title: Global transcriptome analysis of fungal genes affected by a novel antifungal agent KR-72, a 13-(4-isopropylbenzyl)berberine derivative   a 13-(4-isopropylbenzyl)berberine derivative

status: Public on Feb 26 2014

city: Seoul

first: Hyojeong

last: Kwon

address: Yonsei street

country: South Korea

institute: Yonsei university

summary: A 13-(4-isopropylbenzyl)berberine derivative (named KR-72) was synthesized and examined for antifungal activities against various human pathogenic fungi. The synthesized compound exhibited remarkably enhanced antifungal activity than berberine and berberrubine. Regardless of the potent antifungal activity of KR-72, its mode of action and the physiological impacts of the drug on fungal metabolism remain elusive. In this study, we performed the DNA microarray-based transcriptome analysis to identify KR-72 responsive genes and employed reverse genetics approaches to characterize their functions in Cryptococcus neoformans, which causes fatal meningoencephalitis in humans. First, KR-72 treatment altered in remodeling of transcriptome profiles in C. neoformans. Genes involved in translation and transcription were mostly upregulated, while those involved in cytoskeleton, intracellular trafficking, lipid and carbohydrate metabolism and energy production were downregulated. Supporting this, KR-72 has a strong synergistic effect with a calcineurin inhibitor FK506, while it has an antagonistic effect with polyene drug. Finally, KR-72 treatment promoted expression of ECM16, NOP14, HSP10, and MGE1, which we proved to be essential for the growth of C. neoformans. Among them, KR-72 mediated induction of MGE1 also appeared to hamper the viability of C. neoformans, potentially through impaired cell cycle or DNA repair system. This study will proposed mode of action for KR-72.

overall_design: The six slides of Cryptococcus_neoformans 3X20K are used in this analysis, 3 biological replicate experiments are performed, total RNAs are extracted under 2 conditions (with or without treatment of KR-72 with H99 (H99 Wild type strain (Cryptococcus neoformans var. grubii serotype A). We use the KR-72 non-treated RNAs from this experiment as a control RNA. We use Cy5 as Sample dye and Cy3 as a control dye.

first: Soohyun

last: Bang

first: Hyun

last: Hwang

first: Ki

middle: D

last: Park

first: Sung

last: Kim

first: Yong-Sun

last: Bahn


title: M. tuberculosis H37Rv: mutant expressing foreign peptide SL3 Vs control H37Rv

status: Public on Apr 10 2014

city: New Delhi

first: Sachin

middle: Kumar

last: Samuchiwal

address: Aruna Asaf Ali Marg,

department: Recombinant Gene Products Group

country: India

institute: International Centre for Genetic Engineering and Biotechnology (ICGEB)

summary: Transcriptional profiling of M.tb H37Rv cells comparing control wild type H37Rv with H37Rv cells electroporated with constitutive expression plasmid pVV16 expressing ESAT-6 binding peptide SL3. The expression of SL3 makes H37Rv less virulent during ex vivo and BalB/c mice infections, sequesters ESAT-6 inside M.tb cells and cause severe defects in mycobacterial morphology. Goal was to determine the effects of SL3 expression on global H37Rv gene expression.

overall_design: Two color Experiment,Organism: Mycobacterium Tuberculosis, ilife Discoveries designed Custom Mycobacterium tuberculosis on  8x15k GE Microarray. Two-condition experiment, H37Rv vs. H37Rv/SL3. Biological replicates: 2 biological control H37RV replicates labelled with Cy3, 2 SL3 biological expressing replicates labelled with Cy5.

middle: K

first: Ashish

middle: C

last: Trivedi

first: Anand

last: Ranganathan


title: ORC binding profile in Candida albicans

status: Public on Feb 13 2014

city: Minneapolis

first: Hung-Ji

last: Tsai

state: MN

address: 6-170 MCB, 420 Washington Ave. SE

country: USA

institute: University of Minnesota

type: Genome binding/occupancy profiling by genome tiling array

summary: Map ORC binding sites to identify replication origins in C. albicans by using polyclonal ORC antibodies (gift from Stephen Bell Lab).  Due to the unsynchronized nature of Candida cells, log-phase cultures were taken to perfoem ChIP-chip experiments to find the genome-wide ORC binding sites.

overall_design: ChIP-chip experiments from log-phase C. albicans culture. 7 different unsynchronized log-phase cultures as replicates.

first: Joshua

last: Baller

first: Amnon

last: Koren


title: Differential gene expression in 2 days old zebrafish after glucocerebrosidase (GBA1) morpholino-mediated knockdown

status: Public on Feb 07 2014

city: PADOVA

first: Enrico

last: Moro

address: Via U. Bassi 58/B

department: Molecular Medicine

country: Italy

institute: University of Padova

summary: Gene expression signature was explored to identify gene targets regulate by dysfunctional glucocerebrosidase function. We found 131 upregulated genes and 63 downregulated genes. Some of the most upregulated (PON3, PLOD1) and downregulated (gpx-1b and complemewnt c9) genes  were analyzed by q-PCR demonstrating the correct differential gene expression signature among control and morpholino-microinjected fish.

overall_design: Knockdown of GBA1 function was measured in 4 biological replicates at 2 days post fertilization after microinjection of GBA1 morpholino and control morpholino at one -cell stage embryos.

first: Ilaria

last: Zancan

first: Stefania

last: Bellesso

first: Mirella

last: Filocamo


title: Expression data from Pseudomonas putida KT2440: Fuelling the central metabolism with aromatic compounds

status: Public on Feb 01 2014

city: Hannover

first: Sarah

last: Frank

address: Carl-Neuberg-Str. 1

department: Clinic for Paediatric Pneumology and Neonatology

country: Germany

institute: Medical School Hannover

summary: We used Progenika oligonucleotide arrays to monitore the gene expression of P. putida during carbon source stimulus experiments.

overall_design:
After ensuring steady state conditions on benzoate, the stimuli were introduced by changing the carbon source from benzoate to glucose, from glucose to fructose and from fructose to benzoate, respectively. The single stimuli were monitored over a time period from 10 to 120 minutes after changing the carbon source by three representative timepoints. Moreover, the steady state conditions were compared among each other.

Supplementary file: Individual normalized signal intensity VALUES for each channel of each array are provided in the FullNormalizedMatrix.txt file.

first: Suresh

last: Sudarsan


title: Analysis of mature miRNA levels in the context of CHO cell proliferation

status: Public on Jan 07 2014

city: Vienna

first: Matthias

last: Hackl

state: Austria

address: Leberstrasse 20

country: Austria

institute: TAmiRNA GmbH

summary: mature microRNA transcripts were analyzed in 5 CHO cell lines growing at different proliferation rates. The goal was to identify microRNAs that correlate positively or negatively with CHO proliferation rates.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: A common reference design was chosen, where all samples were hybridized against a pool of all RNA samples.

first: Vaibhav

last: Jadhav

first: Gerald

last: Klanert

first: Michael

last: Karbiener

first: Marcel

last: Scheideler

first: Johannes

last: Grillari

first: Nicole

last: Borth


title: Global microRNA expression profiling of serum from healthy controls vs serum from ovarian cancer patients

status: Public on Feb 05 2014

city: Bochum

first: Stephan

middle: A

last: Hahn

address: Universitaetsstrasse 150

department: MGO

institute: Ruhr-University Bochum

summary: Global microRNA expression profiling of serum were collected using Agilent miRNA microarrays (G4471A Human, Amadid 29297, Sanger 14)  carrying 887 individual human miRNA probes. Two different sources of RNA were analyzed: serum from healthy controls (N=5) and patients with ovarian carcinoma (CA, n=5)

overall_design: Two conditions (CA, N), each condition is represented by 5 biological replicates

first: Jan

last: Kuhlmann


title: Phanerochaete chrysosporium gene expression in different media

status: Public on Jan 15 2014

city: Madison

first: Dan

last: Cullen

state: WI

address: One Gifford Pinchot Dr

institute: UW/FPL

summary: Transcript profiles of Phanerochaete chrysosporium grown on different substrates were analyszed. Array design was based on the DoE's Joint Genome Institute's gene models for P. chrysosporium version s. The research goal is to identify genes essential for lignocellulose depolymerization.

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 RP78 (Forest Mycology Center, Forest Products Lab) grown in Highley’s basal salt medium containing 0.5% (w/v) wiley milled (1 mm mesh) wood. For each of the three samples (hybrid line P717, transgenic line 82, transgenic line 64) multiple branches were harvested, debarked and dried.  Each two-liter Erlenmeyer flask contained 250 ml medium and was inoculated with approximately 10e7 P. chrysosporium spores scraped from the surface of YMPG agar.  Cultures were incubated for five days on a rotary shaker (150 RPM) at 37° C.  For RNA, mycelium from triplicate cultures was collected by filtration through Miracloth (Calbiochem, EMD Biosciences, Gibbstown, NJ), squeeze dried and snap frozen in liquid nitrogen. Pellets were stored at -80 °C until use. For mass spectroscopic analysis, culture filtrates were stored at -20 before use. P. chrysosporium Roche NimbleGen array design was similar to GPL8022, but repetitive elements were removed and 25 gene targets were added. The latter corresponded to open reading frames for which peptides had been detected in culture filtrates. Culture condition compariso:  Total RNA was purified from frozen mycelial pellets, converted to Cy3 labeled cDNA, hybridized to microarrays, and scanned as described by Vanden Wymelenberg et al 2010 (Appl Enviro Microbiol 76:3599-3610). The 9 arrays used in these experiments were scanned on the Axon4000B Scanner (Molecular Dynamics) and data extracted using NimbleScan v2.4. Quantile normalization and robust multi-array averaging (RMA) were applied to the raw data using DNASTAR ArrayStar v4 (Madison, WI). Expression levels are based on log2 signals and significant differences in expression were determined using the Moderated t-Test with the FDR  threshold set at P<0.05.
triplicate cultures for each substrate (wood genotype); The three wood substrates are lines 64, 82 and P717; three different media, and each medium was represented by three flasks (reps).


title: Low-level Gamma Ray Exposure to Rice Seedlings in Iitate Village (Fukushima) Activates Self-defense Responses Unraveled by DNA Microarray Analysis

status: Public on Dec 07 2013

city: Tsukuba

first: RANDEEP

last: RAKWAL

state: Ibaraki

address: 1-1-1 Tennodai

department: Institute of Health and Sport Sciences

country: Japan

institute: University of Tsukuba

summary: In the summer of 2012, one year after the 3.11 accident at Fukushima Daiichi nuclear power plant following the Great Tohoku Earthquake, a project was initiated to examine the effects of low-level gamma radiation on rice plants. The site of the experiment was the highly contaminated Iitate village in Fukushima prefecture of Japan. The basic experimental strategy was to expose healthy rice seedlings to continuous low-dose gamma radiation and examine the morphological and molecular genetic changes therien. Selected gene expression profiles of internal control, DNA replication/repair, oxidative stress, photosynthesis, and defense/stress functions were examined by semi-quantitative RT-PCR. Results revealed that low-level gamma radiation affects the expression of numerous genes, in particular showing the early (6 h) induction in DNA repair/damage-related genes and the late (72 h) induction of a previously described marker gene for defense/stress responses. Based on these results, which confirmed our data from preliminary experiments using detached rice leaves for radiation exposure, we proceeded for DNA microarray analysis. Using the established dye-swap approach, we analyzed the differentially expressed genes at 6 and 72 h time points using a whole rice genome 4 x 44 K custom chip. Obtained results showed that exposure to low-level gamma radiation differentially regulated 4481 (induced) and 3740 (suppressed) and 2291 (induced) and 1474 (suppressed) rice leaf genes at 6 and 72 h post-exposure, respectively, by at least two-fold changes. MapMan bioinformatics tool was also used to produce diagrams of the potential pathways, based on the input gene expression data of highly changed genes, operating downstream of the gamma radiation perception by rice plant.Inventory of a large number of gamma radiation-responsive genes in leaves provide new information and increased knowledge on novel regulatory processes in rice.

overall_design: The highly contaminated Iitate Farm (ITF), which is located 31 Km from the damaged nuclear power plant and having a background radiation level over 100 times (~ 5 microSv/h) than normal, was the designated place for the re-examination of low-level gamma radiation experiments using rice as a model system. As our group had a decade of experience and data on the effects of gamma radiation on leaf segments, the experimental was designed in such a way so as to expose whole rice plants to gamma radiation being emitted from the contaminated ground and examine the morphological and molecular genetic changes in the leaves under a dose-dependent manner.

first: Gohei

last: Hayashi

first: Junko

last: Shibato

first: Tetsuji

last: Imanaka

first: Manabu

last: Fukumoto

first: Kyoungwon

last: Cho

first: Akihiro

last: Kubo

first: Shoshi

last: Kikuchi

first: Seiji

last: Shioda

first: Shinzo

last: Kimura

first: Shoji

last: Ozawa

first: Satoshi

last: Fukutani

first: Satoru

last: Endo

first: Katsuki

last: Ichikawa

first: Ganesh

last: Agrawal

first: Randeep

last: Rakwal


title: CCAAT/enhancer-binding protein alpha target genes in myeloid progenitor cells uncovered by chromatin IP

status: Public on Dec 01 2013

city: Rotterdam

first: Erdogan

last: Taskesen

address: dr. molewaterplein 50

country: Netherlands

institute: Erasmus University Medical Center (EMC)

summary: CCAAT/enhancer-binding protein alpha (C/EBPα) is a lineage-specific transcription factor that directs development of granulocytes. To obtain insights into the genome-wide transcriptome of wild type C/EBPα, we have performed chromatin immunoprecipitation on DNA promoter microarrays (ChIP-chip) in the murine 32D myeloid progenitor cell line. These cells expressed an estradiol-inducible form of wild-type C/EBPα.

overall_design: In the murine 32D myeloid progenitor cell line, expressing either an estradiol-inducible form of wild-type C/EBPα. (C/EBPα-ER, n=3, replicates), or as a control ER (n=2, replicates), we have performed chromatin immunoprecipitation on DNA promoter microarrays (ChIP-chip) after 4 hours of estradiol incubation.

first: Renee

last: Beekman

first: Jeroen

last: de Ridder

first: Bas

middle: J

last: Wouters

first: Justine

last: Peeters

first: Ivo

last: Touw

first: Marcel

last: Reinders

first: Ruud

last: Delwel


title: Mutant-CCAAT/enhancer-binding protein alpha target genes in myeloid progenitor cells by chromatin IP

summary: CCAAT/enhancer-binding protein alpha (C/EBPα) is a lineage-specific transcription factor that directs development of granulocytes. To obtain insights into the genome-wide transcriptome of mutant C/EBPα, we have performed chromatin immunoprecipitation on DNA promoter microarrays (ChIP-chip) in the murine 32D myeloid progenitor cell line. These cells expressed an estradiol-inducible form of mutant C/EBPα.

overall_design: In the murine 32D myeloid progenitor cell line, expressing an estradiol-inducible form of C-terminal mutant of C/EBPα. (n=2, replicates). We have performed chromatin immunoprecipitation on DNA promoter microarrays (ChIP-chip) after 4 hours of estradiol incubation.


title: microRNA profiling in pediatric AML

status: Public on Jan 01 2014

first: Maarten

last: Fornerod

address: Dr. Molewaterplein 50

department: Cell Biology

institute: ErasmusMC

summary: MicroRNAs (miRNAs) play a pivotal role in the regulation of hematopoiesis and development of leukemia. Great interest emerged in modulating miRNA expression for therapeutic purposes. In order to identify miRNAs, which specifically suppress leukemic growth of AML with t(8;21), inv(16) or MLL-rearrangement by inducing differentiation, we conducted a miRNA expression profiling in a cohort of 90 cytogenetically characterized, de novo pediatric AML cases. Four miRNAs, specifically downregulated in MLL-rearranged, t(8;21) or inv(16) AMLs, were characterized by their tumor suppressive properties in cell lines representing those respective cytogenetic groups. Among those, forced expression of miR-9 reduced leukemic growth and induced monocytic differentiation of t(8;21) AML cell lines in vitro and in vivo. The tumor suppressive functions of miR-9 were specifically restricted to AML cell lines and primary leukemic blasts with t(8;21). On the other hand, these functions were not evident in AML blasts from patients with MLL-rearrangements. We showed that miR-9 exerts its effects through the cooperation with let-7 to repress the oncogenic LIN28B/HMGA2 axis. Thus, miR-9 is a tumor suppressor-miR which acts in a stringent cell context-dependent manner.

overall_design: In order to identify miRNAs, which specifically suppress leukemic growth of AML with t(8;21) (n=21), inv(16) (n=17) or MLL-rearrangement (n=35) by inducing differentiation, we conducted a miRNA expression profiling in a cohort of 90 cytogenetically characterized, de novo pediatric AML cases, which also included 12 t(15;17) and 5 t(7;12) samples.

first: Stephan

last: Emmrich

first: Jenny

middle: E

last: Katsman-Kuipers

first: Kerstin

last: Henke

first: Mona

last: El Khatib

first: Razan

last: Jammal

first: Felix

last: Engeland

first: Ferhat

last: Dasci

first: C

middle: M

last: Zwaan

first: Monique

middle: L

last: den Boer

first: Lonneke

last: Verboon

first: Jan

last: Stary

first: André

last: Baruchel

first: Valerie

last: de Haas

first: Astrid

last: Danen-van Oorschot

first: Rob

last: Pieters

first: Dirk

last: Reinhardt

middle: H

last: Klusmann

first: Marry

last: van den Heuvel-Eibrink


title: Inhibition of proliferation and induction of autophagy by atorvastatin in PC3 prostate cancer cells correlate with downregulation of Bcl2 and upregulation of miR-182 and p21 [miRNA expression]

status: Public on Sep 30 2013

city: Northbrook

first: Michael

last: Falduto

state: IL

address: 1808 Janke, Unit M

institute: GenUs BioSystems, Inc.

summary: The epidemiologic association between statin use and decreased risk of advanced prostate cancer suggests that statins may inhibit prostate cancer development and/or progression.  Studies were performed to determine the effects of a model statin, atorvastatin (ATO), on the proliferation and differentiation of prostate cancer cells, and to identify possible mechanisms of ATO action.  ATO inhibited the in vitro proliferation of both LNCaP and PC3 human prostate cancer cells in dose-dependent fashion.  The greater inhibitory activity of ATO in PC3 cells was associated with induction of autophagy in that cell line, as demonstrated by increased expression of LC3-II.  miR-182 was consistently upregulated by ATO in PC3 cells, but not in LNCaP cells.  ATO upregulation of miR-182 in PC3 cells was p53-independent and was reversed by geranylgeraniol.  Transfection of miR-182 inhibitors decreased expression of miR-182 by >98% and attenuated the antiproliferative activity of ATO.  miR-182 expression in PC3 cells was also increased in response to stress induced by serum withdrawal, suggesting that miR-182 upregulation can occur due to nutritional stress.  Bcl2 and p21 were identified to be potential target genes of miR-182 in PC3 cells. Bcl2 was downregulated and p21 was upregulated in PC3 cells exposed to ATO.  These data suggest that miR-182 may be a stress-responsive miRNA that mediates ATO action in prostate cancer cells.

overall_design: Gene and miRNA expression in two prostate cancer cell lines treated with Atorvastatin vs. untreated control.

first: Xinjian

last: Peng

first: Wenping

last: Li

first: Liang

last: Yuan

first: Rajendra

middle: G

last: Mehta

first: Levy

last: Kopelovich

first: David

last: McCormick


title: Identification of c-Rel and RelA binding regions in stimulated EL4 cells

status: Public on Dec 29 2013

city: Bruce

first: Kristine

last: Hardy

state: ACT

address: University of Canberra

country: Australia

institute: University of Canberra

summary:
c-Rel and RelA are members of the NF-kappaB family of transcription factors. They both have important roles in T cell activation. To discover where in the genome c-Rel and RelA bind and hence which genes they may directly target, we used ChIP-chip with EL4 cells stimulated with phorbol ester (PMA) and Ionomycin.
We have identified regions in EL4 cells (background strain: C57BL/6N) activated for 2h or 8h by PMA and Ionomycin, that bind the transcription factors c-Rel and RelA.

overall_design: Immunoprecipitated samples from EL4 cells stimulated with PMA and ionomycin for 2 h and 8 h with antibodies against RelA or c-Rel respectively were used for ChIP-on-chip experiments. In addition, samples from total input and mock immunoprecipitation were used as controls. Biological triplicates were used.

first: Seungsoo

last: Lee


title: crl; Transcriptome comparison of the crl mutant and CDT1-RNAi line

status: Public on Sep 01 2013

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

country: France

institute: INRA

summary:
au13-04_cdtbis; cdt1_bis
crl mutants and CDT1-RNAi lines have very similar macroscopic phenotypes as well as identical defects in plastid division and biogenesis. Our goal wwas to determine how much of these similarities originated from similar alterations of gene expression.

Plantlets of crl mutant and CDT1-RNAi lines were grown in vitro on MS1/2 medium for 14 days. CDT1-RNAi lines were compared to the corresponding wild-type (Ws), whereas crl mutants were compared to their wild-type siblings and are in the Col0 ecotype.

overall_design: 4 dye-swap - normal vs rnai mutant comparaison, normal vs transgenic comparaison

first: Sandrine

last: Balzergue

first: Ludivine

last: Taconnat

first: Cécile-

last: Raynaud

first: Marie-Laure

last: Martin-Magniette


title: Comparison of gene expression of miltefosine responsive Vs miltefosine unresponsive  Leishmania donovani promastigotes

status: Public on Aug 05 2013

city: Guwahati

first: Vikash

last: Dubey

state: Assam

address: Room No. 102

department: Department of Biotechnology

institute: Indian Institute of Technology Guwahati

summary: The current study aims to study change in gene expression profile of miltefosine resistance L. donovani with respect to miltefosine responsive L. donovani.

overall_design: Agilent one-color experiment,Organism: Leishmania donovani, Microarray GeneExpression 8x15k designed by Genotypic Technology Private Limited. (AMADID: 035638)

first: Mousumi

last: Das

first: Prakash

last: Saudagar


title: BioTile Identification of Differentially Methylated Regions in Tiling Microarray Data

status: Public on May 24 2013

city: Baltimore

first: Jerry

last: Guintivano

state: MD

address: 720 Rutland Avenue, Ross 1068

institute: Johns Hopkins University

summary: This submission includes simulated data generated to test the BioTile algorithm's capability of identifying differentially methylated regions (DMR) located within an actual tiling array dataset.

overall_design: The data submitted was generated in silico to closely resemble DNA methylation profiles using Affymetrix Mouse Promoter 1.0R Tiling arrays. This simulated dataset of 40 arrays was generated using the "rnorm" function in R to create probe-wise distributions with the same mean and variance as our previously measured dataset (GSE43460).

first: Michal

last: Arad

first: Todd

last: Gould

first: Zachary

last: Kaminsky


title: Genotypic and Phenotypic Versatility of Aspergillus flavus during Maize Exploitation

status: Public on Sep 19 2013

city: Genoa

first: Paolo

last: Uva

address: Via Gerolamo Gaslini, 5

institute: IRCCS Istituto Giannina Gaslini

summary: Several are the inputs which are able to modulate mycotoxin synthesis. In particular, when a fungus receives an external stimulus reacts by activating, through a quite well-defined signal cascade, an evident switch in its lifestyle. This profound change is also due to the activation of global gene regulators and, in particular, of transcription factors able to switch on the mycotoxin gene clusters expression. Aflatoxins (AF) are harmful carcinogenic compounds produced mainly by Aspergillus flavus and A. parasiticus. AF are produced during the contamination of maize kernels into the field, even if their role in phyto-toxicity is not yet assessed. Nevertheless, AF biosynthesis is tightly regulated by host-derived signals. Recently, the nature of some of these signals have been elucidated. In particular, a role in susceptibility and resistance of maize to A. flavus contamination has been assigned to some plant oxylipins. These findings draw a scenario in which a complex interplay is under way between A. flavus and maize. For uncovering all the implications of this cross-talk we decide to follow a holistic approach. In particular, we designed experimental conditions aimed to mimic the different phases of A. flavus infection cycle on maize and then by performing a microarray analysis on the harvested mycelia. The microarray data set has been processed for performing the differential expression analysis of almost 14000 gene probes, the pathway analysis based on the gene ontology and inter pro annotations, the secondary metabolites cluster co-expression analysis and an identification of groups of co-expressed neighbor genes, possibly associated with production of secondary metabolites.

platform_organism:
Zea mays
Aspergillus flavus
Aspergillus oryzae

overall_design: Analysis of 12 microarrays monitoring gene expression of Aspergillus flavus over various growth conditions

first: M

last: Reverberi

last: Punelli

first: V

last: Scala

last: Scarpari

first: P

first: W

middle: I

last: Mentzen

first: A

last: Dolezal

first: C

last: Woloshuk

first: F

last: Pinzari

last: Fabbri

last: Fanelli

first: G

last: Payne


title: NeuCode metabolic labeling reveals a high correlation between mRNA and protein abundance during salt adaptation in S. cerevisiae.

status: Public on Dec 21 2013

first: Audrey

last: Gasch

address: 3456 Biotechnology Center 425G Henry Mall

institute: University of Wisconsin-Madison

summary: Transcriptome profiling of yeast strains responding to 0.7M NaCl treatment for 30 or 60 minutes. This study identified affected genes under both conditions tested. Transcript and protein changes were compared to determine mRNAs contribution to protein levels during salt acclimation.

overall_design: Two-color fluorescence arrays reporting on mRNA abunance in strains before and at 30 min or 60 min after a shock with 0.7M NaCl, hybridized to yeast tile-genome Nimblegen arrays

first: Anna

last: Larson

first: Matt

last: MacGilvray

first: Josh

last: Coon


title: Circulating U2 small nuclear RNA fragments as a novel diagnostic biomarker for pancreatic and colorectal adenocarcinoma

status: Public on Jul 01 2013

first: Stephan

last: Hahn

summary: Global microRNA expression profiling of serum were collected using Agilent miRNA microarrays (G4471A Human, Amadid 29297, Sanger 14)  carrying 887 individual human miRNA probes. Two different sources of RNA were analyzed: serum from NMRI-nu/nu mice carrying a xenograft tumor derived from human primary pancreatic ductal adenocarcinomas (CA, n=6) and serum from tumor free control NMRI-nu/nu mice (N, n=6)

overall_design: Two condition (CA, N), each condition is represented by 6 biological replicates


title: Estrogen Induced DNA Methylation Changes in Mouse Hippocampus

first: Jerry

last: Guintivano

type: Methylation profiling by genome tiling array

summary: Estrogen, specifically estradiol, has been shown to mediate DNA methylation changes at mutiple locations downstream of estrogen response elements (EREs). We identified differentially methylated regions associated with long-term estradiol exposure in the hippocampus of C57BL/6J mice.

overall_design: Hippocampus was collected from ovariectomized (OVX) C57BL/6J mice treated with estradiol (n=5) and vehicle controls (n=5). Genomic DNA was extracted and treated with methylation sensitive restriction enzymes HpaII and HinP1I to enrich for the unmethylated fraction. This fraction was interrogated using the Affymetrix GeneChip®  Mouse Tiling Promoter 1.0R Array

first: Michal

last: Arad

last: Gould

last: Kaminsky


title: Dexamethasone Acutely Down-regulates Genes Involved in Steroidogenesis in Stallion Testes

status: Public on May 01 2013

city: College Station

first: Nancy

last: Ing

state: TX

department: Animal Science

institute: Texas A&M University

summary: Three stallions were treated with 0.1 mg/kg dexamethasone i.v. while three control stallions received an equivalent volume of saline. Serum testosterone dropped 60% in treated stallions at 12 h post-injection. Testes were collected 12 h post-injection and assessed for differential gene expression.

overall_design:
Adult stallions were acclimated to the clinic over a 10 day period, then treated 12 h prior to collection of testes.
Differential gene expression in treated vs. control stallion testes


title: Differences in miRNA Detection Levels are Technology and Sequence Dependent [Agilent array]

status: Public on Mar 01 2013

city: Rehovot

first: Dena

last: Leshkowitz

department: Bioinformatics Unit, Life Sciences Core Facilities

country: Israel

institute: Weizmann Institute of Science

summary: We undertook an integrative technological approach to compare miRNA detection capability of three high-throughput commercial platforms.

overall_design: We artificially introduced human precursor, 2’-O-methyl modified and mature spiked-in miRNAs in a controlled fashion into native human placenta total RNA.

first: Shirley

last: Horn-Saban

first: Yisrael

last: Parmet

first: Ester

last: Feldmesser


title: Expression data from MCF7 Scrambled and SIM2si cells

status: Public on Feb 08 2013

first: Kelly

last: Scribner

state: Texas

address: 448 TAMU

department: VIBS

summary:
MCF7 breast cancer cells are a luminal-type breast cancer with moderate native levels of SIM2s.  To determine effects of SIM2s on tumor progression, cells were stably transduced with SIM2si shRNA to knockdown expression, inducing an EMT effect.  Microarray analysis was performed to determine genetic pathways involved in this phenotype.
The coordination of cellular metabolism is a key factor in the progression of ductal carcinoma in situ (DCIS) to invasive ductal carcinoma (IDC).  Pathways regulating the balance between oxidative phosphorylation and glycolysis are unclear.  We have found that transcription factor Singleminded-2s (SIM2s), commonly lost with breast cancer progression, contributes to metabolic regulation by controlling glycolytic flux and cellular senescence.  Through promotion of p21 and cellular senescence, SIM2s decreases glycolytic enzyme activity and promotes oxidative phosphorylation in breast cancer.  These, coupled with increased autophagy and ROS, inhibit tumor growth and metastasis.
We use microarrays to detail the global gene programming changes that occur with loss of SIM2s gene expression.

overall_design: Scrambled and SIM2si cells were grown in triplicate for  RNA extraction and hybridization on Amersham microarrays.


title: Stemness-related factor Sall4 interacts with transcription factors Oct-3/4 and Sox2 and occupies Oct-Sox elements in mouse embryonic stem cells

status: Public on Dec 28 2012

city: Kyoto

first: Nobuyuki

last: Tanimura

address: Yoshida-Konoe-cho, Sakyo-ku

department: Graduate School of  Biostudies

institute: Kyoto University

summary: A small number of transcription factors, including Oct-3/4 and Sox2, constitute the transcriptional network that maintains pluripotency in embryonic stem (ES) cells. Previous reports suggested that some of these factors form a complex that binds the Oct-Sox element, a composite sequence consisting of closely juxtaposed Oct-3/4-binding and Sox2-binding sites. However, little is known regarding the components of the complex. In this study, we show that Sall4, a member of the Spalt-like family of proteins, directly interacts with Sox2 and Oct-3/4. Sall4 in combination with Sox2 or Oct-3/4 simultaneously occupies the Oct-Sox elements in mouse ES cells. Sall4 knockdown led to differentiation of ES cells. Overexpression of Sall4 in ES cells increased reporter activities in a luciferase assay when the Pou5f1- or Nanog-derived Oct-Sox element was included in the reporter. Microarray analyses revealed that Sall4 and Sox2 bound to the same genes in ES cells significantly more frequently than expected from random coincidence. These factors appeared to bind the promoter regions of a subset of the Sall4- and Sox2-double-positive genes in precisely similar distribution patterns along the promoter regions, suggesting that Sall4 and Sox2 associate with such Sall4/Sox2-overlapping genes as a complex. Importantly, gene ontology analyses indicated that the Sall4/Sox2-overlapping gene set is enriched for genes involved in maintaining pluripotency. Sall4/Sox2/Oct-3/4-triple-positive genes identified by referring to a previous study identifying Oct-3/4-bound genes in ES cells were further enriched for pluripotency genes than Sall4/Sox2-double-positive genes. These results demonstrate that Sall4 contributes to the transcriptional network operating in pluripotent cells, together with Oct-3/4 and Sox2.

overall_design: ChIP-on-chip experiments using anti-Sall4 or anti-Sox2 antibody were performed.

first: Motoki

last: Saito

first: Miki

last: Ebisuya

first: Eisuke

last: Nishida

first: Fuyuki

last: Ishikawa


title: Met synergizes with p53 loss to induce mammary tumors that possess features of claudin-low breast cancer (miRNA expression data).

status: Public on Mar 04 2013

city: St. Louis

first: Robert

last: Lesurf

state: MO

address: 4444 Forest Park Ave

department: McDonnell Genome Institute

institute: Washington University in St. Louis

summary: miRNA profiling of normal and tumorigenic mouse mammary tissue. Mouse genotypes consist of wildtype, MMTV-Met, MMTV-Met;Trp53fl/+;Cre, and Trp53fl/+;Cre.

overall_design: One-color design. Samples consist of 2 normal tissues, 7 MMTV-Met tumors, 8 MMTV-Met;Trp53fl/+;Cre tumors, and 8 Trp53;Cre tumors.

first: Jennifer

last: Knight

first: Dushanthi

last: Pinnaduwage

first: yan

last: Davis

first: Sadiq

last: Saleh

first: Dongmei

last: Zuo

first: Hong

last: Zhao

first: Monica

last: Naujokas

first: Naila

last: Chugthai

first: Jason

last: Herschkowitz

first: Aleix

last: Prat

first: Anna

last: Mulligan

first: William

last: Muller

last: Cardiff

first: Jeffrey

last: Gregg

first: Irene

last: Andrulis

first: Michael

last: Hallett

first: Morag

last: Park


title: The syp locus of Vibrio salmonicida is necessary for biofilm formation and is regulated by the quorum sensing transcriptional regulator LitR

status: Public on Dec 19 2012

city: Tromsoe

first: Espen

middle: Mikal

last: Robertsen

address: Breivika

department: Chemistry

country: Norway

institute: University of Tromsoe

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

overall_design: Refer to individual Series


title: Integrative genomic characterization of oral squamous cell carcinoma identifies frequent somatic drivers (microRNA)

status: Public on Jan 01 2013

city: Houston

first: Jiexin

last: Zhang

address: 1515 Holcombe Blvd

department: Bioinformatics & Computational Biology

institute: UT MD Anderson Cancer Center

summary:
Oral cavity squamous cell carcinoma (OSCC) is a disease with extensive morbidity and mortality and few useful molecular targets.
Multiplatform integrated genomic analysis was performed in order to identify genomic drivers and molecularly discernible tumor subtypes.
mRNA, miRNA and methylation data are all submitted to GEO

overall_design: We measured microRNA expression of 43 OSCC cases with Agilent Human miRNA microarray rel12.0

first: Curtis

middle: R

last: Pickering

first: Mitchell

last: Frederick

middle: N

last: Myers


title: V. salmonicida wild type strain LFI1238 and isogenic DlitR mutant grown as statical biofilm in SWT medium

summary: Quorum sensing (QS) is a cell density regulated communication system that bacteria use to coordinate activities, including biofilm formation, involved in colonization and pathogenesis. We have previously shown that inactivation of the QS master regulator LitR attenuates the Vibrio (Allivibrio) salmonicida strain LFI1238 in a fish model. In this work we show that LFI1238 as well as a panel of naturally occurring V. salmonicidia strains are poor biofilm producers. Inactivation of litR strongly enhances medium and temperature dependent adhesion, rugose colony morphology and biofilm formation. Chemical treatment and scanning electron microscopy of the biofilm identified an extracellular matrix consisting mainly of protein filaments and polysaccharides. Further, microarray analysis of planktonic and biofilm cells identified a number of genes regulated by LitR, and among these were homologues of the Vibrio fischeri symbiosis polysaccharide (syp) genes. Disruption of syp alleviated the different phenotypes regulated by LitR in V. salmonicida. Hence, LitR is a repressor of syp expression that is necessary for rugose colony morphology, adhesion and biofilm formation, three phenotypes of the DlitR mutant that are expressed at temperatures below 12ºC. The DlitR mutant mimics low cell density behavior suggesting that these phenotypes are important during the initial steps of colonization. Although the syp operon in V. salmonicida shows identical gene synteny to the one in the squid symbiont V. fischeri, its regulation is probably more related to vibrio polysaccharide (vps) expression in the human pathogenic Vibrio cholera which is controlled by the LitR homologue HapR.

overall_design: V. salmonicida wild type strain LFI1238 (control) and the isogenic DlitR mutant were grown as statical biofilm in SWT medium, at 4°C and harvested after 72 hours. Biological replicates for each sample: 4 wild type, 4 DlitR mutant (including one dye swap), independently grown and harvested. One replicate per array.

first: Hilde

last: Hansen

first: Maria

last: Ronessen

first: Ane-Mohn

last: Bjelland

first: Espen-Mikal

first: Nils-Peder

last: Willassen


title: Microarray gene expression profiling in central neurocytomas

status: Public on Feb 19 2013

city: Lyon

first: jacques

last: champier

address: rue Guillaume Paradin

department: neuroonology

summary: Microarray gene expression profiling of central neurocytomas (CNs). Comparison between neurocytoma, pineocytoma (PC) and pineoblastoma (PB) relative to normal brain.

overall_design: Gene expression analysis was performed on tumor samples. Tumor tissues of 5 CNs, 2 PCs (low-grade pineal parenchymal tumors (PPTs)) and 2 PBs (high-grade PPTs) were obtained from the NeurobiotecBank (Groupement Hospitalier Est, Bron, France) or from the AP-HM Tissue Bank (Assistance Publique-Hôpitaux de Marseille, France). At surgery, the tumor tissue was divided into 2 fragments, one of which was frozen and stored in liquid nitrogen for RNA extraction, whereas the other was fixed for histopathologic analysis.

first: Alexandre

last: Vasiljevic

first: Jacques

last: Champier

first: Dominique

last: Figarrella-Branger

first: Anne

last: Wierinckx

last: Jouvet

first: Michelle

last: Fèvre Montange


title: DamID LaminB1 data in mouse MEFs, wild-type and POU2F1-/-. DamID LaminA data in mouse Neural Precursor Cells and Astrocytes.

status: Public on Oct 10 2012

city: Amsterdam

first: Bas

last: van Steensel

address: Plesmanlaan 121

department: division of Molecular Biology

institute: Netherlands Cancer Institute

summary:
DamID LaminB1 data were generated in POU2F1-/- MEFs to study the potential role of POU2F1/Oct1 in genome - nuclear lamina interactions.
DamID LaminA data were generated in NPCs and Astrocytes to study similarities/differences between LaminA and LaminB1 binding.

The procedure to arrive at the provided Hidden Markov Model (HMM) state calls is as follows:
We fitted a two-state HMM whereby emissions are distributed as Student's t variables. Mean and variance of DamID signals differ between states, but the degree of freedom (nu) is the same. Gaps in the probe coverage were filled by evenly spaced null probe-values. The parameters were estimated by an adaptation of the ECME algorithm to the HMM framework, showing faster convergence than regular EM when nu is unknown (Filion et al., Cell, 2010). State calls were derived through the Viterbi algorithm. This process was repeated separately for each cell type, yielding per-probe calls. Probes in the ‘bound’ (1) state are indicated as LAD-probes, probes in the ‘unbound’ (0) state as inter-LAD-probes.

overall_design: Comparison of MEF wt versus MEF POU2F1-/-. Comparison of LaminA (NPC & AC) with LaminB1 (NPC & AC data in GSE17051)

first: Wouter

last: Meuleman

first: Daan

last: Peric-Hupkes


title: V. salmonicida wild type strain LFI1238 and isogenic DlitR mutant grown in suspension in SWT medium

first: Espen

last: Robertsen

overall_design: V. salmonicida wild type strain LFI1238 (control) and the isogenic DlitR deletion mutant were grown in suspension in SWT medium at 8°C  with  200 rpm and harvested at OD=0.8. Biological replicates for each sample: 4 wild type, 4 DlitR mutant (including one dye swap), independently grown and harvested. One replicate per array.


title: Cachexia-inducible Transforming growth factor-beta1 stimulated Clone-22 D4 controls acute hepatic lipid homeostasis.

status: Public on Sep 01 2012

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

summary: To explore the molecular basis for TSC22D4 function in hepatic lipid homeostasis in vivo TSC22D4 was knocked down in the mouse liver using adenovirus and performed genome wide expression analysis.

overall_design: 1x10^9 plaque-forming units (pfu) per recombinant virus were administered via tail vein injection. Mice (C57Bl/6) were sacrificed 7 days after infection. Hepatic RNA was isolated and used for whole genome expression analysis.

first: Allan

last: Jones

last: Rohm

first: Oksana

last: Seibert

first: Stefan

last: Kleinsorg

first: Philipp

last: Kulozik

first: Anja

last: Reimann

first: Tjeerd

last: Sijmonsma

first: Daniela

last: Strzoda

first: Angelika

last: Bierhaus

first: Norbert

last: Gretz

first: Geesje

last: Dallinga-Thie

first: Barbara

last: Leuchs

first: Manfred

last: Kögl

first: Mauricio

middle: B

last: Diaz

first: Stephan

last: Herzig


title: Genome-wide location analysis of FLAG-H2BE

city: Cambridge

first: Stephen

middle: W.

last: Santoro

address: 16 Divinity Ave.

department: Molecular and Cellular Biology

institute: Harvard University

summary:
We have identified a replication-independent histone variant, Hist2h2be (referred to herein as H2be), which is expressed exclusively by olfactory chemosensory neurons. Levels of H2BE are heterogeneous among olfactory neurons, but stereotyped according to the identity of the co-expressed olfactory receptor (OR). Gain- and loss-of-function experiments demonstrate that changes in H2be expression affect olfactory function and OR representation in the adult olfactory epithelium. We show that H2BE expression is reduced by sensory activity and that it promotes neuronal cell death, such that inactive olfactory neurons display higher levels of the variant and shorter life spans. Post-translational modifications (PTMs) of H2BE differ from those of the canonical H2B, consistent with a role for H2BE in altering transcription. We propose a physiological function for H2be in modulating olfactory neuron population dynamics to adapt the OR repertoire to the environment.
The objective of generating this dataset was to analyze the occupancy of H2BE protein in the vicinity of gene promoters throughout the genome, relative to histone H3, in olfactory sensory neurons within the main olfactory epithelium (MOE).

overall_design: This dataset analyzes the occupancy of FLAG-H2BE protein in the vicinity of gene promoters throughout the genome, relative to histone H3, in olfactory sensory neurons within the main olfactory epithelium (MOE) of Flag-H2be transgenic mice, which express a FLAG-tagged version of H2BE from the H2be promoter. There are 2 replicates for each ChIP (FLAG and H3).

middle: W

first: Catherine

last: Dulac


title: Microarray profiling of mononuclear peripheral blood cells to identify novel candidate genes related to chemoradiation response in rectal cancer

status: Public on Feb 22 2013

city: Granada

first: Carlos

last: Cano

address: Periodista Daniel Saucedo Aranda S.N.

country: Spain

institute: University of Granada

summary:
Peripheral blood mononuclear cells have emerged recently as pathology markers of cancer and other diseases, making possible their use as therapy predictors. Furthermore, the importance of the immune response in radiosensivity of solid organs led us to hypothesized that microarray gene expression profiling of peripheral blood mononuclear cells could identify patients with response to chemoradiation in rectal cancer.
27 patients with locally advanced rectal cancer were recruited initially to perform the study. Peripheral blood samples were obtained before neaodjuvant treatment. RNA was extracted and purified to obtain cDNA and cRNA for hybridization of microarrays included in Human WG CodeLink bioarrays. Quantitative real time PCR was used to validate microarray experiment data. Results were correlated with pathological response, according to Mandard´s criteria and final UICC Stage (patients with tumor regression grade 1-2 and downstaging being defined as responders and patients with grade 3-5 and no downstaging as non-responders).

overall_design: The group of study consisted of 27 locally advanced rectal cancer (LARC) patients from the Division of Colon & Rectal Surgery, HUVN, Granada, Spain. To qualify for this study, rectal carcinomas had to be on the stage II or stage III according the criteria of the International Union Against Cancer’s (UICC), without systemic metastases in the positron emission tomography scan and no known second neoplasm. The diagnosis of rectal cancer was confirmed by the histopathological analysis of endoscopic biopsies. The study was approved by the local ethics committee. Informed consent was obtained from all patients before the study. After the initial staging, all patients qualifying for this study received neoadjuvant radiotherapy (28 fractions of 1.8 Gy, 5 fractions/week) with concomitant chemotherapy (capecitabine, 825 mg/m2, twice daily alone or in combination with oxaliplatine 50 mg/m2 once weekly). Standardised surgery, including total mesorectal excision, was performed 8 weeks after the standardised CRT protocol described above.

