title: Detection of immunogenic proteins from bacteria

status: Public on Oct 27 2011

city: Potsdam

first: Sebastian

last: Hoppe

address: Am Mühlenberg 13

department: Bioanalytics and Biosensorics

institute: Fraunhofer Institute for Cell Therapy and Immunology

summary:
Detection of immunogenic proteins remains an important task for life sciences as it nourishes the understanding of pathogenicity, illuminates new potential vaccine candidates and broadens the spectrum of biomarkers applicable in diagnostic tools. Traditionally, immunoscreenings of expression libraries via polyclonal sera on nitrocellulose membranes or screenings of whole proteome lysates in 2-D gel electrophoresis are performed. However, these methods feature some rather inconvenient disadvantages. Screening of expression libraries to expose novel antigens from bacteria often lead to an abundance of false positive signals owing to the high cross reactivity of polyclonal antibodies towards the proteins of the expression host. A method is presented that overcomes many disadvantages of the old procedures. We incorporated a fusion tag prior to our genes of interest and attached the expressed fusion proteins covalently on microarrays. This enhances the specific binding of the proteins compared to nitrocellulose. Thus, it helps to reduce the number of false positives significantly. It enables us to screen for immunogenic proteins in a shorter time, with more samples and statistical reliability. We validated our method by employing several known genes from Campylobacter jejuni NCTC 11168.
Four of proteins that have previously been described as immunogenic have successfully been assessed immunogenic abilities with our method. One protein with no known immunogenic behaviour before suggested potential immunogenicity. The method presented offers a new approach for screening of bacterial expression libraries to illuminate novel proteins with immunogenic features. It could provide a powerful and attractive alternative to existing methods and help to detect and identify bacterial virulence factors, vaccine candidates and potential biomarkers.

overall_design:
The overall study was done with five technical replicates. Ten proteins derived from Campylobacter jejuni were tested regarding their immunogenic potential.
The ten proteins derived from Campylobacter jejuni were fusion proteins, i.e., N-terminal HaloTag fused to:
Gene <--> Protein
cjaA <--> putative amino-acid transporter periplasmic solute-binding protein
hisJ <--> histidine-binding protein precursor
pal <--> peptidoglycan associated lipoprotein
flaC <--> flagellin
flaA <--> flagellin
peb1a <--> bifunctional adhesin/ABC transporter aspartate/glutamate-binding protein
pyrC <--> dihydroorotase (EC:3.5.2.3)
pseB <--> UDP-GlcNAc-specific C4,6 dehydratase/C5 epimerase
gapA <--> glyceraldehyde 3-phosphate dehydrogenase (EC:1.2.1.12)
argC <--> N-acetyl-gamma-glutamyl-phosphate reductase (EC:1.2.1.38)


title: DNA Replication Timing is Maintained Genome-wide in Primary Human Myoblasts Independent of D4Z4 Contraction in FSH Muscular Dystrophy

status: Public on Dec 06 2011

city: Tallahassee

first: Benjamin

last: Pope

state: FL

address: 319 Stadium Dr

department: Biological Science

country: USA

institute: Florida State University

type: Genome variation profiling by genome tiling array

summary: Facioscapulohumeral muscular dystrophy (FSHD) is linked to contraction of an array of tandem 3.3-kb repeats (D4Z4) at 4q35.2 from 11-100 copies to 1-10 copies. The extent to which D4Z4 contraction at 4q35.2 affects overall 4q35.2 chromatin organization remains unclear. Because DNA replication timing is highly predictive of long-range chromatin interactions, we generated genome-wide replication-timing profiles for FSHD and control myogenic precursor cells. We compared non-immortalized myoblasts from four FSHD patients and three control individuals to each other and to a variety of other human cell types. This study also represents the first genome-wide comparison of replication timing profiles in non-immortalized human cell cultures. Myoblasts from both control and FSHD individuals all shared a myoblast-specific replication profile. In contrast, male and female individuals were readily distinguished by monoallelic differences in replication timing at DXZ4 and other regions across the X chromosome affected by X inactivation. We conclude that replication timing is a robust cell-type specific feature that is unaffected by FSHD-related D4Z4 contraction.

overall_design: Profile comparison of myoblast cultures from four FSHD patients and three control individuals

middle: D

first: Koji

last: Tsumagari


title: Chip-chip from WI-38 human fibroblast with Argonaute antibody

status: Public on Nov 30 2011

city: paris

first: Moussa

last: BENHAMED

address: Institut pasteur

country: France

institute: Institut Pasteur

type: Genome binding/occupancy profiling by genome tiling array

summary: In humans, there are four Ago proteins (Ago1–4) and AGO1- and 2 were previously implicated in TGS induced by exogenous siRNAs and microRNAs (miRs) directed against gene promoter transcripts via promotion of changes in histone covalent modifications and DNA methylation. Not-with-standing, many mechanistic details of this process remain poorly defined in human cells, and very little is known about the identity of possible endogenous signals, which may drive this process in human cells. Given the evolutionary conserved role of siRNAs and AGO proteins in TGS and heterochromatin formation, we set out to analyse their possible involvement in senesence-associated repression of E2F target genes. To determine, in an unbiased manner, which genes might be under the control of AGO proteins we perfomed genome-wide promoter profiling in senescent and presenescent control WI38 primary fibroblasts applying “ChIP-on-chip” technology using 4 an anti-pan-AGO antibody. DNA from matched genomic inputs and chromatin immunoprecipitation (ChIP) samples were purified, amplified by PCR, and labeled either with Cy3 or Cy5 fluorophores. The labeled DNA from input and ChIP fractions  were then combined and hybridised to human promoter arrays containing ~59,000 promoters.

overall_design: determination of AGO binding sites in WI-38 pre-senescent human fibroblast and in senescent human fibroblast

first: O

last: BISCHOF


title: Gene expression study of bovine skeletal muscle

status: Public on Dec 01 2011

city: St Lucia

first: Sean

last: McWilliam

state: Queensland

address: 306 Carmody Road

department: Agriculture and Food

country: Australia

institute: CSIRO

summary: To investigate the effects that hormone growth promotants, tenderness genotype and state has on the expression levels of genes in the Longissimus dorsi muscle of of cattle

overall_design: The expression of genes were measured from a 4x3 treatment scenario, with animals from 2 sites, 3 tenderness genotypes and hormone treated or not.

first: Nadia

last: de Jager


title: Microarray experiment to identify gene expression changes in response to Phenobarbital treatment and CncC overexpression in Drosophila.

status: Public on Nov 29 2011

city: Salt Lake City

first: Carl

last: Thummel

state: UT

department: Human Genetics

institute: University of Utah

summary: Transcriptional profiling of mature adult w1118 males treated with phenobarbital compared to controls and heat treated HS-CncC flies compared with heat treated w1118 flies.

overall_design: Mature adult w1118 males were treated witheither 5% sucrose alone or 5% sucrose supplemented with 0.3% phenobarbital for six hours, following which RNA was extracted and subjected to micraoarray analysis.Similarly,mature adult w1118 flies or HS-CncC flies were subjected to heat treatment at 37oC for 30 minutes and recovered at room temperature for two hours,after which RNA was exctracted and subjected to microarray analysis.

first: J

middle: R

last: Misra

first: C

middle: S

last: thummel


title: Gene expression in a porcine preadipocyte cell line during differentiation

status: Public on Nov 27 2011

city: Tsukuba

first: Hirohide

last: Uenishi

state: Ibaraki

address: 2-1-2 Kannondai

country: Japan

institute: National Institute of Agrobiological Sciences

summary: These data show time-course transcriptional profiling of porcine subcutaneous preadipocyte cell line (PSPA) during differentiation. In the early stage after stimulation for adipocyte differentiation, upregulation of many genes encoding proteins involved in regulation of cell proliferation and transcription was observed. The data presented here should form a valuable database for exploring candidate genes for fat-related QTLs in pigs, and also for analyses to clarify the physiological characteristics of development of porcine adipose tissues by comparison with the results in humans and mice.

overall_design: The experiments consist of samples at seven different time points with an undifferentiated control. A set of the experiments is repeated three times.

first: Toshimi

last: Matsumoto

first: Ikuyo

last: Nakajima

first: Tomoko

last: Eguchi-Ogawa

first: Yoshiaki

last: Nagamura

first: Noriyuki

last: Hamasima


title: Adult Caenorhabditis elegans: wild-type (N2) and mir-243 mutant worms

status: Public on Sep 16 2011

city: Utrecht

first: Rene

last: Ketting

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

summary: Transcriptional profiling of N2 vs. mir-243 worms, aiming to identify direct and indirect targets of the microRNA.

overall_design: N2 and mir-243 young-adult worms grown at 20C were analyzed. Three biological replicates with dye-swaps were performed.

first: Regis

last: Correa


title: Isolation of a Novel Rat Neural Progenitor Clone that Expresses Dlx Family Transcription Factors and Gives Rise to Functional GABAergic Neurons in Culture

status: Public on Nov 09 2011

city: Piscataway

first: Ronald

middle: P.

last: Hart

state: NJ

address: 604 Allison Rd Rm B430

department: Cell Biology & Neuroscience

institute: Rutgers University

summary:
GABAergic interneurons are lost in conditions including epilepsy and CNS injury, but there are few culture models available to study their function.  Towards the goal of obtaining renewable sources of GABAergic neurons, we used the molecular profile of a functionally-incomplete GABAergic precursor clone to screen 17 new clones isolated from GFP+ rat E14.5 cortex and ganglionic eminence (GE) that were generated by viral introduction of v-myc. The clones grow as neurospheres in medium with FGF2, and after withdrawal of FGF2 they exhibit varying patterns of differentiation. Transcriptional profiling and qPCR indicated that one clone (GE6) expresses high levels of mRNAs encoding Dlx1, 2, 5 and 6, glutamate decarboxylases, and presynaptic proteins including neuropeptide Y and somatostatin. Protein expression confirmed that GE6 is a progenitor with restricted differentiation giving rise mostly to neurons with GABAergic markers. In co-cultures with hippocampal neurons, GE6 neurons became electrically excitable and received both inhibitory and excitatory synapses. After withdrawal of FGF2 in cultures of GE6 alone, neurons matured to express BetaIII-tubulin, and staining for synaptophysin and vesicular GABA transporter (VGAT) were robust after 1-2 weeks of differentiation. GE6 neurons also became electrically excitable and displayed synaptic activity, but synaptic currents were carried by chloride and were blocked by bicuculline. The results suggest that the GE6 clone, which is ventrally derived from the GE, resembles GABAergic interneuron progenitors that migrate into the developing forebrain.  This is the first report of a relatively stable fetal clone that can be differentiated into GABAergic interneurons with functional synapses.
The purpose was to compare differentiation patterns of several different immortalized rat neural progenitor clones to identify early stages in differentiation.  The cell clones studies were: GE6 (GABAergic neuronal precursor), GE2 (non-neuronal precursor, CTX8 (multipotential precursor), L2.2 (interneuronal precursor), and L2.3 (multipotential precursor).

overall_design: Five rat neural precursor cell clones were compared at three different time points following FGF2 withdrawal, which triggers differentiation.  Three sister culture replicates were performed for each cell clone and time point, yielding 45 samples.  One microarray failed so we have 44 microarray results in the dataset.

first: Hedong

last: Li

first: Anna

middle: T

last: Hader

first: Yu

last: Han

first: Joseph

middle: A

last: Wong

first: Joanne

last: Babiarz

first: Christopher

middle: L

last: Ricupero

first: Sasha

middle: B

last: Godfrey

first: John

middle: P

last: Corradi

first: Myels

last: Fennell

first: Mark

last: Plummer

first: Martin

last: Grumet


title: Transcriptional analysis of kidney infiltrating T cells after ischemia reperfusion injury reveals a pathophysiologic role for the chemokine (C-C motif) receptor 5

status: Public on Aug 31 2011

city: Baltimore

first: Dmitry

middle: N

last: Grigoryev

state: MD

institute: JHU

summary: We examined the transcriptional responses in kidney infiltrating T cells 6 hrs after IRI

overall_design: CD3 (+) T cells were purified applying magnetic beads to mononuclear cells extracted from kidney by percoll gradient methods. The total T-cell RNA was isolated, and trabscript abundance measured with array-based PCR

first: Ko-Gang

last: Jee


title: Effect of bacterial ACC deaminase on plant gene expression

status: Public on Nov 01 2011

city: Waterloo

first: Jennifer

last: Stearns

state: Ontario

address: 200 University Ave. W.

country: Canada

institute: University of Waterloo

summary: Canola plants inoculated with plant growth-promoting bacteria either expressing ACC deaminase or not to determine the effect on plant gene expression using an Arabidopsis microarray.

overall_design: 3 replicates for each ACD+ and ACD- bacteria, each compared with untreated control.

first: J

middle: C

first: O

middle: Z

last: Woody

first: B

last: Glick

middle: J

last: McConkey


title: Transcriptional profiling from young, old, healthy, or injured rat iliac arteries.

status: Public on Oct 19 2011

city: Miami

first: Lina

last: Shehadeh

address: 1600 NW 10th Ave

department: Medicine

institute: University of Miami Miller School of Medicine

overall_design: We studied the gene expression profile in a model of mechanical vascular injury in the iliac artery of aging (22 months old) and young rats (4 months old). We investigated aging-related variations in gene expression at 30 min, 3d and 7d post injury.

first: Roberto

middle: I

last: Vazquez-Pardon


title: Functional analysis of HSFB transcription factors [32°C]

status: Public on Sep 07 2011

first: Nobutaka

last: Mitsuda

address: Central 6 Higashi 1-1-1

department: Bioproduction Research Institute

institute: National Institute of Advanced Industrial Science and Technology

summary: To identify biological function of HSFB transcriptional repressor, we subjected hsfb1 hsfb2b double mutant and wild-type Arabidopsis plant under heat condition (32 Celsius degree) and did microarray experiment. The microarray experiment under non-heated condition is described in GSE14702. We found expression of many heat-shock proteins (HSPs) is not fully enhanced in the double mutant when compared to wild-type plant. This data suggest that the inhibition of expression of HSPs in non-heated condition is important for fully heat-stress response in plant.

overall_design: hsfb1 hsfb2b double mutant vs. wild-type seedlings of Arabidopsis thaliana subjected under heat condition (32 Celsius degree). Biological replicates: 4  replicates.

first: Miho

last: Ikeda

first: Masaru

last: Ohme-Takagi


title: Profiling long non-coding RNA expression in oral premalignant lesions.

status: Public on Aug 15 2011

city: Vancouver

first: Ewan

last: Gibb

address: 675 West 10th Ave

institute: BC Cancer Agency Research Centre

summary: Oral epithelial dysplasias are believed to progress through a series of histopathological stages; from mild to severe dysplasia, to carcinoma in situ, and finally to invasive OSCC. Underlying this change in histopathological grade are gross chromosome alterations and changes in gene expression of both protein-coding genes and non-coding RNAs. Recent papers have described associations of aberrant expression of microRNAs, one class of non-coding RNAs, with oral cancer. However, expression profiling of long non-coding RNAs (lncRNAs) has not been reported. Long non-coding RNAs are a novel class of mRNA-like transcripts with no protein coding capacity, but with a variety of functions including roles in epigenetics and gene regulation. In recent reports, the aberrant expression of lncRNAs has been associated with human cancers, suggesting a critical role in tumorigenesis. Here, we present the first long non-coding RNA expression map for the human oral mucosa. We describe the expression of 325 long non-coding RNAs, suggesting lncRNA expression contributes significantly to the oral transcriptome. Intriguingly, 60% of the detected lncRNAs show aberrant expression in oral premalignant lesions. A number of these lncRNAs have been previously associated with other human cancers.

overall_design:
A total of six normal oral samples and ten oral premalignant lesions were used to construct SAGE libraries which were then queried for long non-coding RNA expression profiles.
The six normal oral samples were previously deposited as GSE8127.

first: Katey

last: Enfield

first: Greg

last: Stewart

first: Kim

middle: M

last: Lonergan

first: Raj

last: Chari

first: Raymond

last: Ng

first: Lewei

last: Zhang

first: Calum

middle: E

last: MacAulay

first: Miriam

last: Rosin

first: Wan

last: Lam


title: Lytic Effect of Terpeneless Cold Pressed Valencia Orange Oil on Methicillin-Resistant Staphylococcus aureus

status: Public on Nov 08 2011

city: Fayetteville

first: Arunachalam

last: Muthaiyan

state: AR

address: 2435 N Hatch Ave

department: Food Science

institute: University of Arkansas

summary: Staphylococcus aureus has been recognized as an important cause of human disease for more than 100 years.  Resistance to multiple classes of antibiotics is becoming an increasingly difficult problem in the management of methicillin-resistant S. aureus (MRSA) and vancomycin-intermediate resistant S. aureus (VISA) infections. One approach to the MRSA and VISA problem, involves the discovery and development of new natural antimicrobials. The antimicrobial properties of essential oils of plant origin have been recognized for many years. In this study 0.1% of commercial cold pressed terpeneless Valencia orange oil (CPV) showed inhibitory and lytic activity against MRSA and VISA. To identify the mechanisms of action of CPV genomic response of CPV treated MRSA was analyzed by transcriptional profiling. Results showed alteration in the expression of cell wall peptidoglycan biosynthesis associated genes in the CPV treated cells.  Transmission electron microscopic observation of CPV treated MRSA cells exhibited cell wall damage and cell lysis.  Overall results of this study suggest that CPV may be a potential anti-staphylococcal agent for MRSA.

overall_design:
Overnight grown S. aureus COL was inoculated in TSB medium (20 ml) in a 50 ml Erlenmeyer flask and incubated at 37°C, with shaking at 200 rpm. Growth was measured at regular intervals at 600 nm until OD reached approximately 0.4.  Based on the GIC study ½ x MIC concentration of EO was added for 15 min of challenge. Control cultures were not challenged with EO and were also incubated for 15 min. Total bacterial RNA was isolated as previously described and the RNA samples were then converted to fluorescently-labeled cDNA and hybridized to S. aureus microarrays version 6 (NIAID's Pathogen Functional Genomics Resource Center). Hybridization signals were scanned using an Axon4000B scanner (Molecular Devices, Sunnyvale, CA ) with Acuity 6.0 software and scans were saved as TIFF image. Scans were analyzed using TIGR-Spotfinder (www.tigr.org/software/) software and the local background was subsequently subtracted. The data set was normalized by applying the LOWESS algorithm using TIGR-MIDAS (www.tigr.org/software/) software. The normalized log2 ratio of test/reference signal for each spot was recorded. Genes with less than three data points were considered unreliable, and their data points were discarded. The averaged log2 ratios for each remaining gene on the 6 replicate slides were ultimately calculated. Significant changes of gene expression were identified with SAM (significance analysis of microarrays; www.tat.stanford.edu/~tibs/SAM/index.html.

Contents of raw data files:

Channel A = Cy3 dye
Channel B = Cy5 dye

first: E

last: Martin

first: Senthil

last: Natesan

first: Philip

last: Crandall

first: Brian

last: Wilkinson

first: Steven

last: Ricke


title: Gene expression patterns of chemoresistant and chemosensitive serous epithelial ovarian tumors with possible predictive value in response to initial chemotherapy

status: Public on Jul 24 2011

city: Antwerp

first: Xuan Bich

last: Trinh

address: Oosterveldlaan 24

country: Belgium

institute: TCRU St. Augustinus GZA hospitals

summary: Chemotherapy (CT) resistance in ovarian cancer is broad and encompasses diverse, unrelated drugs, suggesting more than one mechanism of resistance. We aimed to analyze the gene expression patterns in primary serous epithelial ovarian cancer (EOC) samples displaying different responses to first-line CT in an attempt to identify specific molecular signatures associated with response to CT. Initially, the expression profiles of 15 chemoresistant serous EOC tumors [time to recurrence (TTR) ≤6 months] and 10 chemosensitive serous EOC tumors (TTR ≥30 months) were independently analyzed which allowed the identification of specific sets of differentially expressed genes that might be functionally implicated in the evolution of the chemoresistant or the chemosensitive phenotype. Our data suggest that the intrinsic chemoresistance in serous EOC cells may be attributed to the combined action of different molecular mechanisms and factors linked with drug influx and efflux and cell proliferation, as possible implications of other molecular events including altered metabolism, apoptosis and inflammation cannot be excluded. Next, gene expression comparison using hierarchical clustering clearly distinguished chemosensitive and chemo- resistant tumors from the 25 serous EOC samples (training set), and consecutive class prediction analysis was used to develop a 43-gene classifier that was further validated in an independent cohort of 15 serous EOC patients and 2 patients with other ovarian cancer histotypes (test set). The 43-gene predictor set properly classified serous EOC patients at high risk for early (≤22 months) versus late (>22 months) relapse  after initial CT. Thus, gene expression array technology can effectively classify serous EOC tumors according to CT response. The proposed 43-gene model needs further validation.

overall_design: 2 condition experiment: chemoresistant clinical samples versus chemosensitive samples

first: Dimcho

last: Bachvarov


title: Adipocyte Differentiation of Immortalized Human Bone Marrow-derived Stromal Cells is Modulated by microRNA-155, microRNA-221 and microRNA-222

status: Public on Aug 23 2011

city: Oslo

first: Heidi

middle: Maria

last: Namløs

address: PO Box 4953 Nydalen

department: Institute for cancer research, The Norwegian Radium Hospital

country: Norway

institute: Oslo University Hospital

summary:
Human bone marrow mesenchymal stromal cells are capable of limited self-renewal and multi-lineage differentiation in vitro. Several studies have demonstrated that microRNAs, post-transcriptional modifiers of protein expression, play crucial roles in the regulation of these complex processes.
To gain knowledge regarding the role of microRNAs in human adipocyte regulation, we examined the microRNA expression profile of the immortalized human bone marrow-derived stromal cell line hMSC-Tert20. We identified 12 microRNAs that were differentially expressed during adipogenesis, of which several have previously been shown to play important roles in adipocyte biology.
The expression of miR-155, miR-221 and miR-222 decreased during the adipogenic program, suggesting that they act as negative regulators of differentiation. Interestingly, adenovirus-mediated expression of either miR-155 alone or miR-221 plus miR-222 significantly inhibited adipogenesis and repressed induction of the master regulators C/EBP α and PPARgamma Our study provides the first experimental evidence that miR-155, miR-221 and miR-222 function in human adipocyte differentiation.

overall_design:
The telomerase immortalized human bone marrow-derived stromal cell line hMSC-Tert20 was differentiated towards adipocytes, and total RNA was harvested at various time points (0, 8, 24, 32, 48 and 72 hours, and 7, 14 and 21 days).
All hybridizations, except for 0h, 8h and 32h, were performed twice. The expression of each miRNA at a given time point was calculated as a ratio relative to its level on day 0. No dye swaps.

