title: Gene expression from Inducible TOC1 expression in Arabidopsis seedlings

city: Raleigh

first: Colleen

last: Doherty

address: 128 Polk Hall CB7622

department: Biochemistry

institute: North Carolina State University

summary:
The first described feedback loop of the Arabidopsis circadian clock is based on reciprocal regulation between TOC1 and CCA1/LHY. CCA1 and LHY are MYB transcription factors that bind directly to the TOC1 promoter to negatively regulate its expression. Conversely, the activity of TOC1 has remained less well characterized. Genetic data supports that TOC1 is necessary for the reactivation of CCA1/LHY, but there is little description of its biochemical function. Here we show that TOC1 occupies specific genomic regions in the CCA1 and LHY promoters. Purified TOC1 binds directly to DNA through its CCT domain, which is similar to known DNA binding domains. Chemical induction and transient overexpression of TOC1 in Arabidopsis seedlings cause repression of CCA1/LHY expression demonstrating that TOC1 can repress direct targets, and mutation or deletion of the CCT domain prevents this repression showing that DNA binding is necessary for TOC1 action. Furthermore, we use the Gal4/UAS system in Arabidopsis to show that TOC1 acts as a general transcriptional repressor, and that repression activity is in the Pseudoreceiver (PR) domain of the protein. To identify the genes regulated by TOC1 on a genomic scale, we couple TOC1 chemical induction with microarray analysis and identify new potential TOC1 targets and output pathways. Together these results define the biochemical action of the core clock protein TOC1 and refine our perspective on how plant clocks function.

Keywords: Expression profiling by array

overall_design: Wildtype (Col-0) and ALC::TOC1 were sown on Murashige-Skoog with 0.8% agar, stratified for 48 hours and grown in12:12 light:dark(LD) for 12 days and either left in LD or transferred to LL and then grown for one more day before the start of the experiment. Tissue was submerged in Murashige-Skoog media supplemented with 2.5% ethanol or no ethanol (mock) and with 20mM MG132  for 3 hours and harvested at ZT1. Three replicates each of the seedlings were collected and frozen in liquid nitrogen.

first: Joshua

last: Gendron

last: Gross

first: Steve

last: Kay

first: Jose

last: Pruneda-Paz


title: Genome-wide analysis of gene expression and nuclear/cytoplasmic distribution by compound 1 treatment [293T_NS1-1]

status: Public on Jan 17 2012

city: Dallas

first: liang

last: zhang

state: Texas

address: 5323 harry hines blvd k2.202

country: USA

institute: utsw

summary:
Analysis of cellular response to DHODH inhibition at gene expression and nuclear/cytoplasmic distribution level.
The NS1 protein of influenza virus is a major virulence factor essential for virus replication as it re-directs the host cell to promote viral protein expression. NS1 inhibits cellular mRNA processing and export, down-regulating host gene expression and enhancing viral gene expression. We report here the identification of a non-toxic quinoline carboxylic acid that reverts the inhibition of mRNA nuclear export by NS1, in the absence or presence of virus. This quinoline carboxylic acid directly inhibited dihydroorotate dehydrogenase (DHODH), a host enzyme required for *de novo* pyrimidine biosynthesis, and partially reduced pyrimidine levels. This effect induced NXF1 expression, which promoted mRNA nuclear export in the presence of NS1. The release of NS1-mediated mRNA export block by DHODH inhibition also occurred in the presence of VSV M protein, another viral inhibitor of mRNA export. This reversal of mRNA export block allowed expression of antiviral factors. Thus, pyrimidines play a necessary role in the inhibition of mRNA nuclear export by virulence factors.

overall_design: Five million 293T cells were non-transfected or transfected with 6ug of pCAGGS-NS1 for 16h. Then, cells were untreated or treated with compound 1(5uM) for 24h. RNA from total cell extracts or from nuclear or cytoplasmic fractions were obtained

first: Liang

last: Zhang

first: Beatriz

last: Fontoura


title: Genome-wide analysis of gene expression and nuclear/cytoplasmic distribution by compound 1 treatment [293T-M]

overall_design: Five million 293T cells were non-transfected or transfected with 6ug of pEGFPN3-M-GFP for 16h. Then, cells were untreated or treated with compound 1(5uM) for 24h. RNA from total cell extracts or from nuclear or cytoplasmic fractions were obtained


title: Gene expression data from ABA, [5-(3,4-Dichlorophenyl)Furan-2-yl]-Piperidin-1-ylMethanethione (DFPM), and ABA+DFPM treated Arabidopsis thaliana seedlings.

status: Public on Dec 31 2011

city: La Jolla

first: Julian

last: Schroeder

state: CA

address: 9500 Gilman Drive #0116

department: Division of Biological Sciences

institute: UCSD

summary: Coordinated regulation of protection mechanisms against environmental abiotic stress and pathogen attack is essential for plant adaptation and survival. Initial abiotic stress can interfere with disease resistance signaling. Conversely, initial plant immune signaling may interrupt subsequent ABA signal transduction. However, the processes involved in cross talk between these signaling networks have not been determined. By screening a 9,600 compound chemical library, we identified a small molecule [5-(3,4-Dichlorophenyl)Furan-2-yl]-Piperidin-1-ylMethanethione that rapidly down-regulates ABA-dependent gene expression and also inhibits ABA-induced stomatal closure. Transcriptome analyses show that DFPM also stimulates expression of plant defense-related genes. Plate grown 12-day-old seedlings were transferred into 6 well plates with 1:5000 (V/V) DMSO in water as a control, 30uM DFPM, and 10uM ABA in water as a treatment for 6 hours. DFPM was added 30 min prior to ABA treatment. RNA was extracted using Trizol (Invitrogen, Carlsbad, CA, USA) and further purified using RNeasy Plant RNA purification kit (QIAgen, Valencia, CA, USA). Three biological replicates of ATH1 oligonucleotide arrays were hybridized with labeled samples from 1) wild-type Columbia (WT) untreated, 2) WT with 30uM DFPM treatment, 3) WT with 10uM ABA treatment, 4) WT with 30uM DFPM and 10uM ABA treatment. Each biological replicate was prepared by combining 7 independently-treated samples.

overall_design: Seedling treatments, 4 agent, 1 genotype/variation sets.

first: Taehoun

last: Kim

middle: I


title: DUX4 activates germline genes, retroelements and immune-mediators: Implications for facioscapulohumeral dystrophy

status: Public on Jan 03 2012

city: Seattle

first: Janet

middle: M.

last: Young

state: WA

address: 1100 Fairview Avenue N., C3-168,  P.O. Box 19024

department: Division of Human Biology

institute: Fred Hutchinson Cancer Research Center

summary: Facioscapulohumeral dystrophy (FSHD) is one of the most common inherited muscular dystrophies. The causative gene remains controversial and the mechanism of pathophysiology unknown. Here we identify genes associated with germline and early stem cell development as targets of the DUX4 transcription factor, a leading candidate gene for FSHD. The genes regulated by DUX4 are reliably detected in FSHD muscle but not in controls, providing direct support for the model that misexpression of DUX4 is a causal factor for FSHD. Additionally, we show that DUX4 binds and activates LTR elements from a class of MaLR endogenous primate retrotransposons and suppresses the innate immune response to viral infection, at least in part through the activation of DEFB103, a human defensin that can inhibit muscle differentiation. These findings suggest specific mechanisms of FSHD pathology and identify candidate biomarkers for disease diagnosis and progression.

overall_design:
[Overexpression experiment] Quadruplicate total RNA samples were collected from control human primary myoblasts transduced with lentivirus carrying DUX4-fl, DUX4-s or GFP (MOI = 15) for 24 h and from untransduced myoblasts.
[Defensin experiment] Quadruplicate samples were also collected from myoblasts and myotubes grown in media containing human beta-defensin 3 peptide or in control media.

first: Linda

middle: N

last: Geng

first: Zizhen

last: Yao

first: Lauren

last: Snider

first: Abraham

middle: P

last: Fong

first: Jennifer

last: Cech

middle: M

first: Silvere

last: van der Maarel

first: Walter

middle: L

last: Ruzzo

first: Robert

middle: C

last: Gentleman

first: Rabi

last: Tawil

first: Stephen

middle: J

last: Tapscott


title: AhNAS2 suppression in Arabidopsis halleri roots

city: Bayreuth

first: Stephan

last: Clemens

address: Universitaetsstrasse 30

department: Plant Physiology

country: Germany

institute: University of Bayreuth

summary: The model Zn hyperaccumulators Arabidopsis halleri and Noccaea caerulescens share elevated nicotianamine synthase (NAS) expression relative to non-accumulators among a core of alterations in metal homeostasis gene expression. Suppression of AhNAS2 expression by RNAi resulted in strongly reduced root NA accumulation and a concomitant decrease in root-to-shoot-translocation of Zn but not of other micronutrients. Few secondary effects on the root transcriptome were detected by microarray analysis.

overall_design: Vegetatively propagated clones of A. halleri wildtype plants and a line with strong suppression of AhNAS2 were grown hydroponically for weeks in two different media (control Hoagland and 10 µM Zn2+ added). Roots were harvested and analyzed. Three plants were pooled for one sample. Three independent experiments were performed.

first: Ulrich

last: Deinlein


title: Fork head targets in Stage 11 Drosophila embryos

city: Baltimore

first: Deborah

last: Andrew

state: MD

address: 725 N. Wolfe St., Hunterian G-1

department: Cell Biology

institute: Johns Hopkins University School of Medicine

summary: Transcription factors drive organogenesis, from the initiation of cell fate decisions to the maintenance and implementation of these decisions. The Drosophila embryonic salivary gland provides an excellent platform for unraveling the underlying transcriptional networks of organ development because Drosophila is relatively unencumbered by significant genetic redundancy.  The highly conserved FoxA family transcription factors are essential for various aspects of organogenesis in all animals that have been studied.  Here, we explore the role of the single Drosophila FoxA protein Fork head (Fkh) in salivary gland organogenesis using two genome-wide strategies.  A large-scale in situ hybridization analysis reveals a major role for Fkh in maintaining the salivary gland fate decision and controlling salivary gland physiological activity, in addition to its previously known roles in morphogenesis and survival.  The majority of salivary gland genes (59%) are affected by fkh loss, mainly at later stages of salivary gland development.  We show that global expression of Fkh cannot drive ectopic salivary gland formation.  Thus, unlike the worm FoxA protein PHA-4, Fkh does not function to specify cell fate.  In addition, Fkh only indirectly regulates many salivary gland genes, which is also distinct from the role of PHA-4 in organogenesis.  Our microarray analyses reveal unexpected roles for Fkh in blocking terminal differentiation and in endoreduplication in the salivary gland and in other Fkh-expressing embryonic tissues.  Overall, this study demonstrates an important role for Fkh in determining how an organ preserves its identity throughout development and provides an alternative paradigm for how FoxA proteins function in organogenesis.

overall_design: Three wild type (reference) samples were obtained from the Oregon R strain, age matched and treated the same as the three experimental samples isolated from Stage 11 fkh[6] mutant embryos.

first: Rika

last: Maruyama


title: Genome-wide analysis of Prokineticin-1-regulated genes in human term myometrium

city: Edinburgh

first: Roberto

last: Catalano

address: 47 Little France Crescent

department: The Queen's Medical Research Institute

country: United Kingdom

institute: MRC Human Reproductive Sciences Unit

summary: Infiltration of human myometrium and cervix with leukocytes and formation of a pro-inflammatory environment within the uterus has been associated with the initiation of both term and preterm parturition. The mechanism regulating the onset of this pro-inflammatory cascade is not fully elucidated. We demonstrate that prokineticin 1 (PROK1) is up-regulated in human myometrium and placenta during labour. Gene array analysis identified 65 genes up-regulated by PROK1 in human myometrium, mainly cytokines and chemokines including: Interleukin-1beta (IL1B), chemokine C-C motif ligand 3 (CCL3) and Colony Stimulating Factor 3 (CSF3). We additionally demonstrate that PROK1 increases expression of chemokines C-C motif ligand 20 (CCL20), Interleukin-6 (IL-6), Interleukin-8 (IL-8), prostaglandin synthase 2 (PTGS2) and prostaglandin E2 and F2α secretion. We propose that PROK1 is a novel inflammatory mediator that can contribute to onset of human parturition at term and partially mediate premature onset of inflammatory pathways during bacterial infection.

overall_design: Total RNA was extracted from human term non-labour myometrium explants treated with prokineticin for 6 and 24 hours compared to vehicle-treated explants. Six biological replicates were analyzed for each treatment and time point. Two of the 6-hour vehicle samples failed a quality-control analysis and were substituted with a 4-hour vehicle treatment from the same tissue sample in each case.

first: Marta

middle: R

last: Gorowiec

first: Rob

middle: D

first: Jane

middle: E

last: Norman

first: Fiona

last: Denison

first: Henry

last: Jabbour


title: Comparison of gene expression profiles between erf5/6 and WT Arabidopsis in response to chitooctaose

city: Columbia

first: Gary

last: Stacey

state: MO

address: 1201 Rollins Road

department: Plant Sciences

institute: University of Missouri-Columbia

summary: Transcription factors ERF5 and ERF6 may play a regulatory role in regulating the expression of chitin-responsive genes. We compared the gene expression profiles between the double mutant erf5/6 and WT plants in response to chitooctaose using the Affymetrix Arabidopsis Whole Genome Arrays.

overall_design: Both the double mutant erf5/6 and WT plants were grown in liquid MS medium in a growth chamber with constant light. Two-week-old seedlings were treated with chitooctaose at a final concentration of 1 uM for 30 minutes. The controls were similarly treated with an equivalent amount of ddH2O. The treated seedlings were harvested for RNA isolation. Three biological replicates were conducted for the experiment.

first: Jinrong

last: Wan

first: Geon-hui

last: Son


title: IL-22 down-regulates filaggrin expression and affects expression of profilaggrin processing enzymes by keratinocytes

status: Public on Dec 30 2011

city: Oxford

last: Taylor

address: Headington

institute: CBRG

summary: Genome-wide analysis of gene expression after stimulation with cytokines to assess the main processes, molecular functions and cellular components affected as well as genes related to skin barrier function.

overall_design: HaCaT cells were exposed to IL-22 (200ng/ml) for 12h. The cells were lysed, total RNA was extracted and microarray study was performed on Illumina HT12 platform.

first: Graham

middle: S

last: Ogg

first: Danuta

last: Gutowska-Owsiak


title: In vitro knockdown of LAMP3 leads to down-regulation of  interferon-inducible genes

status: Public on Dec 29 2011

city: Bethesda

first: Natalia

last: Shulzhenko

address: 9000 Rockville Pike

department: Laboratory of Cellular and Molecular Immunology

institute: NIAID, USA

summary: We identified LAMP3 as a key driver gene of anti-viral subnetwork genes in cervical cancer patients. Therefore we tested this prediction using an in vitro system. This is the first direct demonstration of LAMP3 regulatory role in interferon-dependent immune response.

overall_design: We first pretreated HeLa cells with control siRNA or LAMP3 siRNA overnight and then added 1 ng/ml of interferon alpha to the cultures for 3 and 4 days

first: Andrey

last: Morgun


title: mRNA microarray analysis on young adult Caenorhabditis elegans, Drosophila melanogaster, and Danio rerio exposed to benzene, toluene, and formaldehyde

city: seoul

first: jinhee

last: choi

address: 90 Jeonnong-dong, Dongdaemun-gu

department: College of Urban Science

country: South Korea

institute: University of Seoul

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

sample_organism:
Caenorhabditis elegans
Drosophila melanogaster
Danio rerio

overall_design: Refer to individual Series


title: mRNA microarray analysis on young adult Drosophila exposed to benzene, toluene, and formaldehyde

summary: In order to evaluate the identification of genes and pathways, the global gene expression profiles were assessed in response to three chemicals (benzene (B), toluene (T), formaldehyde (F)) on Drosophila melanogaster. We performed whole genome DNA microarray experiments with subsequent quantitative analysis conducted on selected genes.

overall_design: We used young adults of D. melanogaster exposed to B, T, or F, and whole genome microarrays to screen for global changes in D. melanogaster transcription profiles. Young adult flies were selected for RNA extraction and hybridization on Affymetrix microarrays.

first: Jinhee

last: Choi

first: Hyun-jeong

last: Eom


title: Routine use of microarray-based gene expression profiling to identify patients with low cytogenetic risk acute myeloid leukemia: accurate results can be obtained even with suboptimal samples. (test samples)

status: Public on Dec 24 2011

city: Angers

first: Philippe

last: Guardiola

state: Maine et Loire

address: 4 rue Larrey

country: France

institute: Angers University Hospital

summary: Background: Gene expression profiling has shown its ability to identify with high accuracy low cytogenetic risk acute myeloid leukemia such as acute promyelocytic leukemia and leukemias with t(8;21) or inv(16). The aim of this gene expression profiling study was to evaluate to what extent suboptimal samples with low leukemic blast load (range, 2-59%) and/or poor quality control criteria could also be correctly identified. Methods: Specific signatures were first defined so that all 71 acute promyelocytic leukemia, leukemia with t(8;21) or inv(16)-AML as well as cytogenetically normal acute myeloid leukemia samples with at least 60% blasts and good quality control criteria were correctly classified (training set). The classifiers were then evaluated for their ability to assign to the expected class 111 samples considered as suboptimal because of a low leukemic blast load (n=101) and/or poor quality control criteria (n=10) (test set). Results: With 10-marker classifiers, all training set samples as well as 97 of the 101 test samples with a low blast load, and all 10 samples with poor quality control criteria were correctly classified. Regarding test set samples, the overall error rate of the class prediction was below 4 percent, even though the leukemic blast load was as low as 2%. Sensitivity, specificity, negative and positive predictive values of the class assignments ranged from 91% to 100%. Of note, for acute promyelocytic leukemia and leukemias with t(8;21) or inv(16), the confidence level of the class assignment was influenced by the leukemic blast load. Conclusion: Gene expression profiling and a supervised method requiring 10-marker classifiers enable the identification of favorable cytogenetic risk acute myeloid leukemia even when samples contain low leukemic blast loads or display poor quality control criterion.

first: Diane

last: de la Blétière

first: Odile

last: Blanchet

first: Pascale

last: Cornillet-Lefèbvre

first: Anne

last: Coutolleau

first: Laurence

last: Baranger

first: Franck

last: Geneviève

first: Isabelle

last: Luquet

first: Mathilde

last: Hunault-Berger

first: Annaelle

last: Beucher

first: Aline

last: Schmidt-Tanguy

first: Marc

last: Zandecki

first: Yves

last: Delneste

first: Norbert

last: Ifrah


title: Transcript profiling of three genotypes by ultraviolet-B (UV-B) radiation

city: Yokohama

first: Miyako

last: Kusano

state: Kanagawa

address: 1-7-22, Suehiro, Tsurumi

country: Japan

institute: RIKEN CSRS

summary: Due to ever increasing environmental deterioration it is likely that influx of solar UV-B radiation (280-320 nm) will increase further due to the depletion of stratospheric ozone. Given this fact it becomes essential that we better understand both rapid and adaptive responses of plants to UV-B imposed stress. Here we compare the transcriptmic responses of wild type Arabidopsis to that of Arabidopsis mutants impaired in flavonoid (TRANSPARENT TESTA4 [tt4] or sinapoyl-malate (sinapoylglucose accumulator 1 [sng1]) biosynthesis, to a short, 24h exposure to this photo-oxidative stress. In control experiments we subjected the same genotypes to 24h treatments of continuous light.

overall_design: Total 18 samples; number of biological replicates, n = 3 each; 2 different light treatments; three genotypes

first: Hitomi

last: Otsuki


title: Expression data from ozone-treated wild-type and G-protein null mutant Arabidopsis lines

first: Fitzgerald

middle: Lewis

last: Booker

state: NC

address: 3127 Ligon Street

department: Plant Science Research

institute: USDA-ARS

summary:
Ozone pollution decreases plant growth and yield worldwide.  Some of the effects are genetically-mediated and are reported to involve G-protein signaling pathways.  Effects of ozone on gene expression were examined in wild-type and G-protein null mutants to determine affected genes and to determine differential responses that may help define affected pathways.
We used microarrays to examine changes in gene expression in response to ozone exposure and identified distinct classes of up- and down-regulated genes in wild-type and G-protein null mutant genotypes.

overall_design: Columbia wild-type and G-protein null mutant gpa1-4/agb1-2 plants were exposed to 5 or 125 ppb ozone in controlled environment chambers for two days.  Leaves were sampled after 3 h and 2 d of exposure to examine early and late gene expression changes.

first: Kent

middle: O

last: Burkey

first: Alan

last: Jones


title: Gene expression profile of STAT3 in ovarian cancer cell (SKOV3ip1)

status: Public on Dec 22 2011

city: Houston

first: Sangbae

last: Kim

state: TX

address: 1 Baylor plaza

department: HGSC

institute: Baylor Colleage of Medicine

summary: RNA interference (RNAi) holds tremendous potential as a therapeutic approach, especially in the treatment of malignant tumors. However, efficient and biocompatible delivery methods are needed for systemic delivery of siRNA. To achieve this goal, we have established a novel formulation of siRNA by incorporating it into reconstituted high density lipoprotein (rHDL) nanoparticles. Here, we demonstrate that rHDL nanoparticles facilitate highly efficient systemic delivery of siRNA in vivo, mediated by the scavenger receptor type B1 (SR-B1). Moreover, in therapeutic proof-of-concept studies, these nanoparticles were effective in targeting either signal transducer and activator of transcription 3 (STAT3) or focal adhesion kinase (FAK) expression in orthotopic mouse models of ovarian and colorectal cancer. These data indicate that an rHDL nanoparticle is a novel and highly efficient siRNA carrier, and therefore this novel technology could serve as the foundation for new cancer therapeutic approaches.

overall_design: To identify the role of STAT3 in ovarian cancer cell, we performed microarray after knocking down STAT3 in ovarican cancer cells (3 siCon and 3 siSTAT3).

first: Mian

last: Shahzad

first: Yun-Yong

last: Park

first: Ju-seog

last: Lee

first: Anil

middle: K

last: Sood


title: Gene expression profile of NR2E3 in MCF7 cells

summary:
While the roles of individual nuclear receptor (NR) in human diseases have been well characterized, interplays among NRs have not been extensively characterized due, in part, to technical difficulties in simultaneously monitoring molecular activities of all 48 NR genes. Using systems-level analysis of publically available gene expression data from NCI-60 cell lines, we uncovered novel interaction between ESR1 and orphan receptor NR2E3. Expression of NR2E3 is significantly associated with expression of ESR1 in NCI-60 cell lines as well as in breast cancer patients. To investigate how NR2E3 gene signatures are globally correlated with ESR1 signaling pathway, we performed microarray after knocking down NR2E3 or ESR1 in MCF-7 cells.

