title: Juvenile obesity in Ossabaw swine produces artery-specific transcriptional changes

status: Public on May 29 2013

city: North Chicago

first: J

middle: Wade

last: Davis

state: IL

address: 1 N Waukegan Rd

institute: AbbVie

summary: We adopted a transcriptome-wide microarray analysis approach to determine the extent to which vascular gene expression is altered as a result of juvenile obesity and identify obesity-responsive mRNAs. We examined transcriptional profiles in the left anterior descending coronary artery (LAD), perivascular fat adjacent to the LAD, and descending thoracic aorta between obese (n=5) and lean (n=6) juvenile Ossabaw pigs (age=22 weeks). Obesity was experimentally induced by feeding the animals a high-fat/high fructose corn syrup/high-cholesterol diet for 16 weeks. We found that expression of 189 vascular cell genes in the LAD and expression of 165 genes in the thoracic aorta were altered with juvenile obesity (FDR≤10%) with an overlap of only 28 genes between both arteries. Notably, a number of genes found to be markedly up-regulated in the LAD of obese pigs are implicated in atherosclerosis, including ACP5, LYZ, CXCL14, APOE, PLA2G7, LGALS3, SPP1, ITGB2, CYBB, and P2RY12. Furthermore, pathway analysis revealed the induction of pro-inflammatory and pro-oxidant pathways with obesity primarily in the LAD. Gene expression in the LAD perivascular fat was minimally altered with juvenile obesity. Together, we provide new evidence that obesity produces artery-specific changes in pre-translational regulation with a clear up-regulation of pro-atherogenic genes in the LAD. Our data may offer potential viable drug targets and mechanistic insights regarding the molecular precursors involved in the origins of over-nutrition and obesity-associated vascular disease. In particular, our results suggest that the oxLDL-LOX-1-NFκB signaling axis may be involved in the early initiation of a juvenile obesity-induced pro-atherogenic coronary artery phenotype.

overall_design: We examined transcriptional profiles in the left anterior descending coronary artery (LAD), perivascular fat adjacent to the LAD, and descending thoracic aorta between obese (n=5) and lean (n=6) juvenile Ossabaw pigs (age= 22 weeks). All three tissue types were taken from each animal, and each was applied to one and only one array array except a single Thoracic aorta (Animal ID 63 because there were not enough arrays), so there were 32 total arrays (11 unique pigs).

middle: W

first: Jaume

last: Padilla

first: Scott

last: Rector

first: Nathan

middle: T

last: Jenkins

first: Harold

last: Laughlin


title: Selective degradation of the miR-17 family members of the miR-17-92 cluster by human Cytomegalovirus

status: Public on May 09 2013

city: Seoul

first: Sanghyun

last: Lee

address: 599 Gwanak-ro, Gwanak-gu

department: Department of biology

country: South Korea

institute: Seoul National University

summary: miRNA microarrays were used to investigate host miRNA expression profiles during HCMV clinical strain infection. Human foreskin fibroblasts (HFFs) were infected with the HCMV clinical strain Toledo. To mimic the attenuated strain, we used ToledoΔ15kb, which lacks the 15-kb genomic segment in the UL/b’ region.

overall_design: Changes in miRNA expression upon HCMV infection. Human foreskin fibroblasts (HFFs) were infected with Toledo-WT or ToledoΔ15kb for miRNA microarray (5 MOI). The miRNA expression levels of virus-infected HFFs at 24 or 72 hpi have been compared with those for the noninfected control.

first: Kwangseog

last: Ahn


title: Dicer deficiency reveals microRNAs predicted to control gene expression in developing adrenal cortex [RT-PCR]

status: Public on May 01 2013

city: Detroit

first: Katherine

last: Gurdziel

state: MI

address: 275 E. Hancock

country: USA

institute: Wayne State University

summary: MicroRNAs (miRNAs) are small, endogenous, non-protein coding RNAs that are an important means of post-transcriptional gene regulation. Deletion of Dicer, a key miRNA processing enzyme, is embryonic lethal in mice, and tissue-specific Dicer deletion results in developmental defects. Using a conditional knockout model, we generated mice lacking Dicer in the adrenal cortex. These Dicer knockout (KO) mice exhibited perinatal mortality and failure of the adrenal cortex during late gestation between embryonic day 16.5 (E16.5) and E18.5. Further study of Dicer KO adrenals demonstrated a significant loss of Sf1 expressing cortical cells that was histologically evident as early as E16.5 coincident with an increase in p21 and cleaved-caspase 3 staining in the cortex. However, peripheral cortical proliferation persisted in KO adrenals as assessed by anti-PCNA staining.  To further characterize the embryonic adrenals from Dicer KO mice, we performed microarray analyses for both gene expression and miRNA on purified RNA isolated from control and KO adrenals of E15.5 and E16.5 embryos. Consistent with the absence of Dicer and the associated loss of miRNA-mediated mRNA degradation, we observed an up-regulation of a small subset of adrenal transcripts in Dicer KO mice, most notably the transcripts coded by the genes Nr6a1 and Acvr1c. Indeed, several miRNAs, including let-7, miR-34c, and miR-21 that are predicted to target these genes for degradation, were also markedly down-regulated in Dicer KO adrenals. Together these data suggest a role for miRNA mediated regulation of a subset of genes that are essential for normal adrenal growth and homeostasis.

overall_design: Adrenals from control and Dicer KO litter mates were pooled separately from 4 individual litters, resulting in a total of 4 control (cre-) and 4 Dicer KO biological

first: Kenneth

last: Krill

first: Joanne

middle: H

last: Heaton

first: Derek

middle: P

last: Simon

first: Gary

middle: D

last: Hammer


title: Distribution, functional impact and origin mechanisms of copy number variation in the barley genome

city: Saint Paul

first: María

last: Muñoz-Amatriaín

state: MN

address: 411 Borlaug Hall, 1991Upper Buford Circle

department: Agronomy and Plant Genetics

institute: University of Minnesota

type: Genome variation profiling by genome tiling array

summary: There is growing evidence for the prevalence of DNA copy number variation (CNV) and its role in phenotypic variation in recent years. Comparative genomic hybridization (CGH) was used to explore the extent of this type of structural variation in the barley genome. In a panel of 14 genotypes including domesticated cultivars and wild barleys, we found that 14.9% of all the sequences on the array are affected by CNV. Higher levels of CNV diversity are present in the wild accessions relative to cultivated barley. A substantial portion (37%) of the CNV events are present in both wild and domesticated barley. CNVs are enriched in telomeric regions for all chromosomes except 4H, which is also the barley chromosome with the lowest proportion of CNVs. CNV affected 9.5% of the coding sequences represented on the array. The genes affected by CNV are enriched for sequences annotated as disease-resistance proteins and protein kinases, suggesting the potential for CNV to influence variation for responses to biotic and abiotic stress. The analysis of CNV breakpoints indicated that DNA repair mechanisms of double-strand breaks (DSBs) via single-stranded annealing (SSA) and synthesis-dependent strand annealing (SDSA) play an important role in the origin of many structural changes in barley. Here we present the first catalog of CNVs in a diploid Triticeae species, which opens the door for future genome diversity research in a tribe that comprises the economically important cereal species wheat, barley and rye. Our findings constitute a valuable resource for the identification of CNV affecting genes of agronomic importance.

overall_design: 1-2 replications of 8 barley cultivars and 6 wild barley accessions were hybridized to an array designed from 115,003 whole genome shotgun (WGS) contigs of the ‘reference’ genome of cv. Morex

last: Muñoz‐Amatriaín

first: Nils

last: Stein

middle: J

last: Muehlbauer


title: Small RNAs in differentiating mouse ES cells

status: Public on May 18 2013

city: Boston

first: Mark

middle: L

last: Borowsky

state: MA

address: 185 Cambridge Street

department: Molecular Biology

institute: MGH

type: Non-coding RNA profiling by high throughput sequencing

summary: RNA-interference (RNAi) refers to a growing class of gene silencing phenomena defined by a requirement for small RNAs of 20-32 nt and the action of the Argonaute (Ago) family of ribonucleases. We have previously identified developmentally regulated small RNAs, using Northern blot analysis, that are expressed during X-chromosome inactivation in differentiating female mouse ES cels. We sought to identify these small RNAs using deep sequencing.  We identified small RNAs that align to retrotransposon sequences and are enriched on the X-chromosome.  LINE elements have been proposed to act as way stations during X-inactivation for the spreading of silencing along the entire chromosome, and our findings suggest that LINE elements found on the X-chromosome may be enriched for small RNAs relative to the genome.  These results suggest that RNAi pathways are involved in regulating LINE elements during X-inactivation and ES cell differentiation.

overall_design:
We size-fractionated total RNA from differentiating female mouse ES cells (day 4) into 18-24 nt and 25-45 nt populations and sequenced each fraction separately using the 454 platform.
We used a karyotypically stable 40XX female ES cell line (EL16.7) with one X each of 129 and M. castaneus origins: 129 x (M.castaneus x 129).

first: Kim

last: Daniel

first: Ogawa

last: Yuya

first: Lee

last: Jeannie

first: Borowsky

last: Mark

first: Ohsumi

last: Toshiro


title: Mechanisms of age-dependent response to winter temperature in perennial flowering of Arabis alpina.

status: Public on May 27 2013

city: Cologne

first: Emiel

last: Ver Loren van Themaat

address: Carl von linneweg

country: Germany

institute: Max Planck Institute

summary: Transcriptomic profile of Arabis alpina apex enriched material. We compared apices from plants grown for 2 weeks in long days (20°C) (juvenile) with apices from plants grown for 8 weeks in long days (20°C) (adult) and apices from plants grown for 2 weeks and then shifted in vernalization for 4 weeks with apices from plants grown for 8 weeks and than shifted to vernalization for 4 weeks.

overall_design: 2x2 factorial design. 2 starting ages (2 weeks and 8 weeks) and 2 developmental conditions (before and after vernalization). 4 biological replicates for each condition (16 arrays). Reference: pool of the 16 arrays.

first: Sara

last: Bergonzi

first: George

last: Coupland


title: Vertebrate GAGA factor associated insulator elements demarcate homeotic genes in the HOX clusters

city: Hyderabad

first: Rakesh

middle: K

last: Mishra

state: Andhra Pradesh

address: Uppal Road

country: India

institute: Centre for Cellular and Molecular Biology

type: Genome binding/occupancy profiling by genome tiling array

summary: Hox genes impart segment identity to body structures along the anterior-posterior axis and are crucial for the proper development of all organisms. Multiple regulatory elements, best defined in Drosophila melanogaster, ensure that Hox expression patterns follow the spatial and temporal colinearity reflected in their tight genomic organization. However, the precise mechanisms that regulate colinear patterns of Hox gene expression remain unclear, especially in higher vertebrates where it is not fully determined how the distinct activation domains of the tightly clustered Hox genes are defined independent of each other. Here, we report the identification of a large number of novel cis-elements at mammalian Hox clusters that can help in regulating their precise expression pattern.

overall_design: Agilent two-color ChIP-on-Chip experiment, Organism: Mus musculus ,Genotypic Technology designed Custom Mouse 1 million ChIP-on-chip Array (AMADID-0245671)

first: Surabhi

last: Srivastava

first: Deepika

last: Puri

first: Hita

middle: S

last: Garapati

first: Jyotsna

last: Dhawan


title: miRNA transcriptional profiling during rainbow trout ovarian development

status: Public on Apr 11 2013

city: Rennes

first: Julien

last: Bobe

address: Campus de Beaulieu

country: France

institute: Institut National de la Recherche Agronomique

summary: The study aimed to characterize miRNA expression in rainbow trout ovary during ovarian development from immature to mature stages. Whole ovary were collected at the following stages: immature pre-vitelogenesis (IMM), mid-vitellogenesis (MV), late vitellogenesis (LV), post-vitellogenesis (PV) and mature while meiotic maturation is in progress (MAT).

overall_design: miRNA expression in rainbow trout ovary was measured at 5 different stages (immature, mid-vitellogenesis, late vitellogenesis, post-vitellogenesis and mature).  Two to three biological replicates were used for each stages.

first: Amelie

last: Juanchich

first: Aurelie

last: Le Cam


title: Transcriptional and miRNA profiling during rainbow trout ovarian development

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

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

overall_design: Refer to individual Series


title: Transcriptional profiling during rainbow trout ovarian development

summary: The study aimed to characterize gene expression in rainbow trout ovary during ovarian development from immature to mature stages. Whole ovary were collected at the following stages: immature pre-vitelogenesis (IMM), mid-vitellogenesis (MV), late vitellogenesis (LV), post-vitellogenesis (PV) and mature while meiotic maturation is in progress (MAT).

overall_design: Gene expression in rainbow trout ovary was measured at 5 different stages (immature, mid-vitellogenesis, late vitellogenesis, post-vitellogenesis and mature).  Three to four biological replicates were used for each stages.

first: Jerome

last: Montfort


title: Expression analysis of A. actinomycetemcomitans wild type (JP2) vs. Mlc deletion mutant both grown aerobically and anaerobically

status: Public on Jun 01 2013

city: SA

first: David

last: Kolodrubetz

state: TX

address: 7703 Floyd Curl Dr

department: Microbiology and Immunology

institute: UTHSCSA

summary: The goal of this analysis is to define the aerobic and anaerobic regulons for the transcription factor Mlc (Makes Large Colonies) in the periodontal pathogen Aggregatibacter actinomycetemcomitans. The objectives were met by comparing the mRNA profile of a wild type strain, JP2, to that of an isogenic mutant deleted of the Mlc gene. Both strains were grown aerobically and anaerobically. The results show that Mlc is involved in the regulation of dozens of genes in both growth conditions.

overall_design: Half of the study (anaerobic samples) was a four biological replicates study using total RNA recovered from four separate anaerobic cultures of wild-type Aggregatibacter (formerly Actinobacillus) actinomycetemcomitans strain JP2 and four separate anaerobic cultures of strain AAM155, an isogenic deletion mutant in which the gene for Mlc (Makes Large Colonies) has been replaced by a spectinomycin resistance gene cassette. The cells were grown anaerobically in pairs (wild type paired with mutant). The second half of the study (aerobic samples) was a four biological replicates study using total RNA recovered from four separate aerobic cultures of wild-type Aggregatibacter actinomycetemcomitans strain JP2 and four separate anaerobic cultures of strain AAM155, an isogenic deletion mutant of Mlc. The cells were grown aerobically in pairs (wild type paired with mutant). Each chip measures the expression level of 2,116 genes from A. actinomycetemcomitans strain HK1651. There were 11 different 60-mer probes /gene for 94% of the genes, and the entire probe set (22,537 probes) was replicated (technical replicates) three times on each array. Each probe set is contained on a quarter of a chip and there were also 4,426 random probes per array. A total of four chips were used in these experiments.

first: Catherine

last: Childress


title: Genomic rearrangements in C3 glomerulopathies

status: Public on May 28 2013

city: Madrid

first: Santiago

last: Rodriguez de Cordoba

state: Madrid

address: Ramiro de Maeztu, 9

department: Medicina Celular y Molecular

country: Spain

institute: Centro de Investigaciones Biologicas

summary:
Copy number variations and genomic rearrangements in the CFH-CFHRs region were assessed with a custom-designed high-density 8x15k oligonucleotide CGH arrays spanning the RCA gene cluster region in human chromosome 1q32 (median resolution of 110 bp) (AMADID 040193, Agilent Technologies, Santa Clara, CA).
A healthy male donor sample, fully genotyped for that region, was used  as hybridization control. Microarray data were extracted and visualized using the Feature Extraction Software v10.7 and Genomic Workbench Standard Edition 7.0 (Agilent Corp, Santa Clara, CA). Copy number altered regions were detected using ADM-2 (set as 5) statistic provided by DNA Analytics, with a minimum number of 5 consecutive probes. Genomic build hg19 was used for the experiment.

overall_design: Only a Sample was analyzed

first: Agustín

last: Tortajada

first: Hugo

last: Yébenes

first: Cynthia

last: Abarrategui-Garrido

first: Jaouad

last: Anter

first: Jesús

middle: M

last: García-Fernández

first: Rubén

last: Martínez-Barricarte

first: María

last: Alba-Domínguez

first: Talat

last: Malik

first: Rafael

last: Bedoya

first: Rocío

middle: C

last: Pérez

first: Margarita

last: Trascasa

first: Matthew

last: Pickering

first: Claire

last: Harris

first: Pilar

last: Sánchez-Corral

first: Oscar

last: Llorca

last: Rodríguez de Córdoba


title: Mechanisms of tentacle morphogenesis in the sea anemone, Nematostella vectensis

city: Kansas City

first: Chris

last: Seidel

state: MO

department: Genomics

institute: Stowers Institute

summary: Evolution of the capacity to form secondary outgrowths from the principal embryonic axes was a crucial innovation that potentiated the diversification of animal body plans.  Nevertheless, precisely how such outgrowths develop in early-branching metazoan species remains poorly understood. To identify genes potentially involved in tentacle initiation, outgrowth, and maintenance, we performed transcriptional profiling at three different stages of Nematostella development:  late planula larvae with tentacle buds, animals with growing tentacles, and mature animals with four-tentacle polyps. At each of these three stages, the animal was bisected such that the oral tentacle portion (head) could be compared to the body column.

overall_design: Tentacle buds, growing tentacles, and mature tentacles, were compared to body columns from each matching stage in duplicate, for a total of 6 samples.

first: Ashleigh

middle: E

last: Fritz

first: Aissam

last: Ikmi

first: Ariel

last: Paulson

last: Gibson


title: Analysis of serum cytokine levels of EAE mice

status: Public on May 31 2013

city: Shanghai

first: Qian-qian

last: Yin

state: Shanghai

address: No280, Chongqing South Road

country: China

institute: Shanghai Jiao Tong University School of Medicine

summary: Sera of experimental autoimmune encephalomyelitis (EAE) or control mice were collected at day 18 post immunization. Comprehensive analysis of cytokine levels were performed by using commercially available RayBio Mouse Cytokine Array 2 (RayBiotech, Inc.) according to manufacturer’s protocol

overall_design: 4 samples.There are  two groups: vehicle control group and EAE group. Each group consists of 2 replications.


title: Comparative analysis of D. shibae wild-type vs. ∆ctrA, ∆chpT and ∆cckA

status: Public on May 30 2013

city: Třeboň

first: Jürgen

last: Tomasch

address: Novohradská 237

country: Czech Republic

institute: Center Algatech, Institute of Microbiology of the Czech Academy of Science

summary: Comparison of D. shibae wild-type with single gene knock-out strains of a phosphorelay conserved in Alphaproteobacteria (∆ctrA, ∆chpT and ∆cckA)

sample_organism: Dinoroseobacter shibae DFL 12 = DSM 16493

overall_design: Loop-design, two biological replicates of D. shibae wild-type, ∆ctrA, ∆chpT and ∆cckA in mid-exponential phase (OD 0.4) and stationary phase (6h after culture reached maximum OD)

first: Hui

last: Wang

first: Oliver

last: Frank

first: Madeleine

last: Martin

first: Jörn

last: Petersen

first: Irene

last: Wagner-Döbler


title: Host microRNA molecular signatures associated with human H1N1 and H3N2 influenza A viruses

status: Public on Apr 03 2013

city: Lyon

first: olivier

last: Terrier

address: Rue Guillaume Paradin

department: Laboratoire de Virologie et Pathologie Humaine

institute: Université Claude Bernard Lyon 1

summary: In this study, we performed a miRNA global profiling in human lung epithelial cells (A549) infected by two different subtypes of human influenza A viruses (H1N1 and H3N2).

overall_design: A549 cells were either mock-infected or infected at a multiplicity of infection (MOI) of 1 with H1N1 or H3N2 viruses, and total RNAs were isolated at 24 hours post-infection (hpi). An MOI of 1 was performed to ensure that 100% of the cells were infected at 24 hpi, a strategy that we have previously validated and used for a transcriptional profiling study of infected cells (Josset et al. , 2010). The purified RNAs were subjected to reverse transcription using a pool of miRNA RT primers (Human pool A v2.1, Applied Biosystems) and subsequently amplified and quantified by RT-qPCR in a TaqMan array MicroRNA card (Applied biosystems).

first: Olivier

first: Julien

last: Textoris

first: Coralie

last: Carron

first: Virginie

last: Marcel

first: Jean-Christophe

last: Bourdon

first: Manuel

last: Rosa-Calatrava


title: Programmed necrosis and apoptosis differentially regulate cancer development and biliary homeostasis in the liver

status: Public on Apr 01 2013

city: Aachen

first: Bernd

last: Denecke

state: NRW

address: Pauwelsstrasse 30

department: IZKF Aachen

institute: RWTH Aachen University

summary: For years, the term apoptosis was used synonymously for programmed cell death. However, it was recently discovered that programmed necrosis – dependent on the kinases Receptor-Interacting-Protein-Kinase (RIP)1 and RIP3 (also called necroptosis) – represents a major programmed cell-death pathway in development and immunity. At present, the functions of necroptosis in hepatitis, liver cancer development and biliary disease are unclear. Here we show that in mice with chronic hepatitis due to conditional ablation of TGF-beta-activated kinase1 (TAK1) in liver parenchymal cells (LPC), both apoptotic and necroptotic signaling pathways are activated. Strikingly, only Caspase-8-dependent apoptosis promotes spontaneous liver cancer development, while in contrast LPC necroptosis inhibits hepatic tumourigenesis. The tumour-promoting effect of apoptosis results from an induction of strong compensatory proliferation of LPC, linked with the paracrine action of growth factors like Insulin-like growth factor-2 (IGF-2) not induced by necroptosis. In addition to prevention of HCC development, induction of necroptosis leads to massive cholestasis and hyperbilirubinemia, resulting from an insufficient ductular reaction and biliary regeneration from the hepatic stem cell niche as a response to chronic hepatitis. These results indicate previously undefined distinctive functions of apoptosis and programmed necrosis in controlling cancer development and cholestasis in the liver with important implications for future therapeutic strategies in chronic liver disease.

overall_design: 8 samples were analysed. We compared groups of 4 Tak1/Caspase8 LPC double knockout mice and 4 Tak1 LPC-KO/Rip3-/- mice to detect genes differentially regulated by apoptotic and necrotic signalling pathways.

first: Tom

last: Lüdde

last: Janssen


title: Mock, latent, and lytic rKSHV.219-infected iSLK cells [Expt3]

status: Public on Mar 29 2013

city: Emeryville

first: Henry

last: Chang

state: CA

address: 4560 Horton Street

department: Infectious Diseases Group

institute: Novartis Institutes for BioMedical Research

type: Expression profiling by genome tiling array

summary: Expression profiling of stably infected epithelial cells using a custom tiling microarray. iSLK was infected with rKSHV.219 and selected with puromycin. Mock infected iSLK served as control for iSLK.219. Lytic reactivation of iSLK.219 was induced with 1 ug/mL doxycycline for 48 hours.

sample_organism:
Homo sapiens
Human gammaherpesvirus 8
Human herpesvirus 8 strain rKSHV.219

platform_organism:
Homo sapiens
Human herpesvirus 8 type M

overall_design: Three condition experiment: mock infected, latently infected, and lytically induced rKSHV.219-infected iSLK cells.

first: Don

last: Ganem


title: Mock and stably infected rKSHV.219 cells (LEC, BEC, HUVEC, and HAEC) [Expt2]

summary: Expression profiling of stably infected primary endothelial cells using a custom tiling microarray. LEC, BEC, HUVEC, and HAEC were infected with rKSHV.219 and selected with puromycin for 2 weeks. Mock infected LEC, BEC, HUVEC, and HAEC served as controls for their infected counterparts. All cells were harvested after 2 weeks of stable infection.

platform_organism:
Homo sapiens
Human herpesvirus 8 strain rKSHV.219

overall_design: Two condition experiment: mock infected vs. stably infected cells. Four cell types.


title: Mock and stably infected rKSHV.219 cells (LEC and BEC) [Expt1]

summary: Expression profiling of stably infected primary endothelial cells using a custom tiling microarray. LEC and BEC were infected with rKSHV.219 and selected with puromycin for 2 weeks. Mock infected LEC and BEC served as controls for their infected counterparts. All cells were harvested after 2 weeks of stable infection.

overall_design: Two condition experiment: mock infected vs. stably infected cells. Two cell types.


title: Identification of differential duodenal gene expression levels correlated with differences in energy utilization in chickens

city: East Geelong

first: Dragana

last: Stanley

state: Victoria

address: 5 Portarlington Rd

department: AAHL

country: Australia

institute: CSIRO

summary: The amount of energy that can be extracted from a diet varies between individuals. Apparent Metabolizable Energy  (AME) is a measure of energy utilization efficiency and represents the difference between the energy consumed and the energy lost via the excreta. There are significant differences in the energy utilization capability of individual birds that have a similar genetic background and are raised under identical conditions. We analyzed duodenal gene expression and microbiota differences between birds with different efficiencies in food to energy conversion using microarrays and sequencing of 16s rRNA genes. Differences were found in duodenal gene expression between high and low AME birds, they were however mostly related to genes of unknown function.

overall_design: The flock of 96 chickens was used to study ability of the bird to utilise the energy from feed. We measured energy content in feed and in excreta of individually housed birds. The microarrays were used to compare expression between the best and worst energy utilisers.

first: Barbara

last: Konsak


title: miR-17~92 Regulates Effector and Memory CD8 T cell Fates by Modulating Proliferation in Response to Infection

status: Public on Apr 16 2013

city: Seattle

first: Surojit

last: Sarkar

state: WA

address: 1100 Olive Way, Suite 100

department: Department of Pediatrics and Laboratory Medicine

institute: University of Washington School of Medicine

summary: miRNA profiling of Db-GP33-41 specific murine CD8 T cells following infection with LCMV Armstrong

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

overall_design: Various in-vivo subsets of antigen-specific CD8 T cells were FACS sorted and analyzed for miRNA expression profiling. Samples were purified from either uninfected animals or after days 4.5, 9 and >60 post infection with LCMV Armstrong.

first: Vandana

last: Kalia


title: A unique herpesviral transcriptional program in KSHV-infected lymphatic endothelial cells leads to mTORC1 activation and rapamycin sensitivity

platform_organism:
Homo sapiens
Human herpesvirus 8 type M
Human herpesvirus 8 strain rKSHV.219


title: Study of microRNA associated with metformin’s anti-tumor effect [pancreatic cancer]

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

country: Japan

institute: Toray Industries,Inc.

summary: The miRNAs expression was markedly altered with the treatment of metformin in vitro and in vivo and various miRNAs induced by metformin also may contribute to tumor regression in vitro and in vivo.

overall_design: Using a custom microarray platform, we analyzed the expression levels of 1042 human miRNA probes in the cell lines in vitro and tumorous tissues in vivo that were treated with and without metformin.

first: Kiyohito

last: Kato

first: Tsutomu

last: Masaki


title: Genomic regions flanking E-box sites influence DNA binding specificity of bHLH transcription factors through DNA shape

city: Durham

first: Raluca

last: Gordan

state: NC

address: 101 Science Dr, CIEMAS 2179

department: Center for Genomic and Computational Biology

institute: Duke University


title: Genomic regions flanking E-box sites influence DNA binding specificity of bHLH transcription factors through DNA shape (validation)

summary: DNA sequence is a major determinant of the binding specificity of transcription factors (TFs) for their genomic targets. However, eukaryotic cells often express, at the same time, TFs with highly similar DNA binding motifs but distinct in vivo targets. Currently, it is not well understood how TFs with seemingly identical DNA motifs achieve unique specificities in vivo. Here, we used custom protein binding microarrays to analyze TF specificity for putative binding sites in their genomic sequence context. Using yeast TFs Cbf1 and Tye7 as our case study, we found that binding sites of these bHLH TFs (i.e., E-boxes) are bound differently in vitro and in vivo, depending on their genomic context. Computational analyses suggest that nucleotides outside E-box binding sites contribute to specificity by influencing the 3D structure of DNA binding sites. Thus, local shape of target sites might play a widespread role in achieving regulatory specificity within TF families.

overall_design: Two protein binding microarray (PBM) experiments of Saccharomyces cerevisiae transcription factors were performed. Briefly, the PBMs involved binding GST-tagged yeast transcription factors Cbf1 and Tye7 to double-stranded 44K Agilent microarrays in order to determine the accuracy of our regression models for TF-DNA binding specificity. Briefly, this  array contains 30-bp genomic sequences from our initial custom array (Gordan et al 2013, submitted), with 0 through 4 mutations designed at various positions in the genomic sequences. Each sequence in represented in 6 replicate spots. We report the PBM signal intensity for each spot. The PBM protocol is described in Berger et al., Nature Biotechnology 2006 (PMID 16998473).

first: Ning

last: Shen

first: Iris

last: Dror

first: Tianyin

last: Zhou

first: John

last: Horton

first: Remo

last: Rohs

first: Martha

last: Bulyk


title: CD4+ Tcell : control vs cocaine treated

city: Nashville

first: Chandravanu

last: Dash

state: TN

address: 1005 Dr. DB Todd Jr Blvd

department: Center for AIDS Health Disparities Research

institute: Meharry Medical College School of Medicine

summary: Changes in miRNA profile of CD4+ T cells treated with cocaine

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: 6 samples were analysed, 3 control and 3 treated with cocaine

first: Chinmay

last: Mantri


title: Production of pyomelanin in the Vibrio campbellii hmgA mutant results in the repression of quorum sensing, bioluminescence and virulence

city: Washington

first: Baochuan

last: Lin

state: DC

address: 4555 Overlook Avenue, S. W.

department: Center for Bio/Molecular Science & Engineering

institute: US Naval Research Laboratory

summary: Vibrio campbellii BAA-1116 was used as model organism from the Harveyi clade to understand how melanization affected cellular phenotype, metabolism and virulence. An in-frame deletion of the homogentisate-1,2-dioxygenase (hmgA) gene resulted in the overproduction of a pigment in cell culture supernatants and cellular membranes that was identified as pyomelanin. Unlike previous demonstrations in Vibrio cholerae, Burkholderia cepacia and Pseudomonas aeruginosa, the pigmented V. campbellii mutant did not show increased UV or hydrogen peroxide resistance and was found to be ~2.7 times less virulent then the wild type strain in Penaeus monodon shrimp virulence assays. Microarray-based transcriptomic analyses revealed that the deletion of the hmgA gene and subsequent pyomelanin production negatively effected the expression of 129 genes involved in protein translation, cell division, membrane transport, electron transfer and amino acid utilization. The response was mediated in part by an impairment of the quorum sensing regulon as transcripts of the quorum sensing high cell density master regulator LuxR and other operonic members of this regulon were significantly repressed in the hmgA mutant. Taken together, the results suggest that the pyomelanization of V. campbellii sufficiently impairs the metabolic activities of this organism and renders it less fit and virulent then its isogenic wild type strain.

platform_organism: Vibrio campbellii CAIM 519 = NBRC 15631 = ATCC 25920

overall_design: Three biological replicates  of V. campbellii BAA-1116 (str) and hmgA mutants were grown to stationary phase (48 h, 200 rpm, 30°C, in 50 mL LM medium) and total RNA was extracted from 1.0E+9 cells. Messenger RNA was isolated from the total RNA extracts treated with DNase, labeled with biotin, fragmented and hybridized to V. campbellii BAA-1116 whole genome microarrays (520694F, Affymetrix).

first: Zheng

last: Wang

first: Anahita

last: Mostaghim

first: Robert

middle: A

last: Rubin

first: Evan

last: Glaser

first: Pimonsri

last: Mittraparparthorn

first: Janelle

middle: R

last: Thompson

first: Gary

last: Vora


title: Increased levels of IAA are required for system 2 ethylene synthesis causing fruit softening in peach (Prunus persica (L). Batsch)

status: Public on Mar 27 2013

city: Shizuoka

first: Hiroshi

last: Fujii

state: Shizuoka

address: 485-6 Okitsunakacho, Shimizu

department: Division of Citrus Research

institute: Institute of Fruit Tree Science, NARO

summary: The fruit of melting-flesh peach cultivars produce high levels of ethylene caused by high expression of PpACS1, resulting in rapid fruit softening at the late-ripening stage. In contrast, the fruit of stony hard peach cultivars do not soften and produce little ethylene due to low expression of PpACS1. To elucidate the mechanism for suppressing PpACS1 expression in stony hard peaches, a microarray analysis was performed. Several genes that displayed similar expression patterns as PpACS1 were identified and shown to be IAA-inducible genes.

overall_design: Change in gene expression according to growth of fruits in 'melting peach ‘Akatsuki’ fruit sampled at 92, 98, 104 and 106 day after full bloom (DAB). Propylene induced gene expression stony peach ‘Manami’ and ‘Odoroki’ harvested at commercial maturity (Tatsuki et al., 2006).

first: Miho

last: Tatsuki

first: Takehiko

last: Shimada

first: Michiharu

last: Nakano


title: Identification of NLP7 direct targets using ChIP-chip in Arabidopsis thaliana

status: Public on Mar 23 2013

first: François

last: ROUDIER

address: 46 Allée d'Italie

department: Biologie

institute: Ecole Normale Supérieure de Lyon

summary: Chromatin immunoprecipitation was performed in nlp7-1 Arabidopsis thaliana seedlings complemented by a pNLP7::NLP7-GFP construct upon 10 minutes NO3- resupply after a 3-day NO3- starvation.

overall_design: Genome-wide profiling of NLP7 binding regions by ChIP-chip, 2 biological replicates in dye-swap

first: Francois

last: Roudier

first: Vincent

last: Colot


title: Protein and histone binding profiles from mouse ES cells during differentiation and after Kdm6a RNAi treatment.

status: Public on Mar 22 2013

first: Joel

last: Berletch

address: 1959 NE Pacific St.

department: Pathology

institute: University of Washington

summary: Here we show binding and occupancy profiles for KDM6A, H3K27me3 and H3K4me3 to address the epigenetic regulation of a subset of Rhox genes, Rhox6 and 9, in female and male ES cells during differentiation. To further address a functional role for KDM6A in the epigenetic regulation of Rhox6 and 9, binding profiles for female ES cells treated with a control siRNA and siRNA specific for Kdm6a are shown. We report that two members of the Rhox cluster, Rhox6 and 9, are regulated by de-methylation of histone H3 at lysine 27 by KDM6A, a histone demethylase with female-biased expression. Our results are consistent with other homeobox genes in that Rhox6 and 9 are in bivalent domains prior to embryonic stem cell differentiation and thus poised for activation. In female mouse ES cells KDM6A is specifically recruited to Rhox6 and 9 for gene activation, a process inhibited by Kdm6a knockdown. In contrast, KDM6A occupancy at Rhox6 and 9 is low in male ES cells and knockdown has no effect on expression.   Our study implicates Kdm6a, a gene that escapes X inactivation, in the regulation of genes important in reproduction, suggesting that KDM6A may play a role in the etiology of developmental and reproduction-related effects of X chromosome anomalies.

overall_design: ChIP-chip was used to analyze the binding profiles of KDM6A, H3K27me3, and H3K4me3 during differentiation in female and male ES cells. Additionally, ChiP-chip of KDM6A binding in control treated and siRNA treated ES cells is presented.

middle: B

first: Xinxian

last: Deng

first: Di

last: Nguyen

first: Christine

last: Disteche


title: Inactivation of TP53 correlates with disease progression and low miR-34a expression in previously treated chronic lymphocytic leukemia patients

status: Public on Mar 21 2013

city: Basel

first: Giuseppe

last: Palermo

address: wettsteinallee 76

country: Switzerland

institute: F. Hoffman-La Roche Ltd.

summary: Micro-RNA expression data of CD19 selected B-cells from previously treated and relapsed chronic lymphocytic leukemia patients. We aimed to correlate miR-34a with TP53 mutation status and del17p status.

overall_design: CD19 B-cells from previously treated and relapsed chronic lymphocytic leukemia patients were selected for RNA extraction and hybridization on Affymetrix microarrays.

first: Annika

last: Dufour

first: Evelyn

last: Zellmeier

first: Gudrun

last: Mellert

first: Guillemette

last: Duchateau-Nguyen

first: Stephanie

last: Schneider

first: Tobias

last: Benthaus

first: Purvi

last: Kakadia

first: Karsten

last: Spiekermann

first: Wolfgang

last: Hiddemann

first: Jan

last: Braess

first: Sim

last: Truong

first: Nancy

last: Patten

first: Lin

last: Wu

first: Sabine

last: Lohmann

first: David

last: Dornan

first: Debraj

last: GuhaThakurta

first: Ru-Fang

last: Yeh

first: Galina

last: Salogub

first: Philippe

last: Solal-Celigny

first: Anna

last: Dmoszynska

first: Tadeusz

last: Robak

first: Marco

last: Montillo

first: John

last: Catalano

first: Christian

last: Geisler

first: Martin

last: Weisser

first: Stephan

last: Bohlander


title: Genomic regions flanking E-box sites influence DNA binding specificity of bHLH transcription factors through DNA shape (different concentrations)

first: Raluca

last: Gordan

overall_design: Three protein binding microarray (PBM) experiments of Saccharomyces cerevisiae transcription factors were performed. Briefly, the PBMs involved binding GST-tagged yeast transcription factors Cbf1 and Tye7 to double-stranded 44K Agilent microarrays in order to determine their binding specificity for putative DNA binding sites in native genomic context. Briefly, we represent three categories of 30-bp genomic sequences: 1) ChIP-chip bound probes, 2) ChIP-chip unbound probes, and 3) negative control probes. ChIP-chip bound probes corresponded to genomic regions bound in vivo by Cbf1 or Tye7 (ChIP-chip P < 0.005 in rich medium  (YPD) (Harbison et al., Nature 2004, PMID 15343339)) contained at least two consecutive 8-mers with universal PBM E-score > 0.35 (Zhu et al., Genome Research 2009, PMID 19158363). All putative binding sites occurred at the same position within the probes on the array. “ChIP-chip unbound” probes corresponded to genomic regions with ChIP-chip P > 0.5  and at least two consecutive 8-mers at a more stringent universal PBM E-score threshold of 0.4. Negative control probes corresponded to S. cerevisiae intergenic regions with a maximum 8-mer E-score < 0.3. We also designed probes that contain, within constant flanking regions, all 10-bp sequences that occur within the “ChIP-chip bound” probes and contain the E-box CACGTG, but are flanked by synthetic rather than native genomic sequence. Each DNA sequence represented on the array is present in 4 replicate spots. We report the PBM signal intensity for each spot. The PBM protocol is described in Berger et al., Nature Biotechnology 2006 (PMID 16998473).

first: Ning

last: Shen

first: Iris

last: Dror

first: Tianyin

last: Zhou

last: Horton

first: Remo

last: Rohs

first: Martha

last: Bulyk


title: Enterococcus faecalis OG1RF control vs. treatment with ampicillin, bacitracin, cephalothin, or vancomycin

status: Public on Mar 19 2013

city: Gainesville

first: Jessica

last: Kajfasz

state: FL

address: 1395 Center Drive

department: Oral Biology

institute: University of Florida

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

overall_design: Refer to individual Series


title: Enterococcus faecalis OG1RF control vs. treatment with ampicillin, bacitracin, or cephalothin

status: Public on Mar 16 2013

summary: Transcriptional profiling to investigate the effect of drug treatment on the E. faecalis cells. For microarray analysis, E. faecalis OG1RF was grown in FMC medium supplemented with 10 mM glucose to an optical density at 600 nm (OD600) of 0.3 and the cultures were divided in 7 aliquots. One aliquot was collected by centrifugation and immediately frozen (untreated control cells). The other aliquots were treated for 30 or 60 min with 1.25 X the minimum inhibitory concentration (MIC) of one of the following CW inhibitors: ampicillin (20 μg ml-1), bacitracin (80 μg ml-1), or cephalothin (80 μg ml-1). After an exposure time of 30 or 60 minutes, each of these cultures was also centrifuged and the pellets frozen. RNA was then isolated from each pellet for microarray analysis. This process was repeated 3 additional times, for a total of four replicates of each condition.

overall_design: RNA was extracted from four replicate samples of each condition of interest (control cells grown to OD600 = 0.3 in FMC medium supplemented with 10mM glucose, then treated with ampicillin, bacitracin, or cephalothin for 30 or 60 minutes) and labeled with Cy3. For each replicate, labeled RNA was hybridized to slides along with Cy5-labeled reference RNA, extracted from E. faecalis OG1RF cells grown in BHI medium to mid-log.

first: Jacqueline

last: Abranches

first: Pamella

last: Tijerina

first: Alejandro

last: Avilés-Reyes

first: Anthony

middle: O

last: Gaca

first: José

last: Lemos


title: eqtl-Identification of expression QTL of ABA response in sunflower

status: Public on Jun 12 2013

city: evry

first: caius

last: jose

state: essonne

address: 2 rue gaston cremieux

department: URGV

institute: transcriptomic platform

summary: affy_eqtl_sunflower - eqtl - Abiotic stress and more specifically drought is the major limiting factor for sunflower production. ABA is a key hormone for drought stress response in plants and sunflower. This experiment aims at identifying ABA responsive pathways in order to better understand sunflower responses to drought. The ultimate goal will be improve sunflower breeding through selection of key drought response genes. The experiment consisted of 1 or 2 (and 3 for the sample 209) repeats of 113 recombinant imbred lines and 11 repeats of the population parents SF1935 (INRA code XRQ), 11 SF326 (INRA code: PSC8) and the F1 hybrid 10 INEDI. The genotypes were grown in growth chamber conditions and submitted to a 6-hour-treatment of 0.5 µM absissic acid or not. Growth conditions were 14h light at 23°C and 10h night at 18°C under fluorescent bulbs. Plants were grown in 18 hydroponic boxes (9 for ABA treatment, 9 for control) containing 20 litres of aerated liquid culture medium (as described in Massonneau et al., 2001 Planta). Leaves (not cotyledons) from the 15-day-old-plantlets of sunflower were harvested 6 hours after treatment; the three repeats were pooled for each genotype and frozen immediately in liquid nitrogen.

overall_design:
236 arrays - SUNFLOWER; treated vs untreated comparison

Grp suffixes such as -A, -AA, and bis, are there to differentiate the same replicates.

last: Caius

first: Nicolas

last: Langlade

first: Sandrine

last: Balzergue

first: Marie-Laure

last: Martin-Magniette


title: Identify the dysregulated miRNA in human colorectal cancer tissues

status: Public on Mar 20 2013

city: Hong Kong

first: Yujuan

last: Dong

address: Ngan Shing Street

department: Surgery

country: Hong Kong

institute: The Chinese University of Hong Kong

summary: Dysregulated miRNA in human colorectal cancer (CRC) were identified through comparison between 4 CRC tumors and their adjacent normal tissues by miRNA array. Histologically-confirmed CRC were included in this study. CRC tissues and paired adjacent normal tissues were obtained from the resected surgical specimens. The adjacent normal tissue is composed of normal colonic mucosa located at approximately 10 cm away from the cancer tissue. miRNA profiling of 754 human miRNAs was performed using TaqMan Human MiRNA Array Set v3.0. Quantitative real-time polymerase chain reaction (Q-PCR) was performed using Applied Biosystems 7900HT Real-Time PCR System (Applied Biosystems). Results were analyzed by the SDS RQ Manager 1.2 software (Applied Biosystems).

overall_design: 4 CRC tissues and 4 adjacent normal tissues were subjucted to qPCR based miRNA expression profiling. Equal amount of total RNA were used for analysis.

first: Simon

last: Ng


title: Gene expression profiling of adult female tissues in feeding Rhipicephalus microplus cattle ticks

status: Public on Mar 15 2013

city: Pretoria

first: Christian

last: Stutzer

state: Gauteng

address: Lynnwood road

department: Biochemistry

country: South Africa

institute: University of Pretoria

summary: Transcriptional profiling of salivary gland, midgut and ovary tissues isolated from  Rhipicephalus microplus females at day 20 post infestation. This enabled the identification of transcripts that are tissue-specific or shared among the tissues tested.

overall_design: Reference pool design: Each tissue tested was compared to a reference pool comprising ticks (immature to adult stages) sampled on day 4, 5, 7, 13, 15 and tissues collected on  day 20 post infestation. Biological replicates: 2; Technical replicates: 2.

first: Willem

last: van Zyl

first: Nicholas

last: Olivier

first: Christine

last: Maritz-Olivier


title: Enterococcus faecalis OG1RF control vs. treatment with vancomycin

last: Kajfasz

summary: Transcriptional profiling to investigate the effect of drug treatment on the E. faecalis cells.  For microarray analysis, E. faecalis OG1RF was grown in FMC medium supplemented with 10 mM glucose to an optical density at 600 nm (OD600) of 0.3 and the cultures were divided in 3 aliquots.  One aliquot was collected by centrifugation and immediately frozen (untreated control cells).  The other aliquots were treated for 30 or 60 min with 1.25 X the minimum inhibitory concentration (MIC) of vancomycin (10 μg ml-1).  After an exposure time of 30 or 60 minutes, each of these cultures was also centrifuged and the pellets frozen.  RNA was then isolated from each pellet for microarray analysis.  This process was repeated 3 additional times, for a total of four replicates of each condition.

overall_design: RNA was extracted from four replicate samples of each condition of interest (control cells grown to OD600 = 0.3 in FMC medium supplemented with 10mM glucose, then treated with vancomycin for 30 or 60 minutes) and labeled with Cy3.  For each replicate, labeled RNA was hybridized to slides along with Cy5-labeled reference RNA, extracted from E. faecalis OG1RF cells grown in BHI medium to mid-log.


title: Aneuploidy, oncogene amplification, and epithelial to mesenchymal transition define spontaneous transformation of murine epithelial cells

status: Public on Mar 14 2013

city: Bethesda

first: Hesed

middle: Maria

last: Padilla-Nash

state: MD

address: 50 South Drive

department: Genetics Branch

institute: NCI

type:
Expression profiling by array
Genome variation profiling by array

first: Nicole

last: McNeil

first: Ming

last: Yi

first: Quang-Tri

last: Nguyen

first: Yue

last: Hu

first: Danny

last: Wangsa

first: David

last: Mack

first: Amanda

last: Hummon

first: Chanelle

last: Case

first: Eric

last: Cardin

first: Robert

last: Stevens

first: Michael

last: Difilippantonio

first: Thomas

last: Ried


title: The transcriptional response of Cryptococcus neoformans to ingestion by Acanthamoeba castellanii and murine macrophages

city: St. Louis

last: Heinz

address: 4320 Forest Park Blvd.

department: Genetics

institute: Washington University School of Medicine

summary: Virulence of Cryptococcus neoformans for mammals was proposed to emerge from evolutionary pressures on its natural environment by protozoan predators, which selected for strategies that allow survival within macrophages. In fact, Acanthamoeba castellanii ingests yeast cells, which then replicate intracellularly. In addition, most fungal factors needed to establish infection in the mammalian host are also important for survival within the amoeba. To better understand the origin of C. neoformans virulence, we compared the transcriptional profile of yeast cells internalized by amoebae and murine macrophages after 6 h of infection. Our results showed 656 and 293 genes whose expression changed at least two-fold in response to the intracellular environments of amoebae and macrophages, respectively. Among the genes common to both groups, we focused on the ORF CNAG_05662, which was potentially related to sugar transport. We constructed a mutant strain and evaluated its ability to grow on various carbon sources. The results showed that this gene, named PTP1 (Polyol Transporter Protein 1), is involved in the transport of 5- and 6-carbon polyols but its absence had no effect on virulence. Overall, our results are consistent with the hypothesis that mammalian virulence originated from fungal-protozoal interactions and provide a better understanding of how C. neoformans adapts to the mammalian host.

overall_design: Four conditions, pairwise-compared: cells in vegetative growth at 28C versus cells within amoebae at 28C; and cells in vegetative growth at 37C/5% CO2 versus cells within macrophages at 37C/5% CO2. Three biological replicates for each condition. One replicate per array.

first: Lorena

last: Derengowski

first: Hugo

last: Paes

first: Patrícia

last: Albuquerque

first: Aldo

last: Tavares

first: Larissa

last: Fernandes

first: Ildinete

last: Silva-Pereira

first: Arturo

last: Casadevall


title: Aneuploidy, oncogene amplification, and epithelial to mesenchymal transition define spontaneous transformation of murine epithelial cells [CGH]

first: Hesed

last: Padilla-Nash

summary:
Human epithelial cancers are defined by a recurrent distribution of specific chromosomal aneuploidies.  In our model system, mouse bladder and kidney epithelial cells spontaneously immortalize, transform and become tumorigenic after prolonged culture. We assessed genome and transcriptome alterations and found wide-spread aneuploidy, early transcriptional deregulation, and massive genomic dereguation of the cellular transcriptome.
The results reveal a remarkable similarity with genome and transcriptome aberrations detected in human tumorigenesis, hence validating our newly derived cancer models.

overall_design: Epithelial cells were isolated from the C57BL/6 mouse bladder and kidney.  These cells underwent spontaneous transformation in culture.  We sought to identify the molecuar genomic alterations that occur during the  transformation process and to compare these with the changes observed in human bladder and kidney cancers.

first: Nicole

last: McNeil

first: Ming

last: Yi

first: Quang-Tri

last: Nguyen

last: Hu


status: Public on Mar 12 2013

city: Berkeley

first: Adam

middle: P.

last: Arkin

address: 1 Cyclotron Road

department: Physical Biosciences Division

institute: Virtual Institute for Microbial Stress and Survival

summary: Using data from microarray experiments, we investigated the transcriptional changes in evolved and ancestor D. vulgaris strains.    gene expression changes in evolved salt-stressed DvH strain (ES, evolved in LS4D + 100 mM NaCl for 1200 generations), evolved control DvH strain (EC, evolved in LS4D for 1200 generations) and ancestor DvH strain grown in non-stress (LS4D), low salt stress (LS4D + 100 mM NaCl) or high salt stress (LS4D + 250 mM NaCl) conditions

sample_organism: Nitratidesulfovibrio vulgaris str. Hildenborough

overall_design: Comparison of gene expression in evolved salt-stressed strain (ES, 1200g) to ancestor (An) or evolved control (EC, 1200g) strains at mid-logarithmic phase under standard growth condition with defined medium LS4D, salt stress conditions LS4D+100 mM NaCl or LS4D+250 mM NaCl.


title: Comparison between HuT78 parental and romidpepsin-selected cell lines

last: Robey

address: 37 Convent Drive Rm 2112

summary:
Gene expression values were determined for HuT78 parental cells and cells selected with romidpesin in the presence of P-glycoprotein inhibitors. HuT78 DpVp35 cells are maintained in 35 ng/ml romidepsin with 2.5 µg/ml verapamil and HuT78 DpP100 cells are maintained in 100 ng/ml romidepsin with 1 µM valspodar
To identify molecular determinants of histone deacetylase inhibitor (HDI) resistance, we selected HuT78 cutaneous T-cell lymphoma (CTCL) cells with romidepsin in the presence of P-glycoprotein (Pgp) inhibitors to prevent transporter upregulation. Resistant sublines were 250- to 385-fold resistant to romidepsin and were resistant to apoptosis induced by apicidin, entinostat, panobinostat, belinostat and vorinostat. A custom Taqman array identified increased insulin receptor (INSR) gene expression; immunoblot analysis confirmed increased expression and a 4- to 8-fold increase in mitogen activated protein kinase (MAPK) kinase (MEK) phosphorylation in resistant cells compared to parental cells. Resistant cells were exquisitely sensitive to MEK inhibitors and apoptosis correlated with restoration of proapoptotic Bim. Romidepsin combined with MEK inhibitors yielded greater apoptosis in cells expressing mutant KRAS compared to romidepsin treatment alone. Gene expression analysis of samples obtained from patients with CTCL enrolled on the NCI1312 Phase II study of romidepsin in T-cell lymphoma suggested perturbation of the MAPK pathway by romidepsin. Immunohistochemical analysis of Bim expression demonstrated decreased expression in some skin biopsies at disease progression.  These findings implicate increased activation of MEK and decreased Bim expression as a resistance mechanism to HDIs, supporting combination of romidepsin with MEK inhibitors in clinical trials.

overall_design: Gene expression in resistant lines was compared to parental lines

first: Ribert

middle: W

first: Arup

last: Chakraborty

first: Victoria

last: Luchenko

first: Zhirong

last: Zhan

first: Richard

last: Piekarz

first: Jean-Pierre

last: Gillet

first: Andrew

middle: V

last: Kossenkov

first: Julia

last: Wilkerson

first: Louise

last: Showe

first: Nathan

last: Collie

last: Gottesman

first: Susan

last: Bates


title: Aneuploidy, oncogene amplification, and epithelial to mesenchymal transition define spontaneous transformation of murine epithelial cells [transcriptome]

last: Padilla-Nash

overall_design: Epithelial cells were isolated from the C57BL/6 mouse bladder and kidney.  These cells underwent spontaneous transformation in culture.  We sought to identify the molecuar genomic alterations that occur during the transformation process and to compare these with the changes observed in human bladder and kidney cancers.

last: McNeil

first: Yue

first: Danny

last: Wangsa

first: David

last: Mack

first: Amanda

last: Hummon

first: Chanelle

last: Case

first: Eric

last: Cardin

first: Robert

last: Stevens

first: Michael

last: Difilippantonio

first: Thomas

last: Ried


title: Gene expression profiles of Head & Neck Squamous and Lung Squamous Cancers

status: Public on Mar 10 2013

city: Redwood City

first: Anita

last: Lal

address: 595 Penobscot Dr

department: Product Development

institute: Pathwork Diagnostics

summary: The differential diagnosis between head & neck squamous cell carcinomas and lung squamous cell carcinomas is often unresolved because the histologic appearance of these two tumor types is similar. In the development of a gene expression profile test (GEP-HN-LS) that distinguishes these 2 cancer types, a collection of poorly differentiated primary and metastatic tumor specimens were used. Here we describe 76 such tumor specimens that were used for validation of GEP-HN-LS. The specimens are either head & neck squamous cell carcinomas or lung squamous cell carcinomas.

overall_design: All tissue specimens were formalin fixed paraffin embedded specimens. Gene expression was profiled using Affymetrix GeneChip platform.

first: Ljubomir

last: Buturovic


title: Lactobacillus rhamnosus LGG and LC705 effects on human primary macrophages

status: Public on Mar 18 2013

city: Helsinki

first: Matti

last: Kankainen

address: PL0056 (Viikinkaari 5)

department: Institute of Biotechnology

country: Finland

institute: University of Helsinki

summary:
Analysis of human primary macrophages after live Lactobacillus rhamnosus GG (LGG) or LC705 stimulation for 6h and 24h. The results reveal novel mechanisms for probiotics-induced activation of the healthy human innate immune system.
Macrophages are phagocytic cells of the innate immune system that perform sentinel functions to initiate appropriate responses to surrounding stimuli. Macrophages that reside at mucosa encounter ingested bacteria. Our understanding of the responses elicited by nonpathogenic bacteria in human innate immune system is limited.  Lactobacillus are nonpathogenic bacteria commonly used in food and as supplements with health-promoting probiotic potential. In this study, we have utilized global gene expression profiling to compare the responses of human primary macrophages to two closely related, well-characterized L. rhamnosus strains LGG and LC705. Our results demonstrate that live LGG and LC705 induced quantitatively different gene expression in macrophages. A gene ontology analysis revealed functional similarities and differences in responses to LGG and LC705. Both LGG and LC705 induced IL-1b production in macrophages that required caspase-1 activity. LC705 but not LGG induced a strong type I IFN-dependent gene activation that correlated with the ability of LC705 to prevent influenza A virus replication and production of viral proteins in macrophages.

overall_design: Differentiated 7d human primary macrophages from 18 healthy individuals were stimulated with either live L. rhamnosus GG (LGG) or LC705 for 6 h and 24 h in RPMI medium containing penicillin and streptomycin. As a control, macrophages were stimulated with the medium only. The experiment was performed three times, each time with cells from six different individuals (samples 1-3). For each experiment, macrophages were stimulated separately as described, and macrophages from different donors were pooled after each stimulation experiment.  Extracted RNA was hybridized to Affymetrix® U133-plus2.0 GeneChip® arrays.

first: Minja

last: Miettinen

first: Riina

last: Kekkonen

first: Riitta

last: Korpela

first: Ilkka

last: Julkunen


title: Genome variation profiling of Glioma Stem Cell lines

status: Public on Mar 08 2013

city: Monza

first: Simona

last: Baronchelli

address: Via Cadore 48

country: Italy

institute: University of Milan-Bicocca

summary: Glioblastoma multiforme (GBM), the most common and malignant type of glioma, is characterized by a poor prognosis and the lack of an effective treatment, which are due to a small sub-population of cells with stem-like properties, termed glioma stem cells (GSCs). The term “multiforme” describes the histological feature of this tumor, i.e. the cellular and morphological heterogeneity. At the molecular level multiple layers of alterations may reflect this heterogeneity providing together the driving force of tumor initiation and development. In order to decipher the common “signature” of the ancestral GSC population, we examined 5 already characterized GSC lines evaluating their copy number alterations using a genome-wide approach.

overall_design: Genomic DNA was isolated from 5 Glioma Stem Cell (GSC) lines. Each sample was labeled with Cy3 dye and then hybridized against the same commercial reference DNA labeled in Cy5.

first: Angela

last: Bentivegna

first: Serena

last: Redaelli

first: Gabriele

last: Riva

first: Valentina

last: Butta

first: Laura

last: Paoletta

first: Leda

last: Dalprà


title: Histone  H2B monoubiquitination facilitates the rapid modulation of gene expression during Arabidopsis photomorphogenesis

status: Public on Mar 13 2013

city: Paris

first: Fredy

last: BARNECHE

address: Rue d'Ulm

department: IBENS

institute: CNRS

summary:
In eukaryotes, chromatin-based mechanisms superimpose with DNA sequence information to determine the transcriptional output of the genome.  Therefore, evaluating the role of chromatin modifications in the regulation of gene expression is key to understand the contribution of chromatin state variations to development. Recent studies identified several transcriptional coactivators that contribute to selectively regulate cellular pathways by coordinating histone H2B monoubiquitination (H2Bub) with other histone modifications. Although H2Bub is present on a large number of genes, loss of H2B monoubiquitination activity was shown to affect RNA steady levels for a small subset of genes and therefore its influence on gene expression is not well understood. In this study we assessed the impact of H2Bub on dynamic expression changes during a rapid developmental tranistion that initiates only when exposing plants to light. This revealed that H2Bub deposition is highly dynamic in a genomic context. Furthermore, plants lacking histone H2B monoubiquitination activity were impaired for rapid changes of RNA levels for a large repertoire of genes, indicating that H2Bub is important for attaining appropriate expression levels /in fine/. Finally, the detection power of the genomic approach has allowed us to define a set of genes impacted by H2Bub dynamics for rapid changes in RNA levels.

The purpose of this study was to integrate the genome-wide distribution of H2Bub chromatin mark together with transcriptome profiles of wild-type and /hub1 /mutant plants (accession GSE21922) at three time points during early photomorphogenesis

overall_design:
H2Bub epigenome in 5-day-old dark-grown seedlings, H2Bub epigenome in 5-day-old dark-grown seedlings +1h light, and H2Bub epigenome in 5-day-old dark-grown seedlings +6h light
2 biological replicates for each time point in dye-swap - ChIP-chip

last: Barneche

first: Clara

last: Bourbousse


title: The gene vitellogenin affects microRNA regulation in honey bee (Apis mellifera) fat body and brain

status: Public on Mar 07 2013

city: São Carlos

first: Francis

middle: M. F.

last: Nunes

state: São Paulo

address: Rodovia Washington Luís, km 235, SP-310

department: Departamento de Genética e Evolução

country: Brazil

institute: Universidade Federal de São Carlos


title: Global Transcriptome Analysis of Spermatogenically Regressed, Recrudescent, and Active Testis of Seasonally Breeding Wall Lizards Hemidactylus flaviviridis

status: Public on Mar 01 2013

city: New Delhi

first: Subeer

last: Majumdar

state: Delhi

address: Aruna Asaf Ali Marg, JNU Complex

institute: National Institute of Immunology

summary: Reptiles are phylogenically important group of animals as mammals are evolved from them. Clearly distinct phases of reproductive cycle in wall lizard enable us to study mechanisms regulating spermatogenesis. We have performed microarray hybridizations on mouse whole genome 60K gene chip using RNA from regressed, recrudescent and active phase of reproductive cycle. Microarray data was analyzed considering regressed phase as control. To the best of our knowledge, this is the first report of transcriptome analysis of whole testis of wall lizard from various phases of reproductive cycle. Microarray results reveal that maximum number of differential gene expression is in between regressed and recrudescent phase than in between recrudescent and active phase. The genes prominently expressed in recrudescent and active phase testis are cytoskeleton organization, cell growth and division, osmo-regulation, differentiation and apoptosis. The genes showing higher expression in regressed phase belonged to functional categories such as negative regulation of growth, repression of transcription, maintenance of stem cell niche and muscle related proteins. Summarily, this is first exploratory study profiling transcriptome of three drastically different conditions of wall lizard testis. This study will pave the way for deeper insight into gene regulatory mechanisms in spermatogenesis and evolution of spermatogene processes.

overall_design: Agilent one-color experiment,Organism: Mouse ,Agilent-Custom Whole Genome Mouse 8x60k designed by Genotypic Technology Pvt. Ltd. (AMADID: 026986)  , Labeling kit: Agilent Quick-Amp labeling Kit (p/n5190-0442)

first: Mukesh

last: Gautam

first: Umesh

last: Rai


title: Apis mellifera brain Vg-miRNA data

summary: In honey bees, Vitellogenin (Vg) is hypothesized to be a major factor affecting hormone signaling, food-related behavior, immunity, stress resistance and lifespan. Likewise microRNAs play important roles in posttranscriptional gene regulation and affect many biological processes thereby showing many parallels to Vg functions. The molecular basis of Vg and microRNA interactions is largely unknown. Here, we exploited the well-established RNA interference (RNAi) protocol for Vg knockdown to investigate its effects on microRNA population in honey bee forager’s brain and fat body tissue. To identify microRNAs that are differentially expressed between tissues in control and knockdown foragers, we used µParaflo® microfluidic oligonucleotide microRNA microarrays. Our results show 76 and 74 miRNAs were expressed in the brain of control and knockdown foragers whereas 66 and 69 miRNAs were expressed in the fat body of control and knockdown foragers respectively. Target prediction identified potential seed matches for differentially expressed subset of microRNAs affected by Vg knockdown. These candidate genes are involved in a broad range of biological processes including insulin signaling, juvenile hormone (JH) and ecdysteroid signaling previously shown to affect foraging behavior. Thus, here we demonstrate a causal link between Vg expression-variation and variation in the abundance of microRNAs in different tissues with possible consequences for regulation of foraging behavior.

overall_design: We knocked down Vitellogenin (Vg) gene expression (using RNAi) in adult workers to identify potential downstream consequences on the expression of microRNA population in the brain compared to control group (dsRNA-GFP injected bees). Six biological samples of brain-derived small RNA fraction were prepared for each treatment group (dsRNA-Vg and dsRNA-GFP). Each biological sample contained pooled RNA from 5 unique individuals. Each brain pool contained a total of 1 µg of small RNA fraction, to which each of the 5 individuals contributed equally (200 ng). Pools were named as “control forager brain” (GFBr) and “knockdown forager brain” (VFBr), followed by a number from 1 to 6.

first: Kate

last: Ihle

first: Navdeep

last: Mutti

first: Zilá

last: Simões

first: Gro

last: Amdam


title: Apis mellifera fat body Vg-miRNA data

overall_design: We knocked down Vitellogenin (Vg) gene expression (using RNAi) in adult workers to identify potential downstream consequences on the expression of microRNA population in the fat body compared to control group (dsRNA-GFP injected bees). Six biological samples of fat body-derived small RNA fraction were prepared for each treatment group (dsRNA-Vg and dsRNA-GFP). Each biological sample contained pooled RNA from 5 unique individuals. Each fat body pool contained a total of 2 µg of small RNA fraction, to which each of the 5 individuals contributed equally (400 ng). Pools were named as “control forager fat body” (GFFb) and “knockdown forager fat body” (VFFb), followed by a number from 1 to 6.


title: Real-time quantitative PCR analysis of murine bone marrow cells

status: Public on Mar 02 2013

city: Rome

first: fiorella

last: ciaffoni

state: Italy

address: Viale Regina Elena 299

department: Cellular Biology and Neurosciences

institute: Istituto Superiore di Sanità

summary: TGF-β1 signaling pathway of bone marrow of the Gata1low mouse model of myelofibrosis

overall_design: Four condition experiment. Biological replicates: 3 control CD1 mice, 3 Gata1low mice, 3 SB431542-treated  Gata1low mice and 3 Vehicle-treated Gata1low mice.

first: Maria

last: Zingariello

first: Fabrizio

last: Martelli

first: Fiorella

last: Ciaffoni

first: Francesca

last: Masiello

first: Barbara

last: Ghinassi

first: Emanuela

last: D'Amore

first: Margherita

last: Massa

last: Sancillo

first: Xiaochun

last: Li

first: Judith

middle: D

last: Goldberg

first: Rosa

last: Rana

first: Anna

last: Migliaccio


title: Real-time quantitative PCR analysis of spleen cells

summary: TGF-β1 signaling pathway of spleen of the Gata1low mouse model of myelofibrosis

first: Laura


title: DNA profiling of human normal colon tissues

status: Public on Feb 14 2013

city: Seodaemun-gu

first: Park

last: Chan Hee

state: Seoul

address: Shinchondong 134

institute: Cancer Metastasis Research Center

summary: To study the field cancerization effect, we screened systemic metastasis-related CNVs from morphologically normal colon tissues adjacent to colon cancer that had systemic metastasis. 89 systemic metastasis-related CNVs, mainly consisting of migration and invasion-, morphology-, cell death and survival-related pathways, were selected. Noticeably, LIM and senescent cell antigen-like domains 2 (LIMS 2, PINCH2) showed copy number amplification and up-regulation of mRNA expression in the non-relapsed group compared to the systemic relapse group. Colon cancer cells had lower expression of PINCH2 protein and mRNA compared with normal epithelial colon cells.

overall_design: Two-condition experiment: 41 colon normal tissue vs. control gDNA.

first: Chan

middle: H

last: Park

first: Hyun

last: Chung


title: Quantitative analysis of miRNA changes in bone marrow stem cells under neural differentiation

status: Public on Jan 19 2013

city: Lodz

first: Mariola

last: Matysiak

address: Kopcinskiego 22

department: Neurology

country: Poland

institute: Medical University of Lodz

summary: Normal SJL mice, 6 to 8 weeks old, were used for the isolation of bone marrow stem cells (BMSC). Bone marrow cells were obtained from the femurs and tibias of euthanized mice by flushing with PBS. Cells were subjected to negative magnetic sorting using the Lineage Cell Depletion Kit. Isolation of murine bone marrow Lin-Sca-1+ cells was performed using MACS Sca-1 MultiSort Kit (fBMSC).  The differentiation of neural stem cells was induced by removing the bFGF-containing medium and resuspending cells in fresh bFGF-free medium. Microarray analysis of miRNA expression profiles was performed comparing non differentiated bone marrow stem cells (fBMSC) to bone marrow stem cells differentiated for 4 or 7 days.

overall_design: The data are from adult mouse stem cells isolated from bone marrow

first: M

last: Fortak-Michalska

first: W

last: Orlowski

first: K

last: Selmaj


title: Transcriptional analysis of development and detoxification in Culex pipiens quinquefasciatus

status: Public on Dec 30 2012

city: Beijing

first: Pengcheng

last: Yang

address: Datun Road

institute: Institute of Zology, Chinese Academy of Sciences

type: Expression profiling by high throughput sequencing

summary:
The genomes of three major mosquito vectors of human diseases, including Anopheles gambiae, Aedes aegypti, and Culex pipiens quinquefasciatus, have been previously sequenced. C. p. quinquefasciatus has the largest number of predicted protein-coding genes, which partially results from the expansion of three detoxification gene families: cytochrome P450 monooxygenases (P450), glutathione S-transferases (GST), and carboxylcholinesterases (CCE). However, unlike A. gambiae and A. aegypti, which have large amounts of gene expression data, C. p. quinquefasciatus has limited transcriptomic resources. Knowledge of complete gene expression information is very important for the exploration of the functions of genes involved in specific biological processes. In the present study, the three detoxification gene families of C. p. quinquefasciatus were analyzed for phylogenetic classification and compared with those of three other dipteran insects. Gene expression during various developmental stages and the differential expression responsible for parathion resistance were profiled using the digital gene expression (DGE) technique.  Results: A total of 291 detoxification genes were found in C. p. quinquefasciatus, including 70 CCE, 186 P450, and 35 GST genes. Compared with three other dipteran species, gene expansion in Culex mainly occurred in the CCE and P450 families, where the genes of α-esterases, juvenile hormone esterases, and CYP325 of the CYP4 subfamily showed the most pronounced expansion on the genome. A total of 13314 genes were expressed in five DGE libraries. Genes with signal transduction and odorant binding functions were prominently expressed during egg development. Genes involved in proteolysis, glycosphingolipid biosynthesis, and purine metabolism were preferentially expressed at the larval stage. Seventy five percent of the detoxification genes were found to be expressed. One fourth of the CCE and P450 genes were expressed at unique stages, indicating their developmentally regulated expression. Fifteen detoxification genes, including 2 CCEs, 6 GSTs, and 7 P450s, were expressed at higher levels in a parathion-resistant strain than in a susceptible strain.  Conclusion: The results of the present study provide new insights into the functions and evolution of three detoxification gene families in mosquitoes and comprehensive transcriptomic resources for C. p. quinquefasciatus, which will facilitate the elucidation of molecular mechanisms underlying the different biological characteristics of the three major mosquito vectors.

Raw data were deposited in SRA and assigned accession number SRA049959:
http://www.ncbi.nlm.nih.gov/sra?term=SRA049959

overall_design: Five DGE libraries were sequenced: the egg, third instar larval, pupal, and adult stages of the SG strain, and the third instar larval stage of the S-lab strain.

first: Liangzhen

last: Yan

first: Feng

last: Jiang

last: Cui

first: Enbo

last: Ma

first: Chuanling

last: Qiao


title: Identification of miRNAs from Eugenia uniflora by high-throughput sequencing and bioinformatics analysis [small RNA-seq]

status: Public on Jan 07 2013

city: Porto Alegre

first: Rogerio

last: Margis

state: RS

address: Av. Bento Goncalves 9500

department: Centro de Biotecnologia

institute: Universidade Federal do Rio Grande do Sul

summary: miRNAs are small non-coding regulatory RNAs that play important functions in the regulation of gene expression at the post-transcriptional level by targeting mRNAs for degradation or by inhibiting protein translation. Eugenia uniflora is a plant native to tropical America with pharmacological and ecological importance without previous studies about its gene expression and regulation. To date, there is not miRNAs reported in species of Myrtaceae. A small RNA library was constructed to identify miRNAs in Eugenia uniflora. Solexa technology was used to perform high throughput sequencing of the library and the data obtained was analysed using bioinformatics tools. From 14,489,131 clean reads, we obtained 1,852,722 small RNAs representing 45 known miRNA families that have been identified in other plant species. Further analysis using contigs assembled from Illumina mRNA sequencing of leaves from the same individual allowed the prediction of secondary structures of 25 known and 17 novel miRNAs. Potential targets were predicted for the most abundant mature miRNAs in the identified pre-miRNAs based on sequence homology. This study provide the first large scale identification of miRNAs and their potential targets of a species from Myrtaceae without previous genomic sequence resources. Our study provides more information about the evolutionary conservation of the regulatory network of miRNAs in plants and highlights the miRNAs species-specific.

overall_design: microRNA profiles in 1 leaf library of Eugenia uniflora by deep sequencing (Illumina HiSeq2000)

first: Frank

last: Guzman

first: Ana

last: Körbes

first: Rogério


title: Isolation of two new Dehalococcoides mccartyi strains with dissimilar dechlorination functions and their characterization by comparative genomics via microarray analysis

first: Patrick

last: Lee

state: CA

address: 209 O'Brien Hall

department: Civil and Environmental Engineering

institute: University of California, Berkeley

summary: Microbial reductive dechlorination of trichloroethene (TCE) in groundwater often results in the accumulation of dichloroethenes (DCEs). Dehalococcoides mccartyi (Dhc) are the only known bacteria capable of dechlorination beyond DCE to non-toxic ethene. In this study, two newly isolated Dhc strains (11a and 11a5) with dissimilar functional abilities are described. Strain 11a reductively dechlorinates TCE, 1,1-DCE, cis-DCE, trans-DCE, and vinyl chloride (VC) to ethene, while strain 11a5 dechlorinates TCE and all three DCE isomers only to VC. Each of these dechlorination reactions are coupled to growth by these strains. The VC dechlorination rate of strain 11a occurs at a rate of 258 nmol per min per mg of protein, about two times faster than previously reported stains. Strain 11a possesses the vcrA gene while strain 11a5 contains the tceA gene. Strains 11a and 11a5 share 100% 16S rRNA gene sequence identity with previously sequenced Dhc strains BAV1 and CBDB1, placing it within the Pinellas subgroup, and 85.4% and 89.5% of all genes present in the CBDB1 and BAV1 genomes were detected in strains 11a and 11a5, respectively, using a custom-designed microarray targeting four sequenced Dhc strains. Genes that were not detected in strains 11a and 11a5 are mostly within the high plasticity regions or integrated elements of the sequenced strains. This study reports the functional description and comparative genomics of two additional Dhc isolates and provides evidence that the observed functional incongruence between the activity and core genome phylogenies of Dhc strains is likely driven by the horizontal transfer of key reductive dehalogenase-encoding genes.

platform_organism:
Dehalococcoides mccartyi BAV1
Dehalococcoides mccartyi 195
Dehalococcoides mccartyi CBDB1
Dehalococcoides mccartyi VS

overall_design: The genomic DNA (gDNA) of each culture was analyzed in triplicate. gDNA from the two newly isolated Dehalococcoides strains 11a and 11a5 were analyzed.

first: Dan

last: Cheng

first: Kimberlee

last: West

first: Lisa

last: Alvarez-Cohen

first: Jianzhong

last: He


title: Pathogen recognition and activation of the innate immune response in zebrafish: MyD88 mutants

status: Public on Dec 10 2012

city: Leiden

first: Michiel

last: van der Vaart

address: Einsteinweg 55

department: IBL

country: Netherlands

institute: University of Leiden

summary: MyD88 is an adaptor protein in Toll-like receptor and interleukin 1 receptor mediated signaling pathways that plays an essential role in activation of immune responses following pathogen recognition. We investigate that role in the zebrafish embryo model by using a zebrafish mutant line that contains a premature stop condon in the gene encoding MyD88, leading to a truncated protein that lacks domains important for its normal function. We infected these MyD88 mutants and wildtype individuals with Salmonella typhimurium and Edwardsiella tarda to compare the resulting immune response by transcriptome profiling on total RNA isolated from single embryos. The data derived from these microarray experiments confirms the vital role of MyD88 in pathogen recognition and provides many leads for further research.

overall_design: This microarray study was designed to determine the effect of a truncation of the MyD88 protein on the innate immune response of zebrafish embryos during infection with Salmonella typhimurium and Edwardsiella tarda. Embryos used in this study are derived from an incross between parents heterozygous for the mutation. Both homozygous mutants and their wildtype siblings were selected by genotyping after being injected with the bacteria or PBS as control. RNA was isolated from single embryos and each treatment group consisted of three embryos: (1) Homozygous mutants injected with PBS 8 hours post infection (hpi), (2) wildtype siblings injected with PBS 8hpi, (3) S. typhimurium-infected homozygous mutants 8hpi, (4) S. typhimurium-infected wildtype siblings 8hpi, (5) Homozygous mutants injected with PBS 8 hours post infection (hpi) (E.tarda control), (6) wildtype siblings injected with PBS 8hpi (E. tarda control), (7) E. tarda-infected homozygous mutants 8hpi, (8) E. tarda-infected wildtype siblings 8hpi. Embryos were grown at 28.5–30°C in egg water and manually dechorionated at 24 hours post fertilization (hpf). Subsequently, embryos were infected at 28 hpf by micro-injecting 200 colony forming units (CFU) of S. typhimurium SL1027 or E. Tarda FL-F60, or were mock-injected with buffer as a control.  After injections embryos were transferred into fresh egg water and incubated for 8 h or 4 days at 28°C. After the incubation period, single embryos were snap-frozen in liquid nitrogen and RNA was isolated for microarray analysis. All treatment groups were analyzed using a common reference approach.

first: M

first: J

middle: J

last: van Soest

first: H

middle: P

last: Spaink

first: A

last: Meijer


title: The Sp100 component of ND10/PML bodies is a potent tumor suppressor

status: Public on Dec 04 2012

city: Philadelphia

first: Louise

last: Showe

state: PA

address: 3601 Spruce St

country: USA

institute: The Wistar Institute

summary: Identifying the functions of proteins, which define specific subnuclear structures and territories, is important for understanding eukaryotic nuclear dynamics. Sp100 is a prototypical protein of ND10/PML bodies and co-localizes with the proto-oncogenic protein PML and Daxx, proteins with critical roles in oncogenic transformation, interferon-mediated viral resistance and response to PML-directed cancer therapeutics. Sp100 isoforms contain PHD, Bromo and HMG domains and are highly sumoylated at ND10/PML bodies, all characteristics suggestive of a role in chromatin mediated gene regulation. However, no clear role for the Sp100 component of PML bodies in oncogenesis has been defined. