title: Exon Expression Changes in the Spinal Cords of Lewis Rats with Myelin Basic Protein-Induced Experimental Autoimmune Encephalomyelitis (EAE)

status: Public on Jun 30 2013

city: Brisbane

first: Hayley

middle: Ruth

last: Inglis

state: Queensland

address: Building 71/918, Royal Brisbane & Women’s Hospital Campus,Herston, QLD, 4029

department: Clinical Neurosciences

country: Australia

institute: University of Queensland , Centre for Clinical Research

summary:
Myelin Basic Protein (MBP) induced experimental autoimmune encephalomyelitis (EAE) in the Lewis rat, produces an an acute weakness, or paralysis of the tail and hind limb ataxia ,weakness or paralysis associated with increased permiability of the blood brain barrier, inflammation and demyelination in central nervous system (CNS).  Clinical symptoms , ascending weakness or paralysis of the tail followed by the hind limbs and in rare cases the fore limbs occurs 8 and 14 days post immunisation (dpi) and is generally resolved completely by day 20  dpi.  We have carried out transcriptome analysis of total RNA from the spinal cords of female Lewis rats at the peak of disease (EAE)  and age matched  healthy controls to identify exon expression changes associated with the disease.
In these data sets we include the exon expression data obtained from total RNA preparations from the spinal cords of female Lewis  rats sacrificed at the clinical peak of MBP induced EAE and age matched , untreated, healthy controls.

overall_design: 8 total RNA samples were prepared.  A two way ANOVA comparison carried out in Partek Genomics Suite was used to detect differences in exon expression in the spinal cord of female lewis rats with MBP induced EAE and age matched healthy controls.

middle: R

first: Judith

middle: M

last: Greer

first: Pamela

middle: A

last: McCombe


title: The genomic landscape of the somatic linker histone subtypes H1.1 to H1.5 in human cells

status: Public on Jun 15 2013

city: Oxford

first: Kinga

last: Kamieniarz-Gdula

address: South Parks Road

department: Sir William Dunn School of Pathology

country: United Kingdom

institute: University of Oxford

type: Genome binding/occupancy profiling by genome tiling array

summary:
We employed the DamID technique to systematically map the genomic distribution of all canonical somatic H1 subtypes (H1.1-H1.5) in human IMR90 cells.
Human cells contain up to eleven histone H1 proteins, with different spatial and temporal expression patterns. These include five canonical, replication-dependent somatic H1 subtypes (H1.1, H1.2, H1.3, H1.4 and H1.5). Despite being a key chromatin component, the genomic distribution of the somatic canonical H1 subtypes is still unknown and their role in chromatin related processes has so far remained elusive.  Here we employed a DamID approach to map for the first time the genomic localization of all somatic canonical  H1 subtypes in human cells. Our integrative analysis reveals novel insights into H1 subtype distribution and uncovers functional chromatin features potentially regulating the H1 genomic landscape. In general H1.2 to H1.5 are depleted from GC-rich regions and regulatory regions associated with active transcription. H1.1 shows a binding profile distinct from the other subtypes, suggesting a unique function for H1.1 in chromatin-regulated processes. Interestingly, our data indicate a novel role for somatic H1 subtypes in the three-dimensional organization of the genome by marking repressive regions within topological domains such as LADs.
Our work integrates the five somatic linker histone H1 subtypes into the epigenome maps of human cells and provides a resource to refine our understanding of the significance of H1 and its heterogeneity in the control of genome function.

overall_design: DamID profiling of somatic linker histone variants H1.1, H1.2, H1.3, H1.4 and H1.5 in human fibroblasts. Two biological replicate samples of all H1 variants were hybridized on NimbleGen Human ChIP-chip 2.1M Economy Whole-Genome Tiling - Array GPL16055 covering small human chromosomes.

first: Robert

last: Schneider

first: Annalisa

last: Izzo


title: Genomic Characterization of Bladder Cancer Cell Lines using CGH Arrays

status: Public on Jun 28 2013

city: Madrid

first: Francesco

last: Acquadro

state: Madrid

address: calle de Melchor Fernandez Almagro 3

department: Molecular Cytogenetics

country: Spain

institute: Centro Nacional de Investigaciones Oncologicas CNIO

summary: Genomic rearrangements involving different chromosome translocation in bladder cancer cell lines and in primary tumor samples

overall_design: DNA extracted from 3 Bladder Cancer Cell lines (SW1710, JON, RT-4), and 1 bladder cancer (372C) in T3 Tumor stage and Grade 3 primary  sample, were processed, Cy5 labeled and hybridized on Agilent CGH Arrays. As control DNA we used Cy3 labeled probes prepared starting from a pool of female DNA obtained mixing the DNA extracted from 20 healthy donors.

first: Acquadro

last: Francesco

first: Menezes

last: Juliane

first: Rio-Machin

last: Ana

first: Rodriguez-Perales

last: Sandra

first: Roncador

last: Giovanna

first: Real

last: Francisco X.

first: Cigudosa

last: Juan Cruz


title: CD8+ T cells: IL-10+ VS IL-10-

status: Public on Jun 21 2013

city: tianjin

first: huiyuan

last: zhao

address: weijin Road 94

country: China

institute: nankai university

summary: Transcriptional profiling and gene expression profiling analysis of sorted CD8+IL-10+ T cells compared to CD8+IL-10- T cells using IL-10-GFP(tiger) reporter mice

overall_design: Two sample, CD8+IL-10+ T cells vs CD8+IL-10- T cells. Three replicate per array.

first: Huiyuan

last: Zhao

first: Yapu


title: Worms spun in centrifuge at elevated g values

status: Public on Jun 22 2013

city: Derby

first: Nathaniel

middle: J

last: Szewczyk

address: Uttoxeter Road

department: MRC/Arthritis Research UK Centre for Musculoskeletal Ageing Research

institute: University of Nottingham, Royal Derby Hospital

summary:
Worms spun at higher than normal g values for 4 days on 20G centrifuge vs. worms kept at 1 X G. Both are mixed stage cultures.
A stimulus or stress experiment design type is where that tests response of an organism(s) to stress/stimulus. e.g. osmotic stress, behavioral treatment
Physical Characteristics: worms kept at increased g values for 4 days (x g value)

first: Catharine

last: Conley

first: John

last: Wang


title: Spirodiclofen resistance in the spider mite Tetranychus urticae

status: Public on Jun 26 2013

city: Ghent

first: Wannes

last: Dermauw

address: Coupure Links 653

department: Crop Protection

country: Belgium

institute: University Ghent

summary: The goal of our microarray experiments was to compare the gene expression profile of two spirodiclofen resistant spider mite strains (SR-VP and SR-TK) with that of a susceptible spider mite strain (LS-VL)

overall_design: 5 samples were analyzed: 3 biological replicates for SR-VP, 2 biological replicates for SR-TK

first: Peter

last: Demaeght

first: Thomas

last: Van Leeuwen


title: Nucleosome mapping in Saccharomyces cerevisiae in different conditions

city: Edinburgh

first: Yatendra

last: Kumar

email: yaten2020@gmail.com, ykumar@ed.ac.uk

address: Crewe Road south

department: MRC HGU

institute: MRC Human Genetics Unit, The University Of Edinburgh

summary: This experiment aims to map nucleosome positions and comparison of the same in WT NORMAL GROWTH vs WT-NUTRIENT STARVATION/isw1∆2∆ MUTANT/rsc4-∆4  MUTANT in Saccharomyces cerevisiae using a custom designed tiling array on  Agilent plat form. The corresponding platform is submitted to GEO under Geo-ID GPL15842. 60mer probes with variable tiling density were designed for all the genes transcribed by RNA polymerase III. Each gene is tiled along with its 1kb downstream and upstream region with the exceptions of RPR1, SCR1, RDN5(1-6) and SNR52. Mononucleosomal DNA and size matched naked DNA was competitively hybridized to the array. Data was extracted and normalized log ratios were calculated using Agilent sofware. Normalized log2 ratio data was used in MLM to detection nucleosome positions.

overall_design: Equal amount of mono-nucleosomal DNA  and sized matched naked DNA prepared from formaldehyde fixed cells (Yuan et al. 2005), was labeled with Cy5 and Cy3 respectively and hybridized to the microarray. Each Hybridization was done in triplicate from three independent biological samples in each condition. Enrichment of mono-nucleosomal DNA over naked genomic DNA is a measure of nucleosome density calculated as Log2(nucDNA/nakedDNA).

first: Purnima

last: Bhargava


title: Structural systems biology evaluation of metabolic thermotolerance in Escherichia coli

status: Public on Jun 20 2013

city: Ulsan

first: Donghyuk

last: Kim

address: 50 UNIST-gil, Eonyang-eup, Ulju-gun

department: Department of Chemical Engineering

country: South Korea

institute: UNIST

summary: Investigation of whole genome gene expression level in E. coli K-12 MG1655 in glucose M9 minimal media with/without heatshock

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

overall_design: A six chip study using total RNA recovered from E. coli K-12 MG1655 grown up to OD600nm 0.6 (mid-exponential phase) in M9 minimal media supplemented with 0.2% glucose with/without heatshock in 42oC. The high-density oligonucleotide tiling arrays used were consisted of 371,034 oligonucleotide probes with 50-bp length that are spaced 25 bp apart across the E. coli genome (NimbleGen). Experiments were performed with three biological replicates.

first: Roger

last: Chang

first: Kathleen

last: Andrews

first: Bernhard

middle: O

last: Palsson


title: Heat and nickel induced mRNA changes in mussels

status: Public on Jun 19 2013

city: Chott-Mariem

first: Mohamed

last: Banni

state: Sousse

address: Route Touristique

department: Life sciences

country: Tunisia

institute: Higher Institut of Agronomy

summary:
Transcriptional profiling of the digestive gland tissue of female mussel Mytilus galloprovincialis exposed to nickel along with a temperature gradient
Background: The exposure of marine organisms to stressing agents may affect the level and pattern of gene expression. Although many studies have examined the ecological effects of heat stress on mussels, little is known about the physiological mechanisms that might be affected by co-exposure to heat stress and environmental contaminants such as nickel (Ni). In the present work we investigated the effects of simultaneous changes in temperature and Ni supply on lysosomal membrane stability (LMS) and malondialdehyde accumulation (MDA) in the digestive gland (DG) of the blue mussel Mytilus galloprovincialis (Lam.). To shed some light into how the molecular response to environmental stressors is modulated, we employed a cDNA microarray with 1,673 sequences to measure the relative transcript abundances in the DG of mussels exposed to Ni along with the temperature increase. Temperature and Ni rendered additive effects on LMS and MDA accumulation, increasing the toxic effects of metal cations. Ni loads in DG tissues was also affected by co-exposure to 26°C. In animals exposed only to heat stress, functional genomics analysis of the microarray data (171 DEGs) revealed 7 biological processes, largely dominated by the up-regulation of folding protein-related genes, and the down regulation of genes involved in cell migration and cellular component assembly. Exposure to Ni at 18°C and 26°C rendered respectively 188 and 262 DEGs showing distinct pattern in term of biological processes. In particular, the response of mussels exposed to Ni at 26°C was characterized by the up regulation of proteolysis, ribosome biogenesis, response to unfolded proteins and catabolic-related genes as well as the down-regulation of genes encoding cellular metabolic processes. Our data provide new insights on the transcriptomic response in mussels challenging temperature increases and Ni exposure and should be carefully considered in view of the biological effects of heat stress and particularly in polluted areas.

overall_design: Digestive gland tissue from individual animals in different experimental conditions were analyzed in a complete loop design. Dual color competitive hybridizations (Control “16°C” vs “20°C” vs “24°C” vs “16°C+Cu”, “20°C” vs “24°C” vs “20°C+Cu”, “24°C” vs “24°C+Cu”, “16°C+Cu” vs”20°C+Cu” vs “24°C+Cu”; “20°C+Cu” vs “24°C+Cu”) including label swap. Single individuals. Four biological replicates. One replicate per array.

last: BANNI

first: Alessandro

last: NEGRI

first: Aldo

last: VIARENGO


title: Leishmania donovani amastigotes: Nelfinavir (NFV)-sensitive (control) vs Nelfinavir-resistant

status: Public on Jun 27 2013

city: Quebec City

first: Frederic

last: Raymond

state: Quebec

address: 2440 Bd Hochelaga Suite 1710

department: École de nutrition

country: Canada

institute: Université Laval

type:
Genome variation profiling by array
Expression profiling by array

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

overall_design: Refer to individual Series

first: Pranav

first: Frédéric

first: Robert

last: Lodge

first: Marc

last: Ouellette

first: Michel

last: Tremblay


title: EpCAM overexpression prolongs proliferative capacity of primary human breast epithelial cells and supports hyperplastic growth

city: Bolzano

first: Johannes

last: Rainer

address: Via A. Volta 21

department: Institute for Biomedicine

country: Italy

institute: Eurac Researc

summary:
Background: The Epithelial Cell Adhesion Molecule (EpCAM) has been shown to be strongly expressed in human breast cancer and cancer stem cells and its overexpression has been supposed to support tumor progression and metastasis. However, effects of EpCAM overexpression on normal breast epithelial cells have never been studied before. Therefore, we analyzed effects of transient adenoviral overexpression of EpCAM on proliferation, migration and differentiation of primary human mammary epithelial cells (HMECs).
METHODS:
HMECs were transfected by an adenoviral system for transient overexpression of EpCAM. Thereafter, changes in cell proliferation and migration were studied using a real time measurement system. Target gene expression was evaluated by transcriptome analysis in proliferating and polarized HMEC cultures. A Chicken Chorioallantoic Membrane (CAM) xenograft model was used to study effects on in vivo growth of HMECs.
RESULTS:
EpCAM overexpression in HMECs did not significantly alter gene expression profile of proliferating or growth arrested cells. Proliferating HMECs displayed predominantly glycosylated EpCAM isoforms and were inhibited in cell proliferation and migration by upregulation of p27KIP1 and p53. HMECs with overexpression of EpCAM showed a down regulation of E-cadherin. Moreover, cells were more resistant to TGF-beta1 induced growth arrest and maintained longer capacities to proliferate in vitro. EpCAM overexpressing HMECs xenografts in chicken embryos showed hyperplastic growth, lack of lumen formation and increased infiltrates of the chicken leukocytes.
CONCLUSIONS:
EpCAM revealed oncogenic features in normal human breast cells by, inducing resistance to TGF-beta1-mediated growth arrest and supporting a cell phenotype with longer proliferative capacities in vitro. EpCAM overexpression resulted in hyperplastic growth in vivo. Thus, we suggest that EpCAM acts as a prosurvival factor counteracting terminal differentiation processes in normal mammary glands.

overall_design: For each gene a representative transcript probe set was selected based on a score that combines average expression and variation of expression across all samples. Transcript probe sets with more than 4 probes were preferred. Differential expression analysis between EPCAM over-expressing and control cells (expressing GFP) was performed using a paired moderated t-test employing functions provided by Bioconductor's limma package. p-values were subsequently adjusted for multiple hypothesis testing using the method from Benjamini and Hochberg for a strong control of the false discovery rate.

first: Agnieszka

last: Martowicz

first: Julien

last: Lelong

first: Gilbert

last: Spizzo

first: Guenther

last: Gastl

first: Gerold

last: Untergasser


title: Gene expression analysis of bovine oocytes with high developmental competence obtained from FSH-stimulated animals

city: Quebec

first: Remi

last: Labrecque

state: QC

address: 2440, boulevard Hochelaga

department: Animal Science

institute: Laval University

summary: The objective of the study was to analyze the impact of various lenght FSH withdrawal period (coasting) after the last FSH injection on transcriptome changes in in vivo bovine oocytes at the GV stage. Oocytes were collected from super-stimulated animals after 20, 44, 68 and 92 hours of coasting.

overall_design: For each cow individually (biological replicate), each coasting time was compared to others (i.e. 20 hrs vs 44 hrs; 20 hrs vs 68 hrs; 20 hrs vs 92 hrs; 44 hrs vs 68 hrs; 44 hrs vs 92 hrs and 68 hrs vs 92 hrs) for a total of six comparisons. Overall, 36 hybridizations, corresponding to the three cows and six comparisons were done using a dye-swap set-up.

first: Christian

last: Vigneault

first: Patrick

last: Blondin

first: Marc-André

last: Sirard


title: Genome-wide microRNA analysis of NPC and non-NPC specimens gene expression

status: Public on Jun 25 2013

city: shanghai

first: shu

last: yang

address: State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Science

institute: Fudan University

summary: Analysis of differential expression between NPC and non-NPC tissues at miRNA expression level.  We used a miRNA microarray platform to investigate the profile between NPC tissues and normal nasopharyngeal tissues to evaluate the relationship between miRNA expression and NPC. Recognition of the aberrant miRNAs and enrichment pathway analysis of predicted target gene may provide some clues to estimate the mechanism of miRNA effects on NPC carcinogenesis mediated by miRNA-mRNA regulation.

overall_design: Total RNA was extracted from 8 NPC tissues compared to 4 nasopharyngeal tissues. We peformed the Illumina miRNA microarray to identify the differentially expressed miRNA between NPC tissues and normal nasopharyngeal tissues.

first: Ting

last: LI

first: Jia-xin

last: CHEN

first: Xu-ping

last: FU

first: Shu

last: YANG

first: Zheng

last: ZHANG

first: Ke-he

first: Yao


title: ChIP-chip from HEK293 cells with YY2-antibody

status: Public on Jun 16 2013

city: Berlin

first: David

last: Drews

address: Augustenburger Platz 1

country: Germany

institute: Charite

summary: The Yin Yang 2 (YY2) gene encodes a zinc finger transcription factor that is not well characterized, yet. By using chromatin immunoprecipitations combined with whole-genome human promoter microarray (ChIP-chip) in HEK293 cells, we identified a multiplicity of YY2-bound annotated promoters as well as additional chromosomal regions. Interestingly, gene ontology analyses linked YY2 to fundamental biological pathways associated to cancer and developmental processes.

overall_design: Identification of YY2 target genes in HEK293 cells in vivo

first: Martin

last: Klar

first: Sandy

last: von Salisch

first: Christof

last: Dame


title: Methylation Analysis of Gastric Cancers

status: Public on Jun 14 2013

city: Nashville

first: Barbara

middle: G

last: Schneider

state: TN

address: 2215 Garland Avenue, 1030C MRB IV

department: Div. of Gastroenterology, Hepatology, & Nutrition

country: USA

institute: Vanderbilt University Medical Center

type: Methylation profiling by genome tiling array

summary: Examine methylation changes in gene promoters in gastric cancers and matched normal control gastric epithelium, using Nimblegen arrays.

overall_design: Direct comparison of gastric cancers and matched normal control gastric epithelium

first: B

first: M

middle: B

last: Piazuelo

first: L

last: Sicinschi

first: K

middle: C

last: Lo

first: R

last: Mera

first: D-F

last: Peng

first: J

last: Roa

last: Romero-Gallo

first: A

last: Delgado

first: T

last: de Sablet

middle: E

last: Bravo

middle: T

last: Wilson

first: W

last: El-Rifai

last: Peek Jr.

first: P

last: Correa


title: Leishmania donovani amastigotes: Nelfinavir (NFV)-sensitive (control) vs Nelfinavir-resistant [Comparative Genomic Hybridization (DNA) profiling]

first: Frederic

last: Raymond

summary: Drug resistance is a major public health challenge in Leishmaniasis chemotherapy, particularly in the case of emerging Leishmania/HIV-1 co-infections. Recently, we have delineated the mechanism of cell death induced by the HIV-1 protease inhibitor, Nelfinavir, in the Leishmania parasite. In order to investigate the underlying molecular mechanism involved in Nelfinavir resistance, in vitro Nelfinavir resistant amastigotes were developed by direct drug pressure in culture. RNA expression profiling analyses of closely related Leishmania species were used as a screening tool to compare Nelfinavir-resistant and -sensitive parasites in order to identify candidate genes involved in drug resistance, and several genes were found to be differentially expressed. Comparative gene hybridization (CGH) analyses of Nelfinavir-resistant and -sensitive Leishmania using whole-genome 60-mer oligonucleotide microarrays were also carried out. RNA expression profiles and the CGH of Nelfinavir resistant vs sensitive Leishmania amastigotes suggest that parasites regulate mRNA levels either by modulating gene copy numbers through chromosome aneuploidy, or gene deletion/duplication by homologous recombination. Interestingly, supernumerary chromosomes 6 and 11 in the resistant parasites lead to upregulation of the ABC class of transporters, which are involved in vesicular trafficking. Transporter assays using radiolabeled Nelfinavir suggest that the drug accumulates in greater amounts in the resistant parasites and in a time dependent manner. Furthermore, high-resolution electron microscopy showed an increased number of vacuoles in Nelfinavir-resistant parasites. Together these results suggest that Nelfinavir is rapidly and dramatically sequestered in these intracellular vesicles.

overall_design: Two condition experiment: NFV-sensitive vs resistant. Biological replicates: Three. One dye swap.

first: Pranav

last: Kumar

first: Frédéric

first: Robert

last: Lodge

first: Marc

last: Ouellette

first: Michel

last: Tremblay


title: Leishmania donovani amastigotes: Nelfinavir (NFV)-sensitive (control) vs Nelfinavir-resistant [RNA expression profiling]


title: Lytic infection of Lactococcus lactis by bacteriophages Tuc2009 and c2 trigger alternative transcriptional host responses

city: Utrecht

first: Aldert

last: Zomer

address: Yalelaan 1

department: Department of Infectious Diseases and Immunology,Faculty of Veterinary Medicine

country: Netherlands

institute: Utrecht University

summary: This study analysed the temporal transcriptional response of L. lactis UC509.9 undergoing infection with either Tuc2009 or c2, representing phages of two different species (P335 and c2, respectively) of the family Siphoviridae. For the first time, to our knowledge, both DNA microarrays of the host and high resolution tiling arrays of each phage were used provide corresponding data sets of the entire transcriptome at various points post-infection.

sample_organism: Lactococcus cremoris subsp. cremoris UC509.9

overall_design: DNA microarrays containing oligonucleotide primers representing each of the 2066 annotated genes on the genome of L. lactis UC509.9 (Genbank accession number: CP003157), in addition to complete genome tiling arrays of bacteriophages Tuc2009 NC_002703) and C2 (NC_001706) at 4 bp resolution, were designed using eArray (https://earray.chem.agilent.com/earray/) and ChipD (http://www.ncbi.nlm.nih.gov/pubmed/20529880) and obtained from Agilent Technologies (Palo Alto, CA). For sample collection, pre-warmed GM17 (30 °C) was inoculated with 2 % of an overnight culture of L. lactis UC509.9. This was grown at 30 °C under static conditions to an OD600 of 0.13 at which point CaCl2 was added to a final concentration of 10 mM. The culture was further incubated for 10 min to allow equilibration. At this point, the culture was split into two equal volumes. To one, phage (either C2 or Tuc2009) in TBT buffer (100 mM Tris pH 7.5, 100 mM NaCl, 10 mM MgCl2), was added to a final multiplicity of infection (MOI) of 5. To the other, acting as control, a corresponding amount of TBT buffer without phage was added. Samples (60 ml) were collected at 2, 5, 10, 15, 25, 35 and, in the case of Tuc2009 only, 45 min post infection (p.i.) by centrifugation. Pellets were flash frozen in a -80 °C EtOH bath. Samples were then maintained at -80 °C until further processing and analysis.

first: Stuart

last: Ainsworth

first: Douwe

last: van Sinderen


title: Profiling of RNA Pol II occupancy in Drosophila neural stem cell populations using TaDa (Targeted DamID)

city: London

first: Tony

middle: David

last: Southall

address: South Kensington Campus

department: Life Sciences

institute: Imperial College London

summary:
Cell-type specific transcriptional profiling is key to understanding cell fate specification and function. In order to achieve this it has been necessary, to date, to isolate specific cell types from complex tissues. We have developed 'TaDa', a technique that enables cell-specific profiling without cell isolation.  TaDa permits genome-wide profiling of DNA- or chromatin-binding proteins without cell sorting, fixation or affinity purification. The method is simple, sensitive, highly reproducible and is in principle transferable to any model system. Here we show that TaDa can be used to identify transcribed genes in a cell-type specific manner. We profile the genome-wide binding of RNA polymerase II (Pol II) in adjacent, clonally related neural stem cells in intact Drosophila brains. Our data reveal the activity of non-canonical metabolic pathways in proliferating neuroepithelial cells, and highlight a possible role for the retinal determination gene regulatory network in patterning neural stem cell fates. We also identify temporal differences in the activity of signalling pathways that control neuroepithelial cell fate by profiling Pol II occupancy at two different stages of brain development.
Using RNA Pol II TaDa to profile, in a cell-type specific manner, the transcriptional state of neuroepithelial cells at two stages of larval brain development. Closely related asymmetrically dividing neural stem cells (neuroblasts) were also profiled, in order to compare the transcriptomes of  two different types of neural stem cells.

overall_design: 3 biological relicates were performed for 3rd instar neuroepithelial cells (with one dye-swap). 2 biological relicates were performed for 3rd instar neuroblasts (with dye-swap). 2 biological relicates were performed for 1st instar neuroepithelial cells (with dye-swap). As additional supporting evidence for the Pol II TaDa technique, 2 biological relicates were performed for 3rd instar salivary glands (with dye-swap) in order to compare with previous Pol II-ChIP data for this tissue [PMID 22821985].

middle: D

first: Andrea

middle: H

last: Brand


title: Mycobacteria-Dependent Expression of microRNA-142-3p Reduces WASP Family Proteins and Controls Phagocytosis

city: Heidelberg

first: Jonathon

last: Blake

state: BW

address: Meyerhofstr 1

institute: EMBL

summary:
Phagocytosis requires the activation of a plethora of mechanisms that include the activation of the actin cytoskeleton guided by the Arp2/3 complex. These are promoted by activators such as the Wiskott Aldrich Syndrome Protein (WASP) family members. In order to further understand the molecular mechanisms involved in the early events leading the phagocytosis of the pathogenic Mycobacterium tuberculosis, we set out to examine potential roles of miRNAs in phagocytosis using genome-wide expression profiling to identify miRNAs differentially regulated following mycobacterial infection.
One of the miRNAs activated upon infection of mouse macrophages with the non-pathogenic Mycobacterium smegmatis, the widely conserved miR-142-3p, was predicted and confirmed to target the Neural-WASP (N-WASP). Upregulating of miR-142-3p in mouse macrophages inversely correlated with levels of N-WASP, upon infection with live pathogenic and non-pathogenic mycobacteria, suggesting an active role of Mycobacterium tuberculosis on the regulation of phagocytosis, at the post-transcriptional level, in host cells. The reduction of N-WASP correlated with a reduced internalization of bacteria per macrophage, independently of the phagocytosis index. Furthermore, the downregulation of WASP levels accompanied those of N-WASP, at early but not at late time points, suggesting a closely regulatory mechanism among both family members, dependent on the time frame of the phagocytosis. Additionally, upregulating of miR-142-3p promoted the change in the protein levels of another predicted and confirmed target, the Cofilin2 protein, in a phagocytosis-independent fashion. Downregulation experiments promoted aberrant morphologic phenotypes in macrophages, similar to observed by others in PBMCs of humans with Wiskott Aldrich Syndrome, suggesting the strong involvement of miR-142-3p on the regulation of the actin machinery in macrophages.
Altogether these results show for the first time that miRNAs are involved in the regulation of actin-mediated phagocytosis of pathogenic bacteria and that these are direct targets of Mycobacterium tuberculosis.

overall_design: Expression analysis of mouse macrophage cell line J774A.1 in response to infection with Mycobacterium smegmatis mc2155 EGFP. Three biological replicates each for uninfected and infected samples.

first: Paulo

last: Bettencourt

first: Sabrina

last: Marion

first: David

last: Pires

first: Leonor

last: Santos

first: Joana

last: Pardal

first: Gareth

last: Griffiths

first: Elsa

last: Anes


title: Autosomal and uniparental portraits of the native populations of Sakha (Yakutia): implications for the peopling of Northeast Eurasia

city: Tartu

first: Mait

last: Metspalu

address: Riia 23

country: Estonia

institute: Estonian Biocentre

summary: Sakha – an area connecting South and Northeast Siberia – is significant for understanding the history of peopling of Northeast Eurasia and the Americas. Previous studies have shown a genetic contiguity between Siberia and East Asia and the key role of South Siberia in the colonization of Siberia. We report the results of a high-resolution phylogenetic analysis of 701 mtDNAs and 318 Y chromosomes from five native populations of Sakha (Yakuts, Evenks, Evens, Yukaghirs and Dolgans) and of the analysis of more than 500,000 autosomal SNPs of 758 individuals from 55 populations, including 40 previously unpublished samples from Siberia. Phylogenetically terminal clades of East Asian mtDNA haplogroups C and D and Y-chromosome haplogroups N1c, N1b and C3, constituting the core of the gene pool of the native populations from Sakha, connect Sakha and South Siberia. Analysis of autosomal SNP data confirms the genetic continuity between Sakha and South Siberia. Maternal lineages D5a2a2, C4a1c, C4a2, C5b1b and the Yakut-specific STR sub-clade of Y-chromosome haplogroup N1c can be linked to a migration of Yakut ancestors, while the paternal lineage C3c was most likely carried to Sakha by the expansion of the Tungusic people. MtDNA haplogroups Z1a1b and Z1a3, present in Yukaghirs, Evens and Dolgans, show traces of different and probably more ancient migration(s). Analysis of both haploid loci and autosomal SNP data revealed only minor genetic components shared between Sakha and the extreme Northeast Siberia. Although the major part of West Eurasian maternal and paternal lineages in Sakha could originate from recent admixture with East Europeans, mtDNA haplogroups H8, H20a and HV1a1a, as well as Y-chromosome haplogroup J, more probably reflect an ancient gene flow from West Eurasia through Central Asia and South Siberia. Our high-resolution phylogenetic dissection of mtDNA and Y-chromosome haplogroups as well as analysis of autosomal SNP data suggests that Sakha was colonized by repeated expansions from South Siberia with minor gene flow from the Lower Amur/Southern Okhotsk region and/or Kamchatka. The minor West Eurasian component in Sakha attests to both recent and ongoing admixture with East Europeans and an ancient gene flow from West Eurasia.

overall_design: 40 samples were analysed with the Illumina platform Human660W-Quad v1.0 and are described herein.

first: Richard

last: Villems

first: Sardana

last: Fedorova

first: Maere

last: Reidla


title: Genome-wide analysis of desiccation tolerance-related genes in Arabidopsis seeds

city: Wageningen

first: Wilco

last: Ligterink

address: Droevendaalsesteeg 1

department: Lab of Plant Physiology

institute: Wageningen University

type: Expression profiling by genome tiling array

summary: The combination of robust physiological models with “omics” studies holds promise for the discovery of genes and pathways linked to how organisms deal with drying. Here we used a transcriptomics approach in combination with an in vivo physiological model of re-establishment of desiccation tolerance (DT) in Arabidopsis thaliana seeds. We show that the incubation of desiccation-sensitive (DS) germinated Arabidopsis seeds in a polyethylene glycol (PEG) solution re-induces the mechanisms necessary for expression of DT. Based on a SNP-tile array gene expression profile, our data indicates that the re-establishment of DT, in this system, is related to a programmed reversion from a metabolic active to a quiescent state similar to prior to germination. Our findings show that transcripts of germinated seeds after the PEG treatment are dominated by those encoding LEA, seed storage and dormancy-related proteins. On the other hand, a massive repression of genes belonging to many other classes such as photosynthesis, cell wall modification and energy metabolism occurs in parallel. Furthermore, comparison with a similar system for Medicago truncatula reveals a significant overlap between the two transcriptomes. Such overlap may highlight core mechanisms and key regulators of the trait DT. Taking into account the availability of the many genetic and molecular resources for Arabidopsis, the described system may prove useful for unraveling DT in higher plants.

overall_design: Desiccation-sensitive seeds vs. desiccation-tolerant seeds in the same developmental stage in triplicate.

first: Julio

last: Maia

first: Bas

last: Dekkers

first: Nicholas

last: Provart

first: Henk

middle: W

last: Hilhorst


title: A small RNA activates CFA synthase by a reprogrammable mechanism of mRNA stabilization

status: Public on Jun 24 2013

city: Würzburg

first: Kai

last: Papenfort

state: Würzburg

address: Josef-Schneider Str.2/BAU D15

department: RNA Biology

institute: IMIB Würzburg

summary: Small RNAs use a diversity of well-characterized mechanisms to repress mRNAs, but how they activate gene expression at the mRNA level remains not well understood. The predominant activation mechanism of Hfq-associated small RNAs has been translational control whereby base-pairing with the target prevents the formation of an intrinsic inhibitory structure in the mRNA and promotes translation initiation. Here, we report a translation-independent mechanism whereby the small RNA RydC selectively activates the longer of two isoforms of cfa mRNA (encoding cyclopropane fatty acid synthase) in Salmonella enterica. Target activation is achieved through seed pairing of the pseudoknot-exposed, conserved 5' end of RydC to an upstream region of the cfa mRNA. The seed pairing stabilizes the messenger, likely by interfering directly with RNase E-mediated decay in the 5' untranslated region. Intriguingly, this activation mechanism is fully generic in that it can be reprogrammed to other seed pairing small RNAs, suggesting this mechanism may be utilised in the design of RNA-controlled synthetic circuits. Physiologically, RydC is the first small RNA known to regulate membrane stability.

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

overall_design: To determine the targets of the small regulatory RNA RydC in S. Typhimurium, we looked at the effect of a short pulse of RydC over-expression on the Salmonella transcriptome. To achieve over-expression, the rydC gene was cloned in the pBAD plasmid and induced with 0.2% L-arabinose for 10 min. We then extracted the total RNA for transcriptional profiling. A strain carrying the pBAD plasmid w/o insert was used as negative control (also induced by L-arabinose). 2 biological replicates were performed. This sRNA target identification strategy has been described in Papenfort et al; Molecular Microbiology (2006) 62(6), 1674–1688.

first: Kathrin

middle: S

last: Fröhlich

first: Agnes

last: Fekete

first: Jörg

last: Vogel


title: Transcriptome analysis of the early response to nickel (Ni) in Acidiphilium sp. PM

status: Public on Jun 18 2013

city: Torrejon de Ardoz

first: Patxi

last: San Martin-Uriz

address: Ctra. de Ajalvir, km. 4

department: Centro de Astrobiologia

institute: Instituto Nacional de Tecnica Aeroespacial

summary: To study the mechanisms of Ni resistance in the metal resistant Acidiphilium sp. PM, the transcriptome of Acidiphilium sp. PM was studied 5min and 30 min after the addition of 10mM Ni and compared to the transcriptome in untreated cells.

overall_design: Two-condition hybridization experiments: untreated cells vs cells treated with 10mM Ni (for either 5 or 30 minutes). Eighteen 100ml-cultures: 6 untreated control cultures (not exposed to Ni), 6 cultures exposed to 10mM Ni for 5min, and 6 cultures exposed to 10mM Ni for 30 min. Cultures were independently grown and harvested. Gene expression levels of one untreated replicate were compared separately with one 5min-exposed replicate and with one 30min-exposed replicate (yielding two microarray data sets. One for each hybridization).

first: Pedro

last: Alcolea

first: Mercedes

last: Moreno-Paz

first: Manuel

last: Gomez

first: Ricardo

last: Amils


title: Protein microarray analysis of antibody responses to Plasmodium falciparum in Western Kenyan highlands

city: Irvine

first: Elisabeth

last: Baum

state: CA

address: Med Surge II

institute: University of California Irvine

summary: Malaria represents a major public health problem in Africa [1]. In the East African highlands, even in high-altitude areas previously considered too cold to support vector population and parasite transmission [2], frequent malaria epidemics have been reported since the 1980’s [3]. Plasmodium falciparum infections have been detected in areas as high as 1,600-2,400m above sea level in Africa [4], albeit there is a marked gradient of parasite prevalence along the altitude transect [5-7].  Both the historical absence of malaria in the African highlands and now the intensive malaria control efforts put in place after the recent outbreaks have reduced malaria prevalence and incidence [8], rendering the East African highlands particularly prone to epidemic malaria due to the lack of the protective immunity, and causing significant human mortality amongst all age groups [9]. Therefore, malaria transmission monitoring in the East African highlands becomes a particularly important public health issue.Despite the overall lower immunity of the population in these historically malaria-free areas, the many successive outbreaks since the 1980’s may have generated some level of immunity against P. falciparum amongst highland residents. The antibody response to Plasmodium is cumulative and long lasting, developing after repeated exposures to the parasite and persisting for months or years after infection was resolved. The antibody response to Plasmodium varies amongst individuals of different age groups (i.e. toddlers, children and adults) as well as amongst individuals of same age groups from areas of different parasite prevalence [10]. The repertoire of targets of the antibody response also expands after multiple infections, with the number of recognized antigens being correlated to parasite prevalence, age and immunity to clinical malaria [11,12]. Serological studies bring forth indirect evidence of human exposure to the parasite, and can reliably assess its prevalence and transmission intensity in an endemic area [13-15]. However, the vast majority of serological studies of malaria have been, hereto, limited to a small number of the parasite’s antigens. The work we present here is an expansion of the study published by Badu et al. [16], in which the antibody response to the 19kDa fragment of merozoite surface protein 1 (MSP-119) was examined in populations from two endemic areas in the western Kenyan highlands. There, the tremendous variations of malaria transmission intensity in a small spatial scale are caused by substantial differences in altitude, topography and other environmental conditions [6,7,17,18]. We now expand our antibody profiling survey to include 854 P. falciparum proteins by using high-throughput proteomic microarray technology.  Protein microarrays have been used to explore the humoral response to P. falciparum in other African settings [19-24], but this is the broadest characterization of the antibody responses of the population of western Kenyan highlands to date. In the present study we: i) determined the serological reactivity against P. falciparum (Pf) in subjects residing in a low transmission area, and detected hotspots of transmission; ii) examined the dynamics of antibody response to hundreds of Pf proteins generated by sera from toddlers, older children and adults residing in two endemic areas differing in transmission intensities, during two distinct malaria seasons, and compared the intensity, breadth and antigenic targets of these responses; and iii) identified candidate Pf antigenic markers that could provide more sensitive serological surveillance to detect micro-geographic variations in malaria transmission levels and differentiate hotspots of infection in low endemic areas. (references provided in the 'readme.txt')

overall_design: Antibody profiling was performed on sera from residents of western Kenyan highlands against Plasmodium falciparum. One-hundred and ten age-stratified serum samples collected during the dry and the wet seasons, from residents of two locations with differing parasite transmission levels (uphill and valley bottom), and 10 unexposed USA controls were probed on a protein microarray displaying 854 unique proteins of P. falciparum.

first: Kingsley

last: Badu

first: Phillip

last: Felgner

first: Guiyun

last: Yan


title: Differential expression of microRNAs in adipose stem cells

city: Shanghai

first: Min

last: Li

address: 50 Chifeng Rd., Yangpu District

department: Life Sciences and Technology

institute: Tongji University

summary: Human adipose derived stem cells (hADSCs) are an attractive multipotent stem cell source with therapeutic applicability in diverse fields for the repair and regeneration of acute and chronically damaged tissues.In the last few years there has been increased interest in hADSCs for tissue engineering applications; however, the molecular mechanisms especially the microRNAs underlying the regulation of hADSCs proliferation and differentiation are not fully understood. To this end, we profiled the global microRNA expression in hADSCs, fibroblasts and endothelial cells by using Exqion mercury LNATM  (Exqion Inc)

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus
Human alphaherpesvirus 1
Human alphaherpesvirus 2
Human betaherpesvirus 5
Murid betaherpesvirus 1
human gammaherpesvirus 4
JC polyomavirus
Human immunodeficiency virus 1
synthetic construct
Murid gammaherpesvirus 4
Human gammaherpesvirus 8
Merkel cell polyomavirus
Betapolyomavirus hominis
Betapolyomavirus macacae

overall_design: To identify the microRNAs significantly expressed in human adipose derived stem cells, eight samples were analyzed using Exqion mercury LNATM  (Exqion Inc) including six hADSCs samples and human endothelial and fibroblast cells as controls.

first: Xiaoqing

last: Liu

first: Cizhong

last: Jiang

first: Guangfeng

last: Chen

first: Xiujuan

last: Shi

first: Qing

last: Zhou


title: Time course experiment of 17β-estradiol (E2) treatment in the zebrafish

city: Jerusalem

first: Amit

last: Cohen

address: Hebrew University

country: Israel

institute: huji

summary: Transcriptional profiling of zebrafish (Danio rerio) livers comparing control untreated fish with fish treated with estrogen [17β-estradiol (E2)] for different time points (4, 12, 24, 48 hours).

overall_design: For the assay experimental design, RNA from one of three different E2-treated fish (representing three biological replicates) of each time point was hybridized with RNA that was pooled from liver samples of 15 untreated fish (control pool) on one chip.


title: Analyses of endogenous rna substrates of xrn and exosome and ptgs pathways; Integrating RNA Quality Control and RNA Silencing Pathways

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

country: France

institute: INRA

summary:
blan08_rnapaths; Analyses of endogenous rna substrates of xrn and exosome and ptgs pathways
What are the endogenous RNA substrates co-regulated by RQC and PTGS pathways?
Genome-wide analyses of endogenous RNA substrates of RNA Quality Control pathways; wild type versus 15 mutants.

overall_design: 30 dye-swap - gene knock in (transgenic), gene knock out

first: Herve

last: Vaucheret

first: Allison-

last: Mallory

first: Eddy

last: Blondet

first: Sandrine

last: Balzergue

first: Marie-Laure

last: Martin-Magniette


title: Rejuvenation of pluripotent stem cells by frequent activation of Zscan4, Part A

status: Public on Jun 12 2013

city: Baltimore

first: Minoru

last: Ko

state: MD

address: 251 Bayview Blvd, Suite 100, 10C

department: National Institute on Aging

institute: NIH

summary: The gold standard for examining pluripotency of stem cells is to see whether cells can contribute to entire body of animals. Here we show that the increased frequency of Zscan4 activation in mouse ES cells not only enhances, but also maintains their developmental potency in long-term cell culture. As the potency increases, even a whole animal can be produced from a single ES cell injected into 4N blastocyst at unusually high success rate. Although Zscan4-activated cells express genes that are also expressed in 2-cell stage mouse embryos, transiently Zscan4-activated state of ES cells is not associated with the high potency of ES cells. It is thus concluded that ES cells acquire higher potency by going through transient Zscan4 activation state more frequently than the regular state. Taken together, our results indicate that frequent activation of Zscan4 can rejuvenate pluripotent stem cells.

overall_design: MC1 ES cells (for pZscan4-Emerald transfection) and R26R6 ES cells (for pZscan4-Cre ERT2 transfection) were grown on gelatin in 6-well plate, 5x10^5cells in suspension were transfected with 1ug of linearized pZscan4-Emerald vector or pZscan4-Cre ERT2 vector using Effectene (QIAGEN) according manufacturer protocol, and plated in gelatin coated 100 mm dishes. Cells were selected with 5 ug/ml blasticidin, colonies were picked on the 8th day, expanded and frozen for further analysis. DNA microarray analysis of pZscan4-Emerald cells was carried out as described. In brief, universal Mouse Reference RNA (Stratagene) were labeled with Cy5-dye, mixed with Cy3-labeled samples, and used for hybridization on the NIA Mouse 44K Microarray v2.2 (manufactured by Agilent Technologies #014117). The intensity of each gene feature was extracted from scanned microarray images using Feature Extraction 9.5.1.1 software (Agilent Technologies). Microarray data analyses were carried out by using an application developed in-house to perform ANOVA and other analyses (NIA Array Analysis software; http://lgsun.grc.nia.nih.gov)

first: Tomokazu

last: Amano

first: Tetsuya

last: Hirata

first: Geppino

last: Falco

first: Manuela

last: Monti

first: Lioudmila

middle: V

last: Sharova

first: Misa

first: Sarah

last: Sheer

first: Hien

last: Hoang


title: Multiple platform assessment and isomir analysis of the EGF dependent microRNA-ome by microarray and deep sequencing analysis [Exiqon]

status: Public on Jun 11 2013

city: Badalona

first: Lauro

last: Sumoy

state: Barcelona

address: Ctra. Can Ruti, Camí de les escoles s/n

department: High Content Genomics and Bioinformatics

institute: IGTP

summary: We have used an integrative high content analysis approach to identify the specific miRNAs implicated in EGF signaling in HeLa cells as potential mediators of cancer mediated functions. We have used microarray and deep-sequencing technologies in order to obtain a global view of the EGF miRNA transcriptome with a robust experimental cross-validation. By applying a procedure based on Rankprod tests, we have delimited a solid set of EGF-regulated miRNAs. After validating regulated miRNAs by RT-qPCR, we have derived protein networks and biological functions from the predicted targets of the regulated miRNAs to gain insight into the potential role of miRNAs in EGF-treated cells. In addition, we have analyzed sequence heterogeneity due to editing relative to the reference sequence (isomirs) among regulated miRNAs.

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

overall_design:
Time course experiment comparing HeLa gene expression in response to EGF analyzed on different microarray platforms and by digital gene expression using short read high throughput sequencing by synthesis. Three independent experiments were performed where HeLa cells were serum deprived for 24 hours and were either left untreated or treated with EGF for 6 h and harvested for RNA extraction.
treated vs. untreated comparison, time course

first: Franc

last: Llorens

last: Hummel

first: Lorena

last: Pantano

first: Xavier

last: Pastor

first: Ana

last: Vivancos

first: Ester

last: Castillo

first: Heidi

last: Mattlin

first: Anna

last: Ferrer

first: Matthew

last: Ingham

first: Marc

last: Noguera

first: Robert

last: Kofler

first: Juliane

last: Dohm

first: Raquel

last: Pluvinet

first: Mònica

last: Bayés

first: Heinz

last: Himmelbauer

first: Jose

last: del Rio

first: Eulàlia

last: Martí


title: Adipose-derived stem cells improved mouse ovary function after chemotherapy-induced ovary failure

city: Xi'an

first: Min

last: Sun

address: No.1, Xinsi Road

institute: Tangdu Hospital

summary: ADSCs are a new type of MSC that is typically abundant in individuals. Numerous investigations reported that adipose-derived stem cell (ADSC) transplantation could ameliorate the structure and function of injured tissues. However, their protective role in premature ovarian failure remains obscure. The aim of this study was to explore the therapeutic efficacy of ADSC transplantation for chemotherapy-induced ovarian damage and microarray analyses were used to assess gene related to ovarian function.

overall_design: Total RNA of ovarians of four groups was extracted using the TRIZOL Reagent according to the manufacturer's instructions. Labeling and hybridization were performed at the CapitalBio Company, according to protocols described in the 32K mouse genome arrays user manual. The data were analyzed using LuxScan 3.0 Image analysis software (CapitalBio company).


title: Comparative analysis of transcriptome profiles of G. hirsutum L. cv. MCU5 and its fuzzless-lintless mutant during fiber development stages.

city: New delhi

first: Padmalatha

state: Delhi

address: Pusa campus

department: Plant Biotechnology

country: India

institute: NRCPB

summary: Cotton is one of the most commercially important Fiber crops in the world and used as a source for natural textile Fiber and cottonseed oil. The fuzzless-lintless ovules of cotton mutants are ideal source for identifying genes involved in Fiber development by comparing with Fiber bearing ovules of wild-type. To decipher molecular mechanisms involved in Fiber cell development, transcriptome analysis has been carried out by comparing G. hirsutum cv. MCU5 (wild-type) with its fuzzless-lintless mutant (MUT). Cotton bolls were collected at Fiber initiation (0 dpa/days post anthesis), elongation (5, 10 and 15 dpa) and secondary cell wall synthesis stage (20 dpa) and gene expression profiles were analyzed in wild-type and MUT using Affymetrix cotton GeneChip Genome array.

platform_organism:
Gossypium barbadense
Gossypium hirsutum
Gossypium arboreum
Gossypium raimondii

overall_design: Cotton plants were grown under field condition. Flowers were tagged and cotton bolls were collected during Fiber development stages. Total RNA was isolated from Fiber bearing ovules of wild-type (WT) and fuzzless-lintless ovules of mutant (MUT) collected at various (0, 5, 10, 15 and 20 dpa) Fiber development stages using SpectrumTM Plant Total RNA kit (Sigma, USA) according to the manufacturer’s protocol. Affymetrix cotton GeneChip Genome array (Affymetrix, USA) having 23,977 probe sets representing 21,854 cotton transcripts was used for transcriptome analysis. Three biological replicates were maintained to test the reproducibility and quality of the chip hybridization. cDNA labeling, array hybridization, staining and washing procedures were carried out as described in the Affymetrix protocols. CEL files having estimated probe intensity values were analyzed with GeneSpring GX-11.5 software (Agilent Technologies, USA) to get differentially expressed transcripts. The Robust Multiarray Average (RMA) algorithm was used for the back ground correction, quantile normalization and median polished probe set summarization to generate single expression value for each probe set. Normalized expression values were log2-transformed and differential expression analysis was performed using unpaired t-test. The p-values were corrected by applying the false discovery rate (FDR) correction (Benjamini and Hochberg, 2000).

first: K

last: Padmalatha

first: G

last: Dhandapani

first: M

last: Kanakachari

first: Neha

last: Jain

first: H

last: Vamadevaiah

first: I

last: Katageri

first: S

last: Leelavathi

middle: K

last: Reddy

first: A

last: Prakash

first: V

middle: P

last: Ananda


title: Homo sapiens Ewing sarcoma cell line RD-ES: Negative control vs. HDGF knockdown

city: Guangzhou

first: yang

last: yang

address: 58, Zhongshan Road II, Guangzhou

institute: Sun Yat-sen University

summary:
Comparing the gene expression profiling of HDGF-silenced RD-ES cells and control RD-ES cells to identify genes regulated by HDGF in RD-ES cells.
Keywords: expression analysis

overall_design: Control RD-ES cells and HDGF-silenced RD-ES cells were profiled on 22K Human Genome Array

first: Yang

last: Yang

first: An-jia

last: Han


title: Expression data from uninephrectomized dogs compared to sham operated dogs

status: Public on Jun 13 2013

city: Rochester

first: Asha

last: Nair

address: 200 1ST ST SW

institute: Mayo Clinic

summary: Renal insufficiency is a risk factor for development of cardiovascular disease. In this study our aim was to investigate functional and structural changes in the heart of dogs with mild renal insufficiency induced by uninephrectomy (UNX).  In addition to comprehensively assessing functional parameters 12 week after UNX or sham surgery, we harvested tissue for assessment of structural changes.  Microarray analyses were performed on snap frosen tissue from the left atrium (LA) and left ventricle (LV) of UNX  and sham operated animals.  Gene expression in LA was compared between the groups, and gene expression in the LV was compared between the groups.  We aimed to assess whether a potentially altered gene expression in the heart of the UNX group also included genes associated with cardiac remodeling.

overall_design: Six dogs were assigned to unineprectomy and 6 dogs were assigned to sham operation.  Microarray analyses were performed on 5 samples from the left atrium of uninephrectomized animals and on 5 samples from the left atrium of sham operated animals.  Further, microarray analyses were performed on 5 samples from the left ventricle of uninephcretomized animals and on 5 samples from the left ventricle of sham operated animals. No replicates were perfomed.

first: Ingrid

last: Andersen

first: Alessandro

last: Cataliotti

first: Sarah

last: Mangiafico

first: Diego

last: Bellavia

first: Brenda

last: Huntley

first: Guido

last: Boerrigter

first: Gail

last: Harty

first: John

last: Burnett


title: PrPC-dependent gene expression and cell signalling signature in Neuro2a cells. Role on mitogenic stimulation and cell morphology.

first: Lauro

last: Sumoy

summary: In this work we present the PrPC-dependent gene expression signature in N2A cells and its implication on the most overrepresented functions; cell cycle, cell growth and proliferation and cell morphology.

overall_design:
To evaluate the genes whose transcription was regulated after Prnp modulation, RNA samples were analyzed with Illumina mouse whole genome beadarrays.
cell type comparison; genetic modification; RNA interference

first: Franc

last: Llorens

first: Patricia

last: Carulla

first: Juan

middle: M

last: Torres

first: Isidre

last: Ferrer

first: José

last: Del Río


title: MicroRNAs Expression Profiles and the target genes in Chinese Non-syndromic isolated Cleft Palate Patients

first: Huijun

last: Wang

state: Shanghai

address: 399 Wanyuan Road,

department: Translational Research Center for Development and Disease

institute: Children Hospital of Fudan University

summary: MicroRNAs (miRNAs) play an important role in organ development. MicroRNA expression profiling is an effective method of acquiring novel and valuable information. In this study, using miRNA microarray technology, we finally validate three over-expressed miRNAs (hsa-miR-1246, hsa-miR-1323 and hsa-miR-93) and one under-expressed miRNA (hsa-miR-143*) in NSCP group. Target gene WNT5A of hsa-miR-143* was up-regulated, while target gene FGFR2 of hsa-miR-1246, hsa-miR-1323 and hsa-miR-93 was down-regulated in the NSCP group compared to the control group. The association of miRNAs expression levels with the risk of developing NSCP, the correlation with age and gender were analyzed. The risk analysis identified that odds ratio (95% CI) of hsa-miR-1246, hsa-miR-1323 and hsa-miR-93 was higher ranged from 9.75 (1.642-57.89) to 13.67 (2.480-75.30) and p＜0.05. Neither age nor gender was associated with the four miRNAs expression levels. In male cases, the association of hsa-miR-1246, hsa-miR-1323, hsa-miR-93 and hsa-miR-143* expression levels with NSCP was observed and the p value was 0.0012, 0.0008, 0.0088 and 0.0385, respectively. Bioinformatics approaches identified nine KEGG pathways enriched in predicted target genes. In summary, we firstly defined miRNAs profiles and target genes in human soft palate tissue. Four distinctive miRNAs and their target genes expression in NSCP will advance our understanding of the genetic progress of this complex disease. Further exploration will be needed to elucidate how these miRNAs and target genes modulate signaling pathways during palatogenesis.

overall_design: Two-condition experiment, control (normal development people) vs. NSCP patients. Biological replicates: 6 control replicates, 10 NSCP patients replicates.

first: Ping

last: Zhang

first: Shouxia

last: Li


title: Expression profile of Chicken Early Embryonic Endodermal Tissues

status: Public on Jun 08 2013

city: Kobe

first: Cantas

last: Alev

state: Chuo-ku

address: 2-2-3 Minatojima Minamimachi

country: Japan

institute: RIKEN CDB

summary: In vertebrates the endoderm which gives rise to the epithelial lining of the digestive tract becomes regionalized along its antero-posterior axis after gastrulation. The molecular basis of the initial step of this regionalization has largely remained unclear. Using chick model, we generated high-quality transcriptomic datasets of different stages/regions of the endoderm and analyzed their molecular heterogeneity.

overall_design: Total RNA from HH stage 4-5 entire definitive endoderm, HH stages 10-11 foregut endoderm and HH stages 8-10 mid/hindgut endoderm were purified.  5 μg of RNA from each sample were used to screen Affymetrix Chicken Genome Array without an amplification step.

first: Wataru

last: Kimura

first: Alev

last: Cantas

first: Sheng

last: Guojun

first: Martin

last: Jakt

first: Sadao

last: Yasugi

first: Kimiko

last: Fukuda


title: Transcriptomic consequence of the mutation in the response regulator gene gacA of the two-component regulatory system GacS/GacA in the rhizosphere biocontrol strain Pseudomonas aeruginosa M18

status: Public on Jun 07 2013

first: xianqing

last: Huang

address: 800 Dong chuan RD

institute: Shanghai Jiao Tong University

summary: To investigate the influence of GacA on the genome-wide transcription of the rhizobacterium P. aeruginosa M18, DNA microarray experiments were carried out to compare the transcriptional profile of M18 with that of the gacA mutant grown to the early stationary phase (OD600 = 5.0 ~ 5.5) in KMB media. When compared with the M18 parental strain, the transcriptomic profile of gacA mutant revealed the significantly differential expression (increased or decreased by at least 2-fold as well as p-value < 0.05) of 839 genes, which represent approximately 15% of all 5696 annotated genes in the M18 genome. Of these 839 genes, 472 were downregulated and 367 genes were upregulated by the gacA mutation.

overall_design: P. aeruginosa M18 and its gacA mutant were grown to OD600=5.0-5.5 (early stationary phase) in KMB medium at 28℃. Three independent experiments were performed at each time.

first: Xianqing


title: Multiple platform assessment and isomir analysis of the EGF dependent microRNA-ome by microarray and deep sequencing analysis [Agilent]

first: Lauro

last: Sumoy

first: Franc

first: Manuela

last: Hummel

first: Lorena

last: Pantano

first: Xavier

last: Pastor

first: Ana

last: Vivancos

first: Ester

last: Castillo

first: Heidi

last: Mattlin

first: Anna

first: Matthew

last: Ingham

first: Marc

last: Noguera

first: Robert

last: Kofler

first: Juliane

last: Dohm

first: Raquel

last: Pluvinet

first: Mònica

last: Bayés

first: Heinz

last: Himmelbauer

first: Jose

middle: A

last: del Rio

first: Eulàlia

last: Martí


title: Comprehensive, high resolution analysis of cis-acting regulatory networks at the alpha globin locus (array)

status: Public on Jun 06 2013

city: Oxford

first: Richard

middle: J

last: Gibbons

state: Oxon

address: John Radcliffe Hospital,

department: MRC Molecular Haematology Unit

institute: Weatherall Institute of Molecular Medicine

summary: We have combined the 4C chromosome conformation capture protocol with high throughput, genome-wide sequence analysis to characterise in full a cis-acting regulatory network at a single locus. In contrast to methods which identify large interacting regions (10-1000kb), the 4C approach provides a comprehensive, high resolution analysis of a specific locus with the aim of defining, in detail, all cis- regulatory elements controlling a single gene or gene cluster. Using the human α-globin locus as a model we detected all known local and long-range interactions with this gene cluster. In addition we identified two interactions with genes located 300 kb (NME4) and 625 kb (FAM173a) from the α-globin cluster. Using paired-end sequencing it was possible for the first time to identify interactions between specific subsets of cis-regulatory elements in populations of cells and within individual cells.

overall_design: Two biological replicates of 4C amplification from the promoters of the human HBA  and HBB genes and B-Cell controls.   Quality of B-cell material was confirmed using amplification from a CTCF bound region associated with Human Axin Gene.

first: Jim

last: Hughes


title: miRNA expression in CD4+CD25- conventional (Tconv) and CD4+CD25+ regulatory T (Treg) cells

city: San Francisco

first: Jeffrey

middle: A.

last: Bluestone

address: 513 Parnassus Ave

department: Diabetes Center

institute: UCSF

summary: miRNA expression profiling in highly purified murine CD4+ Tconv and Treg cells. FoxP3-GFP-hCre1a(high) reporter mice were used to separate both populations based on surface markers and presence or absence of GFP.

overall_design: Two-condition experiment, Tconv vs. Treg. Biological replicates: 1 Tconv, 1 Treg, purified from the same pooled mice. One replicate on 1 array.

first: Lukas

last: Jeker


title: Genes induced by Oxi-beta overexpression in dopaminergic neuronal cell SN4741

status: Public on Jun 05 2013

city: SEOUL

first: Jin

last: Son

address: Daehyun-dong, Seodaemun-gu

department: Brain & Cognitive Sciences

institute: Ewha W. University

summary:
To identify genes regulated by Oxi-beta, differential gene chip analysis was perfomed.
And the greatest upregulation (about 25-fold) of FBXW5 mRNA was observed in response to Oxi-beta overexpression in SN4741 dopaminergic neuronal cells

overall_design: Total RNAs obtained from subjected to overexpression of Oxi-beta for 12 hours compared to control SN4741 cells at 0 hr.

first: Ji-Young

last: Ha


title: Gene deletion expression profiles of SAGA, TREX2 and Sem1

status: Public on Jun 04 2013

city: Utrecht

first: Patrick

last: Kemmeren

state: Utrecht

address: Universiteitsweg 100

department: Department of Molecular Cancer Research

institute: UMC Utrecht

summary: Evidence indicates that transcription and mRNA export are linked processes. The molecular mechanisms of this coordination are not clear however. Sus1 (hENY2) participates in this coordination as part of two protein complexes: SAGA, a transcriptional co-activator and TREX-2 that functions in mRNA biogenesis and export. Here we investigate the coordinated action of SAGA and TREX-2 that is required for gene expression. We demonstrate that the TREX-2/proteasomal subunit Sem1, influences Sus1 role in mRNA export and TREX-2 stability. Wide analyses of gene expression reveal that Sem1 and Sus1 have also overlapping functions in transcription. In the absence of Sem1, expression of some SAGA-dependent genes is compromised with a concomitant decrease of RNAP II recruitment to promoters. Notably, ChIP experiments revealed a distinct dependency for SAGA subunits recruitment on Sem1. While absence of Sem1 lowers Ada2 and Taf9 recruitment to GAL1 promoter upon activation, association of the deubiquitylation module remains intact. However, H2B deubiquitylation activity is dramatically decreased. These results unveil a new role for Sem1 in influencing activation of SAGA-dependent H2B deubiquitylation likely mediated by stabilization of TREX-2 complex and SAGA modular assembly. Our work gives insights in how modular architecture of SAGA is determinant for its function in gene expression.

overall_design: Two channel microarrays were used. RNA isolated from a large amount of wt yeast from a single culture was used as a common reference. This common reference was used in one of the channels for each hybridization and used in the statistical analysis to obtain an average expression-profile for each deletion mutant relative to the wt. Two independent cultures were hybridized on two separate microarrays. For the first hybridization the Cy5 (red) labeled cRNA from the deletion mutant is hybridized together with the Cy3 (green) labeled cRNA from the common reference. For the replicate hybridization, the labels are swapped. Each gene is represented twice on the microarray, resulting in four measurements per mutant. Using the Erlenmeyer growth protocol up to five deletion strains were grown on a single day. In the tecan platereader, up to eleven deletion strains could be grown on a single day. Wt cultures were grown parallel to the deletion mutants to assess day-to-day variance.

first: Encar

last: Garcia-Oliver

first: Pau

last: Pascual-Garcia

first: Ana

last: Llopis

first: Tineke

last: Lenstra

first: Celia

last: Martinez-Jimenez

first: Varinia

last: Garcia-Molinero

first: Frank

last: Holstege

first: Susana

last: Rodriguez-Navarro


title: Quaking is a global regulator of muscle-specific alternative splicing in vertebrates [differentiation data]

city: Santa Cruz

first: Manny

last: Ares

address: 1125 High St

department: Molecular and Cellular Biology

institute: UCSC

summary:
This work provides the first evidence that Qk is a global regulator of splicing in vertebrates, defines a new splicing regulatory network in muscle, and suggests that overlapping splicing networks contribute to the complexity of changes in alternative splicing during differentiation.
Alternative splicing contributes to muscle development and differentiation, but the complete set of muscle splicing factors and their combinatorial interactions are not known. Previously work identifies ACUAA (STAR motif) as an enriched sequence near muscle-specific alternative exons such as Capzb exon 9. We did mass spectrometry of proteins selected by wild type and mutant Capzb intron 9 RNA affinity chromatography, and identified Quaking (Qk), a protein known to regulate mRNA function through ACUAA motifs in 3' UTRs. We show that in myoblasts, Qk promotes inclusion of Capzb exon 9 in opposition to repression by PTB. Qk knockdown in myoblasts has little effect on transcript levels, but alters inclusion of 824 cassette exons whose adjacent intron sequences are enriched in ACUAA motifs. During differentiation to myotubes, Qk levels increase 2-3 fold, suggesting a mechanism for Qk-responsive exon regulation.  We captured the PTB splicing regulatory network and intersected it with the Qk network, identifying overlap between the functions of Qk and PTB. Approximately 60% of exons whose inclusion is altered during myogenesis appear to be under control of one or both of these splicing factors in myoblasts.

overall_design: This series is the C2C12 differentiation data. It is 9 arrays, 3 timepoints, with 3 replicates. The time points are 0 hrs, 24 hrs, and 72hrs.

last: Ares Jr

first: Megan

last: Hall

first: Roland

last: Nagel

first: Samuel

last: Fagg

first: Lily

last: Shiue

first: Melissa

last: Cline

first: Rhonda

last: Perriman

first: John

last: Donohue


title: The Arabidopsis copper transport protein COPT2 and the responses under copper and iron deficiency.

city: Valencia

first: Francisco

last: Vera-Sirera

address: Ingeniero Fausto Elio, s/n

institute: IBMCP (UPV-CSIC)

summary: Copper and iron are essential micronutrients for most living organisms because they participate as cofactors in biological processes including respiration, photosynthesis and oxidative stress protection. In many eukaryotic organisms, including yeast and mammals, copper and iron homeostases are highly interconnected; however such interdependence is not well established in higher plants. Here we propose that COPT2, a high-affinity copper transport protein, functions under copper and iron deficiencies in Arabidopsis thaliana. COPT2 is a plasma membrane protein that functions in copper acquisition and distribution. Characterization of the COPT2 expression pattern indicates a synergic response to copper and iron limitation in roots. We have characterized a  knockout of COPT2, copt2-1, that leads to increased resistance to simultaneous copper and iron deficiencies, measured as reduced leaf chlorosis and improved maintenance of the photosynthetic apparatus. We propose that COPT2 expression could play a dual role under Fe deficiency. First, COPT2 participates in the attenuation of copper deficiency responses driven by iron limitation maybe aimed to minimize further iron consume. On the other hand, global expression analyses of copt2-1 mutants versus wild type Arabidopsis plants indicate that low phosphate responses are increased in copt2-1 plants. In this sense, COPT2 function under Fe deficiency counteracts low phosphate responses. These results open up new biotechnological approaches to fight iron deficiency in crops.

overall_design: Four biological replicates of Arabidopsis seedlings were generated for 2 genotypes, Col-0 and copt2-1 mutant; and 3 growth condictions; first one an iron(Fe) and copper(Cu) sufficient medium (+Fe + Cu), second one  an Fe deficient and Cu sufficient medium (-Fe+Cu)  and third one an Fe and Cu deficient medium (-Fe-Cu). For each growth one comparasion was made, copt2-1 mutant versus Col-0;  in each comparasion four biological replicates were made, two replicas were labeled with Cy5 for the mutant sample and Cy3 for the Col-0  sample, while the other two replicas were reversed-labeled.

last: Perea-García

first: Antoni

last: Garcia-Molina

first: Nuria

last: Andrés-Colás

first: Miguel

last: Pérez-Amador

first: Sergi

last: Puig

first: Lola

last: Peñarrubia


title: Thymidine Kinase and mtDNA Depletion in Human Cardiomyopathy: Epigentic and Translational Evidence for Energy Starvation

city: Atlanta

first: William

last: Lewis

state: Georgia

address: 101 Woodruff Circle

department: Pathology

institute: Emory University

summary:
A comparison of epigenetic nuclear DNA methylation and gene expression changes between human dialated cardiomypathy left ventricle samples and non-failing cardiac left ventricule samples
This study addresses how depletion of huaman cardiac left ventricle mitochondrial DNA and epigentic nuclear DNA methylation promote cardiac dysfunction in human dilated cardiomyopathy.

overall_design: Each sample was fluorescently labeled and hybridized to Roche Nimblegen 2.1M Deluxe Promoter Arrays and Expression arrays.

first: Christopher

last: Koczor


title: Epigenetic marks reduce erythrocyte uptake of antimalarials

status: Public on Jun 03 2013

city: Rockville

first: Sanjay

middle: Arvind

last: Desai

state: Maryland

address: 12735 Twinbrook Parkway

department: Laboratory of Malaria and Vector Research

institute: National Institute of Allergy and Infectious Diseases, NIH

summary: Acquired antimalarial drug resistance produces treatment failures and has led to periods of global disease resurgence. In P. falciparum, resistance is known to arise through genome-level changes such as mutations and gene duplications. We now report an epigenetic resistance mechanism involving genes responsible for the plasmodial surface anion channel, a nutrient channel that also transports ions and antimalarial compounds at the host erythrocyte membrane. Two blasticidin S-resistant lines exhibited markedly reduced expression of clag

overall_design: Mutant FCB-br1 and wild-type FCB samples were hybridized to seven arrays (biological repeats) using forward (n=2) and reverse (n=5) fluoro.


title: Madin-Darby Canine Kidney (MDCK) cells grown in 2-dimensional and 3-dimensional type I collagen culture.

city: New Haven

first: Erika

middle: Krystal

last: Wells

state: CT

address: 333 Cedar Street SHM B117/119

department: Cellular and Molecular Physiology

institute: Yale University

summary: In order to gain insight into epithelial morphogenesis and the influence of culture geometry on gene expression patterns, Madin Darby Canine Kidney (MDCK) epithelial cells  where grown in 2-dimensional (2D) culture or 3-dimensional (3D) culture . MDCK cells cultured in 2D were plated atop a pre-solidified type I collagen gel. Cells cultured under these conditions grew as flat monolayer sheets. In 3D culture, cells are embedded within type I collagen gel. Cells grown under these conditions form large spherical cysts with hollow central lumens. We anticipate, therefore, that these results provide insight into the mechanisms that regulate epithelial cystogenesis.

overall_design: Cells grown in the 2D or 3D geometries were collected from digested type I collagen gels on day 8. The 2D MDCK cells were treated as the control condition and there gene expression patterns were compared to those of 3D grown cells, which served as the experimental condition.

first: OrLando

last: Yarborough

first: Richard

last: Lifton

first: Michael

last: Caplan


title: Quaking is a global regulator of muscle-specific alternative splicing in vertebrates [siRNA data]

first: Manny

last: Ares

overall_design: This series is the C2C12 Qk and PTB siRNA data. It is 12 arrays: 3 PTB siRNA arrays , 3 Qk siRNA arrays, and 6 mock siRNA arrays.

last: Ares Jr

first: Megan

last: Hall

first: Roland

last: Nagel

first: Samuel

last: Fagg

first: Lily

last: Shiue

last: Cline


title: Conjunctival miRNA expression data in scarring and inflammatory trachoma

city: london

first: Tamsyn

middle: Ruth

last: Derrick

address: keppel street

institute: london school of hygiene and tropical medicine

summary: Ocular infection with Chlamydia trachomatis (trachoma) is the leading cause of blindness that results from infection. Chronic inflammation is believed to drive the scarring process and the progressive blinding disease, however the mechanisms by which this occurs are not completely understood. We hypothesized that Micro RNA (miRNA), as key regulators of genes in inflammatory pathways, are involved in the immunopathogenesis and tissue remodeling observed in trachoma. Conjunctival swabs were collected from a total of 63 individuals resident in trachoma endemic communities in The Gambia, West Africa. MiRNA was extracted from the conjunctival swabs of 23 healthy controls (N), 18 cases with trachomatous scarring (TS) and 22 cases with trachomatous scarring in the presence of clinically significant inflammation (TSI) using Qiagen Allprep DNA/RNA/protein kits. Following reverse transcription and pre-amplification, quantitative RT-PCR was performed using TaqMan Array Human MicroRNA genecards (Av2.0 and Bv3.0) on a 7900HT thermal cycler (Life Technologies, Inc). A total of 754 of the most well characterised unique human miRNA from miRBase (www.mirbase.org/) were screened. Data from each array were uploaded and analysed using the high throughput qPCR package in bioconductor R. Samples with a global miRNA median cycle threshold of 40 were filtered out. A and B cards were analysed separately due to differences in performance of samples on each card. In the A card group 40 samples were normalized and tested: 8 TSI, 16 TS and 16 N. In the B card group 29 samples were normalized and tested: 6 TSI, 13 TS and 10 N. Results were normalized by rank invariant normalization as it reduced the coefficient of variation and increased sample distribution homology more than any other normalization procedure tested. Data in each group were tested for differential expression by Limma.

overall_design: 63 total Samples. In the A card group 40 samples were normalized and tested: 8 TSI, 16 TS and 16 N. In the B card group 29 samples were normalized and tested: 6 TSI, 13 TS and 10 N. Results were normalized by rank invariant normalization as it reduced the coefficient of variation and increased sample distribution homology more than any other normalization procedure tested.

first: Chrissy

last: Roberts

first: Megha

last: Rajasekhar

first: Sarah

last: Burr

first: Pateh

last: Makalo

first: Hassan

last: Joof

first: Emma

last: Harding-Esch

first: Robin

middle: L

last: Bailey

first: David

middle: C

last: Mabey

first: Matthew

last: Burton

first: Martin

last: Holland


title: Gene expression analysis of primary human myeloid precursor cells treated with O6-benzylguanine (6BG)  and Temozolomide (TMZ)

city: Bergisch Gladbach

first: Silvia

last: Rueberg

address: Friedrich-Ebert-Str. 68

department: Genomic Services Department

institute: Miltenyi Biotec GmbH

summary: For the comparison of 6BG/TMZ with control sample, the predominant annotation among the upregulated genes is ‘apoptosis’. The majority of the downregulated genes is assigned to heat shock proteins and proteins which bind unfolded proteins.

overall_design: To look at early changes in gene expression, primary human myeloid precursor cells (40 x 10^6 per sample) derived from 3 pooled CD34+ products were treated for 18 hours with control (vehicle), 6BG, TMZ, or 6BG/TMZ and cell pellets flash frozen. Total RNA were isolated at Miltenyi Biotec (Cologne, Germany) and bioinformatics analysis of four microarray datasets was performed by their Bioinformatics Group.  The direct comparisons were: 6BG/TMZ vs Control, TMZ vs 6BG, 6BG/TMZ vs 6BG, 6BG/TMZ vs TMZ. A two-dye competitive hybridization of mRNAs derived from differently treated human cells in comparison to a reference mRNA derived from cells which underwent a different treatment was conducted. After treatment with two different drugs or a combination of both drugs, respectively, RNA was extracted from the cells and hybridized against the corresponding reference mRNA. As microarray platform, the PIQOR™ Cell Death Microarray with 494 probes was used.

first: Karen

middle: E

last: Pollok


title: Expression data: Venous malformation-causative TIE2-mutations mediate an AKT-dependent decrease in PDGFB

city: Brussels

first: Miikka

last: Vikkula

address: 74(+5) Avenue Hippocrate

institute: de Duve Institute, Université catholique de Louvain

summary:
Comparison of transcriptional profiles of human umbilical vein endothelial cells (HUVECs) expressing wild-type vs. VM-causative mutant forms of TIE2/TEK.
The effects of the most common Venous Malformation-causative mutations in the endothelial cell tyrosine kinase receptor: R849W and L914F, were tested. 743 genes were differentially expressed across the four groups. The 80 genes distinguishing between L914F and wild-type TIE2-expressing HUVECs were analyzed in greater detail.

overall_design: 3 batches each of: non-transfected, and wild-type TIE2, R849W-TIE2, and L914F-TIE2 overexpressing HUVECs were compared by exon-array profiling.

first: Melanie

last: Uebelhoer

first: Nisha

last: Limaye


title: Quaking is a global regulator of muscle-specific alternative splicing in vertebrates

first: Manny

last: Ares

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

overall_design: Refer to individual Series


title: Listeria monocytogenes strain F2365 has reduced ability to survive stress while maintaining virulence characteristics

status: Public on Jun 01 2013

city: West Lafayette

first: Haley

last: Oliver

state: IN

address: 745 agriculture mall dr

summary: Listeria monocytogenes strain F2365 was the first strain representative of serotype 4b (lineage I)  to be sequenced in 2004, suggesting it could become the model organism for this serotype, which is associated with most human outbreaks of listeriosis worldwide to date. F2365 itself is an outbreak strain involved in the Mexican-style soft cheese outbreak in California in 1985. In this study we show through phenotypic and transcriptomic analysis that L. monocytogenes strain F2365 has reduced ability to respond to stress due to the absence of a functional σB-dependent stress response system. F2365 shows no B-dependent ability to survive acid or oxidative stress nor B-dependent ability to infect Caco-2 epithelial cell in vitro or guinea pigs in vivo. Therefore, there is substantial evidence that F2365 is an atypical strain and is not a suitable representative of outbreak-associated serotype 4b strains.

overall_design: Independent RNA isolations were performed for F2365 and ΔsigB strains from cells grown to early stationary phase. Three biological replicates were used in competitive whole-genome microarray experiments. For each set of hybridizations, RNA from a L. monocytogenes wildtype strain was hybridized with RNA from its isogenic ΔsigB null mutant.

first: H

middle: F

first: R

last: Orsi

first: M

last: Wiedmann

first: K

last: Boor


title: Granulosa cell differentiation in vivo and developmental competence of oocytes in the bovine model

city: Québec

first: Anne-Laure

last: Nivet

state: Québec

address: 2440 Hochelaga Blvd

institute: Laval University

summary: Transcriptional profiling of in vivo granulosa cells collected at 20h, 44h, 68h, and 92h of coasting in lactating cow (breed Holstein)

overall_design: 4 conditions experiment, 3 biological replicates, one repliacte per array, dye swap experiment, two colors, 20h vs 44h, 44h vs 68h, 68h vs 92h, 20h vs 68h, 20h vs 92h, 44h vs 92h

first: Anne-laure

first: Patrick

last: Blondin

first: Marc-André

last: Sirard


title: Expression analysis of Caenorhabditis elegans Bristol N2 rsd-2 and rsd-6 single mutants at 25°C and 20°C

city: Cambridge

first: Eric

last: Miska

address: Tennis Court Rd

department: Wellcome Trust/Cancer Research UK Gurdon Institute, The Henry We

institute: University of Cambridge

summary: Investigation of whole genome gene expression level changes in early generation Caenorhabditis elegans Bristol N2 rsd-2 and Bristol N2 rsd-6 single mutants, compared to late-generation strains at 25°C and 20°C

overall_design: A six chip study using total RNA recovered from two separate alleles of Caenorhabditis elegans Bristol N2 rsd-2 and one allele Bristol N2 rsd-6 , in which the effects of transgeneration aging are studied in early generation animals and late generation animals at the restrictive temperature of 25°C and the permissive temperature, 20°C.


title: CpG Methylation profile of Invasive Pancreatic Cancer Cells compared to Non-invasive

city: Frederick

first: Lei

last: Sun

address: 1050 Boyles Street

department: Laboratory of Cancer Prevention

institute: Frederick National Laboratory for Cancer Research

summary:
Two established cell lines, PANC1 and HPAC, were invaded toward a stem cell media through Matrigel.
DNA was isolated from Non-invasive cells and invasive cells.

overall_design: Methylated DNA was isolated from each sample using the Methyl Collector kit from Active Motif. Methylated and Non-Methylated DNA was dye labeled and applied to 244K Human promoter tiling arrays.

first: William

last: Farrar


title: Red algae Gracilaria tenuistipitata: control vs. high copper and high cadmium concentration

city: São Paulo

first: Paulo

last: Zaini

state: São Paulo

address: Av. Prof. Lineu Prestes, 748 - Butantã

department: Bioquímica

country: Brazil

institute: Universidade de São Paulo

summary: The study of macroalgae capacity to acclimate and recover in environments contaminated with Cu and Cd could prove a promising way to understand the tolerance mechanisms of these seaweeds against different pollutants. This study used as a model organism Gracilaria tenuistipitata (Rhodophyta), a macroalga with economic and ecological importance. The partial transcriptome of G. tenuistipitata was profiled using cDNA microarrays in the sixth day of exposition to EC50 metals. Genes involved in Cu and Cd chronic stress belonging to various functional categories suffered shallow modifications. This possibly indicates that G. tenuistipitata would be in the acclimatization process. In addition, the expression of nine stress genes accompanied by analysis of the photosynthetic rate of seaweed to both metals in three different time frames was analyzed. Genetic variation linked to the mechanism of resistance of the algae, determined from EC50 culture conditions established for two metals, occurred in the early hours of treatment. It was found that G. tenuistipitata was able to accumulate these two metals and to resist and acclimate to the negative effects produced by these elements. The temporal analysis from the nine specific genes showed some specific transcriptional responses of the G. tenuistipitata, exposed to Cu and Cd.

overall_design: Three-condition experiment, control cells cultivated in seawater enriched with von Stosch solution vs. copper and cadmium (indepedent) treated cells. Biological replicates: 4 control, 2 copper treated, 2 cadmium treated. All independently grown and harvested. Four replicates per array.

first: Angela

last: Tonon

first: Pio

last: Colepicolo


title: SAM domain polymerization links subnuclear clustering of PRC1 to silencing (ChIP-chip)

city: Yokohama

first: Takaho

last: Endo

state: Kanagawa

address: 1-7-22 Suehiro, Tsurumi

department: IMS

institute: RIKEN

type: Genome binding/occupancy profiling by array

summary: Polycomb group (PcG) proteins mediate heritable but reversible silencing of developmental regulator genes by modifying their chromatin configuration. Accumulating evidence documents a role for PcG proteins in regulating higher order chromatin structures likely by their clustering, however, underlying mechanisms and its impact on transcriptional regulation remain obscure. In this study, we found that subnuclear clustering of PRC1 at canonical PcG target genes depended on head-to-tail polymerization property of SAM domain of Phc2 and likely Phc1. We show that Phc2-SAM polymerization limits the dynamic nature of PRC1, thereby promotes stable association of PRC1 with PcG target genes and contributes to their robust silencing. Our findings suggest a novel model by which SAM polymerization of Phc2 modulates the structural organization of PcG complexes to enable robust yet reversible PcG-mediated repression during development.

overall_design: ChIP on chip analysis was carried out using the Mouse Promoter ChIP-on-chip Microarray Set (G4490A, Agilent, Palo Alto, Calif., USA). MEFs were subjected to ChIP assay using a Ring1B antibody. Purified immunoprecipitated and input DNA was subjected to T7 RNA polymerase-based amplification. Labeling, hybridization and washing were carried out according to the Agilent mammalian ChIP-on-chip protocol (ver.9.0). Scanned images were quantified with Agilent Feature Extraction software under standard conditions.

first: Masako

last: Fujita

first: Daisuke

last: Yamada


title: β-catenin signaling is a critical event in ErbB2-mediated mammary tumor progression.

status: Public on Jun 02 2013

city: St. Louis

first: Robert

last: Lesurf

state: MO

address: 4444 Forest Park Ave

department: McDonnell Genome Institute

institute: Washington University in St. Louis

summary: Although ERBB2 amplification and overexpression is correlated with poor outcome in breast cancer, the molecular mechanisms underlying the aggressive nature of these tumors has not been fully elucidated. To investigate this further, we have used a transgenic mouse model of ErbB2-driven tumor progression (ErbB2KI model) that recapitulates clinically relevant events, including selective amplification of the core erbB2 amplicon. By comparing the transcriptional profiles of ErbB2KI mammary tumors and human ERBB2-positive breast cancers, we demonstrate that ErbB2KI tumors possess molecular features of the basal subtype of ERBB2-positive human breast cancer, including activation of canonical β-catenin signaling. Inhibition of β-catenin-dependent signaling in ErbB2KI-derived tumor cells using RNA interference impaired tumor initiation and metastasis. Furthermore, treatment of ErbB2KI or human ERBB2-overexpressing tumor cells with a selective β-catenin/CBP inhibitor significantly decreased proliferation and ErbB2 expression. Collectively, our data indicate that ERBB2-mediated breast cancer progression requires β-catenin signaling and can be therapeutically targeted by selective β-catenin/CBP inhibitors.

overall_design: Common reference design. 9 samples (including 2 normal tissue, 2 NIC tumors, and 5 KI tumor tissue samples) replicated twice as dye swaps, generating a total of 18 arrays.

first: Babette

last: Schade


title: Toxicogenomics and phenotypic characterization of adult male zebrafish liver treated with estradiol

city: Singapore

first: Choong Yong

last: UNG

address: 14 Science Drive 4

department: Department of Biological Sciences

country: Singapore

institute: National University of Singapore

summary: We performed microarray-based expression profiling on liver of male zebrafish exposed to 0.5, 5, and 50 µg/L of estradiol for 24 and 96 hours, to identify global transcriptional programs and biological pathways involved in estradiol-induced adaptive responses under in vivo environment.

overall_design: We analyzed 35 arrays of estradiol-treated adult male zebrafish liver and 15 arrays of control fish.

first: Choong-Yong

last: Ung

first: Sie-Hong

last: Lam

first: Hlaing

last: Myintzu

first: Sinnakarupan

last: Mathavan

first: Zhiyuan

last: Gong


title: ChIP-chip from KG-1 cells with HIV Tat

status: Public on May 31 2013

city: BOSTON

first: NAYOUNG

last: KIM

state: MA

address: 61 BINNEY

department: MEDICINE

institute: BOSTON CHILDREN'S HOSPITAL

summary:
HIV-1 Tat can modulate the expression of both HIV and cellular genes. In antigen-presenting cells Tat induces the expression of a subset of interferon-stimulated genes (ISGs) in the absence of interferons (IFNs). We investigated the genome-wide Tat association with cellular promoters in immature dendritic cells (iDC) and in monocyte derived macrophages (MDM).
Chromatin immunoprecipitation (ChIP) of Tat together with chromatin profiling by ChIP-on-chip analysis demonstrated that Tat associates with the MAP2K6 and MAP2K3 promoters and mediates its increase, which also affects the induction of some ISGs.

overall_design: comparison of KG-1 cells expressing tTA control vs Tat or mutant TatSF2G48R57A

first: Nayoung

last: Kim

first: Sumeet

last: Gupta


title: Differences in gene expression of delta-fmt and wild-type Staphylococcus aureus RN4220

city: Tübingen

first: Diana

last: Mader

address: Morgenstelle 28

institute: University of Tübingen

summary:
Formyltransferase lacking mutants exhibit reduced growth rates in exponential phase indicating that the function of certain proteins depends on formylated N-termini but it has remained unclear, which cellular processes are abrogated by the lack of formylation.
In order to elucidate how global metabolic processes are affected by the absence of formylated proteins the transcription of the fmt mutant was compared with that of the parental strain.

sample_organism: Staphylococcus aureus subsp. aureus RN4220

overall_design: Bacteria were grown under aerobic and anaerobic conditions and harvested in the exponential growth phase. Here we have expected the most effects of lacking formyltransferase.

first: Andreas

last: Peschel


title: Microarray Analysis on the Differences of Gene Expression in Longissimus Dorsi Muscle Tissue between 1-month and 24-month Chinese Red Steppes

city: Changchun

first: qin

middle: li

last: hong

state: jilin

address: 5333,xi'an road

department: College of Animal Science and Veterinary Medicine

institute: Jilin University

summary:
In order to establish the correlation between biological processes and the mechanisms of gene expression controlling beef traits formation in bovine, microarray analysis was performed to capture the differences in gene expression related to beef traits profile in Longissimus Dorsi muscle tissue between 1-month and 24-month Chinese Red Steppes. 1282 (5.6%) probes showed significant differences at the two stages in the experiment, and 1008 differential gene annotations were obtained using Capitalbio molecule annotation system. BLAST analysis revealed that 1001(78.1%) probe genes shared significant similarity in amino acid sequence with other functional genes (As of June 2009). 126 genes showing strong correlation with beef traits were gained by the GO analysis. With the KEGG analysis, 63 pathways were found to be related to beef traits which involved 73 genes. 28 genes were found in a single pathway, while 35 genes were found in 2-16 pathways respectively. The panels of transcripts and gene pathways analysis in different growth stages may be helpful for the study on beef traits formation, and the gene expression profile construction in Longissimus Dorsi muscle tissues, would make a foundation for screening candidate genes which have genetic effect on meat quality in bovine.
Keywords: Microarray analysis; Beef traits; Differences of gene expression; Longissimus Dorsi muscle tissue; Chinese Red Steppe

overall_design: A total of 18 bulls of the same breed (Chinese Red Steppe) were included in the study; 9 were 1month old while another 9 were 24 months old and were provided by Jilin Academy of Agricultural Sciences. They were maintained in standard conditions and fed with standard diet. The bulls were humanely killed at the slaughter house of the academy, and fresh longissimus dorsi muscle tissues were obtained during slaughter, immediately frozen in liquid nitrogen and stored at -80°C for microarray analysis.

first: Lihong

last: Qin

first: Guoliang

last: Zhang

first: Yang

last: Cao

first: Jiabao

first: Yumin

last: Zhao

first: Zhihui


title: the transcript profiles of Thermoanaerobacter sp. X514 (wild type) and its ethanol tolerant mutants (Xm and Xe) with or without ethanol

city: Qingdao

first: Lu

last: Lin

state: Shandong

address: 189 Songling RD

institute: QIBEBT

summary: The ethanol shock and stress response mechanisms by Thermoanaerobacter sp. X514 (wt) and mutants (Xm and Xe) were characterized by whole genome cDNA micorarrays.

overall_design: In this study, X514 (wt) and mutants (Xm and Xe) cell grew in difeined medium supplement with 50mM glucose under different ethanol treatment. Each sample was prepared harvested at different treated times respectively. Samples were used to acquire expression profiles of total 2322 unique genes, leading to metabolic mechanism construction.