Keywords: DNA microarray (Illumina human Ht12 V3)

overall_design: 3 shControl, 3 shNR2E3, 3 siLuc, 3 siESR1


title: Routine use of microarray-based gene expression profiling to identify patients with low cytogenetic risk acute myeloid leukemia: accurate results can be obtained even with suboptimal samples (training samples)

status: Public on Dec 21 2011

first: Philippe

last: Guardiola

summary: Background: Gene expression profiling has shown its ability to identify with high accuracy low cytogenetic risk acute myeloid leukemia such as acute promyelocytic leukemia and leukemias with t(8;21) or inv(16). The aim of this gene expression profiling study was to evaluate to what extent suboptimal samples with low leukemic blast load (range, 2-59%) and/or poor quality control criteria could also be correctly identified. Methods: Specific signatures were first defined so that all 71 acute promyelocytic leukemia, leukemia with t(8;21) or inv(16)-AML as well as cytogenetically normal acute myeloid leukemia samples with at least 60% blasts and good quality control criteria were correctly classified (training set). The classifiers were then evaluated for their ability to assign to the expected class 111 samples considered as suboptimal because of a low leukemic blast load (n=101) and/or poor quality control criteria (n=10) (test set). Results: With 10-marker classifiers, all training set samples as well as 97 of the 101 test samples with a low blast load, and all 10 samples with poor quality control criteria were correctly classified. Regarding test set samples, the overall error rate of the class prediction was below 4 percent, even though the leukemic blast load was as low as 2%. Sensitivity, specificity, negative and positive predictive values of the class assignments ranged from 91% to 100%. Of note, for acute promyelocytic leukemia and leukemias with t(8;21) or inv(16), the confidence level of the class assignment was influenced by the leukemic blast load. Conclusion: Gene expression profiling and a supervised method requiring 10-marker classifiers enable the identification of favorable cytogenetic risk acute  myeloid leukemia even when samples contain low leukemic blast loads or display poor quality control criterion.

overall_design: Training set.

first: Diane

last: Raingeard de la Blétière

first: Odile

last: Blanchet

first: Pascale

last: Cornillet-Lefèbvre

first: Anne

last: Coutolleau

first: Laurence

last: Baranger

first: Franck

last: Geneviève

first: Isabelle

last: Luquet


title: MicroRNAs and their isomiRs function cooperatively to target common biological pathways (Illumina expression beadchip)

city: Brisbane

first: Nic

last: Waddell

address: St Lucia

country: Australia

institute: Queensland Centre for Medical Genomics

summary: Variants of microRNAs, (isomiRs) are commonly reported in deep-sequencing studies; however the functional significance of these variants remains controversial. To assess their biological relevance, we have performed ultra-deep miRNA-seq on ten adult human tissues, and created an analysis pipeline (miRNA-MATE) to align, annotate, and analyze miRNAs and their isomiRs. We find that isomiRs share sequence and expression characteristics with canonical miRNAs, and are generally strongly correlated with canonical miRNA expression. We isolated polyribosome-associated mRNA, and captured the mRNA-bound miRNAs, and found that isomiRs and canonical miRNAs are equally associated with translational machinery. Finally, we transfected cells with biotinylated RNA duplexes encoding isomiRs or their canonical counterparts and directly assayed their mRNA targets. These studies showed substantial overlap in functional mRNA networks suppressed by both canonical miRNAs and their isomiRs. Together, these results find isomiRs to be biologically relevant and functionally synergistic partners of canonical miRNAs that act coordinately to target pathways of functionally related genes. This work exposes the complexity of the miRNA-transcriptome, and helps explain a major miRNA paradox: how specific regulation of biological processes can occur with predominantly non-specific miRNA-mRNA interactions.

overall_design:
HEK293T cells were transfected with biotinylated miRNAs (either mir-10a-iso, mir-10a, mir-10b-iso or mir-10b) or a mock control. The miRNAs and target mRNA were pulled down with streptavidin. The pulled down RNA was hybridised to Illumina microarrays.

The miRNA-Seq data have been submitted to the short read archive under SRA number SRP006043: http://www.ncbi.nlm.nih.gov/sra?term= SRP006043

first: Nicole

last: Cloonan


title: Drosophila brain gene expression with age: mRNA profiling

status: Public on Dec 23 2011

city: Philadelphia

first: Bonini

last: Nancy

state: PA

address: 415 S University Ave

institute: University of Pennsylvania

summary: gene expression profiles in fly brains with age

overall_design: gene expression profiles in fly brains, 3d, 30d and 60d

last: Liu


title: Genome-wide analysis of gene expression profiles in individuals infected with the Human T-Lymphotropic virus Type 1 (HTLV-1) - train set

status: Public on Jan 01 2012

city: London

first: Charles

middle: R. M.

last: Bangham

address: Norfolk Place

department: Immunology

institute: Imperial College London

summary: Infection with the human T lymphotropic virus type 1 (HTLV-1) remains asymptomatic in the majority of carriers; however, some 5% develop a chronic inflammation of the central nervous system termed HTLV-1-associated myelopathy (HAM). It is not well understood how the virus triggers the onset of HAM after many years of clinical latency and importantly, what distinguishes hosts who develop the disease from those who remain asymptomatic. In this study we tested the hypothesis that patients with HAM can be distinguished from asymptomatic HTLV-1 carriers (ACs) and uninfected subjects by their whole blood transcriptional profiles. Here, we compare unstimulated whole blood gene expression profiles of 20 asymptomatic HTLV-1 carriers (ACs), 10 patients with HAM and 9 uninfected healthy control subjects to (1) identify a transcriptional signature associated with presence of HAM and (2) identify cell types and pathways abnormally regulated in HAM by canonical and modular pathway analysis.

overall_design: Patients attending the HTLV-1 clinic at St Mary’s hospital in London, UK were classified according to their clinical status as asymptomatic HTLV-1 carriers (ACs, n=20), patients with HTLV-1-associated meylopathy (HAM, n=10) or uninfected control subjects (n=9). HTLV-1 proviral load (PVL) can differ among individuals by more than 10-fold and is typically higher in patients with HAM than in ACs, with a 1% PVL cut off generally separating disease from asymptomatic carriage. Thus, ACs were subdivided into AC low PVL (<1% infected PBMCs) and AC high PVL (>1% infected PBMCs). Three ml of blood were drawn into a Tempus tube (Applied Biosystems, Foster City, CA, USA). Total RNA was extracted, globin mRNA depleted and following cRNA generation samples were analysed on HUmanHT12 v3 Illumina BeadChip arrays.

first: Sonja

last: Tattermusch

first: Jason

middle: A

last: Skinner

first: Damien

last: Chaussabel

first: Jacques

last: Banchereau

first: Matthew

last: Berry

first: Finlay

middle: W

last: McNab

last: O'Garra

first: Graham

last: Taylor


title: Trachealess (Trh) regulates all tracheal genes during Drosophila embryogenesis

first: Deborah

last: Andrew

summary:
Abstract: The Drosophila trachea is a branched tubular epithelia that transports oxygen and other gases. trachealess (trh), which encodes a bHLH-PAS transcription factor, is among the first genes to be expressed in the cells that will form the trachea. In the absence of trh, tracheal cells fail to invaginate to form tubes and remain on the embryo surface. Expression of many tracheal-specific genes depends on trh, but all of the known targets have relatively minor phenotypes compared to loss of trh, suggesting that there are additional targets. To identify uncharacterized transcriptional targets of Trh and to further understand the role of Trh in embryonic tracheal formation, we performed an in situ hybridization screen using a library of ~100 tracheal-expressed genes identified by the Berkeley Drosophila Genome Project (BDGP). Surprisingly, expression of every tracheal gene we tested was dependent on Trh, suggesting a major role for Trh in activation and maintenance of tracheal gene expression. A re-examination of the interdependence of the known early-expressed transcription factors, including trh, ventral veinless (vvl) and knirps/knirps-related (kni/knrl), suggests a new model for how gene expression is controlled in the trachea, with trh regulating expression of vvl and kni, but not vice versa. A pilot screen for the targets of Vvl and Kni/Knrl revealed that Vvl and Kni have only minor roles compared to Trh. Finally, genome-wide microarray experiments identified additional Trh targets and revealed that a of biological processes are affected by the loss of trh.
Goals:  The goals of the microarray experiments were to identify additional targets of the Trh transcription factor to learn the range of genes regulated by this transcription factor during embryogenesis.  Our in situ screen revealed that Trh is required for all tested tracheal genes.  Our new data now shows that Trh affects a range of biological processes.

overall_design: RNA was isolated from stage 11-16 wild type Drosophila embryos and compared to RNA from trh null mutant embryos of the same age; all samples were hybridized to the Drosophila Genome 2.0 Affymetrix array.  Three individual replicates were obtained for each sample.

first: SeYeon

last: Chung


title: MicroRNAs and their isomiRs function cooperatively to target common biological pathways

type:
Expression profiling by array
Non-coding RNA profiling by array

overall_design:
Refer to individual Series
This represents the miRNA placenta samples and mRNA + miRNA pulldown only
The miRNA-Seq data have been submitted to the short read archive under SRA number SRP006043: http://www.ncbi.nlm.nih.gov/sra?term= SRP006043


title: Drosophila brain gene expression between wildtype and miR-34 null flies

summary: gene expression profiles in fly brains between wildtype and miR-34 null flies

overall_design: gene expression profiles in fly brains, wild type (3d, 20d) and miR-34 null flies (3d, 20d)


title: Depot-dependent effects of maternal nutrient restriction on baboon fetal preadipocyte global gene profiles

status: Public on Dec 16 2011

city: Baton Rouge

first: Yourka

last: Tchoukalova

state: LA

address: 6400 Perkins Road

institute: Penninton BioMedical Research Center

summary: Suboptimal intrauterine nutrition predisposes the fetus to central obesity and metabolic syndrome in adult life,  suggesting nutritional programming of the fat distribution. However, the underlying mechanisms are not elucidated. We hypothesized that prenatal nutritional deprivation leads to stimulation of adipogenesis, as an adaptive mechanism, in a depot-dependent manner.  The induction of adipogenesis is most enhanced in the subcutaneous lower-body  depots, followed by the subcutaneous upper-body and visceral adipose tissue depots.  Stimulation of adipogenesis may lead to an early consumption of the stem cell pool, and thus, may impair adipose tissue expandability postnatally, which may lead to differences in regional adipose tissue growth.  We tested this hypothesis by analyzing global gene expression to identify expression patterns in subcutaneous abdominal, subcutaneous  femoral, and omental adipose depots of baboon fetuses that have been altered by nutritional maternal deprivation. Adipose tissue was collected from baboon fetuses at 165 dG from mothers fed control or 30% nutrient-restricted diets (three females and one male in each group).

overall_design: 24 samples, each consisted of pooled total RNA from triplicate wells (6-well plate).

first: Ursula

last: White

first: Xiaobing

last: Fang

first: Peter

last: Nathanielsz


title: Differential gene expression in ovarian cancer cell lines treated with vehicle or norepinephrine

status: Public on Dec 14 2011

first: Guillermo

last: Armaiz-Pena

address: 1515 Holcombe Blvd

institute: University of Texas MD Anderson Cancer Center

summary: Gene expression profiling was carried out HeyA8 and SKOV3-ip1 ovarian cancer cell lines, treated either with vehicle control or 10 uM norepinephrine.  The primary research question is whether ovarian cancer cell gene expression differs as a function of norepinephrine exposure.