first: Magne

last: Skårn

first: Paul

last: Noordhuis

first: Leonardo

last: Meza-Zepeda

first: Ola

last: Myklebost


title: X chromosome gene expression in D. melanogaster testes

status: Public on Jul 22 2011

city: Bloomington

first: Colin

middle: D

last: Meiklejohn

state: IN

address: Jordan Hall, 1001 E. 3rd St.

department: Biology Department

institute: Indiana University

summary: Whole genome expression analyses reveal little evidence for X chromosome dosage compensation or meiotic inactivation in Drosophila testes, whereas testes-specific transgene reporters suggest a novel form of X chromosome-specific regulation.

overall_design: Gene expression was measured in RNA extracted from adult male and female dissected thorax, and in cells dissected from the apical tip of 2-4 day old adult male testes. Each tissue was assayed on four replicate arrays.

first: Emily

last: Landeen

first: Jodi

last: Cook

first: Sarah

last: Kingan

first: Daven

last: Presgraves


title: LATE-REPLICATING HETEROCHROMATIN IS CHARACTERISED BY DECREASED CYTOSINE METHYLATION IN THE HUMAN GENOME (HELP assay)

status: Public on Aug 06 2011

city: Bronx

first: John

last: Greally

state: NY

address: 1301 Morris Park Avenue

department: Genetics

institute: Albert Einstein College of Medicine

type: Methylation profiling by genome tiling array

summary: Heterochromatin is believed to be associated with increased levels of cytosine methylation.  With the recent availability of genome-wide, high-resolution molecular data reflecting cytosine methylation or heterochromatic organization, such relationships can be explored systematically.  As a well-defined surrogate for heterochromatin, we tested the relationship between DNA replication timing and cytosine methylation in two human cell types, unexpectedly finding that the later-replicating, more heterochromatic regions to be less methylated than early-replicating regions.  When we integrated gene expression data into the study, we found that regions of increased gene expression were earlier replicating, as previously identified, and that transcription-targeted cytosine methylation (TTCM) in gene bodies accounts for the positive correlation with early replication.  A Self-Organising Map (SOM) approach was able to identify genomic regions with early replication and increased methylation but lacking annotated transcripts, which would have been missed in simple two variable analyses and may encode unrecognized intergenic transcripts.  We conclude that the relationship of cytosine methylation with heterochromatin is not simple, and depends on whether the genomic context is tandemly-repetitive sequences often found near centromeres, which are known to be heterochromatic and methylated, or the remaining majority of the genome, where cytosine methylation is targeted preferentially to the transcriptionally-active, euchromatic compartment of the genome.

overall_design: comparison of human fibroblast and GM06690

first: Masako

last: Suzuki

first: Mayumi

last: Oda

first: María-Paz

last: Ramos

first: Marién

last: Pascual

first: Kevin

last: Lau

first: Edyta

last: Stasiek

first: Frederick

last: Agyiri

first: Reid

middle: F

last: Thompson

first: Jacob

last: Glass

first: Qiang

last: Jing

first: Richard

last: Sandstrom

first: Melissa

last: Fazzari

first: R

last: Hansen

last: Stamatoyannopoulos

first: Andrew

last: McLellan


title: Streptococcus gordonii gene response to the binding of human salivary amylase.

status: Public on Sep 03 2011

city: Buffalo

first: Anna

last: Nikitkova

address: 3435 Main St.

institute: University at Buffalo

summary: Streptococcus gordonii, an important primary colonizer of dental plaque biofilm, specifically binds to salivary amylase via the surface-associated amylase-binding protein A (AbpA). We hypothesized that amylase binding to S. gordonii modulates expression of chromosomal genes, which could influence bacterial survival and persistence in the oral cavity. Gene expression profiling by microarray analysis was performed to detect differentially expressed genes in S. gordonii strain CH1 in response to the binding of purified human salivary amylase as compared to exposure to heat-denatured amylase. Selected genes found to be differentially expressed were validated by qRT-PCR. Five genes from the fatty acid synthesis (FAS) cluster were highly (10-35 fold) up-regulated in amylase treated S. gordonii CH1 cells compared to the denatured-amylase treated cells. An abpA-deficient strain of S. gordonii exposed to amylase did not show a similar response in FAS gene expression as observed in the parental strain. Predicted phenotypic effects of amylase binding to S. gordonii strain CH1 associated with increased expression of FAS genes leading to changes in fatty acid synthesis were noted, as evidenced by increased bacterial growth, survival at low pH, and resistance to triclosan. These changes were not observed in the amylase exposed abpA-deficient strain, suggesting for the role of AbpA in amylase-induced phenotype. These results provide evidence that the binding of salivary amylase elicits a differential gene response in S. gordonii, resulting in a phenotype adjustment that is potentially advantageous for bacterial survival in the oral environment.

overall_design:
In order to identify amylase-regulated genes, S. gordonii CH1 was grown statically in 40 ml CDM at 37°C in a candle jar to mid-log phase corresponding to an optical density at 600 nm of 0.5 to 0.6.The  mid-log phase bacterial culture was divided into two aliquots of equal volume. Bacterial cells from all aliquots were pelleted by centrifugation at 6,000 x g in a Sorvall RC6 centrifuge at 20°C, and washed once with simulated salivary buffer preconditioned to 37°C. Simulated salivary buffer containing 0.4 mg/ml purified, non-glycosylated salivary amylase (native amylase) and preconditioned to 37°C was added to the cells of the fist aliquot; to the cells of the second aliquot simulated salivary buffer containing 0.4 mg/ml of the same salivary amylase denatured by heating to 100°C {Heinen, 1976} and cooled to 37°C was added, as a negative control. Each aliquot, amylase treated and control, was incubated statically for 15 min at 37°C in a candle jar.
	Total RNA was immediately isolated by the hot acid phenol method as described previously {Vickerman, 2007}, followed by treatment with TurboDNase (Applied Biosystems/Ambion, Austin, TX) according to manufacturer’s protocol. Remaining contaminants were removed using the RNeasy minikit column (Qiagen, Valencia, CA) with the cleanup protocol. Total RNA was quantified using the Nanodrop 2000 spectrophotometer and RNA integrity determined by agarose gel electrophoresis. Total RNA was used immediately for cDNA synthesis. The Cy dye-labeled cDNA from the amylase-treated aliquot of the culture was mixed with Cy dye-labeled cDNA from the denatured amylase-treated control aliquot, and used to probe the S. gordonii microarray slides.
Each amylase-exposure experiment was repeated from four biological replicates. To confirm microarray results the cDNA from each strain was labeled with the opposite Cy dye and hybridized to similar arrays for the flip-dye comparison.
Overall design 4 samples were analyzed. The quality controls were 4 biological replicates and dye-swap technical replicates for each biological replicate.

first: Elaine

last: Haase

first: Margaret

last: Vickerman

first: Steven

middle: R

last: Gill

first: Frank

last: Scannapieco


title: Quantitative analysis of thyroid response in zebrafish embryos

status: Public on Jul 08 2011

city: Barcelona

first: Sergi

middle: Pelayo

last: Martinez

state: Barcelona

address: Jordi Girona n.18

department: IDAEA

country: Spain

institute: CSIC

summary: In the further study we have employed the Zebrafish gene expression microarray (v2) as a discovery platform to analysis the trancriptome of 5dpf (days post fertilization) embryos exposed from the 2dpf to 5dpf to nanomolar concrations of thyoid hormone. Only less than 5% genes were affected by the treatment. Gene ontology (GO) analyses show that these genes are involved in the haematopoietic system, visual function and skeletal system. Representatives of each GO functional groups were selected and quantified by real-time PCR to validate the microarray data and to use them as a quantitative biomarkers of thyroid receptor activator.

overall_design: The gene expression in Zebrafish was measured in 5 dpf's embryos under 72h Thyroid Hormone treatment at 50nM.

first: S

last: Pelayo

first: E

last: Oliveira

first: B

last: Thienpont

first: P

last: Babin

first: D

last: Raldua

last: Piña


title: Comparison of Arabidopsis callus

status: Public on May 18 2011

first: Nobutaka

last: Mitsuda

summary: Arabidopsis thaliana plant expressing 35S:WIND1 shows callus-like morphology without hormone treatment. Transcriptomes of the callus-like cell expressing 35S:WIND1, callus of T87 cultured cell, 2,4-D-induced callus and control seedling plant were compared by Agilent microarray.

overall_design: Comparison of four kinds of Arabidopsis thaliana plants. Biological replicates: three for each.

first: Akira

last: Iwase

first: Yuko

last: Takiguchi

first: Masaru

last: Ohme-Takagi


title: Diagnostic microRNA profiling in cutaneous T-cell lymphoma (CTCL)

status: Public on Nov 22 2011

city: Lund

first: Rolf

last: Søkilde

address: Scheelevägen 2

department: Department of Oncology

country: Sweden

institute: Lund University, Sweden

summary: Cutaneous T-cell lymphomas (CTCL) are the most frequent primary skin lymphomas. Nevertheless, diagnosis of early disease has proven difficult due to a clinical and histological resemblance to benign inflammatory skin diseases. To address if microRNA (miRNA) profiling can discriminate CTCL from benign inflammation, we study miRNA expression in 199 patients with CTCL, peripheral T-cell lymphoma (PTL), and benign skin diseases (psoriasis and dermatitis). Using microarrays we show that the most induced- (miR-326, miR-663b, miR-711) and repressed- (miR-203, miR-205) miRNAs distinguish CTCL from benign skin diseases with > 90% accuracy in a training set of 90 samples and a test set of 58 blinded samples. These miRNAs also distinguish malignant and benign lesions in an independent set of 50 patients with PTL and skin inflammation and in experimental human xenograft mouse models of psoriasis and CTCL. Q-RT-PCR analysis of 104 patients with CTCL and benign skin disorders validates differential expression of 4 out of the 5 miRNAs and confirms previous reports on miR-155 in CTCL. A q-RT-PCR-based classifier consisting of miR-155, miR-203, and miR-205 distinguishes CTCL from benign disorders with high specificity, sensitivity, and a classification accuracy of 95% indicating that miRNAs have a high diagnostic potential in CTCL.

platform_organism:
Homo sapiens
Human alphaherpesvirus 1
Human betaherpesvirus 5
Murid betaherpesvirus 1
human gammaherpesvirus 4
JC polyomavirus
Human immunodeficiency virus 1
Murid gammaherpesvirus 4
Human gammaherpesvirus 8
Betapolyomavirus hominis
Betapolyomavirus macacae

overall_design: miRNA microarray. From each sample 100 ng of total RNA was labeled with Hy3 fluorescent dye using the miRCURY LNA Array power labeling kit (Exiqon, Denmark). All samples were labeled the same day with the same master mix, in order to minimize technical variation. The Hy3-labelled samples were hybridized to miRCURY LNA arrays (v11.0) (Exiqon, Denmark), containing capture probes targeting all human miRNAs registered in the miRBASE version 15.0 at the Sanger Institute. The hybridization was performed overnight at 56°C according to manufacturer specifications using a Tecan HS4800 hybridization station (Tecan, Austria). Since it was not possible to hybridize all arrays in one go, samples were randomly split into 5 batches as to minimize day to day variation in the hybridization process. After hybridization the microarray slides were scanned using an Agilent G2565BA Microarray Scanner System (Agilent Technologies, Inc., USA) at 5µm resolution, and the resulting TIFF images were analyzed using the ImaGene 8.0 software on standard settings (BioDiscovery, Inc., USA).

first: Ulrik

last: Ralfkiaer

first: Peter

middle: H

last: Hagedorn

first: Nannie

last: Bangsgaard

first: Marianne

last: Løvendorf

first: Charlotte

last: Ahler

first: Lars

last: Svensson

first: Katharina

last: Kopp

first: Marie

middle: T

last: Vennegaard

first: Britt

last: Lauenborg

first: John

last: Zibert

first: Thorbjørn

last: Krejsgaard

last: Bonefeld

first: Lise-Mette

last: Gjerdrum

first: Tord

last: Labuda

first: Anne-Merete

last: Mathiesen

first: Kirsten

last: Grønbæk

first: Mariusz

last: Wasik

first: Thomas

last: Litman

first: Malgorzata

last: Sokolowska-Wojdylo

first: Catherine

last: Queille-Roussel

first: Robert

last: Gniadecki

first: Elisabeth

first: Carsten

last: Geisler

first: Anders

last: Woetmann

first: Christian

last: Glue

first: Mads

last: Røpke

first: Lone

last: Skov

first: Niels

last: Odum


title: Microarray analysis for M1SF370 Streptococcus pyogenes internalized in Detroit 562 human pharyngeal cells.

status: Public on Jun 10 2011

city: Columbus

first: Vijay

last: Pancholi

state: OH

address: 420W 12th Ave, TMRF-288

department: Pathology

institute: Ohio State University

summary:
A total of 432 genes were found to be differentially expressed in M1SF370 bacterial population internalized in Detroit 562 human pharyngeal cells when compared with the same strain incubated in the absence of Detroit 562 cells. While most of them (349/432 i.e. 80.8%) were up regulated, 83 genes were down regulated contributing to 19.2% of the total differentiated genes. The major contributor of the latter category was phage-related genes (35 genes).
Almost ¼ of these genes (106) belonged to a category of Unknown or possible predicted function. Most notably,  up-regulated genes belonged to  amino acid transport , cell division, cell envelope biogenesis, DNA replication correlated well with up-regulated 67 genes  belonged to translation and ribosomal structure.  Further, up-regulation of 12/15 virulence-related genes indicated that human host cell internalized bacteria are highly virulent as compared to laboratory grown culture in test-tubes.

overall_design:
S. pyogenes strain type M1 SF370 (wild-type) was procured from ATCC (ATCC 700294). Detroit 562 pharyngeal cells were obtained from ATCC and maintained in MEM with 10% FBS in humidified CO2-incubator.
Purified cDNA preparations from the Detroit cells-internalized bacteria  and that were cultured without Detroit cells, were labeled with either Alexafluor-555 or Alexafluor-647 depending on the experimental design ( i.e. dye swap experiment). Differentially labeled probes were then combined and purified. Using  four independently isolated RNA preparations (biological replicates), a total of 8 experiments (incorporating 4 dye swaps) were performed. Accordingly eight hybridization measurements for this mutant were obtained.
Exp-1 and -2 (GSM687276, GSM687310-dye swap) are the technical replicates of the biological sample-1, Exp-3 and -4 (GSM687311, GSM687312-dye swap) are technical replicates of biological sample-2, Exp-5 and -6, (GSM687313,GSM687319-dye swap,) are technical replicates of the biological sample-3, and finally Exp-7 and -8, (GSM687320,GSM687321-dye swap) are technical replicates of the biological sample-4. .


title: h3k4me3_roots_gw-Establishing a reference epigenome in arabidopsis seedlings

status: Public on Apr 19 2011

city: Lyon

first: François

last: ROUDIER

address: 46 Allée d'Italie

department: Biologie

institute: Ecole Normale Supérieure de Lyon

summary: gfe_epigenome - h3k4me3_roots_gw - Epigenomic mapping - H3K4me3 profiling in Col-0 roots.

overall_design: 2 dye-swap - chip-chip

first: Vincent

last: Colot

first: Francois

last: Roudier

first: Marie-Laure

last: Martin-Magniette


title: Custom MHC array analysis of lymphoblastoid cell lines

status: Public on May 23 2011

city: Paris

first: Claire

last: Vandiedonck

address: 10 avenue de Verdun

department: Faculte de Medicine Villemin

institute: Inserm U958, Universite Paris Denis Diderot - Paris 7

type: Expression profiling by genome tiling array

summary:
The human MHC is a paradigm for genomics, showing striking association with disease but functional variants remain largely unresolved. Using an original hybrid microarray (containing tiling and junction probes) for the MHC and accounting for known sequence diversity, we have drawn the first high-resolution, strand-specific transcriptional map of the MHC, defining differences in gene expression for three common haplotypes associated with autoimmune disease. In total, 6% of the MHC is transcribed with one transcript per 1.4kb, including previously unrecognized intergenic transcription. The distributions of differentially expressed probes and polymorphisms between haplotypes are significantly correlated, arguing for cis effects. Haplotype-specific transcription involved 96 differentially expressed genes, including ZFP57, which was validated in a cohort of healthy volunteers, while 526 exons show haplotypic differences. We also find splicing events are significantly more extensive in the MHC than in the rest of the genome. This study marks a new step in immunogenetics.
The results files (.bedgraph and .gff) contain tiling data for both the shared-path and the alternate paths (shared and haplotype-specific) , defining transcriptional activity across the entire MHC region in each sample.

overall_design: Lymphoblastoid cell lines carrying three common autoimmunity haplotypes (COX, PGF, QBL) were analysed in triplicate using the custom MHC array, under both unstimulated and stimulated (200nM PMA and 125nM ionomycin for 6 hours) conditions.

first: Martin

middle: S

last: Taylor

first: Helen

last: Lockstone

first: Katharine

last: Plant

first: Jennifer

first: Caroline

last: Durrant

first: John

last: Broxholme

first: Benjamin

last: Fairfax

first: Julian

last: Knight


title: h3k27me3_roots_gw-Establishing a reference epigenome in arabidopsis seedlings

summary: gfe_epigenome - h3k27me3_roots_gw - Epigenomic mapping - H3K27me3 profiling in Col-0 roots


title: Low P stress transcriptome of control rice variety (Dongjin-byeo) and NtPT1-trasngenic rice (PT 1-7-8)

status: Public on Apr 20 2011

city: Suwon

first: Myoung Ryoul

last: Park

address: 126 Suin-ro

country: South Korea

institute: National Institute of Crop Science

summary: To understand expression of candidate gene located on QTLs for phosphate sensitivity traits under low P using NtPT1-transgenic rice with increased Pi uptake efficiency and gene expression profile at the V3-stage seedling through the 60K Rice Whole Genome Microarray

overall_design: Uniformly germinated seedlings were transferred to a hydroponic system filled with aerated standard solution (normal P, 320 μM Pi) and grown for 2 weeks in a glasshouse at 25°C/18°C (day/night) under a natural photoperiod (about 16 h). The composition and concentration of each element in the standard solution were as follows: N (1.43 mM), P (0.32 mM), K (0.51 mM), Ca (0.75 mM), Mg (1.64 mM), Fe (59.37 μM), B (18.92 μM), Mn (9.50 μM), Mo (0.10 μM), Zn (0.15 μM), Cu (0.16 μM), and citric acid (70.72 μM) (Yoshida et al., 1976). Some of the two-week-old seedlings were transferred to the low P solution (the same nutrient solution containing 32 μM Pi) over a period of 5 days to expose them to P-deficiency condition. Control plants were maintained in the standard solution for the entire period.

first: Myoung-Ryoul

first: So-Hyeon

last: Baek

first: Song-Joong

last: Yun


title: h3_gw-Establishing a reference epigenome in arabidopsis seedlings

first: François

summary: gfe_epigenome - h3_gw - Epigenomic mapping - H3 profiling in Col-0 seedlings


title: h3k27me1_gw-Establishing a reference epigenome in arabidopsis seedlings

summary: gfe_epigenome - h3k27me1_gw - Epigenomic mapping - H3K27me1 profiling in Col-0 seedlings

first: Vincent


title: h3k36me3_gw-Establishing a reference epigenome in arabidopsis seedlings

summary: gfe_epigenome - h3k36me3_gw - Epigenomic mapping - H3K36me3 profiling in Col-0 seedlings

first: Francois


title: 5mc_gw-Establishing a reference epigenome in arabidopsis seedlings

summary: gfe_epigenome - 5mc_gw - Epigenomic mapping - Dna methylation profiling in Col-0 seedlings

first: Marie-Laure


title: Comparison between blood myeloid-derived suppressor cells (MDSCs) extracted from syngeneic kidney transplanted recipient and tolerant kidney allografted recipient induced by anti-CD28 antibody

status: Public on Apr 13 2011

city: NANTES

first: Nahzli

last: DILEK

address: 30 Bd Jean-Monnet, CHU Hôtel-Dieu

institute: INSERM UMR643

summary: The goal is to identify molecules involved in the accumulation of blood MDSCs in tolerant kidney allografted recipients when compared to syngeneic grafted recipients.

overall_design: In this study 27,088 individual rat genes expression from total mRNA of blood MDSCs from 3 tolerated allogeneic kidney transplanted recipient by anti-CD28, were compared to MDSCs from 3 syngeneic kidney transplanted recipient at day 100 post transplantation.

first: Anne-Sophie

last: DUGAST

first: Bernard

last: VANHOVE


title: Transcriptome analysis of avian pathogenic Escherichia coli O1 in chicken serum compared to LB

status: Public on Apr 01 2011

city: Birmingham

first: Chrystala

last: Constantinidou

department: School of Biosciences

country: United Kingdom

institute: University of Birmingham

summary: Colisepticemia caused by avian pathogenic Escherichia coli (APEC) results in annual multimillion dollar losses to the poultry industry.  Recent research suggests that APEC may have an important role in public health as well. Generally, colisepticemia follows a respiratory tract infection in which APEC penetrate the respiratory epithelium to enter the bloodstream. From the bloodstream, bacteria may spread to various internal organs resulting in perihepatitis, pericarditis, and other conditions. The aim of this study was to identify molecular mechanisms enabling APEC to survive and grow in the bloodstream. To do so, we compared the transcriptome of APEC O1 during growth in Luria-Bertani broth and chicken serum. Selected genes that were significantly up-regulated in chicken serum were then subjected to mutational analysis to confirm their role in APEC pathogenesis. Several categories of genes, predicted to contribute to adaptation and growth in the avian host, were identified. These included several known virulence genes and genes involved in adaptive metabolism, protein transport, biosynthesis pathways, stress resistance, and virulence regulation. Several genes with unknown function, which were localized to pathogenicity islands or APEC O1’s large virulence plasmid, were also identified, suggesting that they too contribute to survival in chicken serum. This genome-wide analysis provides novel insight into processes that are essential to APEC O1’s survival and growth in chicken serum.

overall_design: Two-condition experiment: LB vs. chicken serm; four biological replicates, independently grown and harvested.

first: Ganwu

last: Li

first: Peng

last: Liu

first: Lisa

middle: K

last: Nolan


title: Estrogen receptor regulation of the social transcriptome

city: Austin

first: Lauren

middle: A

last: O'Connell

state: TX

address: 1 University Station-CO930

department: Section of Integrative Biology

institute: University of Texas at Austin

summary: We investigated the gene regulatory network of the estrogen receptor in the preoptic region of dominant and subordinate male Astatotilapia burtoni.  We compared dominant males receiving either an ER antagonist or vehicle control and seperately compared subordinate males receiving either an ER antagonist or control. 8.25% of all genes examined changed expression in DOMs in comparison to only 0.56% in SUBs.

overall_design: Two separate loops (one for dominant males and one for subordinate males) with dye-swap containing 16 arrays each from 2 sources (an ER antagonist treated animal or a vehicle treated animal)

first: Hans

last: Hofmann


title: Colony stimulating factor 2 causes changes in the transcriptome of the bovine preimplantation embryo

status: Public on Mar 31 2011

city: Gainesville

first: Peter

last: Hansen

address: 1812 Shealy Drive

department: Animal Sciences

institute: University of Florida

summary: The objective of this study was to identify changes on the CSF2 embryo transcriptome that make them more able to become a blastocyst and more likely to survive after transfer. Embryos were treated with CSF2 at day 5 after fertilization and at day 6 morulae and blastocysts were select for the microarray analysis. A total of 160 genes that had a 1.5-fold difference in expression and a significance of P ≤ 0.05 could be annotated.  Analysis of the data identified 13 biological process ontologies that could be grouped into four functional groups (development and differentiation process, cell communication, apoptosis and cell adhesion).

overall_design: Experimental conditions: CSF2 treated vs. CSF2 nontreated bovine in vitro produced preimplantation embryos. Biological replicates: CSF2 treated vs. nontreated bovine preimplantation embryos were used in a dye switch two-color microarray experimental design. Ratio data was not used in these experiments.

first: Barbara

last: Loureiro

first: Lilian

last: Oliveira

first: Mauricio

middle: G

last: Favoreto


title: Manduca sexta differential gene expression, male & female antenna, larval midgut

status: Public on Mar 01 2011

city: Jena

first: Heiko

last: Vogel

address: Hans-Knoell-Strasse 8

department: Dpt. of Entomology

country: Germany

institute: Max Planck Institute for Chemical Ecology

summary: To allow estimation of the complexity of the antennal transcriptome between sexes as well as in comparison with a non-antennal tissue, microarrays were designed based on an assembly of new 454 sequence data from the antenna and publicly available data including 454 data from the larval midgut. The microarrays were hybridized with samples generated from the repsecitve tissues from 3 (antenna) and 5 (midgut) animals per sample, with four independent samples per sex (antenna) and tissue (midgut).

overall_design: Sequence assembly of included Manduca antennal and gut ESTs (63) and all publicly available Genbank sequences was used with eArray (Agilent Technologies) for the design of 4 x 44K microarrays based on 60mer oligo probes.   For sex-specific antennal microarray hybridizations, RNA of three individuals of one sex was pooled per preparation, and 5 larvae each were dissected for gut tissue isolation with four biological replicates per sex (antennae) and tissue (gut), respectively. Double purified total RNA was added to Agilent Technologies spike-in RNA and labeld using QuickAmp Amplification kit (Agilent Technologies) and the Kreatech ULS Fluorescent Labeling Kit with cyanine 3-CTP dye following the manufacturer´s instructions.  Amplified cRNA samples were used for microarray hybridization, scanned with the Agilent Microarray Scanner and data was extracted from TIFF images with Agilent Feature Extraction software version 9.1. Raw data output files were analyzed using the GeneSpring GX11 and GeneSifter microarray analysis softwares.

first: Ewald

last: Grosse-Wilde

first: Sascha

last: Bucks


title: Expression Profiling of Erythroid Progenitors After MYB shRNA Knockdown

status: Public on Jan 03 2011

city: Boston

first: Vijay

middle: G.

last: Sankaran

state: MA

address: 300 Longwood Avenue

department: Department of Medicine

institute: Children's Hospital Boston

summary: MYB plays a critical role as a regulator of erythropoieisis.  We have shown that MYB silences epsilon and gamma-globin expression in erythroid progenitors.  We here examine erythroid cells at the basophilic erythroblast stage of differentiation with MYB shRNA or control lentiviral transduction prior to differentiation.

overall_design: We have cultured CD34 cells and transduced the cells with lentiviruses harboring shRNAs targeting MYB or controls and then allowed the cells to differentiate down the erythroid lineage.  At the basophilic erythroblast stage of differentiation, the cells were harvested and total RNA was extracted.  This was used to hybridize to Affymetrix expression arrays using the HG-U133 Plus 2.0 platform to ascertain expression differences that occur with the knockdown of MYB.


title: Comparison between syngeneic kidney transplant and a model of allogeneic kidney transplant tolerance induced by anti-classII regimen in the rat

status: Public on Apr 09 2011

city: Nantes

first: Romain

last: Vuillefroy de Silly

address: 30 Bvd Jean Monnet

summary: The goal is to identify new molecules implicated in tolerance, to determine the implication of these molecules in immune responses to transplantation by gene expression comparison of 27,088 individual rat genes between tolerated kidney allotransplant and syngeneic kidney transplant.

overall_design: In this study 27,088 individual rat genes expression from total mRNA of 3 tolerated allogeneic kidney transplants by anti-classII, were compared to 3 syngeneic kidney transplants at day 100 post transplantation.

first: Vojislav

last: Jovanovic

first: Richard

last: Danger

first: Sophie

last: Brouard


title: Cuc1 mutants expressing the chimeric repressor TCP3-SRDX

status: Public on Dec 27 2010

city: Tsukuba

first: Nobutaka

last: Mitsuda

address: Central 6 Higashi 1-1-1

institute: National Institute of Advanced Industrial Science and Technology

summary: Downstream genes of Arabidopsis TCP3 transcription factor were tried to be identified. The expression of TCP3-SRDX was induced after germination by estrogen-induction system in a wild type and cuc1 mutant background to reduce an effect of CUC induction by TCP3-SRDX.

overall_design: Two Two-condition experiments, induced vs. non-induced and induced in cuc1 vs non-induced in cuc1. Biological replicates: 3 or 4 replicates.

first: Tomotsugu

last: Koyama

first: Motoaki

last: Seki

first: Kazuo

last: Shinozaki

first: Masaru

last: Ohme-Takagi


title: Genes for embryo development are packaged in blocks of multivalent chromatin in zebrafish sperm

status: Public on Jan 13 2011

city: Salt Lake City

first: Shan-Fu

last: Wu

address: 2000 Circle of Hope

department: Oncological Sciences

institute: University of Utah

summary: In mature human sperm, genes of importance for embryo development (i.e. transcription factors) lack DNA methylation and bear nucleosomes with distinctive histone modifications, suggesting the specialized packaging of these developmental genes in the germline. Here, we explored the tractable zebrafish model and found conceptual conservation as well as several new features. Biochemical and mass spectrometric approaches reveal the zebrafish sperm genome packaged in nucleosomes and histone variants (and not protamine), and we find linker histones high and H4K16ac absent - key factors which may contribute to genome condensation. We examined several activating (H3K4me2/3, H3K14ac, H2AFV) and repressing (H3K27me3, H3K36me3, H3K9me3, hypoacetylation) modifications/compositions genome-wide, and find developmental genes packaged in large blocks of chromatin with coincident activating and repressing marks and DNA hypomethylation, revealing complex ‘multivalent’ chromatin. Notably, genes that acquire DNA methylation in the soma (muscle) are enriched in transcription factors for alternative cell fates. Remarkably, we find H3K36me3 located in ‘silent’ developmental gene promoters, and not present at the 3’ ends of coding regions of genes heavily transcribed during sperm maturation, suggesting different rules for H3K36me3 in the germline and soma. We also reveal the chromatin patterns of transposons, rDNA, and tRNAs. Finally, high levels of H3K4me3 and H3K14ac in sperm are correlated with genes activated in embryos prior to the mid-blastula transition (MBT), whereas multivalent genes are correlated with activation at or after MBT. Taken together, gene sets with particular functions in the embryo are packaged by distinctive types of complex and often atypical chromatin in sperm.

overall_design:
[DNA profiling]: H3K4me3, H3K4me2, H3K14ac, H3K36me3, H3K27me3, H3K9me3, and H2AFV ChIP-chip in zebrafish sperm; DNA methylation in zebrafish sperm and muscle by MeDIP-chip. (two replicates and dye-swaps for all experiments). Antibodies: H3K4me3 (Abcam ab8580 and Active Motif 39159), H3K4me2 (Abcam ab7766), H3K14Ac (Upstate 07-353), H2AZ (Abcam ab4174), H3K27me3 (Upstate 07-449), H3K9me3 (Active Motif 39161), H3K36me3 (Abcam ab9050), 5-methylcytidine (Eurogentec BI-MECY-1000).  Supplementary files: Processed data files reporting calculated enrichment log2 ratio (mean ChIP/mean Input in the log2 ratio). Note: For analysis, "mean Input" from H3K4me3-rep1 ch1, H3K4me2-rep1 ch2, and H3K36me3-rep2 ch1 for all ChIP eluates.

[mRNA profiling]: Transcripts in zebrafish mature sperm using zebrafish expression microarray from Agilent. (two replicates)

first: Haiying

last: Zhang

first: Bradley

last: Cairns


title: SAGE analysis of human glomerular endothelial cell

status: Public on Dec 01 2010

city: Vienna

first: Gürkan

last: Sengoelge

address: Waehringer Guertel 18-20

department: Medicine/Division of Nephrology

country: Austria

institute: Medical University Vienna

summary: Tissue from macroscopically healthy parts of nephrectomized kidneys. Endothelial cells were purified from the cell outgrowth of glomeruli twice using CD31 magnetic beads and cultured on fibronectin coated surface. Cells were not passaged more than eight times and stained with vWf, CD31, and after stimulation with TNF alpha also with CD62E/P.

overall_design: This GEO Series was created by the GEO staff as part of a cleanup effort to ensure that all GEO Samples are included within a Series entry.


title: Peripheral Blood Cells Gene Expression Profiles from Discordant Monozygotic Twins with Systemic Autoimmune disease (SAIDs)

status: Public on Dec 30 2010

city: Durham

first: Rick

middle: David

last: Fannin

state: NC

address: 111 T.W. Alexander Drive

department: Office of the Director

institute: The National Institute of Environmental Health Sciences

summary: Gene expression profiling in peripheral blood cells from monozygotic twin pairs with various sytemic autoimmune diseases revealed 92 genes that could discriminate between MZ twin pairs and unrelated-matched controls. No genes were found that could discriminate between proband and unaffected twin pairs, or between the various disease phenotypes.

overall_design: RNA microarray analyses (Agilent Human 1A(V2) 20K oligo arrays) quantified differential gene expression in blood from 20 monozygotic (MZ) twin pairs, to minimize polymorphic gene effects, discordant for SAID (six with systemic lupus erythematosus (SLE), six rheumatoid arthritis (RA), eight idiopathic inflammatory myopathies (IIM)) and 40 unrelated - matched controls. Multiple statistical and pathway analyses were performed to assess differences in profiles of gene expression among the subject SAID groups and controls. ID's  -xx-00 = Matched Control 1; xx-60 = second matched control; xx-01 = Affected MZ twin; xx-02 = unaffected MZ twin

first: Fred

last: Miller

first: Terrance

last: O'Hanlon


title: Breaking endodormancy in leafy spurge crown buds by dehydration-stress and vernalization identifies overlapping molecular networks linked to growth regulators

status: Public on Apr 05 2011

city: Fargo

first: Munevver

last: Dogramaci

state: ND

address: 1605 Albrecht Blvd N

institute: USDA-ARS

summary: Persistence of the invasive perennial weed leafy spurge is mainly attributed to seasonal production of underground adventitious buds (UABs), which undergo well-defined phases of dormancy (para-, endo- and eco-dormancy). These well-defined phases of dormancy also allow UABs of leafy spurge to survive extreme seasonal variations, including dehydration-stress. Consequently, objectives of this study include understanding the effects of dehydration-stress on vegetative reproduction, flowering competence, and transcript profiles at different phases of bud dormancy. The vegetative growth potential of UABs was monitored by removing the aerial portion of dehydration-stressed plants and re-watering the root system. Further, microarray analysis was used to follow transcriptome profiles to identify critical defense- and signaling-pathways at different phases of dormancy in UABs. Surprisingly, only 3 days of dehydration-stress is required to break the endodormant phase in UABs. In leafy spurge, vernalization of endodormant UABs has previously been shown to induce flower competence, while breaking of endodormancy via dehydration-stress did not induce floral induction. Thus, these two environmental treatments open a unique approach to independently dissect molecular mechanisms involved in endodormancy maintenance and floral competence. Bioinformatics analysis of transcriptome data helped to identify models and overlapping pathways. During endodormancy break, LEC1, PHOTOSYSTEM I RC, and brassinosteroids were identified as ooverlapping hubs of up-regulated genes, and DREB1A, CBF2, GPA1, MYC2, BHLH, BZIP, and flavonoids were identified as overlapping hubs of down-regulated genes. Additionally, key genes involved in metabolic activity, chromatin modification, and cross-talk between growth regulators were identified as playing a role during endodormancy maintenance.

platform_organism:
Manihot esculenta
Euphorbia esula

overall_design:
Plant material, controlled environmental treatments, and vegetative growth:

Three-month-old paradormant leafy spurge plants grown in a greenhouse were acclimated for one week, under growth chamber conditions, prior to being subjected to a ramp-down in temperature (27 °C → 10 °C) and photoperiod (16 h → 8 h light) for 12 weeks to induce endodormancy, as previously established (Doğramacı et al. 2010; Foley et al. 2009). Endodormancy status was confirmed by comparing vegetative growth rates of plants with and without a ramp-down treatment. To study the effects of dehydration-stress on vegetative growth from UABs, water was withheld from endodormant plants up to 21 days. After dehydration for 0, 1-, 3-, 7-, 14-, and 21-days, the aerial portion of the plants were decapitated at the soil surface and vegetative growth and floral competence of UABs were monitored under growth-conducive conditions by re-watering the root system. Vegetative shoot growth from six plants was recorded weekly for four weeks, and results of four replications were analyzed using SAS 9.2 (SAS Institute, Cary, NC, 2008) software as described by Doğramacı et al. (2010).

Microarray analysis:

At the end of each treatment, crown buds were collected, and RNA extraction, cDNA synthesis, fluorescent labeling, microarray hybridization using ~23K element arrays, and spot intensity analyses were performed as previously described by Doğramacı et al. (2010). Based on unexpected vegetative growth results obtained from this study, only microarray data obtained from 0-, 1-, and 3-day dehydration-stressed endodormant UABs, which were compared with microarray data for endodormant, and flowering competent ecodormant UABs from our previous study (Doğramacı et al. 2010; GSE19217), were used for bioinformatics analyses. However, to merge the datasets from these two separate experiments, T-tests were first performed on microarray data obtained from endodormant UABs from each experiment, and differentially-expressed genes (p<0.005) were removed from the dataset (~5% of the spots). After removing the outliers, the two endodormant transcriptome data sets were grouped together and used as the baseline control for further ANOVA, T-tests and other analyses. Array normalization, statistical analyses and clustering of the dataset and Venn diagram generation were done using GeneMaths XT 5.1 software as previously described by Doğramacı et al. (2010).

first: Münevver

last: Doğramacı

first: David

middle: P

last: Horvath

first: Michael

middle: J

last: Christoffers

first: James

middle: V

last: Anderson


title: Midgut - CGH Differential Replication

status: Public on Mar 25 2011

city: Toronto

first: DCC

last: modENCODE

address: MaRS Centre, South Tower, 101 College Street, Suite 800

institute: Ontario Institute for Cancer Research

summary:
modENCODE_submission_3278
This submission comes from a modENCODE project of David MacAlpine. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We will precisely identify sequence elements that direct DNA replication by using chromatin immunoprecipitation of known replication initiation complexes.  These experiments will be conducted in multiple cell types and developmental tissues.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: tiling array analysis. BIOLOGICAL SOURCE: Strain: Oregon-R(official name : Oregon-R-modENCODE genotype : wild type ); Tissue: midgut; Developmental Stage: L3 stage wandering larvae; Genotype: wild type;  NUMBER OF REPLICATES: 2;  EXPERIMENTAL FACTORS: strain Oregon-R; tissue Mid gut; Developmental Stage L3 stage wandering larvae

last: MacAlpine

first: Terry

last: Orr-Weaver

first: Jarred

last: Norman

first: Sharon

last: Li

first: Joseph

last: Prinz


title: SAGE analysis of normal human thyroid tissue

city: Amsterdam

first: Erwin

last: Pauws

address: Meibergdreef 9

institute: Academic Medical Center

summary:
This library was generated from normal human thyroid tissue collected at routine autopsy.
Standard SAGE protocol was used (Velculescu et al. Science 1995).
Data from this library was published in: 'Pauws E, Moreno JC, Tijssen M, Baas F, de Vijlder JJ, Ris-Stalpers C. J Clin Endocrinol Metab. 2000 May;85(5):1923-7'
Data was generated and analyzed at the laboratory of Pediatric Endocrinology, Academic Medial Center, Amsterdam, The Netherlands.


title: Fat Body - CGH Differential Replication

summary:
modENCODE_submission_3277
This submission comes from a modENCODE project of David MacAlpine. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We will precisely identify sequence elements that direct DNA replication by using chromatin immunoprecipitation of known replication initiation complexes.  These experiments will be conducted in multiple cell types and developmental tissues.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: tiling array analysis. BIOLOGICAL SOURCE: Strain: Oregon-R(official name : Oregon-R-modENCODE genotype : wild type ); Tissue: fat body; Developmental Stage: L3 stage wandering larvae; Genotype: wild type;  NUMBER OF REPLICATES: 2;  EXPERIMENTAL FACTORS: strain Oregon-R; tissue fat body; Developmental Stage L3 stage wandering larvae


title: Gene expression profiling of the early-stage CD34+ differentiation process

city: Ribeirão Preto

first: Daniel

middle: Guariz

last: Pinheiro

state: São Paulo

address: Rua Tenente Catão Roxo, 2501

department: Departamento de Genética

country: Brazil

institute: Faculdade de Medicina de Ribeirão Preto (Universidade de São Paulo)

summary: To better understand the early events regulating lineage-specific hematopoietic differentiation, we analyzed the transcriptional profiles of CD34+ human hematopoietic stem and progenitor cells (HSPCs) subjected to differentiation stimulus.

overall_design: CD34+ cells were cultured for 12 and 40 hours in liquid cultures with supplemented media favoring myeloid or erythroid commitment. Serial analysis of gene expression (SAGE) was employed to generate four independent libraries. CD34+ Hematopoietic Stem Progenitor Cells with no differentiation stimulus were used as a control library.

first: Greice

last: Molfetta

first: Dalila

middle: L

last: Zanette

first: Rodrigo

last: Panepucci

first: Wilson

last: Silva Jr

first: Marco

last: Zago


title: Expression array for Trichoderma harzianum T34 and nox1 overexpressed transformant Tnox5 strains in dual culture with Pythium ultimum

status: Public on Oct 13 2010

city: Salamanca

first: Enrique

last: Monte

state: Salamanca

address: Rio Duero

department: Spanish-Portuguese Centre for Agricultural Research

institute: University of Salamanca

summary:
A self-designed Trichoderma high density oligonuclotide (HDO) microarray  (Roche-NimbleGen, Inc., Madison, WI, USA) was constructed in a similar way  than a previous Trichoderma HDO microarray (Samolski et al., 2009). The microarray was composed of 392,779 60-mer probes designed against 13,443 EST-derived transcripts (Trichochip-1) and the genomes of T. atroviride (11,100 genes) and T.  virens (11,643 genes). The Trichochip-1 ESTs were obtained from 28 cDNA libraries from eight different species (representing the biodiversity of this genus: T. harzianum, T. atroviride, T. asperellum, T. viride, T. longibrachiatum, T. virens, T. stromaticum and T. aggresivum), under a wide range of growth conditions, including biocontrol-related conditions and different nutritional situations (Vizcaíno et al., 2006).
The Trichochip1 EST database was generated in the TrichoEST project funded by the EU (QLK3-CT-2002-02032).

sample_organism:
Trichoderma harzianum
Globisporangium ultimum

platform_organism:
Trichoderma virens
Trichoderma atroviride

overall_design: Confrontations were carried out between the T. harzianum T34 or nox1 overexpressed transformant Tnox5 and P. ultimum. Agar plugs cut from the growing edge of a 4-day colony of Trichoderma and Pythium were placed 2 cm from the border on the opposite side of the same petri plates containing PDA covered with sterile cellophane sheets. Dual cultures were allowed to grow at 25 ºC and mycelia were collected from the interaction zone in confrontations between P. ultimum and T. harzianum T34 or Tnox5 strains. Seven PDA plates were used for each condition considered and RNAs were extracted and the corresponding cDNAs were use to hybridize by triplicate the Trichoderma HDO microarray.

first: Marta

last: Montero-Barrientos

first: Fran

last: González

first: Rosa

last: Hermosa


title: Expression profiling of DHR38-dependent transcripts in Drosophila larvae

first: Carl

last: Thummel

department: Human Genetics

summary: Transcriptional profiling of Drosophila third instar larvae comparing control (w1118) and DHR38 mutants (DHR38Y214/Df(2)KetelRX32)

overall_design: Two-condition experiment, control vs. DHR38 mutant larvae. Biological replicates: 3 replicates.

first: Anne-Françoise

last: Ruaud


title: Danio spinal cord injury

status: Public on Oct 19 2010

city: Piscataway

first: Ronald

middle: P.

last: Hart

address: 604 Allison Rd Rm B430

department: Cell Biology & Neuroscience

institute: Rutgers University

summary: Adult zebrafish have the ability to recover from spinal cord injury and exhibit re-growth of descending axons from the brainstem to the spinal cord. We performed gene expression analysis using microarray to find damage-induced genes after spinal cord injury, which shows that Sox11b mRNA is up-regulated at 11 days after injury. However, the functional relevance of Sox11b for regeneration is not known. Here, we report that the up-regulation of Sox11b mRNA after spinal cord injury is mainly localized in ependymal cells lining the central canal and in newly differentiating neuronal precursors or immature neurons. Using an in vivo morpholino-based gene knockout approach, we demonstrate that Sox11b is essential for locomotor recovery after spinal cord injury. In the injured spinal cord, expression of the neural stem cell associated gene, Nestin, and the proneural gene Ascl1a (Mash1a), which are involved in the self-renewal and cell fate specification of endogenous neural stem cells, respectively, is regulated by Sox11b. Our data indicate that Sox11b promotes neuronal determination of endogenous stem cells and regenerative neurogenesis after spinal cord injury in the adult zebrafish. Enhancing Sox11b expression to promote proliferation and neurogenic determination of endogenous neural stem cells after injury may be a promising strategy in restorative therapy after spinal cord injury in mammals.

overall_design: Spinal cord injury or control sham injury was performed on adult zebrafish.  After 4, 12, or 264 hrs, a 5 mm segment of spinal cord was dissected and processed (as a pool from 5 animals) in three replicate groups for each time point and treatment.

first: Yuji

last: Guo

first: Liping

last: Ma

first: Massimiliano

last: Cristofanilli

first: Melitta

last: Schachner


title: Human_SAGE_cervix_normal_B_1

city: Mexico

first: Carlos

last: Perez-Plasencia

address: Cuauhtemoc 300

department: UIMEO

country: Mexico

institute: Mexican Institute for Social Security

summary: Uterine cervix normal SAGE, CGAP non-normalized SAGE library, bulk method , HPV negative


title: SAGE analysis of Type 2 Gaucher brain

city: Bethesda

first: Richard

middle: Leonard

last: Proia

institute: NIDDK

summary: This library was constructed from mRNA derived from an eight month old female with type 2 Gaucher disease according to the SAGE protocol of V. E. Velculescu et al. (1995), in the laboratory of R. L.  Proia (NIDDK, NIH).


title: SAGE analysis of normal human mammary epithelial cells, breast carcinoma (malignant effusion), and breast adenocarcinoma (malignant pleural effusion)

city: Smithville

first: C

middle: Marcelo

last: Aldaz

department: Science Park Research Division, Carcinogenesis

institute: M.D. Anderson Cancer Center

summary:
These libraries represent Cancer Genome Anatomy Project libraries, which are either produced through CGAP funding, or donated to CGAP.
The Cancer Genome Anatomy Project (CGAP: http://cgap.nci.nih.gov) is an interdisciplinary program established and administered by the National Cancer Institute (NCI: http://www.nci.nih.gov) to generate the information and technological tools needed to decipher the molecular anatomy of the cancer cell.


title: Transcriptomic changes following hybridization and allopolyploidy in two salt marsh species

status: Public on Nov 10 2010

city: RENNES

first: Chelaifa

last: Houda

address: Bat 14A campus de beaulieu

institute: Rennes1 university

summary:
Transcriptomic changes following recent natural hybridization and allopolyploidy in the salt marsh species Spartina x townsendii and Spartina anglica (Poaceae)

Allopolyploidy results from two events: the merger of divergent genomes and genome duplication. Both events have important functional consequences for the evolution and adaption of newly formed allopolyploid species.  In spite of significant progress made the last years, a few studies have decoupled the effects of hybridization from genome duplication in the observed patterns of expression changes accompanying allopolyploidy in natural conditions.    We used Agilent Rice oligo-microarrays to explore gene expression changes following allopolyploidy in Spartina that includes a classical example of recent allopolyploid speciation, S. anglica formed during the 19th century following genome duplication of the hybrid S. x townsendii.   Our data indicate important, thought different effects of hybridization and genome duplication in the expression patterns of the hybrid and allopolyploid. Deviation from parental additivity was most important following hybridization and was accompanied by maternal expression dominance, although transgressively expressed genes were also encountered.   Maternal dominance is attenuated following genome duplication in S. anglica while this species exhibits an increased number of transgressively over expressed genes.  These results reflect the decoupled effects of the “genomic shock” following hybridization and genome redundancy, on the genetic, epigenetic and regulatory mechanisms characterizing transcriptomic evolution in allopolyploids.

sample_organism:
Sporobolus alterniflorus
Sporobolus anglicus
Sporobolus maritimus
Sporobolus x townsendii

overall_design: We used Agilent Rice oligo-microarrays to explore gene expression changes among Spartina species, following interspesific hybridization and genome duplication (allopolyploidy). The analysed species included the parents S. maritima & S.alterniflora, the hybrid F1 S x. towensendii and the allopolyploid S.anglica. A total of 20 slides (five replicates per species) were hybridized on a 44 K Rice Agilent array using a one color desgin.

first: Houda

last: Chelaifa

first: Annabelle

last: Monnier

first: Malika

last: Ainouche


title: Atlas of gene expression in the mouse kidney

status: Public on Nov 11 2010

city: Paris

first: Lydie

last: Cheval

address: 15 rue de l'école de Médecine

institute: Institut des Cordeliers

summary: To gain molecular insight into kidney function, we performed a high-resolution quantitative analysis of gene expression in glomeruli and nine different nephron seg-ments dissected from mouse kidney using the long-SAGE method. We also developed dedicated bioinformatics tools and databases to annotate mRNA tags as transcripts. Over 800,000 mRNA SAGE tags were sequenced corresponding to >20,000 different mRNA tags present at least twice in at least one library. Hierarchical clustering analysis of tags demonstrated similarities between the three anatomical sub-segments of the proximal tubule, between the cortical and medullary segments of the thick ascending limb of Henle’s loop, and between the three segments constituting the aldosterone sensitive distal nephron segments, whereas the glomerulus and distal convoluted tubule clusterized independently. We also identified highly specific mRNA markers of each subgroup of nephron segments and of most nephron segments. Tag annotation also identified numbers of putative antisense mRNAs. This database constitutes a reference resource in which the quantitative expression of a given gene can be compared with that of other genes in the same nephron segment, or between different segments of the nephron. To illustrate possible applications of this database, we performed a deeper analysis of the glomerulus transcriptome which unexpectedly revealed expression of several ion and water carriers; within the glomerulus, they were found to be preferentially expressed in the parietal sheet. It also revealed the major role of the zinc finger transcription factor Wt1 in the specificity of gene expression in the glomerulus. Finally, functional annotation of glomerulus-specific transcripts showed the high proliferation activity of glomerular cells. Immunolabelling with anti-PCNA antibodies confirmed a high percentage of proliferating glomerular parietal cells.

overall_design: Approximately 1000 tubules from each different nephron segments were microdissected from 6-8 male CD1 mice. Over 800,000 mRNA SAGE tags were sequenced corresponding to >20,000 different mRNA tags present at least twice in at least one library.

first: Fabien

last: Pierrat

first: Carole

last: Dossat

first: Mathieu

last: Genete

first: Martine

last: Imbert-Teboul

first: Jean-Paul

last: Duong van Huyen

first: Julie

last: Poulain

first: Patrick

last: Wincker

first: Jean

last: Weissenbach

first: David

last: Piquemal

first: Alain

last: Doucet


title: Yeast D10 Small ~ WT San I

status: Public on Sep 03 2010

city: Ljubljana

first: Peter

last: Juvan

address: Zaloska 4

department: Institute of Biochemistry

country: Slovenia

institute: Faculty of Medicine, University of Ljubljana

summary: Transcriptional profiling of parental S. cerevisiae San I cells in comparison with its translocant derivative D10 Small strain. The latter strain was obtained using Bridge Induced translocation technique between DUR3 gene (Chromosome VIII) and ADH1 gene (Chromosome XV), and exhibited an abnormal phenotype comprising elongated buds and multi-budded, unevenly nucleated pseudo-hyphae. Goal was to demonstrate how chromosomal translocations can influence gene expression of translocant and other chromosomes.

overall_design: Two-condition experiment, direct comparison of Saccharomyces cerevisiae D10 small (4 biological replicates) vs. pooled WT San I (reference) cells.

first: Dmitri

last: Nikitin


title: Effects of purine de novo synthesis knockdown on gene expression in Drosophila melanogaster S2 tissue culture cells

city: Fredericton

first: Denise

last: Clark

state: NB

address: 10 Bailey Drive

department: Biology

institute: University of New Brunswick

summary: The effect of inhibiting expression of the ade2 gene by RNA interference in Drosophila S2 tissue culture cells was examined.

overall_design: S2 cells underwnt three different dsRNA treatments.  Two were for non-overlapping sequences of ade2 transcripts and the third was for a non-specific Chlamydomonas reinhardtii lhcb sequence.  3 samples from ade2 dsRNA-1 treated cells, 2 samples from ade2 dsRNA-2, and 3 samples from lhcb dsRNA treated cells were used on two 4x44K format slides (G2519F).


title: Determinants of divergent adaptation and Dobzhansky-Muller interaction in experimental yeast populations

status: Public on Jul 15 2010

city: Cambridge

first: Jason

last: Funt

address: 7 Cambridge Center

country: USA

institute: MIT

summary: Divergent adaptation can be associated with reproductive isolation in the process of speciation.  We recently demonstrated the link between divergent adaptation and the onset of reproductive isolation in experimental populations of the yeast Saccharomyces cerevisiae evolved from a single progenitor in either a high-salt or a low-glucose environment. However, the genetic basis for adaptation and reproductive isolation remained unknown in this system.  Here, we use whole-genome re-sequencing of representatives of three populations to identify 15 candidate mutations, six of which explained the adaptive increases in mitotic fitness in the two environments.  In two populations evolved in high salt, two different mutations occurred in the proton efflux pump gene PMA1 and the global transcriptional repressor gene CYC8; the ENA genes encoding sodium efflux pumps were over-expressed once through expansion of this gene cluster and once as a result of the mutation in the regulator CYC8.  In the population from low glucose, one mutation occurred in MDS3, which modulates growth at high pH, and one in MKT1, a global regulator of mRNAs encoding mitochondrial proteins, the latter recapitulating a naturally-occurring variant.  A Dobzhansky-Muller (DM) incompatibility between the evolved alleles of PMA1 and MKT1 strongly depressed fitness in the low-glucose environment.  This DM interaction is the first reported between experimentally evolved alleles of known genes and shows how reproductive isolation can arise rapidly when divergent selection is strong.

overall_design: Evolved and progenitor strains were grown in stressed and unstressed conditions to identify role of mutations in gene expression.

first: James

middle: B

last: Anderson


title: Gene expression along the human epididymis

status: Public on Aug 26 2010

city: Pointe-Claire

first: Daniel

last: Cyr

state: Québec

address: 245, Boulevard Hymus

institute: INRS-Institut Armand-Frappier

summary:
SUBMITTER_CITATION: Dubé E and Cyr DG, The Blood-Epididymis and Human Male Fertility. In: Biology and Regulation of Blood-Tissue Barriers, Cheng CY Editor. 2010, Landes Bioscience.

The epididymis can be subdivided into three regions, the caput, corpus and cauda epididymidis, that have different characteristics and functions. Goal was to determine the differential pattern of gene expression along the regions of the human epididymis.

overall_design: Two-condition experiment, region 1 vs region 2. Replicates: 4 biological replicates from each epididymal region.

first: Evemie

last: Dubé

first: Louis

last: Hermo

last: Chan


title: Whole-genome gene expression profiling of dorsal root ganglion neurons after nerve damage

status: Public on Sep 01 2010

first: Harold

middle: D

last: MacGillavry

address: De Boelelaan 1087

department: Center for neurogenomics and cognitive research

institute: Vrije Universiteit

summary: We generated whole-genome gene expression profiles of dorsal root ganglion (DRG) neurons following nerve damage. DRG neurons extend one peripheral axon into the spinal nerve and one central axon into the dorsal root. The peripheral axon regenerates vigorously, while in contrast the central axon has little regenerative capacity. For this study, two groups of animals were subjected either to sciatic nerve (SN) or dorsal root (DR) crush, and at 12, 24, 72 hours and 7 days after the crush, lumbar DRGs L4, L5 and L6 were dissected and total RNA was extracted.

overall_design: For each time point after lesion, three biological replicate RNA samples  were hybridized together with the common reference sample consisting of labeld RNA pooled from three unlesioned animals.

first: Geert

last: Geeven

first: Ruben

last: Eggers

first: Joost

last: Verhaagen

first: August

last: Smit

first: Mathisca

middle: C

last: de Gunst

first: Ronald

middle: E

last: van Kesteren


title: Hif1α down-regulation is associated with transposition of great arteries in mice treated with a RA antagonist

status: Public on Sep 20 2010

city: Roma

first: Francesca

last: Amati

address: Via Montpellier 1

department: Biomedicine and Prevention

country: Italy

institute: University of Rome Tor Vergata

summary:
Aims: Congenital heart defect (CHD) account for 25% of all human congenital abnormalities. Very few CHD-causing genes have been identified so far; so, to discover further genes we performed a global transcriptome analysis in mouse models of CHD.
Methods and results: By the use of a retinoic acid competitive antagonist (BMS-189453) we caused CHD, thymic abnormalities and neural tube defects in mouse newborns. Transposition of great arteries was the prevalent cardiac defect observed (61%). Recently we were able to partially rescue this abnormal phenotype by oral administration of folic acid. Now we have performed a microarray analysis in mouse embryos (8.5 dpc) treated with BMS-189453 alone and with BMS-189453 plus folic acid (FA). On the basis of microarray and QRT-PCR results, we deeper analysed Hif1α because of its down-regulation in BMS-treated embryos vs WT and its increased expression level in BMS+FA treated embryos compared to BMS-treated ones. Immunofluorescence experiments confirmed the under-expression of Hif1α protein in BMS-treated embryos compared to WT and BMS+FA treated ones and moreover demonstrated that at 8.5 dpc Hif1α is mainly expressed in the embryo's heart.
Conclusion: We propose that Hif1α down-regulation by blocking retinoic acid binding, may contribute to the development of the cardiac defects of mouse newborns. In line with our hypothesis, when Hif1α expression level is restored (by supplementation of folic acid) a decrement of CHD is found. At the best of our knowledge this is the first report that link retinoic acid metabolism to Hif1α regulation and the development of TGA

overall_design: 2 samples w/ 2 dye-swaps

first: F

first: L

last: Diano

last: Campagnolo

last: Vecchione

first: D

last: Cipollone

first: S

last: Bueno

first: G

last: Prosperini

first: A.

last: Desideri

last: Siracusa

last: Chillemi

first: B

last: Marino

last: Novelli


title: Changes in H2A.Z occupancy and DNA methylation during B-cell lymphomagenesis

status: Public on Aug 09 2010

city: Seattle

first: Jorja

last: Henikoff

state: WA

address: 1100 Fairview AV N, A1-162

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

summary:
The histone variant H2A.Z has been implicated in the regulation of gene expression, and in plants antagonizes DNA methylation. Here we ask whether a similar relationship exists in mammals, using a mouse lymphoma model, where chromatin states can be monitored during tumorigenesis. Using native ChIP-on-chip, we found a progressive depletion of H2A.Z around transcriptional start sites (TSSs) during cell state transformations. In addition, we found that H2A.Z and DNA methylation are anti-correlated around TSSs in wild-type and Myc-transformed cells. Surprisingly, approximately 30% of genes show a redistribution of H2A.Z from around TSSs to bodies of active genes during oncogenesis but not before, and these changes are accompanied by DNA methylation changes in the opposite direction. Our results suggest that antagonism between H2A.Z deposition and DNA methylation is a conserved feature of eukaryotic genes, and that transcription-coupled H2A.Z changes may play a role in cancer initiation and progression.

Keywords: Chromatin affinity-purification on microarray

overall_design: Two types of experiments were performed on wild type pre-B cells, Myc induced pre-B cells, and B cell tumors: H2AZ profiling was performed by comparing DNA isolated by Chromatin immunoprecipitation (ChIP) using antibody against H2AZ, to total MNase fragmented genomic DNA isolated from each of the three cell types.  Methylation profiling was performed by comparing DNA isolated using immunoprecipitation with an antibody against single stranded DNA (MeDIP) to total sonicated genomic DNA isolated from each of the three cell types. For each sample, the input and IP material was differentially labeled and cohybridized to a promoter microarray chip.  Expression analysis was done using single channel microarrays.  In brief, total RNA was isolated from each of the three cell types, followed by poly-AAA CDNA synthesis and labeling.

first: Steven

first: Melissa

last: Conerly

first: Sheila

middle: S

last: Teves


title: Gene expression profiles of ALL cells

status: Public on Sep 10 2010

city: St. Peter

first: Sanjive

last: Qazi

state: MN

address: 800 west College Av

institute: Gustavus Adolphus College

summary: Using using ATLAS cDNA expression arrays, we performed gene expression profiling of primary leukemia cells from 31 infants and 30 non-infant children (pediatric patients) with ALL to determine if any of these signature genes are differentially expressed in infant ALL vs. pediatric ALL.  Reduced expression levels of 6 of the 9 CD22deltaE12 signature genes that were represented on the human cDNA arrays, including TP53 and APC as well as MDM2, SATB1, CCNG1 and GNB2 discriminated infant BPL from non-infant BPL.

overall_design: Total RNA was extracted from primary ALL cells and human ATLAS c DNA expression arrays were used for gene expression profiling.

first: Fatih

last: Uckun

first: Pat

last: Goodman


title: Paramecium tetraurelia autogamy series 2 (ND7-silenced and control cells)

status: Public on Jul 07 2010

city: Villerubanne

first: Jean-François

last: Gout

address: 43 Bld du 11 Novembre 1918

country: France

institute: Laboratoire Biométrie et Biologie Evolutive

summary: P. tetraurelia, like all ciliates, is a unicellular eukaryote processing two different kinds of nuclei, germline micronuclei (mic) and somatic macronucleus (mac). The diploid micronuclei undergo meiosis during sexual events to transmit the germline genome to the next generation. The highly polyploid mac (~800 n) is responsible for transcription during the life cycle but is lost after fertilisation; the new mic and mac develop from mitotic copies of the zygotic nucleus. During development of the new mac, the germline genome is amplified from 2n to ~800n and is extensively rearranged by two distinct kinds of DNA elimination. The micronuclear 50 to 60 Chromosomes are fragmented into ~200 shorter molecules caped by de novo telomere addition as a result of the imprecise elimination transposons and minisatellites. Moreover, approximately 60,000 short, single-copy elements called internal eliminated sequences (IESs) are precisely removed from coding and non-coding sequences. It was shown that the rearrangements in the developing mac appear to reproduce the rearrangements observed in the old mac, implying the existence of homology dependent cross talk between germline and somatic genomes during sexual event. To understand the molecular mechanisms and the genetic control involved in genome rearrangements, we studied the evolution of the transcriptome during Paramecium tetraurelia sexual reproduction.

overall_design: RNA samples were extracted at different time points of mass cultures undergoing autogamy on normal food bacteria and on bacteria producing dsRNA to induce ND7 silencing. ND7 is a non-essential gene involved in the regulated discharge of trichocysts; the loss of function of this gene by with dsRNA feeding results in a mutant phenotype: non-discharge of trichocysts (Skouri and Cohen 1997).

first: Khaled

last: Bouhouch


title: Benzo(a)pyrene induces similar gene expression changes in testis of DNA repair proficient and deficient male mice

status: Public on Aug 24 2010

city: Maastricht

first: Nicole

last: Verhofstad

address: Universiteitssingel 50

department: Health Risk Analysis and Toxicology

institute: Maastricht University

summary: DNA damage induced by benzo(a)pyrene may lead to the formation of mutations and as a consequence to the development of diseases. However, it is uncertain whether benzo(a)pyrene causes heritable mutations in male germ cells, which would increase health risks in offspring. In a previous study, benzo(a)pyrene induced DNA damage was observed at all stages of spermatogenesis and in testis. In addition, we observed that spermatogonial stem cells and testis rely, at least in part, on nucleotide excision repair for the removal of this damage, because removal was less efficient in Xpc-/- than in wild type mice. Efficient removal will protect the germ cells against the formation of heritable mutations. By using microarray technology, we investigated in this study the consequences of this difference in DNA adduct removal at the level of gene expression in testis 4 days after a single exposure to benzo(a)pyrene.

overall_design: We analyzed 20 testis samples of mice divided into 4 groups (5 mice per group): C57BL/6 control mice, C57BL/6 mice exposed to B[a}P, Xpc-/- control mice, Xpc-/- mice exposed to B[a]P. We used a pool of 3 C57BL/6 control mice as a reference.

first: Jeroen

last: Pennings

first: Conny

middle: T

last: van Oostrom

first: Jan

last: van Benthem

first: Frederik

last: van Schooten

first: Harry

last: van Steeg

first: Roger

middle: W

last: Godschalk


title: Paramecium tetraurelia autogamy series 4

summary: In the ciliate Paramecium tetraurelia, autogamy is a self-fertilization process, during which the zygotic nucleus results from the fusion of two identical gametic nuclei. This phenomenon occurs in response to starvation. It starts with meiosis of the germline nuclei (micronuclei or MIC) and fragmentation of the parental somatic nucleus (macronucleus or MAC). This is followed by mitotic division of one haploid nucleus issued from meiosis to yield two identical gametic nuclei, then karyogamy takes place, followed by mitosis of zygotic nucleus and differentiation of new MICs and MACs from the resulting copies of the zygotic nucleus. Within the developing new MACs, developmentally programmed DNA amplification and extensive genome rearrangements (precise excision of short non coding Internal Eliminated Sequences and chromosome fragmentation associated with the imprecise elimination of repetitive DNA) give rise to the highly polyploid somatic genome. To gain further insight into the complex regulation of these successive steps, we used whole genome microarrays to study the different gene networks that become activated throughout autogamy.

overall_design: Total RNA was extracted before the begining of autogamy (reference sample) and at 3 different time points during the process of autogamy.

first: Mireille

last: Betermier


title: Paramecium tetraurelia autogamy series 3

overall_design: Total RNA was extracted before the begining of autogamy (c3_vegetative cells : reference sample) and at 5 different time points during the process of autogamy.

first: Aurélie

last: Kapusta


title: Paramecium tetraurelia trichocyst exocytosis recovery

summary: Paramecium cells possess a few thousand trichocysts (big secretory granules of 3~4 um long) docked at their surface and whose discharge in the external medium can be triggered using aminoethyldextran (a modified dextran positively charged) without damage to the cells. After discharge, new trichocysts are re-synthesized by the cells. We studied the evolution of the transcriptome during this synthesis.

overall_design: Our experimental design was to extract total RNA before trichocyst discharge triggering and at two time points after discharge, 40 and 210 minutes. Four biological replicates are included for each time point and the untriggered control.

first: Jean

last: Cohen

last: Bouhouche

first: Linda

last: Sperling


title: Preferential re-replication of Drosophila heterochromatin

status: Public on Mar 18 2010

city: Durham

first: David

middle: M

last: MacAlpine

address: Box 3813 DUMC

department: Pharmacology and Cancer Biology

institute: Duke University Medical Center

summary: DNA copy number profile of Drosophila Kc167 cells comparing control pUC dsRNA treated cells and geminin dsRNA treated cells.

overall_design: CGH: 2 controls, 2 geminin knockdowns, 2 platforms

first: Queying

last: Ding