first: P

last: Palma

first: M

last: Cuadros


title: Mutualism between gut microbiota and the host as revealed in a comparative study of breast-fed versus formula-fed infants

status: Public on Mar 19 2012

first: Jennifer

last: Goldsby

address: 112 Cater-Mattil

department: Nutrition and Food Sciences

summary:
On going efforts are directed at understanding the mutualism between the gut microbiota and the host in breast-fed versus formula-fed infants. Due to the lack of tissue biopsies, no investigators have performed a global transcriptional (gene expression) analysis of the developing human intestine in healthy infants. As a result, the crosstalk between the microbiome and the host transcriptome in the developing mucosal-commensal environment has not been determined.  In this study, we examined the host intestinal mRNA gene expression and microbial DNA profiles in full term 3 month-old infants exclusively formula fed (FF) (n=6) or breast fed (BF) (n=6) from birth to 3 months. Host mRNA microarray measurements were performed using isolated intact sloughed epithelial cells in stool samples collected at 3 months. Microbial composition from the same stool samples was assessed by metagenomic pyrosequencing. Both the host mRNA expression and bacterial microbiome phylogenetic profiles provided strong feature sets that clearly classified the two groups of babies (FF and BF). To determine the relationship between host epithelial cell gene expression and the bacterial colony profiles, the host transcriptome and functionally profiled microbiome data were analyzed in a multivariate manner. From a functional perspective, analysis of the gut microbiota's metagenome revealed that characteristics associated with virulence differed between the FF and BF babies.  Using canonical correlation analysis, evidence of multivariate structure relating eleven host immunity / mucosal defense-related genes and microbiome virulence characteristics was observed. These results, for the first time, provide insight into the integrated responses of the host and microbiome to dietary substrates in the early neonatal period. Our data suggest that systems biology and computational modeling approaches  that integrate “-omic” information from the host and the microbiome can identify important mechanistic pathways of intestinal development affecting the gut microbiome in the first few months of life.
KEYWORDS: infant, breast-feeding, infant formula, exfoliated cells, transcriptome, metagenome, multivariate analysis, canonical correlation analysis

overall_design: 12 samples, 2 groups

first: Scott

last: Schwartz

first: Iddo

last: Friedberg

first: Ivan

middle: V

last: Ivanov

first: Laurie

last: Davidson

middle: S

first: David

last: Dahl

first: Damir

last: Herman

first: Mei

last: Wang

first: Sharon

last: Donovan

first: Robert

last: Chapkin


title: Small RNA Solexa sequencing of 4 Plant Species in the Cucurbitaceae family

status: Public on Aug 03 2012

city: Kunming

first: Yun

last: Zheng

state: Yunnan

address: 452 Fengyuan Road

country: China

institute: Yunnan Agricultural University

type: Non-coding RNA profiling by high throughput sequencing

summary: Total RNA was isolated from different tissues (leaf, stem and flesh, rind and placenta of the fruits) using TRIzol reagent and small RNA libraries were generated from four cucurbit species: bottle gourd (Lagenaria siceraria (accession Grif 1617 collection from India)), Cucurbita moschata (accession Grif 14244 Early Butternut) Cucurbita pepo (accession NSL98075 Table King), and watermelon (Citrullus lanatus var. lanatus) (PI 438676 Charleston Grey) by pooling equimolar amounts of total RNA from the aforesaid tissues. Construction of small RNA libraries from size fractionated RNA was carried out as described previously. In brief, small RNA fractions of 18–28 nt were isolated from 15% denaturing polyacrylamide gels and sequentially ligated to 5′ and 3′ RNA adapters. Small RNAs ligated with adapters were converted to DNA by RT-PCR following Solexa protocol. The final PCR product was gel purified and sequenced by Genome Analyser II (Illumina).

sample_organism:
Citrullus lanatus
Cucurbita moschata
Cucurbita pepo
Lagenaria siceraria

overall_design: Examination of small RNA transcriptomes in four plants species using Illumina/Solexa GA-II.

first: Ramanjulu

last: Sunkar


title: Genome-wide HSF1 binding sites in control and heat shocked spermatocytes and hepatocytes

status: Public on Aug 28 2012

city: Gliwice

first: Joanna

last: Polanska

address: Akademicka 16

department: Automatic Control

country: Poland

institute: Silesian University of Technology

summary:
In somatic cells elevated temperature induces activation of the heat shock transcription factor 1 (HSF1) what leads to heat shock proteins synthesis and cytoprotection. However, in the male germ cells (spermatocytes) upon HSF1 activation, caspase-3 dependent apoptosis is induced and spermatogenic cells are actively eliminated.
To find out molecular targets of HSF1 in all promoter regions, and to elucidate a mechanism of such diverse HSF1 activity we carried out genome-wide HSF1 binding analysis in control and heat-shocked cells, either spermatogenic or somatic. As model somatic cells we used hepatocytes that respond to hyperthermia in a classical way by induction of heat shock genes transcription. As spermatogenic cells we used a fraction of cells enriched with spermatocytes, which are the most sensitive to damage in elevated temperatures. Using isolated spermatocytes we avoided the influence of the somatic testicular component on the our final results.

overall_design: On Affymetrix GeneChip® Mouse Promoter 1.0R Arrays we analyzed DNA immunoprecipitated (using anty-HSF1 antibody) from spermatocytes or hepatocytes, either untreated (control) or immediately after heat shock performed in vitro for 5-20 minutes. ChIP on chip analyses were done in triplicate.

first: Wieslawa

last: Widlak

first: Malgorzata

last: Kus-Liskiewicz

first: Magdalena

last: Olbryt


title: Analysis of the early transcriptome signature of Nipah virus infection in primary endothelial cells

status: Public on Aug 24 2012

city: LYON

first: HORVAT

last: Branka

address: 21 avenue Tony Garnier

department: human virology

institute: INSERM

summary: Nipah virus (NiV) is a recently emerged zoonotic Paramyxovirus that causes regular outbreaks in East Asia with mortality rate exceeding 75%. Major cellular targets of NiV infection are endothelial cells and neurons. To better understand virus-host interaction, we analysed the transcriptome profile of NiV infection in primary human umbilical vein endothelial cells. We found that NiV infection strongly induces genes involved in interferon response in endothelial cells. Among the top ten upregulated genes, we identified the chemokine CXCL10 (interferon-induced protein 10, IP-10), an important chemoattractant involved in the generation of inflammatory immune response and neurotoxicity.

overall_design: We performed microarray gene expression profiling of NiV infected HUVEC cell (2 replicates) and of uninfected HUVEC cell (2 replicates).

first: Cyrille

last: MATHIEU

first: Vanessa

last: GUILLAUME

first: Catherine

last: LEGRAS-LACHUER

first: Branka

last: HORVAT


title: Multiple changes at the mucosal surface are induced by protective SIV vaccination

status: Public on May 31 2012

city: Minneapolis

first: Anthony

middle: James

last: Smith

address: 420 Delaware Street S.E.

department: Microbiology

institute: University of Minnesota

summary: Systemic vaccination with the attenuated virus SIVmac239-∆Nef provides sterilizing or partial protection to rhesus monkeys challenged with WT SIV strains, providing important opportunities to study key immunological components of a protective host response.  Here we show that intravenous vaccination with SIVmac239-∆Nef provides two potentially crucial immunological barriers localized at mucosal surfaces that correlate with the vaccine’s protective effects against WT SIVmac251 vaginal challenge: 1) a conditioned and coordinated response from the mucosal epithelium that blunts the early inflammatory and chemotactic signalling cascade that aids virus propagation and expansion; 2) early on-site generation/diversification of SIV-specific Abs from ectopic germinal center-like lymphoid aggregates.  This unique host response to WT SIVmac251 in the female reproductive tract of SIVmac239-∆Nef-vaccinated animals points to a multi-layered strategy for a protective host response during immunodeficiency virus exposure—rapid induction of humroal immunity at mucosal surfaces without the deleterious inflammatory side effects tied to innate recognition of virus.  This vaccine-induced host response highlights potential key protective mechanisms needed for an effective HIV vaccine

overall_design: Total RNA was isolated from the cervix of 17 Indian Rhesus macaques (3 uninfected animals; 5 unvaccinated animals 4-5 days post vaginal exposure with SIVmac251; 4 SIVmac239-∆Nef-vaccinated animals before challenge; 5 SIVmac239-∆Nef-vaccinated animals 4-5 days post vaginal exposure with SIVmac251) and prepared for hybridization on Affymetrix GeneChip Rhesus Macaque Genome Arrays.  Replicate arrays were performed for a number of the samples to minimize assay noise and significant host genes altered during virus exposure in female reproductive tract tissue were identified by their associated q-values (< 0.2) and fold change in expression (> 1.2).

first: Steve

last: Wietgrefe

first: Cavan

last: Reilly

first: Lijie

last: Duan

first: Liang

last: Shang

first: Qingsheng

last: Li

first: Paul

last: Johnson

first: Ashley

middle: T

last: Haase


title: Analysis of the early transcriptome signature of infection of primary endothelial cells by Nipah virus vs. Nipah virus deleted for the expression of non-structural C protein

status: Public on Oct 01 2012

summary: Nipah virus (NiV) is a highly pathogenic, negative strand RNA paramyxovirus that has recently emerged from flying foxes to cause serious human disease. To study the poorly-understood role of nonstructural NiV proteins in NiV pathogenesis, we generated recombinant viruse lacking the expression of accesory NiV C protein (NiV∆C).

overall_design:
To analyse the molecular basis of NiV∆C attenuation we have used the gene microarray approach to study early changes of gene expression in infected primary human endothelial cells, which is a major cellular target of human NiV infection.
We performed microarray gene expression profiling of NiV infected HUVEC cell (2 replicates), of uninfected HUVEC cell (2 replicates) and of NiV∆C infected HUVEC cell (2 replicates).

first: Joel

last: LACHUER


title: Comparative genomic hybridization analysis shows different epidemiology of chromosomal and plasmid-borne cpe-carrying Clostridium perfringens type A strains

status: Public on Mar 01 2012

city: Helsinki

first: Panu

last: Somervuo

address: Viikinkaari 4

country: Finland

institute: University of Helsinki

summary:
Enterotoxin-producing C. perfringens type A is a common cause of food poisonings. The cpe encoding the enterotoxin can be chromosomal (genotype IS1470) or plasmid-borne (genotypes IS1470-like-cpe or IS1151-cpe). The chromosomal cpe-carrying C. perfringens are a more common cause of food poisonings than plasmid-borne cpe-genotypes.

The chromosomal cpe-carrying C. perfringens type A strains are generally more resistant to most food-processing conditions than plasmid-borne cpe-carrying strains. On the other hand, the plasmid-borne cpe-positive genotypes are more commonly found in human feces than chromosomal cpe-positive genotypes, and humans seem to be a reservoir for plasmid-borne cpe-carrying strains. Thus, it is possible that the epidemiology of C. perfringes type A food poisonings caused by plasmid-borne and chromosomal cpe-carrying strains is different.

A DNA microarray was designed for analysis of genetic relatedness between the different cpe-positive and cpe-negative genotypes of C. perfringens strains isolated from human, animal, environmental  and food samples. The DNA microarray contained two probes for all protein-coding sequences in the three genome-sequenced strains (C. perfringens type A strains 13, ATCC13124, and SM101).

The chromosomal and plasmid-borne C. perfringens genotypes were grouped into two distinct clusters, one consisting of the chromosomal cpe-genotypes and the other consisting of plasmid-borne cpe-genotypes. Analysis of the variable gene pool complemented with the growth studies demonstrate different carbohydrate and amine metabolism in the chromosomal and plasmid-borne cpe-carrying strains, suggesting different epidemiology of the cpe-positive C. perfringens strain groups.

overall_design: Array CGH. Two-color hybridizations on 8x15K Agilent arrays. Eight reference strain hybridizations. Normalization was based on log-ratios against the reference strain. For each sample, 8 normalization factors were calculated, one against each reference hybridization, and the median normalization factor was used. This was repeated for each sample hybridization separately.

first: Päivi

last: Lahti

first: Miia

last: Lindström

first: Annamari

last: Heikinheimo

first: Hannu

last: Korkeala


title: DNA methylation profiling of embryonic stem cell differentiation into the three germ layers [MeDIP analysis]

status: Public on Feb 15 2012

city: Tokyo

first: Takayuki

last: Isagawa

address: 4-6-1 Komaba, Meguro-ku

department: RCAST

institute: The University of Tokyo

summary: Embryogenesis is tightly regulated by multiple levels of epigenetic systems such as DNA methylation, histone modification, and chromatin remodeling.  DNA methylation patterns are erased in primordial germ cells and in the interval immediately following fertilization.  Subsequent reprogramming occurs by de novo methylation and demethylation.  Variance of DNA methylation patterns between different cell types is not well understood.  Here, using methylated DNA immunoprecipitation and tiling array technology, we have comprehensively analysed DNA methylation patterns at proximal promoter regions in mouse embryonic stem (ES) cells, ES cell-derived early germ layers (ectoderm, endoderm and mesoderm) and four adult tissues (brain, liver, skeletal muscle and sperm).  Most of the methylated regions in the three germ layers and in the three adult somatic tissues are shared in common.  This commonly methylated gene set is enriched in germ cell associated genes that are generally transcriptionally inactive in somatic cells.  We also compared DNA methylation patterns with global mapping of histone H3 lysine 4/27 trimethylation, and found that gain of DNA methylation correlates with loss of histone H3 lysine 4 trimethylation.  Taken together, our findings indicate that differentiation from ES cells to the three germ layers is accompanied by an increase in the number of commonly methylated DNA regions and that these tissue-specific alterations are present for only a small number of genes.  Our findings indicate that DNA methylation at the proximal promoter regions of commonly methylated genes act as an irreversible mark which fixes somatic lineage by repressing transcription of germ cell specific genes.

overall_design: Using the MeDIP on chip protocol, we immunoprecipitated methylated DNA from R1 ES cell, SK7 cell, as well as SK7 derived-Ectoderm, - Endoderm, -Paraxial mesoderm, brain, liver, skeletal muscle, and sperm, and hybridized to a genome tiling array. The three germ layer lineages from ES cells were confirmed by the expression of specific marker genes in each germ layer (see related expression analysis).

first: Genta

last: Nagae

first: Nobuaki

last: Shiraki

first: Takanori

last: Fujita

first: Noriko

last: Sato

first: Shumpei

last: Ishikawa

first: Shoen

last: Kume

first: Hiroyuki

last: Aburatani


title: Comparison of gene expression between wild type and AP2-G KO parasites.

status: Public on May 01 2012

city: tsu

first: masao

last: yuda

state: mie

address: edobashi 2-174

institute: mie university

summary: In the rodent malaria parasite Plasmodium berghei, we found that an AP2 family transcription factor designated AP2-L plays a critical role in the development of the liver stage. Using DNA microarray analysis we showed that the expression of several genes, including those of parasitophorous vacuole membrane proteins, was significantly decreased in the early liver stage of AP2-L-depleted parasites.

overall_design: Gene expression of P. berghei  sporozoites was compared between wild type and AP2-G KO parasites. Five biologically independent experiments were performed for each genotype.

first: Masao

last: Yuda

first: Izumi

last: kaneko


title: Gene expression profiles in the Leiden Longevity Study

status: Public on Sep 04 2011

city: Leiden

first: Willemijn

last: Passtoors

state: Zuid-Holland

department: Molecular Epidemiology

institute: Leiden University Medical Center

summary: Biomarkers of familial longevity may represent mechanisms underlying healthy aging. To identify gene expression profiles marking human familial longevity, an explorative genome-wide expression study was performed among 50 families from the Leiden Longevity Study who have a life-long survival advantage of 30%.  Gene expression profiles were compared between 50 nonagenarians (mean age 93.4 years) and 50 controls (mean age 61.9 years) to investigate differential gene expression that may arise as a function of both chronological age and familial longevity. Differential expression was observed for 2953 probes (FDR≤0.05) and for 109 GO terms, which corresponded well with previously reported findings on gene expression changes associated with chronological age, such as ‘immune response’, ‘signal transduction’ and ‘regulation of gene transcription’. To explore which of the 2953 chronological age-related probes also marked familial longevity, we compared gene expression profiles of 50 offspring of the nonagenarians (mean age 60.8 years) with the same 50 controls. Since the average gene expression levels did not differ between offspring and controls, we tested for differential expression as a function of age (age range 43-79 years). We identified 360 probes (FDR≤0.1) and the ‘Rho protein signal transduction’ GO biological process (FWER = 0.079) whose expression signatures marked familial longevity already at middle-age. Of these probes, 236 were annotated and represent 244 known genes, including WRN and MYC. Interestingly, 51 genes are involved in the regulation of gene expression. Further investigation into the genes involved may be important for unraveling mechanisms underlying longevity.

overall_design: From the Leiden Longevity Study 50 long-lived siblings, 50 of their offspring and 50 partners thereof were analysed in this study. From one individual per group two technical replicates were included in the measurement, but left out in the analysis.

first: Judith

last: Boer

first: Jelle

middle: J

last: Goeman

first: Erik

last: van den Akker

first: Bas

last: Zwaan

first: Ann

last: Scarborough

first: R

last: van der Breggen

first: J

last: Deelen

first: Gert-Jan

last: van Ommen

first: Rudi

last: Westendorp

first: Anton

last: de Craen

first: Andrew

last: White

first: David

middle: A

last: Gunn

first: P

last: Slagboom

first: Marian

last: Beekman


title: Mosaic Analysis with Double Markers Reveals Tumor Cell of Origin in Glioma

status: Public on Jul 01 2011

first: Roel

last: Verhaak

address: 1400 Pressler St

department: Bioinformatics and Comp Bio

institute: MD Anderson Cancer Center

summary: Cancer results from molecular mutations occurring in specific cell types, thus determining the cell-of-origin is critical for effective cancer treatment. Inferring such information from terminal tumors can be misleading because malignant tumor cells tend to acquire aberrant properties. Animal models are widely used because one can initiate mutations in specific cell types. However, cell-of-mutation that harbors initial molecular changes may not directly transform, rather merely passes along mutations to its progeny cell lineage, which then serves as cell-of-origin and finally transforms into malignancy.   Such a problem is exemplified in the glioma field: glioma can be induced either by mutating tumor suppressor genes in neural stem cells (NSCs) or by over-expressing oncogenes in restricted progenitor cells such as oligodendrocyte precursor cells (OPCs). However, for the NSC glioma model, it remains unknown whether NSCs directly transform or simply pass along mutations to OPC lineage for malignancy. Here we use a genetic system termed Mosaic Analysis with Double Markers (MADM) to study the earliest stage of gliomagenesis from mutated NSCs.   At an in vivo single-cell resolution, we unbiasedly analyzed tumorigenic potential of NSCs and all cell lineages derived from them. At pathologically undetectable pre-transforming phases, we found no significant aberrant growth of mutant NSCs and their derivatives except for the OPC lineage. We then tracked the tumor progression from earliest stage and confirmed the expansion of OPCs lead to gliomagenesis. Consistently, transcriptome profiling reveals that terminal-stage tumor cells display salient OPC features and resemble human proneural subtype of glioblastoma multiform (GBM).  Most importantly, introducing the same mutations directly into OPCs was sufficient for malignant transformation and these tumor cells are indistinguishable in their gene expression profiles from those in which the first mutations were introduced into NSCs. Our findings strongly implicate OPCs as the transforming cell type for glioma even when initial mutations could occur in NSCs, and highlight the importance of analyzing early phases of tumorigenesis to distinguish cell-of-origin from cell-of-mutation.

overall_design: 44K Mouse Development Oligo Microarrays from Agilent Technologies were used for microarray analysis. For each experiment, total RNA was fluorescently labeled and hybridized directly against a common reference sample generated from the RNA pool of four WT P17 mouse brain neocortex.

first: Chong

last: Liu

first: Jonathan

middle: C

last: Sage

first: Michael

last: Miller

first: Simon

last: Hippenmeyer

first: Hannes

last: Vogel

first: Oded

last: Foreman

first: Akiko

last: Nishiyama

first: Liqun

last: Luo

first: Hui

last: Zong


title: Multifaceted neuro-regenerative activities of human dental stem cells promote locomotor recovery after complete transection of the rat spinal cord

status: Public on Jan 01 2012

city: Nagoya

first: Akihito

last: Yamamoto

state: Aichi-ken

address: 65 Tsurumai-Cho, Showa-Ku

department: Department of Oral and Maxillofacial Surgery

institute: Nagoya University Graduate School of Medicine

summary: Spinal cord injury (SCI) often leads to persistent functional deficits due to severe neuron and glial loss, and to limited axonal regeneration after injury. Here we show that the transplantation of human dental stem cells into the completely transected adult rat spinal cord resulted in a significant recovery of hindlimb locomotor functions. These stem cells exhibited three major neuro-regenerative activities. First, they inhibited the SCI-induced apoptosis of neurons, astrocytes, and oligodendrocytes, improving the preservation of neuronal filaments and myelin sheaths. Second, they promoted the regeneration of transected axons by directly inhibiting multiple axon growth inhibitors, including chondroitin sulfate proteoglycan and myelin-associated glycoprotein, by paracrine mechanisms. Third, they replaced lost cells by differentiating into mature oligodendrocytes under the extreme conditions of SCI. Our data demonstrate that tooth-derived stem cells may provide novel therapeutic benefits for treating SCI through both cell-autonomous and paracrine neuro-regenerative activities.

overall_design:
Human dental stem cells were isolated from exfoliated deciduous teeth extracted for clinical purposes were collected at Nagoya University School of Medicine, under approved guidelines set by Nagoya University (H-73, 2003). The ethics committee of Nagoya University approved the experimental protocols (permission number 8-2). Mesenchymal stem cells of human Bone marrow line were obtained from Lonza.

Total RNAs were isolated and quantified by spectrophotometer. RNA integrity was checked on 1% agarose gels. RT reactions were carried out with Superscript III reverse transcriptase (Invitrogen) using 1 μg of total RNA in a 50 μl total reaction volume.

Microarray experiments were carried out using a CodeLink™ Human Whole Genome Bioarray (Applied Microarrays, Inc. Tempe, AZ) at Filgen, Inc. (Nagoya, Japan). The arrays were scanned using a GenePix4000B Array Scanner (Molecular Devices, Sunnyvale, CA), and the data was analyzed by using MicroArray Data Analysis Tool Ver3.2 (Filgen, Inc.).

first: Kiyoshi

last: Sakai


title: To study glycosaminoglycan (GAG) glycogene expression in cutaneous lupus erythematosus (CLE) skin lesions and normal skin

status: Public on Jun 14 2011

city: La Jolla

first: Steven

last: Head

state: CA

address: 10550 N Torrey Pines Rd

institute: The Scripps Research Institute

summary: Cutaneous lupus erythematosus (CLE) is an autoimmune disease that localizes to the skin and is known to contain elevated glycosaminoglycans (GAGs) on Hale’s stain of skin biopsy specimens. Recently, different GAG species have been shown to have distinct effects on the recruitment and activation of immune cells and stimulation of cytokine production (Taylor and Gallo, FASEB, 2006; 20: 9-22). Thus, we speculate that the elevated GAGs observed in CLE play a role in the local inflammatory process that produces skin lesions in these patients.

overall_design:
In order to further investigate a molecular basis for the elevated expression of these GAGs in CLE skin lesions, we would like to determine the gene expression profiles of GAG synthesis, degradation, and modifier genes in lesional and non-lesional skin samples from CLE patients and compare to those from healthy controls. A microarray approach will give us a broader understanding of the genetic regulation of the expression of various GAG species in CLE skin. We will then be able to target future quantitative gene expression experiments by real-time RT-PCR to the genes that are shown to be involved in CLE. In order to accomplish our goal, we would like to examine the GAG gene expression profiles of DLE, TLE, and SCLE subtypes due to the differences in CS and HA staining that we found among these subtypes. Since HA and CS are elevated in DLE and HA in TLE, but not in SCLE, the SCLE samples will also serve as an internal control. We would like to examine both lesional and non-lesional skin biopsies to determine if CLE skin prior to developing a lesion is different at the genetic level from healthy control skin and how it changes once a lesion does develop.
We will separate the dermis from the epidermis of the skin biopsies and extract RNA just from the dermis to enrich for dermal fibroblast RNA. We aim to submit four patient biopsies per subtype as well as four samples from healthy control skin for comparison. This number is necessary in order to account for the biologic variability among different patients. We would submit more samples per subtype but are limited by availability of patients in clinic. Thus, we will have a total of 28 samples to submit for microarray. This study design will allow us to analyze the GAG gene expression profiles among different CLE subtypes and enable us to identify which GAc

first: Victoria

last: Werth


title: Novel Targets of the Transcription Factor Sox9 in Neonatal Mouse Limb

status: Public on Nov 01 2011

city: Miami

first: Joy

last: Lincoln

address: 1600 NW 10th Ave.

institute: University of Miami

summary: Sox9 is an SRY-related transcription factor required for expression of cartilaginous matrix genes in the developing skeletal system and heart valve structures. In contrast to positively regulating formation of cartilaginous matrix, Sox9 has also been shown to negatively regulate matrix mineralization associated with bone formation. While the transcriptional activation of Sox9 target genes during chondrogenesis has been well studied, the mechanisms by which Sox9 represses osteogenic processs are not so clear. To address this, we performed a genome-wide Sox9 ChIP-on-chip approach using neonatal mouse lim tissue.

overall_design: Chromatin immunoprecipitation was performed with pooled Sox9 antibodies and normal rabbit IgG as control using neonatal mouse limb tissue. Samples include Sox9 IP and IgG IP.

first: Jacqueline

middle: D

last: Peacock

first: Hasini

last: Ediriweera


title: A time-course transcriptome study of hrpG and hrpX regulons in Xanthomonas axonopodis pv. citri

status: Public on Jun 09 2011

city: Lake Alfred

first: Yinping

last: Guo

state: FL

address: 700 Experiment station road

department: Microbiology and cell science; Citrus research and education center

institute: Xanthomonas axonopodis pv. citri

summary: Xanthomonas axonopodis pv. citri (XAC) is the causal agent of citrus canker which is one of the most serious diseases of citrus.  To understand the virulence mechanism of XAC, we designed and conducted genome-wide microarray analyses to characterize the regulons of HrpG and HrpX, which are critical for the pathogenicity of XAC. Our analyses revealed that the expression of 232 genes and 181 genes belonged to the HrpG and HrpX regulons, respectively. Totally, 123 genes were overlapped in the two regulons at any of the three time-points.  Our results showed that HrpG and HrpX regulated all 25 T3SS genes, 22 T3SS effector genes, and 29 T2SS substrate genes. Our data showed that XAC regulates multiple cellular activities responding to the host environment, such as amino acid biosynthesis, oxidative phosphorylation, pentose-phosphate pathway, transport of sugar, iron and potassium, the phenolic compounds catabolism pathway (pcaQ) through HrpX and HrpG.   We also identified 124 and 90 unknown genes controlled by HrpG and HrpX, respectively.  Our data suggest that a cross-talk exists between HrpG and quorum sensing system in XAC.   We also identified genes involved in chemotaxis and flagellar biosynthesis, production of extracellular enzymes, metabolic pathways, as well as signal transduction controlled by HrpG/HrpX. Our results suggest that HrpG and HrpX interplay with global signaling network and co-ordinate the expression of multiple virulence factors for modification and adaption of host environment during XAC infection.

overall_design: Two mutants and three time-points experiment. Four biological and dye-swap replicates of each strain per each time-point were used. Totally, there were three datasets of hrpG mutant: 1) hrpG mutant vs. wild type strain at time-point A; 2) hrpG mutant vs. wild type strain at time-point B; 3) hrpG mutant vs. wild type strain at time-point C. There are also three datasets of hrpX mutant:  1) hrpX mutant vs. wild type strain at time-point A; 2) hrpX mutant vs. wild type strain at time-point B; 3) hrpX mutant vs. wild type strain at time-point C.

first: Nian

last: Wang


title: Retroviral Integration Mutagenesis in Mice and Comparative Analysis in Human AML Identify Reduced PTP4A3 Expression as a Prognostic Indicator

status: Public on Oct 27 2011

city: Rotterdam

first: Erdogan

last: Taskesen

address: dr. molewaterplein 50

institute: Erasmus University Medical Center (EMC)

summary: Acute myeloid leukemia (AML) results from multiple genetic and epigenetic aberrations, many of which remain unidentified. Frequent loss of large chromosomal regions marks haplo-insufficiency as one of the major mechanisms contributing to leukemogenesis. However, which haplo-insufficient genes (HIGs) are involved in leukemogenesis is largely unknown and powerful experimental strategies aimed at their identification are currently lacking. Here, we present a new approach to discover HIGs, using retroviral integration mutagenesis in mice in which methylated viral integration sites and neighbouring genes were identified. In total we mapped 6 genes which are flanked by methylated viral integration sites (mVIS). Three of these, i.e., Lrmp, Hcls1 and Prkrir, were up regulated and one, i.e., Ptp4a3, was down regulated in the affected tumor. Next, we investigated the role of PTP4A3 in human AML and we show that PTP4A3 expression is a negative prognostic indicator, independent of other prognostic parameters. In conclusion, our novel strategy has identified PTP4A3 to potentially have a role in AML, on one hand as a candidate HIG contributing to leukemogenesis in mice and on the other hand as a prognostic indicator in human AML.

overall_design: We designed a new strategy to specifically identify DNA methylated proviral integrations on a large scale by combining methylated DNA immunoprecipitation (MeDIP), inverse PCR and promoter array hybridization. We used 6 murine leukemia samples from a previous screen that were induced by injecting Gr 1.4 MLV into newborn mice.

first: Renee

last: Beekman

first: Marijke

last: Valkhof

first: Stefan

last: Erkeland

first: Veronika

last: Rockova

first: Justine

middle: K

last: Peeters

first: Peter

last: Valk

first: Bob

last: Löwenberg

first: Ivo

middle: P

last: Touw


title: CCN5, a novel transcriptional repressor

status: Public on Nov 30 2011

city: paris

first: Michèle

last: SABBAH

address: 184 rue du faubourg Saint-Antoine

institute: INSERM U938

summary: CCN5 is a member of the CCN (Connective Tissue Growth Factor/Cysteine-rich 61/Nephroblastoma overexpressed) family and was identified as an estrogen-inducible gene in estrogen receptor-positive cell lines. However, the role of CCN5 in breast carcinogenesis remains unclear. We report here that CCN5 protein is localized mostly in the cytoplasm, and in part in the nucleus, of human tumor breast tissue. Using a heterologous transcription assay, we demonstrate that CCN5 can act as a transcriptional repressor, presumably through association with histone deacetylase HDAC1. Microarray gene expression analysis showed that CCN5 represses expression of genes associated with epithelial-mesenchymal transition (EMT) as well as expression of key components of the TGF-beta signaling pathway, prominent among them TGF-betaRII receptor. We show that CCN5 is recruited to the TGF-betaRII promoter, thereby providing a mechanism by which CCN5 restricts transcription of the TGF-betaRII gene. Consistent with this finding, we found that CCN5 functions to suppress TGF-beta-induced transcriptional responses and invasion that is concomitant with EMT. Thus, our data uncovered CCN5 as a novel transcriptional repressor that plays an important role in regulating tumor progression functioning, at least in part, by inhibiting the expression of genes involved in the TGF-beta signaling cascade that is known to promote EMT.

overall_design: We performed microarray gene expression profiling of one MCF-7-sh-CCN5 sample and one MCF-7-sh-scrambled sample (control sample).

last: Sabbah

first: Prunier

last: Céline

first: Nathalie

last: Ferrand

first: Virginie

last: Megalophounos

first: Kathleen

last: Lambein

first: Olivier

last: De Wever

first: Nicolas

last: Nazaret

first: Joël

last: Lachuer

first: Sylvie

last: Dumont

first: Gérard

last: Redeuilh


title: Genomic analysis of microRNA time-course expression in liver of mice treated with genotoxic carcinogen N-ethyl-N-nitrosourea

status: Public on Nov 04 2010

city: Jefferson

first: Zhiguang Li

state: AR

address: HFT130, 3900 NCTR Road

department: Division of Genetic an Reproductive Toxicology

institute: National Center for Toxicological Research

summary:
Dysregulated expression of microRNA (miRNA) has been extensively detected in human cancer tissues and has shown promise in defining tumor status.  It, however, is little known whether and when expression of miRNAs can be changed in normal tissues after carcinogen exposure.  To explore possible time-course changes of miRNA expression induced by carcinogens, we treated mice with one dose of 120 mg/kg body weight model genotoxic carcinogen N-ethyl-N-nitrosourea (ENU) and vehicle control.  The miRNA expression profiles were determined in the mouse livers in a time-course manner.  MiRNAs were isolated from the livers of ENU-treated and control mice at days 1, 3, 7, 15, 30 and 120 after the treatment.  The miRNA expressions were determined using RT2-mouse miRNA PCR Array.  Principal component analysis of the gene expression profiles showed that miRNA expression at post-treatment days 7 and 15 were different from those at the other time points and the controls.  The numbers of the dysregulated miRNAs changed with time, being 3, 5, 14, 32, 5 and 5 at post-treatment days 1, 3, 7, 15, 30 and 120, respectively.  Functional analysis of the differentially expressed miRNA at post-treatment days 7 and 15 indicated that the major functions of these ENU-induced dysregulated miRNAs were mainly associated with DNA repair and tumorigenesis, suggesting the microRNA expression is related to genotoxicity of ENU.  These results propose that one to two weeks after ENU exposure is the best time for miRNA expression sampling; and that a large number of miRNAs whose expression is dysregulated after carcinogen exposure could be an indicator for carcinogenic damage.

Series type: Non-coding RNA profiling by RT-PCR

overall_design: Six-month-old female mice were injected intraperitoneally with a single dose of 120 mg / kg body weight ENU or the vehicle dimethylsulfoxide.  Groups of 4 or 5 animals were sacrificed on post-treatment days 1, 3, 7, 15, 30, and 120 for the ENU treatment and post-treatment days 1 and 30 for the control treatment. MicroRNA expressions in the livers were investigated using SABiosciences 384-well Mouse Genome microRNA real-time PCR Array.

first: Zhiguang

last: Li

first: Lei

last: Guo

first: William

last: Branham

first: Yexun

last: Wang

first: Leming

last: Shi

first: Tao

last: Chen


title: The expression profiles of PSPTO_2222 and PSPTO_2222-2223 mutants in MM or KB

status: Public on Dec 31 2010

city: manhattan

first: Xiaoyan

last: Tang

email: xtang@ksu.edu, llan@ksu.edu

state: KS

address: 4702 Throckmorton

department: Plant Pathology

institute: Kansas State University

summary: PSPTO_2222 and PSPTO_2222-2223 deletions mutants were grown in MM or KB, and their expression profiles were analyzed.

sample_organism: Pseudomonas syringae pv. tomato str. DC3000

overall_design:
2222MM: PSPTO_2222 mutants cultured in MM.
3/2 MM: PSPTO_2222-2223 deletion mutants cultured in MM.
3-2 kb: PSPTO_2222-2223 deletion mutants cultured in KB.
P2KB:  PSPTO_2222 mutants cultured in KB.

first: Lefu

last: Lan


title: MeDIP-on-chip and Pol-II ChIP-on-chip during C2C12 myogenic and BMP2-induced osteogenic differentiation

status: Public on Feb 07 2011

city: Nijmegen

first: Marlinda

last: Hupkes

address: Heyendaalseweg 135

department: Cell and Applied Biology

institute: Radboud University Nijmegen

summary: Differentiation of pluripotent embryonic stem cells, via more restricted multipotent adult stem cells, towards the multitude of terminally differentiated, specialized cell types that make up the adult body is a multi-step process characterized by a progressive restriction of differentiation potential. Previous studies have demonstrated tissue-specific differences in DNA methylation patterns that might play a role in lineage restriction and tissue-specific gene expression. However, these studies have mainly focused on either the differentiation of pluripotent ES cells or on comparing somatic cells from different tissues, so that it remains unclear at which stages during development these differences in DNA methylation profiles are established. Since data on the role of DNA methylation during late-stage development is limited, we have examined the role of this epigenetic mark during the terminal differentiation of a multipotent adult stem cell, using C2C12 as a model system. Using parallel MeDIP- and Pol-II ChIP-on-chip approaches, we demonstrate a mutually exclusive relationship between high Pol-II occupancy and high DNA methylation levels. In addition, we observe that in undifferentiated progenitor cells, osteoblast-related genes have in general higher methylation levels than myoblast-related genes, while myoblast-related genes have higher Pol-II occupancy. Induction of osteogenesis with BMP2 leads to a rearrangement of Pol-II towards osteoblast-related genes. However, methylation patterns remain unchanged. These results indicate that DNA methylation primes C2C12 multipotent stem cells for myogenic differentiation and permits induction of the osteogenic gene expression program upon growth factor stimulation. We propose that cell type-specific DNA methylation patterns are established prior to terminal differentiation of adult stem cells.

overall_design: C2C12 cells were grown for 0, 1, 3 and 6 days in the presence or absence of BMP2. DNA was isolated and ChIPed with anti-Pol-II or IP-ed with anti-5-methyl-cytosine. non-IP'd input DNA was used as a reference sample

first: Eugene

last: van Someren

first: Ester

last: Piek

first: Koen

last: Dechering

first: Everardus

last: van Zoelen


title: Transcriptomic dysregulation in aggressive and malignant prolactin tumours

status: Public on Mar 16 2011

city: BRON

first: Joël

last: LACHUER

address: 16 avenue du Doyen Lépine

summary: Pituitary tumours are generally benign. However, many are invasive and some of these are aggressive with high proliferation and recurrence rates. Only metastatic tumours are considered malignant and are rare (0.2%). To identify molecular events associated with the aggressive and malignant phenotypes, we combined a comparative genomic hybridization and transcriptomic analysis of 13 prolactin (PRL) tumours classified as non-invasive (NI; n=5), invasive (I; n=2) or aggressive-invasive (AI; n=6). Each tumour showed copy number alterations which appeared to be varied and discrete in the NI and I tumour groups, and more numerous and extensive in the AI tumour group. Allelic loss within the p arm region of chromosome 11 was detected in five of the AI tumours. This region contains the cytobands 11p15.2, 11p15.1, 11p14.3, 11p14.2, 11p14.1, 11p13, 11p12 and 11p11.2. Furthermore, an allelic loss in the 11q arm was also observed in three of these five tumours, which were considered malignant based on the presence of metastases. The comparison of genomic and transcriptomic data showed that allelic loss impacted upon the expression of genes located in the imbalanced region. An original data filtering strategy allowed us to highlight five genes (DGKZ, CD44, TSG101, GTF2H1 and HTATIP2), within the missing 11p region, potentially responsible for triggering the aggressive and malignant phenotypes of PRL tumours. Our novel combined genomic and transcriptomic analysis underlines the importance of chromosome 11 allelic loss in aggressive and malignant PRL tumours and led us to propose a new strategy to find markers of progression in rare tumours.

overall_design: Transcriptomic analysis of Codelink Human Whole Genome Bioarray was performed for 13 prolactin tumors: 6 aggressive-invasive, 2 invasive, and 5 non-invasive.

first: Anne

last: WIERINCKX

first: Magali

last: ROCHE

first: Catherine

last: LEGRAS-LACHUER

first: Nicolas

last: NAZARET

first: Séverine

last: CROZE

first: Gérald

last: RAVEROT

last: REY

first: Carole

last: AUGER

first: Emmanuel

last: JOUANNEAU

first: Philippe

last: CHANSON

first: Jacqueline

last: TROUILLAS


title: ChIP-chip from mouse embryonic stem (mES) cells

status: Public on Oct 14 2010

city: Boston

first: Jonghwan

last: Kim

state: MA

address: 1 Blackfan circle Karp-7

institute: HMS/CHB

summary:
c-Myc (Myc) is an important transcriptional regulator in embryonic stem (ES) cells, somatic cell reprogramming, and cancer, yet functionally differs from the core pluripotency transcription factors, such as Oct4, Sox, and Nanog. Here, we identify a Myc-centered regulatory network in ES cells by combining protein-protein interaction and protein-DNA interaction studies, and show that Myc interacts with the NuA4 histone acetyltransferase complex, previously identified as a critical regulator in ES cell identity. In combination with previously studied transcriptional regulatory network information, we construct three ES cell modules (Core, Polycomb, and Myc) and show that these modules are functionally separable in ES, iPS, MEFs, and partial iPS cells, suggesting that the overall ES cell transcription program is comprised of distinct functional units. With these regulatory modules as an analytical tool, we have reassessed data suggesting that cancer cells reactivate an ES cell-like transcriptional program. We find that the Myc module, independent of the Core module, is active in various cancers and predicts cancer outcome. These observations argue against the hypothesis linking an embryonic gene expression signature with cancer or cancer stem cells. The apparent similarity of cancer and ES cell signatures reflects in large part the pervasive nature of Myc regulatory network.
Keywords: Biotin-mediated Chip-chip, Antibody ChIP-chip, Mouse embryonic stem cells

overall_design: Genomic targets of 5 transcription factors (Max, Dmap1, Tip60, Gcn5, and E2F4) and 2 histone modification signatures (AcH3, AcH4) were identified by biotin-mediated ChIP-chip (bioChIP-chip) in mouse ES cells.

first: J

first: A

last: Woo

last: Chu

last: Snow

first: Y

last: Fujiwara

first: C

middle: G

last: Cantor

first: S

middle: H

last: Orkin


title: Genome-Wide CRX Binding Sites in adult mouse photoreceptors

status: Public on Aug 17 2010

city: Regensburg

first: Thomas

last: Langmann

address: Franz-Josef-Strauss-Allee 11

department: University of Regensburg

institute: Institute of Human Genetics

summary: CRX is a key transcript factor for photoreceptor development and homeostasis. We have characterized the CRX-dependent cis-regulatory network by ChIP-chip analysis of 2 month old BL/6 mouse retinas using Affymetrix Mouse Promoter 1.0 arrays

overall_design: CRX versus IgG immunoprecipitations, 3 independent biological replicates were performed for each CRX and IgG immunoprecipitation


title: Genome-wide Sall1 and Nanog binding sites in mouse embryonic stem cells

status: Public on Nov 23 2010

city: Heraklion

first: Androniki

last: Kretsovali

state: Crete

address: Plastira 100

department: Institute of Molecular Biology & Biotechnology

country: Greece

institute: Foundation of Research & Technology

summary: Sall1 is a multi-zinc finger transcription factor that regulates kidney organogenesis. It is considered to be a transcriptional repressor, preferentially localized on heterochromatin. Mutations or deletions of the human SALL1 gene are associated with the Townes-Brocks syndrome. Despite its high expression, no function was yet assigned for Sall1 in embryonic stem (ES) cells. In the present study we show that Sall1 is expressed in a differentiation-dependent manner and physically interacts with Nanog and Sox2, two components of the core pluripotency network. Genome-wide mapping of Sall1-binding loci has identified 591 genes, 80% of which are also targeted by Nanog. A large proportion of these genes are related to self-renewal and differentiation. Sall1 positively regulates and synergizes with Nanog for gene transcriptional regulation. In addition, our data show that Sall1 suppresses the ectodermal and mesodermal differentiation. Specifically, the induction of the gastrulation markers T brachyury, Goosecoid and Dkk1 and the neuroectodermal markers Otx2 and Hand1 was inhibited by Sall1 overexpression during embryoid body differentiation. These data demonstrate a novel role for Sall1 as a member of the transcriptional network that regulates stem cell pluripotency.

overall_design: Stem cell Chromatin ChIPed with anti-Sall1 and anti-Nanog vs. anti-Fras (control ab) and INPUT

first: Efthimia

last: Karantzali

first: Vassilios

last: Lekakis