first: G

last: Pena


title: Gene expression profilling of poorly metastatic MDA cells and highly metastatic LM2 cells.

city: New York

first: Nils

last: Halberg

state: NY

address: 1230 York Avenue

institute: Rockefeller University

summary: Comparison of gene expression between the breast cancer cell line MDA-MB-231 and its highly metastatic deriviate LM2 cells (described in Minn et al., Nature 2005). Results hilghlights potential metastasis promoting and suppressing genes.

overall_design: 4 Samples

first: Halberg

last: Nils

first: Png

last: Kim

first: Tavazoie

last: Sohail


title: dKDM2 couples histone H2A ubiquitylation to histone H3 demethylation during Polycomb group silencing.

status: Public on Dec 13 2011

city: Rotterdam

first: Yuri

last: Moshkin

address: Dr. Molewaterplein 50

country: Netherlands

institute: Erasmus University Medical Center

summary:
Transcription regulation involves enzyme-mediated changes in chromatin structure. Here, we describe a novel mode of histone crosstalk during gene silencing, in which histone H2A monoubiquitylation is coupled to the removal of histone H3 Lys 36 dimethylation (H3K36me2). This pathway was uncovered through the identification of dRING-associated factors (dRAF), a novel Polycomb group (PcG) silencing complex harboring the histone H2A ubiquitin ligase dRING, PSC and the F-box protein, and demethylase dKDM2. In vivo, dKDM2 shares many transcriptional targets with Polycomb and counteracts the histone methyltransferases TRX and ASH1. Importantly, cellular depletion and in vitro reconstitution assays revealed that dKDM2 not only mediates H3K36me2 demethylation but is also required for efficient H2A ubiquitylation by dRING/PSC. Thus, dRAF removes an active mark from histone H3 and adds a repressive one to H2A. These findings reveal coordinate trans-histone regulation by a PcG complex to mediate gene repression.
Microarray analysis of dKDM2, dRING, PC, PH and PSC target genes in Drosophila S2 cells

overall_design: Expression profiles of Drosophila S2 cells RNAi depleted (KD) for dKDM2, dRING, PC, PH or PSC were compared with expression profile of untreated S2 cells (Mock)

first: Anna

last: Lagarou

first: Adone

last: Mohd-Sarip

first: C

last: Verrijzer


title: Cooperation between Androgen Receptor and Polycomb in oncogenic transformation

status: Public on Dec 11 2011

city: Chicago

first: Jindan

last: Yu

state: IL

address: 303 E. Superior St.

department: Medicine - Hem/Onc

institute: Northwestern University

summary:
Androgen receptor (AR) is a hormone-activated transcription factor that plays important roles in prostate development, function, as well as malignant transformation.  The downstream pathways of AR, however, are incompletely understood.  AR has been primarily known as a transcriptional activator inducing prostate-specific gene expression.  Through integrative analysis of genome-wide AR occupancy and androgen-regulated gene expression, here we report AR as a globally acting transcriptional repressor.  This repression is mediated by androgen responsive elements (ARE) and dictated by Polycomb group protein EZH2 and repressive chromatin remodeling.  In embryonic stem cells, AR-repressed genes are occupied by EZH2 and harbor bivalent H3K4me3 and H3K27me3 modifications that are characteristic of differentiation regulators, the silencing of which maintains the undifferentiated state.  Concordantly, these genes are silenced in castration-resistant prostate cancer rendering a stem cell-like lack of differentiation and tumor progression.   Collectively, our data reveal an unexpected role of AR as a transcriptional repressor inhibiting non-prostatic differentiation and, upon excessive signaling, resulting in cancerous de-differentiation.  It provides an innovative mechanism for castration resistance and highlights novel therapeutic strategies to treat advanced prostate cancer.
Keywords: Genetic Modification

overall_design: compare gene expression in different cell lines with or without androgen treatment or EZH2 knockdown


title: Expression data from Control and Yorkie overexpression  pupal eye discs

status: Public on Dec 20 2011

city: Los Angeles

first: Shubha

last: Gururaja Rao

address: 5032 Terasaki Life Sciences Building, 621 Charles E. Young Drive South

department: MCDB

institute: UCLA

summary: To probe mechanistic determinants of Yki function in mitochondrial biogenesis, we conducted a genome-wide microarray experiment, and specifically compared expression patterns of genes from control (GMR gal4) and Yorkie over-expressing (GMR gal4; UAS yki) pupal eye discs.

overall_design: The above mentioned genotypes were grown at 29 deg C and at about 40 hrs after pupariation, the pupal eye discs were dissected. RNA was extracted from the pupal eye discs, purified and used to generate microarray probes that were hybridized to the Drosophila genome 2 arrays (Affymetrix). The Gene Chip Operating system (Affymetrix) and dCHIP program (Harvard University) were used to generate pairwise comparisons between the transcription profiles of control and Yorkie over-expressing discs.

middle: G

last: Rao

first: Utpal

last: Banerjee


title: Transcriptome analysis of genes regulated by overexpression of LATERAL ORGAN BOUNDARIES (LOB) in Arabidopsis thaliana

status: Public on Dec 07 2011

city: Riverside

first: Patricia

last: Springer

address: 900 University Ave

department: Botany and Plant Sciences

institute: University of California

summary: The Arabidopsis thaliana transcription factor LATERAL ORGAN BOUNDARIES (LOB) is expressed in the boundary between the shoot apical meristem and initiating lateral organs. To identify genes regulated by LOB activity, we used an inducible 35S:LOB-GR line. This analysis identified genes that are differentially expressed in response to ectopic LOB activity.

overall_design: 35S:LOB-GR and Col wild-type seedlings were treated with dexamethasone (DEX) or mock-treated. Three biological replicates were conducted for each treatment.

first: P


title: Transient MPK6 activation in response to oxygen deprivation and reoxygenation is mediated by mitochondria and aids seedling survival in Arabidopsis.

status: Public on Dec 03 2011

first: Charles

last: Jang

address: 2215 Batchelor Hall

institute: UC Riverside

summary:
MPK6 shows transient increase in activity under hypoxia with maximal activity at 2 hrs.  To study the role of MPK6 in hypoxia in Arabidopsis, 10 do seedlings of WT, mpk6 and MPK6 plants were exposed to 2 hrs hypoxia and 2hr air (mock).
Because there are no major phenotypic differences between the genotypes, microarray was used to determine if there were transcript level differences between the genotypes.

overall_design: Wild type Col-0, MPK6 overexpression and mpk6 knockout mutants were exposed to 2 hr hypoxia and air and separated into root and shoot in order to determine the role of MPK6 in hypoxia in both root and shoot.

first: Ruth

last: Chang

first: Cristina

last: Branco-Price

last: Nghiem

first: Julia

last: Bailey-Serres


title: Selective roles of p300 and CBP in androgen regulated gene expression

status: Public on Dec 15 2011

first: Dai-Ying

last: Wu

address: 1441 Eastlake Ave, NOR 6314

institute: University of Southern California

summary:
C4-2B prostate cancer cells were transfected with siRNA against a non-specific (NS) sequence, siRNA specifically targeting EP300, or siRNA specifically targeting CREBBP.
We tested the hypothesis that their exists different subgroups of genes that are preferentially affected by p300 or CBP depletion.

overall_design: Cells were treated with 10nM dihydrotestosterone (DHT) for 16 hours and total RNA was extracted to check for changes in gene expression.

first: Michael

last: Stallcup

first: Irina

last: Ianculescu


title: Drosophila miR-34 mechanistically links aging and neurodegeneration

first: Bonini

last: Nancy

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

overall_design: Aging is the most prominent risk factor for human neurodegenerative disease, but underlying mechanisms that connect two processes are less well characterized.  With age, the brain undergoes functional decline and perhaps degeneration.  Such decline may not just contribute to normal aging, but also enhance susceptibility to and progression of age-related neurodegenerative diseases. Therefore, defining intrinsic factors and pathways that underline the normal integrity of the adult nervous system may lead to insights that potentially link aging and neurodegeneration.  Here, we report a highly conserved microRNA (miRNA), miR-34, as a modulator of aging and neurodegeneration.  Using Drosophila, we show that fly miR-34 expression is brain-enriched and strikingly upregulated with age.  Functional studies reveal that, whereas animals without miR-34 are normal as young adults, upon aging, they gradually show late-onset deficits characteristic of accelerated brain aging; these include a transcriptional signature of aged animals, coupled with rapid functional decline, loss of brain integrity, followed by a catastrophic decline in adult viability.  Moreover, upregulation of miR-34 protects against neurodegeneration induced by pathogenic human polyglutamine (polyQ) disease protein.  We next reveal a dramatic effect of miR-34 to silence the Eip74EF gene of steroid hormone pathways in the adult, which is crucial to maintain the normal aging.  Collectively, these data define a miR-34-mediated mechanism that specifically affects long-term integrity of the adult nervous system.  miR-34 function in Drosophila may thus present a link that functionally connects aging and neurodegeneration.  Our studies implicate essential roles of miRNA- dependent pathways in maintenance of the adult brain, disease pathogenesis and healthy aging.


title: A novel recurrent mutation in MITF predisposes to familial and sporadic melanoma

status: Public on Dec 01 2011

first: Glen

last: Boyle

state: Queensland

address: 300 Herston Road Herston

department: Department of Cell and Molecular Biology, Cancer Program

institute: QIMR Berghofer Medical Research Insitute

summary: We identified a novel germline mutation of the microphthalmia-associated transcription factor (MITF - E318K).  This mutation was found to be present in numerous melanoma families, as well as the general population, where its association with melanoma has a significant effect.  We determined the effect of the E318K mutation on global MITF target gene transcription. We developed a tetracycline-inducible system for expression of wild type MITF or the E318K variant in melanoma cell lines with constitutively low or undetectable levels of endogenous MITF (HT144 and C32).  We examined whole-genome expression profiles in these cells following induction of either wild-type or E318K MITF for 48 hours.  Analysis suggests that the MITF E318K mutant exhibits differential transcriptional activity against some, though not all, target genes.

overall_design: Expression profiling by array

first: Satoru

last: Yokoyama

first: Susan

last: Woods

first: Lauren

last: Aoude

first: Stuart

last: MacGregor

first: Victoria

last: Zismann

last: Gartside

first: Anne

last: Cust

first: Rizwan

last: Haq

first: Mark

last: Harland

first: John

last: Taylor

first: David

last: Duffy

first: Kelly

last: Holohan

first: Ken

last: Dutton-Regester

first: Jane

last: Palmer

first: Vanessa

last: Bonazzi

first: Mitchell

last: Stark

first: Judith

last: Symmons

first: Matthew

middle: H

last: Law

first: Christopher

last: Schmidt

first: Cathy

last: Lanagan

first: Linda

last: O'Connor

first: Elizabeth

last: Holland

first: Helen

last: Schmid

last: Maskiell

first: Jodie

last: Jetann

first: Megan

last: Ferguson

last: Jenkins

first: Richard

middle: F

last: Kefford

first: Graham

last: Giles

first: Bruce

last: Armstrong

first: Joanne

last: Aitken

last: Hopper

last: Whiteman

first: Paul

last: Pharoah

first: Douglas

last: Easton


title: Deciphering the genetic architecture of variation in the immune response to Mycobacterium tuberculosis infection (expression)

status: Public on Dec 06 2011

city: Montreal

first: luis

last: Barreiro

state: Quebec

address: 3175 Chemin de la Côte Sainte-Catherine

country: Canada

institute: luis

summary: Identification of genetic polymorphisms associated with inter-individual variation in immune response to Mycobacterium tuberculosis infection.

overall_design: We performed a genome-wide mapping study of loci that are associated with functional variation in immune response to MTB. Specifically, we characterized transcript and protein expression levels and mapped expression quantitative trait loci (eQTLs) in primary dendritic cells from 65 individuals, before and after infection with MTB

first: Luis

middle: B

first: Ludovic

last: Tailleux

first: Athma

last: Pai

first: Brigitte

last: Gicquel

first: John

last: Marioni

first: Yoav

last: Gilad


title: A systemic view of coordinated root responses to NO3- heterogeneous environment in Arabidopsis

city: NYC

first: Sandrine

last: Ruffel

address: 100 Washington Square East. 1009 Main Building

department: Biology

institute: New York University

summary:
We investigated the morphological roots decisions of Arabidopsis in a NO3- heterogeneous medium. To do so, we used the Split-Root System which is an experimental set up to assess root decisions in nutrient heterogeneous medium. Split-root plants have been subjected to three different treatments. ‘Control KNO3’ plants received KNO3 on both sides of the root system (C.NO3) and ‘Control KCl’ plants received KCl on both sides (C.KCl) as a nitrogen deprivation treatment. 'Split' plants received KNO3 on one side (Sp.NO3) and KCl on the other side (Sp.KCl) of the root system to assess the root decision-making in a heterogeneous environment.
We observed that the total lateral roots length in the Sp.NO3 and C.KCl compartments is induced as compared to C.NO3 and Sp.KCl compartments. This corresponds to a root proliferation response in strategic territories to compensate the nitrogen deprivation. To decipher the molecular basis of this morphological root response on day 4 after the beginning of the split-root treatment, we used a transcriptomic approach on roots at 2hours, 8 hours and 2 days after the beginning of the treatment. From our microarrays data, we have identified a global set of 150 genes for which the expression pattern match with the lateral roots responses. Among them, we selected 8 early marker genes of the root decisions, which allowed us to show that the shoots and the NO3- itself are essential for the decision. Finally, we tested the role of the cytokinins phytohormones as a NO3--derived systemic signal in the root decision. Interestingly, we have demonstrated that the systemic cytokinins are involved into the decision of inducing maker genes expression and making lateral roots in the Sp.NO3 compartment specifically.

overall_design: 36 samples were analyzed. They correspond to three biological repeats of the C.NO3, Sp.NO3, Sp.KCl and C.KCl root samples (12 samples) that we have collected at 2hours, 8 hours and 2 days (12 samples x 3 time points) after the beginning of the split-root treatment. We analyzed the normalized microarrays data by using a three way ANOVA. The three factors of the ANOVA are 1) presence/absence of NO3-, 2) split/control and 3) time. The measures of the significance of each probe were done by the Q-value method (q<0.2, panova<0.001). The genes differentially expressed between the C.NO3 and Sp.NO3 samples, and the C.KCl and Sp.KCl samples were determined by the post-hoc Tukey test (p<0.05).

first: Gabriel

last: Krouk

first: Gloria

middle: M

last: Coruzzi

first: Kenneth

last: Birnbaum


title: NSD2 links dimethylation of histone H3 at lysine 36 to oncogenic programming [TKO]

status: Public on Nov 29 2011

first: kaifu

last: chen

address: 1 Baylor plaza, suite 450A

institute: Baylor College of Medicine

summary: NSD2 (also named MMSET and WHSC1) is a histone lysine methyltransferase that is implicated in diverse diseases and commonly overexpressed in multiple myeloma due to a recurrent t(4;14) chromosomal translocation.  However, the precise catalytic activity of NSD2 is obscure, preventing progress in understanding how this enzyme influences chromatin biology and myeloma pathogenesis.  Here we show that dimethylation of histone H3 at lysine 36 (H3K36me2) is the principal chromatin-regulatory activity of NSD2.  Catalysis of H3K36me2 by NSD2 is sufficient for gene activation.  In t(4;14)-positive myeloma cells, the normal genome-wide and gene-specific distribution of H3K36me2 is obliterated, creating a chromatin landscape that selects for a transcription profile favorable for myelomagenesis.  Catalytically active NSD2 confers xenograft tumor formation and invasion capacity upon t(4;14)-negative cells and NSD2 promotes oncogenic transformation of primary cells in an H3K36me2-dependent manner.  Together our findings establish H3K36me2 as the primary product generated by NSD2, and demonstrate that genomic disorganization of this canonical chromatin mark initiates oncogenic programming.

overall_design: Genome-wide expression profiling of KMS11 and t(4;14) translocation knockout (TKO) cells. Each cell line is tested in triplicate.

first: Alex

last: Kuo

first: Peggie

last: Cheung

first: Kaifu

last: Chen

first: Barry

last: Zee

first: Josh

last: Lauring

first: Yuanxin

last: Xi

first: Ben

last: Park

first: Xiaobing

last: Shi

first: Mitomu

last: Kioi

first: Benjamin

last: Garcia

first: Wei

last: Li

first: Or

last: Gozani


title: Gene Expression Analyisis of T-ALL LOUCY cell lines treated with ETV6 siRNA vs. scramble control siRNA

status: Public on Nov 24 2011

first: Alberto

last: Ambesi-Impiombato

address: 1130 St. Nicholas Avenue

department: ICG

institute: Columbia University

summary: Transcriptional effects of ETV6 inactivation in immature T-ALL were investigated by gene expression analysis upon siRNA-mediated knockdown of ETV6 in LOUCY cells, a T-ALL cell line with a transcriptional program highly related to that of immature T-ALLs. Gene Set Enrichment Analysis (GSEA) of the ETV6 knockdown signature showed a significant enrichment in genes characteristically upregulated in ETV6 mutant immature T-ALLs including HOXA13, PRDM16, PTEN and CD33.

overall_design: 4 samples were analyzed: two biological replicates for each experimental group.

first: Pieter

last: Van Vlierberghe

first: Arianne

last: Perez-Garcia

first: Erika

last: Haydu

first: Isaura

last: Rigo

first: Michael

last: Hadler

first: Valeria

last: Tosello

first: Giusy

last: Della Gatta

first: Elisabeth

last: Paietta

first: Janis

last: Racevskis

first: Peter

last: Wiernik

first: Jacob

last: Rowe

first: Montserrat

last: Rue

first: Adolfo

last: Ferrando


title: Genome-wide analysis of gene expression perturbed by Pontin shRNA in MCF7 subjected to normoxic and hypoxic conditions

status: Public on Dec 02 2011

city: Pohang

first: Bhin

last: Jin-hyuk

address: Ji-gok research center, hyoja-dong, Nam-gu

department: Department of Chemical engineering

institute: POSTECH

summary: In order to investigate the role of Pontin methylation on the expression of hypoxia responsive genes across the whole genome, we performed a microarray analysis from RNAs isolated from MCF7 cells expressing either control shRNA (shNS) or Pontin shRNA(shPontin) in normoxic and hypoxic conditions.

overall_design: MCF7 cells were transiently transfected with either non-specific shRNA or Pontin shRNA in replicates. Cells were grown for 24 hours before being exposed to either normoxic (21% Oxygen) or hypoxic condition (1% oxygen) for 6,9 hours. Cells were then lysed and RNA isolated.

first: Sung

last: Baek

first: Daehee

last: Hwang

first: Jason

last: Lee

first: Yunho

last: Kim

first: Jinhyuk

last: Bhin


title: Comparative Expression Profile of miRNA and mRNA in Primary Peripheral Blood Mononuclear Cells Infected with Human Immunodeficiency Virus (HIV-1)

status: Public on Nov 23 2011

city: Pittsburgh

first: Pruthvi S. R.

last: Nagilla

address: 416 Parran Hall, 130 DeSoto Street

department: Infectious Diseases and Microbiology

institute: University of Pittsburgh

overall_design: Refer to individual Series


title: Comparative Expression Profile of miRNA and mRNA in Primary Peripheral Blood Mononuclear Cells Infected with Human Immunodeficiency Virus (HIV-1) [mRNA]

summary: Host cells respond to exogenous infectious agents such as viruses, including HIV-1. Studies have evaluated the changes associated with virus infection at the transcriptional and translational levels of the cellular genes involved in specific pathways. While this approach is useful, in our view it provides only a partial view of genome-wide changes. Recently, technological advances in the expression profiling at the microRNA (miRNA) and mRNA levels have made it possible to evaluate the changes in the components of multiple pathways. To understand the role of miRNA and its interplay with host cellular gene expression (mRNA) during HIV-1 infection, we performed a comparative global miRNA and mRNA microarray using human PBMCs infected with HIV-1. The PBMCs were derived from multiple donors and were infected with virus generated from the molecular clone pNL4-3. The results showed that HIV-1 infection led to altered regulation of 21 miRNAs and 444 mRNA more than 2-fold, with a statistical significance of p<0.05. Furthermore, the differentially regulated miRNA and mRNA were shown to be associated with host cellular pathways involved in cell cycle/proliferation, apoptosis, T-cell signaling, and immune activation. We also observed a number of inverse correlations of miRNA and mRNA expression in infected PBMCs, further confirming the interrelationship between miRNA and mRNA regulation during HIV-1 infection. These results for the first time provide evidence that the miRNA profile could be an early indicator of host cellular dysfunction induced by HIV-1.

overall_design: Total RNA isolated from PBMC subjected to 7 days of HIV-1 infection compared to uninfected control PBMC

first: Pruthvi

first: Velpandi

last: Ayyavoo


title: Gene expression during Arabidopsis flower maturation

status: Public on Dec 10 2011

city: Chapel Hill

last: Reed

address: CB #3280, Coker Hall

institute: University of North Carolina at Chapel Hill

summary: Flower maturation consists of several events that contribute to reproductive success as flowers open, including petal expansion, stamen filament elongation, pollen release, nectary maturation, stigma growth, and gynoecium maturation to support pollen tube growth.  The Arabidopsis transcription factors ARF6 (Auxin Response Factor 6) and ARF8 regulate all of these processes, in part by activating jasmonate biosynthesis.  Jasmonates in turn activate genes encoding the transcription factors MYB21 and MYB24, which mediate a subset of the processes controlled by ARF6 and ARF8.  This experiment was designed to characterize gene expression in flowers before and after they open, and to determine how arf6 arf8 and myb21 myb24 mutation combinations affect these gene expression patterns.

overall_design: Three biological replicates were prepared at each of two developmental stages, stage 12 (oldest closed buds) and stage 13 (youngest open flowers), for three genotypes (Wild type, arf6-2 arf8-3, and myb21-5 myb24-5).  For the mutant genotypes, stage 13 flowers do not actually open, so corresponding flowers of equivalent age were chosen based on the position of open flowers in wild-type inflorescences.

first: Punita

last: Nagpal

first: Sara

last: Ploense


title: Expression analysis of the effect of protoplasting and sorting in roots exposed to low pH

city: Durham

first: Anjali

last: Iyer-Pascuzzi

institute: Duke University

summary:
To estimate the effect of protoplasting and sorting on low pH-regulated gene expression, we generated expression profiles for whole roots treated with low pH for 24 hours and whole roots that had been protoplasted and FACS sorted after 24 hours of exposure to low pH.
Stress responses in plants are tightly coordinated with developmental processes, but the interaction between these pathways is poorly understood. Here we use genome-wide assays at high spatial and temporal resolution to understand the processes that lnk development and stress in the Arabidopsis root. Our meta-analysis finds little evidence for a universal stress response. Common stress responses appear to exists and, analagous to animal systems, many of them show cell-type specificity, suggesting a convergent evolutionary theme in multicellular organisms. Common stress responses may be mediated by cell identity regulators, as mutations in these genes resulted in altered responses to stress. Our results reveal surprising linkages between stress and development at cellular resolution, and show the power of multiple genome-wide datasets to elucidate biological processes.

overall_design: 3 replicates of protoplasted, FACS sorted whole roots exposed to low pH and 2 replicates of whole roots exposed to low pH

first: Philip

middle: N

last: Benfey


title: Expression analysis of developmental stages of Arabidopsis roots exposed to low pH

summary:
To understand the effect of low pH on developmental stages in the root, we dissected the root into four developmental zones after exposure to low pH and expression profiled each zone.
Stress responses in plants are tightly coordinated with developmental processes, but the interaction between these pathways is poorly understood. Here we use genome-wide assays at high spatial and temporal resolution to understand the processes that lnk development and stress in the Arabidopsis root. Our meta-analysis finds little evidence for a universal stress response. Common stress responses appear to exists and, analagous to animal systems, many of them show cell-type specificity, suggesting a convergent evolutionary theme in multicellular organisms. Common stress responses may be mediated by cell identity regulators, as mutations in these genes resulted in altered responses to stress. Our results reveal surprising linkages between stress and development at cellular resolution, and show the power of multiple genome-wide datasets to elucidate biological processes.

overall_design: 2 replicates each of 4 developmental stages exposed to standard and low pH


title: Expression analysis of root cell types after treatment with low pH

summary:
Cell-type specific transcriptional profiles were generated by FACS (Fluorescence Activated Cell Sorting) sorting of roots that express cell-type specific GFP-reporters. Five different GFP-reporter lines were used. FACS cell populations were isolated from roots grown under standard pH (pH 5.7) or roots that had been transfered to low pH (pH 4.6) media for 24 hours.
Stress responses in plants are tightly coordinated with developmental processes, but the interaction between these pathways is poorly understood. Here we use genome-wide assays at high spatial and temporal resolution to understand the processes that lnk development and stress in the Arabidopsis root. Our meta-analysis finds little evidence for a universal stress response. Common stress responses appear to exists and, analagous to animal systems, many of them show cell-type specificity, suggesting a convergent evolutionary theme in multicellular organisms. Common stress responses may be mediated by cell identity regulators, as mutations in these genes resulted in altered responses to stress. Our results reveal surprising linkages between stress and development at cellular resolution, and show the power of multiple genome-wide datasets to elucidate biological processes.

overall_design: 3 replicates for each of 5 cell types for low pH and standard pH (30 samples total).


title: Time-course expression analysis of the low pH (pH 4.6)  response in  Arabidopsis whole roots

summary:
We preformed at time-course of the expression of whole Arabidopsis roots for 30 minutes, 1H, 3H, 6H 12H, 24H, and 48H after transfer to low pH (pH 4.6). Controls at the standard pH (pH 5.7) were included at each time-point. We combined these data with 13 other datasests and performed a meta-analysis to ask whether a universal stress response exists in Arabidopsis roots.
Stress responses in plants are tightly coordinated with developmental processes, but the interaction between these pathways is poorly understood. Here we use genome-wide assays at high spatial and temporal resolution to understand the processes that lnk development and stress in the Arabidopsis root. Our meta-analysis finds little evidence for a universal stress response. Common stress responses appear to exists and, analagous to animal systems, many of them show cell-type specificity, suggesting a convergent evolutionary theme in multicellular organisms. Common stress responses may be mediated by cell identity regulators, as mutations in these genes resulted in altered responses to stress. Our results reveal surprising linkages between stress and development at cellular resolution, and show the power of multiple genome-wide datasets to elucidate biological processes.

overall_design: 28 samples: 7 time points, with two replicates for each timepoint for both the control (pH 5.7) and treatment (pH 4.6)


title: Gene and pathways affected by CAG-repeat RNA-based toxicity in Drosophila

status: Public on Nov 22 2011

first: Bonini

last: Nancy

address: 415 S University Ave

institute: University of Pennsylvania

summary:
Spinocerebellar ataxia type 3 (SCA3) is one of the polyglutamine (polyQ) diseases, which are caused by a CAG repeat expansion within the coding region of the associated genes.
The CAG repeat specifies glutamine, and the expanded polyQ domain with mutation confers dominant toxicity on the protein.
Traditionally, studies have focused on protein toxicity in polyQ disease mechanisms.
Recent findings, however, demonstrate that the CAG repeat RNA, which encodes the toxic polyQ protein, also contributes to the disease in Drosophila.
To provide insight into the nature of the RNA toxicity,
we extracted brain-enriched RNA from flies expressing a toxic CAG repeat mRNA (CAG100) and a non-toxic interrupted CAA/G mRNA repeat (CAA/G105) for microarray analysis.
This approach identified a set of genes that are differentially expressed specifically in CAG100 flies.

overall_design:
Four independent replicates of flies expressing CAG0, CAG100, or CAA/G105 by elav-GAL4 were collected at 3 days.
The transgenes are DsRed with either (CAG0) no CAG repeat in the 3'UTR, (CAG100) a CAG repeat of 100 CAGs in the 3'UTR, or (CAA/G105) an interrupted CAA CAG repeat in the 3'UTR (ref: Li et al., Nature 453:1107)
The transgenes were adjusted to match in mRNA expression such that CAG0 flies had one copy of the transgene, CAG100 flies had 5 copies, and CAA/G105 had two copies.
Fly brain tissue (about 20 brains per sample, dissected from head capsule, eyes, lamina and outer medulla removed) was dissected in cold phosphate buffered saline (PBS) and stored in Trizol reagent (Invitrogen Corporation, Carlsbad, CA) at -80˚C.
Total brain RNA was extracted and purified using TRIzol reagent (Invitrogen) and the RNeasy Mini system (Qiagen), and treated with RNase-free DNase I (Qiagen).
To define genes whose expression is altered in response to a toxic CAG repeat RNA, we compared CAG100 flies with age-matched flies expressing CAG0.
To exclude transcriptional changes in response to a non-toxic trinucleotide repeat, a second gene list was generated by comparing CAA/G105 flies with age-matched CAG0 flies.

first: Shin-Yi

last: Shieh

first: Nancy

last: Bonini


title: Differential gene expression profiles of side population and non-side population cells of malignant pleural mesothelioma

status: Public on Nov 18 2011

city: detroit

first: naimei

last: tang

state: mi

address: 110 E warren ave

department: internal medicine

institute: wanye state university

summary: Malignant pleural mesothelioma (MPM), which is associated with occupational asbestos exposure, is a deadly disease with no effective treatments due mainly to its high resistance to anti-cancer drugs. The molecular mechanisms responsible for its chemotherapeutic resistance are complicated and undefined. However, the presence of side population cells (SP cells) in tumors is a well-accepted explanation for their anti-cancer drug resistance. To identify SP cell-specific gene expression signature, microarray technique has been employed. Our data show differential gene expression profiles between SP and non-SP cells of H2714 mesothelioma cells. SP cells over-expressed genes associated with cancer stem cell (CSC) and drug resistance: DUSP6, SPRY2 and IL6, as well as multi-pathways, including the cancer stem cell-associated pathways Notch and c-Kit.  Therefore, we believe that targeting CSC-specific genes and pathways in SP cells may hold the key to the discovery of effective treatments for reversing chemotherapeutic resistance to MPM treatment.

overall_design: 4 samples

first: Naimei

last: Tang

first: Xinbo

last: Zhang


title: Expression analysis time-course of Arabidopsis roots to sulfur deficiency

summary:
We preformed at time-course of the expression of whole Arabidopsis roots for 3H, 12H, 24H, 48H and 72H after transfer to media lacking sulfur. We combined these data with 13 other datasests and performed a meta-analysis to ask whether a universal stress response exists in Arabidopsis roots.
Stress responses in plants are tightly coordinated with developmental processes, but the interaction between these pathways is poorly understood. Here we use genome-wide assays at high spatial and temporal resolution to understand the processes that lnk development and stress in the Arabidopsis root. Our meta-analysis finds little evidence for a universal stress response. Common stress responses appear to exists and, analagous to animal systems, many of them show cell-type specificity, suggesting a convergent evolutionary theme in multicellular organisms. Common stress responses may be mediated by cell identity regulators, as mutations in these genes resulted in altered responses to stress. Our results reveal surprising linkages between stress and development at cellular resolution, and show the power of multiple genome-wide datasets to elucidate biological processes.

overall_design: 2 replicates of each timepoint (3H, 12H, 24H, 48H, 72H) and the 0H control.

first: Terry

last: Jackson


title: Expression data from  third instar Drosophila larvae offspring from maternal control or high-sucrose fed diets

status: Public on Nov 30 2011

city: St. Louis

first: Jennifer

last: Duncan

address: 660 S. Euclid, Box 8208

department: Pediatrics

institute: Washington University School of Medicine

summary:
Maternal obesity and diabetes is associated with increased risk of obesity and diabetes in offspring.  We generated a model of maternal caloric excess in Drosophila and noted altered body composition in offspring from females fed a high-sucrose diet. To gain insight into the mechanisms underlying this response, we profiled gene expression in mid-third instar larvae (mid-L3) offspring from either control or high-sucrose fed females.  All offspring were raised on control food.
We used microarrays to detail the response of Drosophila larvae to maternal high calorie diet

overall_design: Virgin female w1118 flies were fed control (0.15M) or high (1M) sucrose food for 7 days, mated with male w1118 flies such that all embryos were laid on control food.    Mid-L3 larvae were selected for RNA extraction and hybridization on Affymetrix microarrays.  Mid-L3 were selected as L2, aged overnight until early L3, then transferred to fresh control food for 12 more hours before selection.

first: Laura

middle: P

last: Musselman


title: Knockdown of the psychosis susceptibility gene ZNF804A alters expression of genes involved in cell adhesion

status: Public on Nov 16 2011

city: Cardiff

first: Matthew

middle: James

last: Hill

address: Maindy Road

institute: Cardiff University

summary: Genome-wide association studies have convincingly implicated several novel genes in susceptibility to schizophrenia and bipolar disorder. The first genome-wide significant association with the broad phenotype of psychosis was with a polymorphism in the ZNF804A gene. However, the biological function(s) of ZNF804A have, to date, been entirely unknown. In this study, we manipulated the expression of ZNF804A in neural progenitor cells derived from human cortical neuroepithelium and assessed its effects on the cellular transcriptome. Gene ontology analysis of differentially expressed genes indicated a significant effect of ZNF804A knockdown on the expression of genes involved in cell adhesion, suggesting a role for ZNF804A in processes such as neural migration, neurite outgrowth and synapse formation. Several highly significant gene expression changes were confirmed in repeat cell culture experiments. Most consistent gene expression changes were seen for C2ORF80, a gene of as yet unknown function, and STMN3, a gene involved in neurite outgrowth and axonal and dendritic branching. These data, generated in a hypothesis-free manner, provide a basis for more targeted investigations of ZNF804A function.

overall_design: Total RNA extracted from human neural progenitor cells manipulated with three siRNAs: control siRNA , siRNA_ZNF804A 1 (HSS150612) and siRNA ZNF804A 2 (HSS150613). 4 replicates per group. Genome wide transcript levels were then measured using gene expression microarrays.

first: Aaron

last: Jeffries

first: Richard

last: Dobson

first: Jack

last: Price

first: Nick

last: Bray


title: Effects of acute dietary zinc depletion on the gene expression profile of whole blood in human male adults

status: Public on Nov 15 2011

city: Gainesville

first: Robert

middle: J.

last: Cousins

state: Florida

address: 359 FSHN Bldg. Newell Dr. PO Box 110370

department: Food Science and Human Nutrition Department, Center for Nutritional Sciences

institute: University of Florida

summary: Even though the importance of adequate zinc intake has been known for around half a century, a reliable diagnostic tool to assess the dietary zinc status of individual humans or populations is in absence. The specific aim of this study was to examine differential expression of specific gene transcripts that occur when the dietary intake of zinc is acutely reduced below the dietary requirement for a period of ten days. Gene expression profiles of whole blood collected before and after dietary zinc restriction were determined by microarray analyses. The data provide potential signature genes of suboptimal zinc consumption and relevant bioinformatic interpretation indicate immune response and cell cycle regulation as biological processes associated with the zinc-responsive genes.

overall_design: To identify candidate markers holding the potential to indicate zinc status, a 24-day observational study comprised of acclimation (7 d; 10.4 mg Zn/d), zinc depletion (10 d; 0.3 mg Zn/d), and zinc repletion (7 d; 29.5 mg Zn/d) phases was conducted with healthy male subjects (n = 9). On day 0, 6 and 10 of zinc depletion, whole blood was collectedunder morning fasting state. RNA profiles were stabilized by using PAXgene reagents during the collection process and globin RNA reduction was conducted to improve the detection of transcripts at low abundance. Genes responding to dietary zinc restriction were determined by array results from individual samples collected before and after 10 d of zinc depletion. Pooled RNA samples from each day of blood collection, i.e., baseline, 6 d and 10 d of depletion, respectively, were used to determine the temporal expression pattern of the zinc-responsive genes during dietary zinc depletion.

first: Moon-Suhn

last: Ryu

first: Bobbi

last: Langkamp-Henken

first: Shou-Mei

last: Chang

first: Meena

last: Shankar

middle: J


title: Identifcation of Human B1 cells

status: Public on Nov 08 2011

city: Manhasset

first: Thomas

middle: L

last: Rothstein

address: 350 Community Drive

department: Oncology and Cell Biology

institute: The Feinstien Institute for Medical Research

summary:
The mission of B lymphocytes is considered to reside primarily in immunoglobulin production; however, the success of B cell depletion in autoimmune diseases previously thought to be T cell-mediated suggests that some B cells fulfill other roles in autoimmunity.  We examined the recently identified human B1 cell population for T cell stimulatory activity.  We found two kinds of B1 cells that are distinguished by multiple surface markers and distinct transcriptomic profiles. In both umbilical cord and adult peripheral blood, the larger of the two, which is CD11b-, constitutes about 90% of B1 cells, whereas the smaller of the two, which is CD11b+, constitutes about 10% of B1 cells. These B1 cell populations differ functionally.  CD11b- B1 cells spontaneously secrete much more IgM than CD11b+ B1 cells.  In contrast, CD11b+ B1 cells express more CD86, and efficiently stimulate more T cell expansion, than CD11b- B1 cells.   These CD11b+ B1 cells are markedly elevated in lupus patients and express increased CD86 and increased T cell stimulating activity in disease. This work distinguishes a novel, T cell-interacting B1 cell population whose expression and activity may be a reflection of, and a therapeutic target in, autoimmune disease.
abstract

overall_design: Four groups each group comprising 3 samples for a total of 12 samples of human B cells were analyzed

first: Daniel

last: Griffin


title: Expression profiling of sorted human Thymocyte populations

status: Public on Nov 05 2011

first: Alberto

last: Ambesi-Impiombato

summary:
Thymus samples were obtained as surgical tissue discards from 3 pediatric patients (age from 7 days to 6 months) undergoing cardiac surgery at the New York Presbyterian Hospital.
RNA was excracted and processed for expression analysis from 7 isolated T-Cell populations.

overall_design: Gene expression analysis of 7 T-Cell populations isolated from surgical samples of 3 human thymi

first: Giusy

last: Della Gatta

first: Valeria

last: Tosello

first: Adolfo

last: Ferrando


title: Cell-type, developmental stage, and whole root responses to low pH and sulfur deficiency

first: Anjali

middle: S

last: Iyer-Pascuzzi

type: Genome binding/occupancy profiling by genome tiling array

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


title: NSD2 links dimethylation of histone H3 at lysine 36 to oncogenic programming [RNAi]

city: Houston

first: kaifu

last: chen

summary: NSD2 (also named MMSET and WHSC1) is a histone lysine methyltransferase that is implicated in diverse diseases and commonly overexpressed in multiple myeloma due to a recurrent t(4;14) chromosomal translocation.  However, the precise catalytic activity of NSD2 is obscure, preventing progress in understanding how this enzyme influences chromatin biology and myeloma pathogenesis.  Here we show that dimethylation of histone H3 at lysine 36 (H3K36me2) is the principal chromatin-regulatory activity of NSD2.  Catalysis of H3K36me2 by NSD2 is sufficient for gene activation.  In t(4;14)-positive myeloma cells, the normal genome-wide and gene-specific distribution of H3K36me2 is obliterated, creating a chromatin landscape that selects for a transcription profile favorable for myelomagenesis.  Catalytically active NSD2 confers xenograft tumor formation and invasion capacity upon t(4;14)-negative cells and NSD2 promotes oncogenic transformation of primary cells in an H3K36me2-dependent manner.  Together our findings establish H3K36me2 as the primary product generated by NSD2, and demonstrate that genomic disorganization of this canonical chromatin mark initiates oncogenic programming.

overall_design: Genome-wide expression profiling of KMS11 cells stably transduced with control vector in comparison to two independent shRNAs against NSD2. Each cell line is tested in duplicate.

first: Alex

last: Kuo

first: Peggie

last: Cheung

first: Kaifu

last: Chen

first: Barry

last: Zee

first: Josh

last: Lauring

first: Yuanxin

last: Xi

first: Ben

last: Park

first: Xiaobing

last: Shi

first: Mitomu

last: Kioi

first: Benjamin

last: Garcia

first: Wei

last: Li

first: Or

last: Gozani


title: Transcriptome profiling identified genes and pathways associated with arsenic toxicity and tolerance in Arabidopsis

status: Public on Nov 26 2011

city: Changhua

first: Shih-Feng

last: Fu

state: Changhua

address: No.1 Jin-De Road

country: Taiwan

institute: National Changhua University of Education

summary:
Transcriptional profiling of arsenic-induced toxicity and tolerance in Arabidopsis plants of different ecotypes
Arsenic (As) is a toxic metalloid found ubiquitously in the environment and has widely been known as an acute poison and carcinogen.  As toxicity is a major factor leading to root growth inhibition in plants.  However, the molecular mechanisms of plants in response to As has not been extensively characterized.  In this study, Arabidopsis ecotypes that are As-tolerant (Col-0) and -sensitive (Ws-2) were used to conduct a transcriptome analysis of the response to As (V).  To begin elucidating the molecular basis of As toxicity and tolerance in Arabidopsis, seedlings of Col-0 and Ws-2 were subjected to As treatment.   The root elongation rate of Col-0 was significantly higher than that of Ws-2 when exposed to As.  The tolerant ecotype (Col-0) demonstrated lower accumulation of As when compared to the responses observed in the sensitive Ws-2.  Subsequently, the effect of As exposure on genome-wide gene expression was examined in the two ecotypes.  Comparative analysis of microarray data identified groups of genes with common and specific responses to As between Col-0 and Ws-2.  The genes related to heat responses and oxidative stresses belonged to common responses, indicating conserved stress-associated changes across two ecotypes.  The majority of specific responsive genes were those encoding heat shock proteins, heat shock factors, ubiquitin and transporters.  The data suggested that metal transport and maintenance of protein structure may be important mechanisms for toxicity and tolerance to As.  This study presents comprehensive surveys of global transcriptional regulation and identifies stress- and tolerance-associated genes in response to As.

overall_design:
Comparison of Arabidopsis ecotype Col-0 and Ws-2 in response to As (V) for 1.5 and 3 hr
Affymetrix GeneChip assay were performed by the Affymetrix Gene Expression Service Lab (http://ipmb.sinica.edu.tw/affy/), supported by Academia Sinica, Taiwan

first: Po-Yu

first: Guan-Ru

last: Zeng

first: Chung-Yi

last: Lin

first: Tsai-Lien

last: Huang

first: Hao-Jen


title: Apoptosis induced by Piroxicam/Cisplatin combined treatment is triggered by p21 in mesothelioma

status: Public on Nov 20 2011

city: Torino

first: Raffaele

last: Calogero

state: To

address: Via Nizza 52

department: Molecular Biotechnology Center

country: Italy

institute: University of Torino

summary: Here we report that piroxicam/cisplatin combined treatment exerts an apoptotic effect on mesothelioma cells. Genome-wide transcriptome analyses lead us to identify p21 as the possible apoptosis mediator acting as downstream target of the piroxicam/cisplatin treatment.

overall_design: To analyze the potential therapeutic effect of the piroxicam/cisplatin treatment at molecular level, and to identify gene expression pattern modifications following the combined treatment, we performed a transcriptional profiling on HGU133A arrays, using cells treated with piroxicam, cisplatin or with piroxicam and cisplatin, choosing the time exposures in which apoptosis induction was absent or evident (8 and 24 hours). Biological duplicates or triplicates were generated for each prototypic situation and data were analyzed using the oneChannelGUI Bioconductor package (Sanges et al., 2007), comparing untreated cells with cells treated in single or combined treatment. After quality controls, the complexity of the data set was reduced removing the non-significant probe sets, resulting in a total of 4,247 out of the 22,283 probe sets present in the microarray. To assess differential expression, linked to piroxicam, cisplatin- and the combined treatment we used an empirical Bayes method together with a false discovery rate (FDR) correction of the P-value. Specifically genes were selected using a corrected p-value ≤0.05 and |log2(fc)| ≥1. We detect a total of 536 differentially expressed genes.

first: ALFONSO

last: BALDI

first: MARIAROSARIA

last: BOCCELLINO

first: ALDO

last: DONIZETTI

first: RAFFAELE

last: LAPORTA

first: ENRICO

last: SPUGNINI

first: IRENE

last: CARDILLO

first: GENNARO

last: CITRO

first: LUCIO

last: QUAGLIUOLO

first: MASSIMO

last: MENEGOZZO

first: FRANCESCA

last: CORDERO

last: CALOGERO

first: STEFANIA

last: CRISPI


title: Complete TLR3 deficiency

status: Public on Nov 02 2011

city: Dallas

first: Damien

last: Chaussabel

address: 3434 Live Oak

institute: Baylor Institute for Immunology Research

summary: The objective of this study is to study the Toll-like receptor 3 (TLR3)-dependent gene expression in human fibroblast cells and peripheral blood mononuclear cells (PBMCs)

overall_design: Fibroblast cells and PBMCs from donors with autosomal recessive (AR) complete TLR3 deficiency and autosomal dominant (AD) partial TLR3 deficiency were collected for microarray analysis to measure the transcriptional responsiveness of TLR3 in fibroblast and PBMCs.  A total of 3 healthy controls, 1 AD TLR3-deficient patient, 1 AR TLR3-deficient patient, 1 AR UNC-93B-deficient patient, 1 MyD88 deficient patien were used in this study.  The fibroblast cells were cultured in DMEM medium supplemented with 10% fetal calf serum (FCS).  The PBMCs were cultured in RPMI medium complemented with 10% FCS. Different kinetics (2 hours and 8 hours) of poly(I:C) (25ug/ml, purchased from Amersham) stimulations were performed, aiming to define TLR3-inducible genes in these human cells. A stimulation of IL-1β (20ng/ml, purchased from R&D system Inc.) was used as a positive activation control with same kinetics of stimulations.  A total of one million cells per stimulation were used for fibroblasts, and around 1.5 million cells per stimulation for PBMCs.

first: Yigi

last: Guo

first: Magali

last: Audry

first: Michael

last: Ciancanelli

first: Laia

last: de Lara

first: Joana

last: Azevedo

first: Melina

last: Herman

first: Esperanza

last: Anguiano

first: Vanessa-Sancho

last: Shimizu

first: Lazaro

last: Lorenzo

first: Elodie

last: Pauwels

first: Paul

last: Philippe

first: Rebeca

last: de Diego

first: Annabelle

last: Cardon

first: Guillaume

last: Vogt

first: Capucine

last: Picard

first: Zafitsara

middle: Z

last: Andrianirina

first: Flore

last: Rozenberg

first: Pierre

last: Lebon

first: Sabine

last: Plancoulaine

first: Marc

last: Tardieu

first: Valerie

last: Doireau

first: Emmanuelle

last: Jouanguy

first: Frederic

last: Geissman

first: Laurent

last: Abel

first: Jean-Laurent

last: Cassanova

first: Shen-Ying

last: Zhang


title: Expression data of T87 Arabidopsis cultured cells in the presence of ABA, SA, JA, ABA+SA, or ABA+JA for 3hr or 24hr

status: Public on Dec 01 2011

city: Kurashiki

first: Takashi

last: Hirayama

state: Okayama

department: Institute of Plant Science and Resources

institute: Okayama University

summary: Plant hormones involved in environmental stresses, namely abscisic acid (ABA), salicylic acid (SA), and jasmonic acid (JA), have been shown to interact with each other in a complex manner. To address the network of the hormone interactions, we have investigated the changes in expression under multiple hormone treatments, ABA+SA and ABA+JA. We chose cultured cells to remove the difference in the response to hormones among developmental cells or tissues. The cells were treated for 3hr and 24hr to see the rapid or transient response and steady-state response. The obtained data indicate that ABA and SA affect antagonistically, but these hormones affected many genes collaboratively. Indeed, according to the microarray data, there are many genes that responded only to ABA+SA. In addition, the ABA+SA responsive genes also responded to ABA+JA. These data suggest that hormone crosstalk is more complicated than expected and that more systematic analysis is required to untangle the hormone crosstalk network.

overall_design: To investigate the hormonal interactions, Arabidopsis T87 cultured cells were exposed to ABA, SA, or JA alone, or two hormones simultaneously, ABA+SA or ABA+JA, for 3hr and 24 hr. Comparing the data among those treatments, the relationships among these hormones were deduced.


title: Identification of DNA Methylation Markers for Lineage Commitment of in vitro Hepatogenesis

status: Public on Nov 25 2011

city: Daejeon

first: Mirang

last: Kim

address: 52 Eoeun-dong

department: human genome center

institute: KRIBB

type:
Expression profiling by array
Methylation profiling by array

overall_design: Refer to individual Series


title: Expression analysis of root cell types after treatment with sulfur deficient media

first: Anjali

last: Iyer-Pascuzzi

summary:
Cell-type specific transcriptional profiles were generated by FACS (Fluorescence Activated Cell Sorting) sorting of roots that express cell-type specific GFP-reporters. Five different GFP-reporter lines were used. FACS cell populations were isolated from roots grown under sulfur deficient conditions for 3 hours.
Stress responses in plants are tightly coordinated with developmental processes, but the interaction between these pathways is poorly understood. Here we use genome-wide assays at high spatial and temporal resolution to understand the processes that lnk development and stress in the Arabidopsis root. Our meta-analysis finds little evidence for a universal stress response. Common stress responses appear to exists and, analagous to animal systems, many of them show cell-type specificity, suggesting a convergent evolutionary theme in multicellular organisms. Common stress responses may be mediated by cell identity regulators, as mutations in these genes resulted in altered responses to stress. Our results reveal surprising linkages between stress and development at cellular resolution, and show the power of multiple genome-wide datasets to elucidate biological processes.

overall_design: 3 replicates for each of 5 cell types for sulfur deficient media

first: Philip

last: Benfey


title: Genes affected upon dsRNA knockdown treatment for nbr/CG9247 in Drosophila DL1 cells

status: Public on Nov 01 2011

city: Philadelphia

first: Bonini

last: Nancy

summary:
nbr/CG9247 gene function regulates the length of the 3'end of miRNAs.
Such 3'end heterogeneity of miRNAs may impact miRNA target gene silencing.
To address this, we performed microarray analysis for genes altered upon nbr knockdown in Drosophila DL1 cells.
This approach revealed a subset of genes upregulated upon nbr knockdown.

overall_design:
Five independent replicates of DL1 cells treated with control (dsRNA to renilla) or nbr (dsRNA RNA to nbr/CG9247) were collected 5 days after dsRNA bathing.
Total RNA from from each replicate was extracted using TRIzol reagent (Invitrogen).
A portion of total RNA for each replicate was used to confirm the effect of nbr knockdown on one of the nbr-dependent miRNAs, miR-34, by small RNA northern.

first: Masashi

last: Abe

first: Nancy

last: Bonini


title: Proteasome inhibition blocks estrogen-dependent gene transcription by decreasing histone H2B monoubiquitination in human breast cancer cells

city: Goettingen

first: Frank

last: Kramer

address: Humboldtallee 32

department: Department of Medical Statistics

institute: University Medical Center Göttingen

summary: The estrogen receptor-alpha (ERα) determines breast cancer cell phenotype and is a prognostic indicator. A better understanding of the mechanisms controlling ERα function may uncover improved strategies for the treatment of breast cancer. Proteasome inhibition was previously reported to regulate estrogen-induced transcription but the mechanisms by which it influences ERα function remain controversial. In this study we investigated the transcriptome-wide effects of the proteasome inhibitor Velcade on estrogen-regulated transcription in MCF7 human breast cancer cells and demonstrate a specific global decrease in estrogen-induced transcription.

overall_design: This set contains 12 microarray samples. 3 controls, 3 estrogen stimulated,  3 Bortezomib stimulated, 3 Bortezomib + estrogen stimulated

first: Tanja

last: Prenzel

first: Yvonne

last: Begus-Nahrmann

first: Magali

last: Hennion

first: Chieh

last: Hsu

first: Theresa

last: Gorsler

first: Corinna

last: Hintermayr

first: Dirk

last: Eick

first: Elisabeth

last: Kremmer

first: Mikael

last: Simons

first: Tim

last: Beissbarth

first: Steven

last: Johnsen


title: The target genes of EGFR activity in glioma cells

city: LaJolla

last: Furnari

state: CA

address: 9500 Gilman Drive

institute: Ludwig Institute

summary:
As a first step towards identifying the target genes of EGFR activity in glioma cells, genome-wide expression analyses were performed using the Affymetrix GeneChip Human Genome U133A array.
To accomplish this, mRNA expression levels of these genes were measured in the glioblastoma cell lines, U87 and U178, engineered with EGFR by retrovirus transduction (termed U87-EGFR and U178-EGFR respectively), with or without 20 ng/mL EGF treatment for 3 h.

overall_design: U87 and U178 cells engineered to express EGFR were stimulated with or without  EGF. The experiment was replicated twice for each U87 and U178 cells.

first: Ming

last: Li

first: Akitake

last: Mukasa

first: Yoshitaka

last: Narita


title: Microarray data from pre-germinated seeds and hypoxia-treated seedlings of Arabidopsis prt6-1 and ate1 ate2 mutants of the N-end rule pathway of targeted proteolysis pathway

status: Public on Oct 23 2011

city: Riverside

first: Takeshi

last: Fukao

address: Department of Botany and Plant Sciences

institute: University of California, Riverside

summary: This study analyzes transcriptome profiles in pre-germinated seeds and hypoxia-treated seedlings of Arabidopsis thaliana wild type (Col-0) and homozygous mutants (prt6-1 and ate1 ate2). This dataset includes CEL files, RMA signal values and MAS5 P/M/A calls. For pre-germinated seeds, seeds imbibed for 24 h were used for total RNA extraction. For hypoxia treatment, 7-d-old seedlings were incubated in a hypoxia chamber for 2 h and the entire seedling was subjected to RNA extraction. Quantitative profiling of cellular mRNAs was accomplished with the Affymetrix ATH1 platform. Changes in the transcriptome during early seed germination stage and in response to hypoxia in seedlings were evaluated. The data led to identification of mRNAs with abundance regulated by PRT6 and ATE1 / ATE2, which are essential components for the N-end rule pathway of targeted proteolysis (NERP). A combination of genetic, biochemical and molecular analyses reveal that NERP coordinates the stability of key ethylene responsive factor (ERF) family transcription factors, which regulate expression of core hypoxia response genes and tolerance to low oxygen stress. This indicates that the NERP functions as a homeostatic sensor of low oxygen in plants.

overall_design: Pre-germinated seeds; 2 genotypes (Col-0 and prt6-1) x 3 independent biological replicate experiments: Hypoxia treated seedlings; 3 genotypes (Col-0, prt6-1, and ate1 ate2) x 2 treatments (2h aerobic and 2h hypoxia) x 2 independent biological replicate experiments.

first: Seung

middle: C

last: Lee

first: Nurulhikma

last: Isa

first: Michael

last: Holdsworth

first: Julia

last: Bailey-Serres


title: The MOF-containing NSL complex associates globally with housekeeping genes, but activates only a defined subset (RNAi)

status: Public on Oct 29 2011

city: Munich

first: Christian

last: Feller

address: Schillerstraße 44

department: Molecular Biology

institute: Adolf-Butenandt Institute at the LMU University Munich

summary: The MOF-containing NSL complex binds to many but not all promoters of active genes and potentially contributes to their proper gene expression. It is currently unknown what determines whether an active gene is bound or not. Here, we provide evidence that the NSL complex primarily targets active promoters of most housekeeping genes. There, it co-localizes with the chromatin remodeler NURF and the histone methyltransferase Trithorax. Moreover, despite binding to most housekeeping genes, the NSL complex regulates only a subset of them, which are depleted for certain insulator binding-proteins and enriched for the core promoter motif “Ohler 5”. We suggest that the combination of general chromatin factors and core promoter motifs is predictive for whether a housekeeping gene is transcriptionally regulated by the NSL complex.

overall_design: Transcriptome expression profiling comparing NSL1 RNAi-depleted cells with control RNAi cells using Affymetrix microarrays.

first: Peter

last: Becker