostate cancer cells to taxane by modulating mitosis

status: Public on Mar 01 2016

city: Vancouver

first: Shawn

last: Anderson

state: BC

address: 2660 Oak Street

country: Canada

institute: Vancouver Prostate Centre

summary: Clusterin (CLU) is a stress-activated molecular chaperone that confers treatment resistance to taxanes when highly expressed. While CLU inhibition potentiates activity of taxanes and other anti-cancer therapies in preclinical models, progression to treatment resistant disease still occurs implicating additional compensatory survival mechanisms. Taxanes are believed to selectively target cells in mitosis, a complex mechanism controlled in part by balancing antagonistic roles of Cdc25C and Wee1 in mitosis progression. Our data indicate that CLU silencing induces a constitutive activation of Cdc25C, which delays mitotic exit and hence sensitizes cancer cells to mitotic-targeting agents such taxanes. Unchecked Cdc25C activation leads to mitotic catastrophe and cell death unless cells upregulate protective mechanisms mediated through the cell cycle regulators Wee1 and Cdc2. In this study we show that CLU silencing induces a constitutive activation of Cdc25C via the phosphatase PP2A but leads to relief of negative feedback inhibition and activation of Wee1-Cdc2 to promote survival and limit therapeutic efficacy. Simultaneous inhibition of CLU-regulated cell cycle effectors, like PP2A and Wee1, may improve synergistic responses of biologically rational combinatorial regimens using taxanes and CLU inhibitors

overall_design: Biological triplicate of PC3  treated with siClusterin were compared to biological trplicate of PC3  treated with siScramblein

first: Nader

last: al Nakouzi

first: Chris

last: Wang

first: Eliana

last: Beraldi

first: Susan

last: Ettinger


title: Pig-specific skin transcriptional responses after intradermal administration of flagellin

status: Public on Jan 31 2016

city: Berlin

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

institute: Max-Planck-Institute for Infection Biology

summary: The study aimed at defining the skin innate responses after intradermal injection of flagellin. For this purpose, pigs were immunized by intradermal route with flagellin and H1N1 antigen. Skin was then sampled for microarray analyses.

overall_design: Pigs were immunized with the TLR5 agonist flagellin and the H1N1 antigen by intradermal route. Punch biopsies of skin were sampled post-injection. Total RNA was extracted and microarray experiments were performed as single-color hybridizations on Agilent 4x44K pig  (Sus Scrofa) whole genome catalog arrays (Agilent-014868) according supplier's recommendations.

first: Jean-Claude

last: Sirard

first: Nicolas

last: Collin

first: Norbert

last: Stockhofe


title: The miRNA profiling in MDA-MB-231, MDA-MB-231/E1A and knockdown of Dicer in MDA-MB-231/E1A cells

status: Public on Jan 16 2016

city: Miaoli County

first: Jen-Liang

last: Su

address: No.35, Keyan Road, Zhunan, Miaoli County 35053, Taiwan.

country: Taiwan

institute: National Health Research Institutes

summary: Dicer, RNase III endonuclease, is an essential enzyme in miRNA biogenesis that regulates target gene expression, and it has been reported that aberrant expressions of Dicer associate with the clinical outcomes of patients in various cancers. To explore the miRNA differencial expression regulated by Dicer in MDA-MB-231/E1A cells, the microarray profiling analysis was employed to conduct differentially expressed miRNAs in stable MDA-MB-231/vector, MDA-MB-231/E1A, and MDA-MB-231/E1A/shDicer cells.

overall_design: The four groups including vector control, E1A-expressing and Dicer knockdown in E1A-expressing MDA-MB-231 cells were harvested and RNA were isolated. Two independent experiments were performed for each group.

first: T

middle: Y

last: Chang


title: C.elegans gene expression study for single, double or triple genetic perturbations of regulators in AMPK, Insulin and TOR pathway

status: Public on Jan 22 2016

city: Shanghai

first: Jing-Dong

middle: Jackie

last: Han

address: Yueyang Road 320

department: CAS-MPG Partner Institute for Computational Biology

institute: Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences

summary: We use genetic manipulations of regulators representing different pathways to examine whether transcriptomes progressively resemble dietary restriction when multiple regulators are perturbed.

overall_design: Worms under 10 different treatments with 2 replicates each were collected on adult day (AD) 4, fed by HT1115 bacteria under ad libitum (AL) with concentration of 1x10^10 bacteria/ml.

first: J


title: Transcriptomic effects of prenatal exposure to corticosteroids on synaptic transmission

status: Public on Jan 09 2016

city: Prairie View

first: Dumitru

middle: Andrei

last: Iacobas

state: TX

address: Ann Preston St

department: Undergraduate Medical Academy

institute: Prairie View A&M University

summary: Prenatal exposure to synthetic corticosteroids can significantly alter postnatal development through changes in neurotransmitters and their receptors, and thus having long-lasting behavioral effects. Some of these changes have been observed in animal experiments, others also in humans prenatally exposed to synthetic corticosteroids. Here, we focused on transcriptomic changes within the prefrontal cortex of female rats prenatally exposed to either betamethasone or saline. The transcriptome has been assessed by novel computational tools to determine complex changes that may have life-long effects on phenotype, i.e., behavior. We analyzed how composition, topology and modulatory networks of the genomic fabric of the dopaminergic, GABAergic, and glutamatergic synapse (the transcriptome of the most interconnected and stably expressed gene network responsible for specific transmission) are affected by prenatal exposure to corticosteroids and postnatal ketamine/saline treated NMDA-induced seizures.

overall_design: One sex (F) x two prenatal exposures (B = betamethasone, S = saline) x two postnatal treatments (K = ketamine, S = saline). Biological replicates: 4 FSS, 4 FBS, 4 FBK.

middle: A

first: Sanda

first: Tamar

last: Chachua

first: Galyna

last: Sidyelyeva

first: C

last: Goletiani

first: Jana

last: Velíšková

first: Libor

last: Velíšek


title: The expression of microRNAs in embryoid bodies derived from mouse embryonic stem cells

status: Public on Jan 08 2016

city: Cincinnati

first: JIALIANG

last: LIANG

address: 231 Albert Sabin Way

department: Department of Pathology and Laboratory Medicine

institute: University of Cincinnati

summary: Mouse embryonic stem cells can spontaneously differentiate and assemble into a spherical embryoid body (EB) during suspension culture. The initial study aims to identify the up-regulated or down-regulated microRNAs during the differentiation process of pluripotent stem cells. From the microRNA profiling, we will focus on the microRNAs associated with mesodermal and endothelial differentiation of embryonic or induced pluripotent stem cells.

overall_design: In this study, the EBs were collected at 0 and 10-day differentiation of ESCs (ATCC: CRL-1934). The miRNA transcripts listed in Sanger miRBase Release 19.0 was detected by microarray.

first: Jialiang

last: Liang

first: Yigang


title: Expression profile of HCT116 cells treated with TNF-α/IFN-ɣ, both TNF-α/IFN-ɣ and silibinin, and without treatment.

status: Public on Dec 31 2015

city: Singapore

first: Lee

middle: Guat Lay

last: Caroline

address: 11 Hospital Drive

department: Department of Biochemistry, National University of Singapore

country: Singapore

institute: National Cancer Centre Singapore

summary: Expression profiling of HCT116 colon cancer cells with different treatments. Illumina HumanHT-12 V4.0 expression beadchip was used to obtain expression profiles across more than 31,000 annotated genes.

overall_design: Total RNA obtained from HCT116 cells with different treatments, namely, cells with TNF-α (50ng/ml)/IFN-ɣ (50U/ml) treatment, cells with TNF-α (50 ng/ml)/IFN-ɣ (50 U/ml) and silibinin (100 uM) treatment and cells without any treatment. Each sample has 2 biological replicates.

first: Yun

last: GAO

first: Way-Champ

last: MAH

first: Steven

last: THENG

first: Caroline

last: Lee


title: Gene expression profiling in humna HCC, lung, and pancreas cell lines.

status: Public on Mar 16 2016

city: Daejeon

first: Yang

last: Suk-Jin

address: 125 Gwahak-ro, Yuseong-gu

country: South Korea

institute: KRIBB (Korea Research Institute of Bioscience and Biotechnology)

summary: To investigate the role for LSD1 in solid cancer cell growth, we depleted LSD1 with siRNA in 50 different cancer cell lines derived from various tissues. By the degree to the cell growth defect mediated by LSD1 knock down, we stratified the cell lines into three groups. Then, to determine differential gene expressions related to the LSD1-dependent cell growth, we performed gene expression microarray analyses of the most and the least LSD1-dependent cell lines.

overall_design:
Gene expression analysis of 21 cell lines under normal cell culture condition.
Determined the gene expression profile of the most and the least LSD1-dependent group by Gene Set Enrichment Analysis (GSEA), and decided to identify the biological pathways correlated with the LSD1 dependence of cell growth.

first: Suk-Jin

last: Yang

first: Ye

middle: J

last: Jang

first: Jung-Ae

last: Kim

first: Young

middle: I

last: Yeom


title: Genome wide profiling of Su(H) [CSL] binding in Drosophila melanogaster larval CNSs where Notch is hyperactive in neuroblasts for 24 hours

status: Public on Dec 15 2015

city: Cambridge

first: Sarah

last: Bray

address: Downing Street

department: PDN

country: United Kingdom

institute: University  of Cambridge

summary: The Notch pathway is a well conserved cell to cell communication mechanism that is normally involved in many developmental processes and when aberrantly activated it leads to diseases such as cancer. One such example is the neural stem cell tumours that arise from constitutive Notch activity in Drosophila neuroblasts from the larval Central Nervous System (CNS). To investigate how hyper-activation of Notch in larval neuroblasts leads to tumours, we mapped genome-widely the regions that are bound by Su(H) (the core Notch pathway transcription factor, known as CSL in mammals). We combined these results with the profiling of upregulated mRNAs in CNSs where Notch is hyper-activated for 24h vs control CNSs and identified 127 putative direct Notch targets in the hyperplastic CNSs. Included were genes associated with the neuroblast maintenance and self-renewal programme and genes coding for temporal transcription factors, which are involved in neuroblast progression and generation of progeny with specific identity over time. Thus, Notch induces neural stem cell tumors by promoting the expression of genes that contribute to stem cell identity and by reprogramming expression of temporal factors that regulate maturity.

overall_design: Su(H) binding profile in Drosophila larval CNSs where Notch is constitutively active for 24 hours. In total there are 3 samples of  Su(H) ChIP in Notch hyper-activated larval CNSs.

first: Evanthia

last: Zacharioudaki

first: Ben

last: Housden

first: Bettina

last: Fischer


title: C.elegans time course study on dietary restriction and aging

first: Jing-Dong

last: Han

summary: Dietary restriction (DR) is the most powerful natural means to extend lifespan. Here we obtain temporally resolved transcriptomes during calorie restriction and intermittent fasting in Caenorhabditis elegans, and find that early and late responses involve metabolism and cell cycle/DNA damage, respectively.

overall_design: 15 samples of N2 worms were collected every two days from adult day (AD) 2 under three dietary regimens: ad libitum (AL), calorie restriction (CR) and intermittent fasting (IF) in this time course Affymetrix microarray experiment. AL, CR and IF treatments were carried out following published protocols (Honjoh et al., 2009, Nature) except the concentration of AL was set to 1x10^10 bacteria/ml while that of CR was set to 1x10^8 bacteria/ml.

first: J

middle: D


title: Dynamic expression of chromatin modifiers during developmental transitions in preimplantation embryos

status: Public on Dec 01 2015

city: Basel

first: Antoine

last: Peters

address: Maulbeerstrasse 66

institute: Friedrich Miescher Institute for Biomedical Research (FMI)

summary: There are two major developmental transitions that take place during the first four days of mouse embryogenesis. The first one is the maternal-to-zygotic transition in the zygote and 2-cell embryo, the second one is the first cell lineage commitment at the 32-cell stage. A number of transcription factors govern zygotic expression and the specification of pluripotent versus trophectoderm cells, while at the same time there are dynamic changes in DNA methylation and chromatin organization. It is not fully understood which chromatin modifying complexes take part in these processes and whether there is a particular spatiotemporal distribution of certain chromatin players in preimplantation development. To address this question, we performed gene expression profiling of single cells from the oocyte to the blastocyst stage. We describe the patterns of expression of over 100 genes involved in histone methylation, DNA methylation and chromatin remodelling. For a number of these genes we observed differential maternal versus zygotic expression. This is particularly the case for homologous genes like Tet1 and Tet3 (zygotic and maternal respectively), or Suv39h1 and Suv39h2 (zygotic and maternal respectively). In contrast to the maternal-to-zygotic switch, most chromatin modifying genes are ubiquitously expressed in the subsequent lineage specification at the 32-cell stage. The few exceptions that showed a differential expression pattern are Kdm1b, Tet1 and Prdm14. Our data suggests that genes coding for histone modifying complexes are ubiquitously expressed in early embryos and that there are maternal and zygotic variants of most of these complexes. Furthermore, the method that we applied, allows the distinction of female versus male embryos based on the expression of Xist (X-linked, expressed in female embryos) and Kdm5d (Y-linked, expressed strongly in male embryo). With the exception of the X- and Y-linked genes, we did not observe sex-specific gene expression patterns of chromatin modifiers or transcription factors.

overall_design: 189 samples screened for the expression of 192 genes by Fluidigm qPCR

first: Peter

last: Nestorov

first: Hans-Rudolf

last: Hotz

middle: H


title: A Systems Approach to Reverse Engineer Lifespan Extension by Dietary Restriction

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

overall_design: Refer to individual Series


title: The expression profile of 5-fluorouracil pathway genes in colorectal carcinoma

status: Public on Aug 31 2015

city: Prague 10

first: Pavel

last: Soucek

address: Srobarova 48

country: Czech Republic

institute: National Institute of Public Health

summary:
This study addressed involvement of fourteen 5-fluorouracil pathway genes in the prognosis of colorectal carcinoma patients. The major goal of our study was to investigate associations of gene expression of enzymes metabolizing 5-fluorouracil with therapy response and survival of colorectal carcinoma patients
Downregulation of DPYD and upregulation of PPAT, UMPS, RRM2, and SLC29A1 transcripts were found in tumors compared to adjacent mucosas in testing and validation sets of patients. Low RRM2 transcript level significantly associated with poor response to the first-line palliative 5-FU-based chemotherapy in the testing set and with poor disease-free interval of patients in the validation set.

overall_design: Testing and validation sets comprising paired tumor and adjacent mucosa tissue samples from 119 patients were used for transcript profiling by quantitative real-time PCR. Intratumoral gene expression levels were correlated with clinical data of patients.


title: Remodeling of Brown and White Adipose Tissue by NT-PGC-1α-Mediated Gene Regulation

status: Public on Aug 07 2015

city: Baton Rouge

first: Ji Suk

last: Chang

state: LA

address: 6400 Perkins Rd.

department: Gene Regulation and Metabolism

institute: Pennington Biomedical Research Center

summary: The β-adrenergic receptor signaling pathway is a major component of adaptive thermogenesis in brown and white adipose tissue during cold acclimation. The β-AR activation highly induces transcriptional coactivator PGC-1α and its splice variant N-terminal (NT)-PGC-1α, promoting the transcription program of mitochondrial biogenesis and thermogenesis. In the present study, we evaluated the role of NT-PGC-1α in brown adipocyte energy metabolism by genome-wide profiling of NT-PGC-1α-responsive genes. Canonical pathway analysis revealed that a number of genes upregulated by NT-PGC-1α are highly enriched in mitochondrial pathways including fatty acid transport and β-oxidation, TCA cycle and electron transport system, thus reinforcing the crucial role of NT-PGC-1α in the enhancement of mitochondrial function. Moreover, gene expression profiling of NT-PGC-1α revealed activation of distinct metabolic pathways such as glucose, lipid and nucleotide metabolism and of signaling pathways such as RAR and PPAR-γ/RXRα activation in brown adipocytes. Together, our data strengthen our previous findings that NT-PGC-1α is a key regulator of mitochondrial oxidative metabolism and thermogenesis in brown adipocytes and further suggest that NT-PGC-1α influences a broader spectrum of thermogenic processes to meet cellular needs for adaptive thermogenesis.

overall_design: Two samples from two groups: NT-PGC-1α overexpression and empty vector. There are technical replicates (A and B) for each group. Two RNA samples were pooled for each group.

first: Jihyun

first: Vivian

last: Fernand

first: Tara

last: Henagan

first: Jeho

last: Shin

last: Huypens

first: Susan

last: Newman

first: Thomas

middle: W

last: Gettys

first: Ji

last: Chnag


title: MeDIP-chip of adult mouse hippocampus exposed to neonatal ethanol

status: Public on Jul 25 2015

city: Toronto

first: Eric

last: Chater-Diehl

state: ON

address: 686 Bay St.

institute: SickKids Research Institute

type: Methylation profiling by genome tiling array

summary: In this experiment, we exposed mice to ethanol injections on postnatal days 4 and 7. We then extracted whole-hippocampus on postnatal day 70. We performed MeDIP-chip  using an antibody against 5mC. We also perfomed MEDME anaylsis using a chip with fully methylated DNA to act as a control. We found alterations in both modifications at many sites, including oxidative stress genes and imprinted loci. We also found many affect lipid metabolism pathways.

overall_design: Comparision of neonatal ethanol-injected  with saline injected C57BL/6J mouse hippocampus in adulthood (day 70)

first: E

last: Diehl

first: S

middle: M

last: Singh


title: Increased plasma matrix metalloproteinase 1 is associated with the presence of esophageal squamous cell carcinoma

status: Public on Jul 01 2015

city: Kaohsiung

first: Chun-Wei

last: Tung

address: No. 100, Shih-Chuan 1st Rd.

institute: Kaohsiung Medical University

summary: Esophageal squamous cell carcinoma (ESCC) patients are usually diagnosed at late stages, prohibiting the chance of surgical cure. The obstacle partly comes from the lack of molecular markers for early detection. Moreover, there is no consensus about endoscopic surveillance for ESCC. This study aimed to identify noninvasive markers for ESCC detection. By microarray-based screening of 17 pairs of human ESCC specimens, we identified that secreted protein matrix metalloproteinase-1 (MMP1) may be associated with the presence of ESCC.

overall_design: The tumor and adjacent normal tissues were obtained from 17 male ESCC patients who underwent total esophagectomy without previous cancer treatment at Kaohsiung Medical University Hospital (KMUH)

first: Wu

last: I-Chen


title: Phanerochaete chrysosporium gene expression on different substrates

status: Public on May 19 2015

first: Shawn

last: Mansfield

address: 2424 Main Mall

department: Department of Wood Science

institute: University of British Columbia

summary:
Using whole genome microarrays based on the annotated genomes of Phanerochaete chrysosporium, we monitored the changes in its transcriptomes relevant to cell wall degradation during growth on three chemically distinct Populus trichocarpa (poplar) wood substrates.
Results of this study are sumbitted for review in Biotechnology for Biofuels

overall_design: From a data set of 10004 unique gene models, each NimbleGen (Madison, WI) array targeted 9959 genes and featured 12 unique 60mers per gene, all in triplicate. RNA and protein were obtained from P. chrysosporium strain RP-78 (USDA Forest Mycology Center, Forest Products Laboratory, Madison WI) grown in malt extract agar for 10 days prior to inoculation with wood wafers. Three poplar wood substrates with distinct cell wall chemical properties were selected from several hundred 4-year old Populus trichocarpa trees grown in a common garden field trial at the University of British Columbia (Canada). We selected three poplar genotypes based on cell wall chemical traits. Substrate A corresponds to a genotype with a higher than average lignin content and lower that average glucose content; Substrate B, a lower than average lignin content and higher that average glucose content; Substrate C lignin and glucose contents are near the population average. Poplar wood stems were cut into 0.5 mm wafers on a microtome, sterilized for 20 min at 121°C, dried at 50°C overnight, and cooled to room temperature. The specimens were then inoculated in Petri dishes with actively growing mycelia. Approximately 5 g of wood wafers were placed in each Petri dish (exact weights were recorded), sealed and incubated at 22°C and 70 ± 5% relative humidity for 10, 20 or 30 days. For RNA, the degraded wafers were removed from the Petri dishes, immediately snap-frozen in liquid nitrogen and stored at -80°C for later use. Total RNA was converted to Cy3 labelled cDNA, hybridized to microarrays and scanned as previously described by Vanden Wymelenberg et al 2010 (Appl Enviro Microbiol 76:3599-3610).The 24 arrays per fungal species were scanned and data extracted using NimbleScan v.2.4. The raw data was loaded into GeneSpring, where the intensities were converted to log2 and quantile normalized, and all probes per gene averaged. This data was then exported and further analyzed in R. For substrates “A” and “B”, three replicates were used for each wood substrate/fungus and incubation period combination. For substrate “C” only 2 biological replicates were employed.

first: Oleksandr

last: Skyba


title: ene expression patterns of wood decay fungi Postia placenta and Phanerochaete chrysosporium are influenced by wood substrate composition during degradation

sample_organism:
Rhodonia placenta
Phanerodontia chrysosporium

platform_organism:
Rhodonia placenta
Phanerochaete chrysosporium RP-78


title: Postia placenta gene expression on different substrates

summary:
Using whole genome microarrays based on the annotated genomes of Postia placenta, we monitored the changes in its transcriptomes relevant to cell wall degradation during growth on three chemically distinct Populus trichocarpa (poplar) wood substrates.
The research goal is to identtify genes essential for cellulose depolymerization.

overall_design: From a data set of 12438 unique gene models, each NimbleGen (Madison, WI) array targeted 9959 genes and featured 10 unique 60mers per gene, all in triplicate. RNA and protein were obtained from P. placenta  strain MAD-698-R (USDA Forest Mycology Center, Forest Products Laboratory, Madison WI) grown in malt extract agar for 10 days prior to inoculation with wood wafers. Three poplar wood substrates with distinct cell wall chemical properties were selected from several hundred 4-year old poplar (Populus trichocarpa) trees grown in a common garden field trial at the University of British Columbia (Canada). We selected three poplar genotypes based on cell wall chemical traits. Substrate A corresponds to a genotype with a higher than average lignin content and lower that average glucose content; Substrate B, a lower than average lignin content and higher that average glucose content; Substrate C lignin and glucose contents are near the population average. Poplar wood stems were cut into 0.5 mm wafers on a microtome, sterilized for 20 min at 121°C, dried at 50°C overnight, and cooled to room temperature. The specimens were then inoculated in Petri dishes with actively growing mycelia. Approximately 5 g of wood wafers were placed in each Petri dish (exact weights were recorded), sealed and incubated at 22°C and 70 ± 5% relative humidity for 10, 20 or 30 days. For RNA, the degraded wafers were removed from the Petri dishes, immediately snap-frozen in liquid nitrogen and stored at -80°C for later use. Total RNA was converted to Cy3 labelled cDNA, hybridized to microarrays and scanned as previously described by Vanden Wymelenberg et al 2010 (Appl Enviro Microbiol 76:3599-3610).The 24 arrays per fungal species were scanned and data extracted using NimbleScan v.2.4. The raw data was loaded into GeneSpring, where the intensities were converted to log2 and quantile normalized, and all probes per gene averaged. This data was then exported and further analyzed in R. For substrates “A” and “B”, three replicates were used for each wood substrate/fungus and incubation period combination. For substrate “C” only 2 biological replicates were employed.


title: Gene expression profiling of recent thymic emigrants (RTEs) from a mouse strain with an ENU-induced mutation in Zfp335

status: Public on Oct 17 2014

first: Brenda

middle: Yuyuan

last: Han

address: 61 Biopolis Drive, Proteos

institute: Institute of Molecular and Cell Biology, A*STAR

summary: The generation of naïve T lymphocytes is critical for immune function yet the mechanisms governing their maturation remain incompletely understood. We have identified a mouse mutant, bloto, that harbors a hypomorphic mutation in the zinc finger protein Zfp335. Mutant blt/blt mice exhibit a naïve T cell deficiency due to an intrinsic developmental defect that begins to manifest in the thymus and continues into the periphery, affecting T cells that have recently undergone thymic egress. Zfp335 binds to promoter regions via a consensus motif, and its target genes are enriched in categories related to protein metabolism, mitochondrial function and transcriptional regulation. Restoring the expression of one target, Ankle2, partially rescues T cell maturation. Our findings identify Zfp335 as a transcription factor and essential regulator of late-stage intrathymic and post-thymic T cell maturation.

overall_design: WT and blt/blt CD4+ RTEs were sorted from mixed hematopoietic chimeras for RNA extraction and gene expression analysis on Affymetrix arrays. 6 samples were analyzed in total, with 3 biological replicates per genotype.

first: Shuang

last: Wu

first: Chuan-sheng

last: Foo

first: Robert

last: Horton

first: Craig

middle: N

last: Jenne

middle: R

last: Watson

first: Belinda

last: Whittle

first: Christopher

middle: C

last: Goodnow

first: Jason

last: Cyster


title: Gene expression profiling of mature CD4 SP thymocytes from a mouse strain with an ENU-induced mutation in Zfp335

overall_design: WT and blt/blt mature CD4SP thymocytes were sorted from mixed hematopoietic chimeras for RNA extraction and gene expression analysis on Affymetrix arrays. 6 samples were analyzed in total, with 3 biological replicates per genotype.

first: Susan

middle: G


title: Small molecule transcriptional responses in Plasmodium falciparum

city: Notre Dame

first: Michael

middle: T

last: Ferdig

state: IN

address: 100 Galvin Life Sciences Center

department: Biological Sciences

institute: University of Notre Dame

summary:
Comparison of whole genome gene expression profiles for Plasmodium falciparum parasites perturbed with small molecules with diverse mechanisms of action.
Perturbations were performed by treating each synchronized parasite culture with a given small molecule at 24 hrs post-eryhrocyte invasion and RNA collected 2 hrs post-exposure

overall_design: Pertubations were performed on 2 laboratory clones of P. falciparum (HB3 and Dd2) and RNA collected from perturbed cultures and controls

first: Geoffrey

last: Siwo

first: Roger

last: Smith

first: Katrina

last: Button-Simons

first: Lisa

last: Checkley


title: Identification of a novel, recurrent MBTD1-CXorf67 fusion in low-grade endometrial stromal sarcoma (aCGH)

status: Public on Mar 31 2015

city: Stanford

first: Joanna

last: Przybyl

address: 300 Pasteur Drive

department: Department of Pathology

institute: Stanford University

summary:
Endometrial stromal sarcomas (ESSs) are a genetically heterogeneous group of rare uterine neoplasms that are frequently driven by recurrent gene rearrangements. In conventional low-grade ESSs, JAZF1-SUZ12, PHF1-JAZF1, EPC1-PHF1 and MEAF6-PHF1 chimeric fusions have been reported in > 50% of cases. The recently described t(10;17)(q22;p13) translocation yields YWHAE-FAM22A/B chimeric proteins that are associated with histologically high-grade and clinically more aggressive ESS.
Integrating whole-transcriptome paired-end RNA sequencing with fluorescence in situ hybridization (FISH) and conventional cytogenetics, we identified MBTD1 (Malignant Brain Tumor Domain-containing 1) and CXorf67 (Chromosome X open reading frame 67) as the genes involved in the novel reciprocal t(X;17)(p11.2;q21.33) translocation in two independent low-grade ESS of classical histology. The presence of the MBTD1-CXorf67 fusion transcript was validated in both cases using RT-PCR followed by Sanger sequencing.
A specific FISH assay to be used on paraffin tissues was developed to detect the novel t(X;17) translocation, and resulted in identification of an additional low-grade ESS case positive for the MBTD1-CXorf67 fusion among 14 uterine stromal tumours [9 ESSs and 5 undifferentiated endometrial sarcomas (UESs)] that were negative for JAZF1 and YWHAE rearrangements.
Gene expression profiles of 3 ESSs with YWHAE- and 4 classical ESSs with JAZF1-rearrangements, and 4 UESs without known gene rearrangements, indicated clustering of tumours with MBTD1-CXorf67 fusion together with low-grade JAZF1-associated ESSs.
The chimeric MBTD1-CXorf67 fusion identifies yet another cytogenetically distinct subgroup of low-grade ESS and offers the opportunity to shed light on the functions of two poorly characterized genes.

overall_design: Genomic DNA extracted from 2 low-grade ESS frozen tumor samples; Agilent CGH+SNP 4x180K array. Reference female DNA supplied with the SureTag Complete DNA Labeling Kit was used for the aCGH experiments.

first: Barbara

last: Dewaele

first: Anna

last: Quattrone

first: Julio

last: Finalet-Ferreiro

first: Vanessa

last: Vanspauwen

first: Ellen

last: Geerdens

first: Valentina

last: Gianfelici

first: Zeynep

last: Kalender

first: Agnieszka

last: Wozniak

first: Philippe

last: Moerman

first: Raf

last: Sciot

first: Sabrina

last: Croce

first: Frederic

last: Amant

first: Peter

last: Vandenberghe

first: Jan

last: Cools

first: Maria

last: Debiec-Rychter


title: Expression data from multiple strains of Francisella

status: Public on May 02 2015

city: Hannibal

first: Siva

middle: Tej

last: Sarva

state: Missouri

address: 6500 Hospital Dr

department: Division of Pulmonary Critical Care

institute: Hannibal Regional Medical Group

summary:
Comparison of expression profiles of strains of Francisella to identify virulence factors
We used custom microarrays to detail the global gene expression of four strains of Francisella (Schu4, LVS, OR960246, U112) and identified distinct classes of differentially expressed genes during this process.

sample_organism: Francisella tularensis subsp. tularensis SCHU S4

sample_organism: Francisella tularensis subsp. holarctica LVS

sample_organism: Francisella tularensis subsp. novicida U112

sample_organism: Francisella tularensis subsp. holarctica OR96246

overall_design:
All the strains of Francisella were grown to optical density of 0.6 in a chemical defined medium and their expression profiles were compared.

The comparative gene expression analyses of the strains of Francisella are reported in PMID 27537327.
The manuscript detailing the comparative intergenic expression of the strains of Francisella is under preparation.

first: Robert

last: Waldo

last: Belland

first: George

last: Hilliard

first: Karl

middle: E

last: Klose


title: Identification of Novel Pre-Erythrocytic Malaria Antigen Candidates for Combination Vaccines with Circumsporozoite Protein

status: Public on Jul 01 2014

city: Seattle

last: Morrison

state: WA

address: 307 Westlake Ave N

institute: Center for Infectious Disease Research

summary:
Determination of gene expression level changes of whole genome during Plasmodium falciparum development in early liver stage (at 24h and 48h), compared to mixed blood stage and sporozoite stage.
A set of Genes selected from this expression analysis are further verified by qPCR and a sub-set were tested for their vaccine efficacy.

overall_design: 6 genomic tiling arrays:  3 time points in early liver infection (spz, hr24, hr48), and 3 blood stage isolates

first: Cate

last: Speake

first: Tejram

last: Sahu


title: Histone ChIP-chip of adult hippocampus tissue from fetal alcohol exposed mice

status: Public on Sep 18 2014

first: Eric

last: Chater-Diehl

summary: In this experiment, we exposed mice to ethanol injections on postnatal days 4 and 7. We then extracted whole-hippocampus on postnatal day 70. We performed two ChIP-chip experiments on all mice form the same tissue using antibodies against H3K4me3 and H3K27me3. We found alterations in both modifications at many sites, including CTCF motifs of protocadherin genes and imprinted loci. We also found many affect lipid metabolism pathways.

first: E

last: Diehl

first: S

last: Singh


title: CGH analysis of melanomas and germline samples from Braf mutant mouse model

status: Public on Jun 11 2014

city: Manchester

first: Simon

last: Furney

state: Lancashire

address: Wilmslow road

institute: CRUKMI

summary: We investigated copy number alterations in melanomas from two cohorts of Braf mutant mice (UV exposed and no UV exposure) by comparing tumour DNA to germline DNA by array CGH

overall_design: There were 15 tumour samples in each cohort (UV exposed and no UV exposure)

first: Richard

last: Marais


title: Genome-wide analysis of mRNA transcriptomes in dendritic cell and exosome-treated dendritic cell

status: Public on Mar 20 2015

city: Hangzhou City, Zhejiang Province

first: Liangjing

last: Zhou

address: no. 3,QingChun east road,Jianggan District, Hangzhou City, Zhejiang Province

department: Department of General Surgery

institute: Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China

summary:
The present research aimed to demonstrate that pancreatic cancer related miRNAs can be transferred from exosome to dendritic cells and influence mRNA expression, inducing immune tolerance of dendritic cells
.Immature dendritic cells were induced from peripheral blood monocytes and stimulated by exosomes collected from PANC-1 cell culture.Genome-wide mRNA chip were performed in iDC and exosome stimulated iDC to detect the change of mRNA expression level.

overall_design: examination of 2 cells:Immature dendritic cell and exosome-treated dendritic cell

first: Guoping

last: Ding

first: Jionghuang

last: Chen

first: Jianyang

last: Xiang

first: Zhengrong

last: Wu

first: Guixing

last: Jiang

first: Liping

last: Cao


title: CNV analysis of iPS cell lines and H2A.X knockout ES cell

status: Public on Sep 07 2014

city: New Haven

first: Andrew

middle: Zhuo

last: Xiao

state: CT

address: 10 Amistad St

department: Genetics

institute: Yale Stem Cell Center

summary: It is well-known that embryonic stem cells (ESC) are much more sensitive to replication-induced stress than differentiated cells but the underpinning mechanisms are largely unknown. H2A.X, a minor variant of H2A, constitutes only 1-10% of the mammalian genome.  H2A.X plays a well-known for role in the DNA damage response and maintaining stability in the genome, including the regions frequently experiencing replication stress, such as the fragile sites. Intriguingly, several recent studies have reported that H2A.X function is elevated in ESC; and others reported that H2A.X function is provoked during cellular reprogramming (in induced pluripotent stem cells, iPSC), indicating that increased proliferation during iPS may trigger replication stress and the H2A.X DNA damage response.  However, several studies of genomic instability in iPSC led to different conclusions on this important issue. For example, frequent copy number variants (CNV) were reported at the genomic regions sensitive to replication stress, such as the fragile sites. On the other hand, another study reported the lack of genomic instability in mouse iPS clones that are able to generate “all-iPS” animals in tetraploid complementation assays (4N+ iPSC), indicative of a potential link between pluripotency and genome integrity. However, whether if high level genomic instability occurs in the 4N- iPSC iPSC clones at replication stress sensitive regions is unknown.  Moreover, due to the lack of mechanistic insights on genome integrity maintenance, how pluripotency and genome integrity are connected remains elusive. Here we show that H2A.X plays unexpected roles in maintaining pluripotency and genome integrity in ESC and iPSC. In ESC, it is specially enriched at genomic regions sensitive to replication stress so that it protects genome integrity thereat. Faithful H2A.X deposition is critical for genome integrity and pluripotency in iPSC. H2A.X depositions in 4N+ iPSC clones faithfully recapitulate the ESC pattern and therefore, prevent genome instability. On the other hand, insufficient H2A.X depositions in 4N- iPSC clones at such regions lead to genome instability and defects in replication stress response and DNA repair, reminiscent of the H2A.X deficient ESC.

overall_design: In this study, male 129sv/C57 ES cell genomic DNA was used as reference control, to identify CNV sites in iPS cell lines. And also detect H2A.X (-/-) ES cell (129/Sv) CNVs, with the H2A.X(f/f) ES cell DNA (129/Sv) as control. DNA samples were compared on NimbleGen Mouse CGH 3x720K Whole-Genome Tiling Array (Build MM9).

first: Tao

first: Matthias

last: Stadtfeld

first: Zito

last: Tseng

first: Martik

last: Tahmasian

first: Yifei

last: Liu

first: Konrad

last: Hochedlinger


title: Dual Mechanisms by which MiR-125b Represses IRF4 to Induce Myeloid and B cell Leukemias

status: Public on Jun 27 2014

city: Madison

first: Karen

middle: Dyer

last: Montgomery

state: WI

address: 504 S Rosa Rd, Ste 101

department: Cytogenetics

institute: WiCell

summary: The oncomir microRNA-125b (miR-125b) is up-regulated in a variety of human neoplastic blood disorders and constitutive up-regulation of miR-125b in mice can promote myeloid and B cell leukemia. We found that miR-125b promotes myeloid and B cell neoplasm by inducing tumorigenesis in hematopoietic progenitor cells. Our study demonstrates that miR-125b induces myeloid leukemia by enhancing myeloid progenitor output from stem cells as well as inducing immortality, self-renewal, and tumorigenesis in myeloid progenitors. Through functional and genetic analyses, we demonstrated that miR-125b induces myeloid and B cell leukemia by inhibiting IRF4 but through distinct mechanisms; it induces myeloid leukemia through repressing IRF4 at the mRNA level without altering the genomic DNA and induces B cell leukemia via genetic deletion of the gene encoding IRF4.

overall_design: The cancer myeloid (Cd11b+ sorted) and B cells (CD19+ sorted) were harvested from mice that over-express miR-125b.  The genomic DNA was extracted from these cells.  A total of 4 cancer samples (Two myeloid cancer samples and two B cell cancer samples) were analyzed.  As control, genomic DNA from cells harvested from healthy C57bl/6 mice were harvested.

first: Alex

last: So

first: Benjamin

middle: S

last: Nisler

last: Dyer Montgomery


title: ChIP-chip with anti-HP1 from third instar larvae

status: Public on Aug 28 2014

city: Taipei

first: Che-Kun

middle: James

last: Shen

address: 128 Academia Road, Section 2, Nankang

department: Institute of Molecular Biology

institute: Academia Sinica

summary: To investigate how dSETDB1 regulated the genome-wide distribution of HP1 proteins, we performed ChIP-chip assay on the third instar larval lysate from the dSETDB1null mutants in comparison to the wild type.

overall_design: Third instar larvae from the wild type and dSETDB1null mutants were collected. Three independent biological replicates of ChIP with anti-HP1 were performed.

first: Lee

last: Chi-Hua

first: James

last: Che-Kun


title: Comparison of exosomal and cellular miRNA from patients with chronic lymphocytic leukaemia

status: Public on Jul 25 2014

city: Leicester

first: Simon

middle: David

last: Wagner

address: Lancaster Road

department: CSMM

institute: University of Leicester

summary:
Exosomes are secreted into the intercellular space and carry a diverse cargo of proteins, mRNA and miRNA that have important roles in cell-to-cell communication. We found that exosomes from primary human leukaemic B-cells contain a population of miRNAs that has been selected from the general cellular pool to be enriched in miR-323-3p, miR-374b, miR-363 and miR-494. Gene targets of these miRNA are found within the TGFβ pathway, but we noted that CD69, a protein that is essential for the regulation of normal lymphocyte egress from lymph nodes was the top predicted target of miR-363. Utilising luciferase reporter assays we demonstrate that CD69 is a target of miR-363. The interaction between miR-363 and CD69 is functionally important as demonstrated by repression of CD69 expression by a miR-363 mimic in the Jurkat T-cell line.
MicroRNA expression profiles of isolated exosomes and CLL cells cultured on CD154/IL-4 feeder layers for 24 hours were determined using Taqman low-density miRNA (TLDA) arrays.  Patient samples were layered on Ficoll and centrifuged for 20 minutes at 2500 rpm following which the interface layer conatining mononuclear cells was removed. The cells were washed in PBS and cultured on a feeder layer of mouse fibroblasts transfected with human CD154 in the presence of IL-4 (10 ng/ml) for 24 hours MiRNA extracts were made using a miRvana miRNA isolation kit (Applied Biosystems, Paisley, UK), and reverse transcribed using MegaPlex RT Primers and a TaqMan MicroRNA Reverse Transcription Kit (Applied Biosystems).  Equal amounts of RNA were added to each microarray plate. Human microRNA Array (A) plates (containing assays for 377 miRNA) were used (Applied Biosystems, #4398965) and reactions carried out on a 7900HT Real Time PCR system.

overall_design: MiRNA expression was compared in paired samples of chronic lymphocytic leukaemia cells and exosomes utilising Taqman Real-Time PCR.

first: Shaun

last: Willimott


title: Genome-wide gene expression profiling reveals unsuspected molecular alterations in Pemphigus Foliaceus

status: Public on Jan 08 2014

city: Curitiba

first: Danielle

last: Malheiros

state: Paraná

address: Centro Politecnico

country: Brazil

institute: Federal University of Paraná

summary: Pemphigus foliaceus (PF) is a complex autoimmune disease characterized by bullous skin lesions and the presence of antibodies against desmoglein 1. In this study we sought to contribute to a better understanding of the molecular processes in endemic PF, since the identification of factors that participate in the pathogenesis is a prerequisite for understanding its biological basis and may lead to novel therapeutic interventions. CD4+ T lymphocytes are central to the development of the disease. Therefore, we compared genome-wide gene expression profiles of peripheral CD4+ T cells of various PF patient subgroups with each other and with that of healthy individuals. The patients sample was subdivided in three groups: untreated patients with the generalized form of the disease, patients submitted to immunosuppressive treatment, and patients with the localized form of the disease. Comparisons between different subgroups resulted in 135, 54 and 64 genes differentially expressed. These genes are mainly related with lymphocyte adhesion and migration, apoptosis, cellular proliferation, cytotoxicity and antigen presentation. Several of these genes were differentially expressed when comparing lesional and uninvolved skin from the same patient. The chromosomal regions 19q31 and 12p13 concentrate differentially expressed genes and are candidate regions for PF susceptibility genes and disease markers. Our results reveal genes involved in severity, potential therapeutic targets and previously unsuspected processes involved in the pathogenesis. Besides, this study adds original information that will contribute to the understanding of PF’s pathogenesis and of the still poorly defined in vivo functions of most of these genes.

overall_design: 24 samples were analyzed, no replicates. Three groups of patients were analyzed: (1) patients with the generalized form of the disease and without treatment; (2) patients with the generalized form undergoing immunosuppressive therapy (prednisone); and (3) patients with the localized form of the disease and without treatment. A fourth group consisted of healthy control subjects.

first: Rodrigo

middle: A

last: Panepucci

first: Ana

last: Roselino

first: Amélia

last: Araújo

first: Marco

last: Zago

first: Maria

middle: L

last: Petzl-Erler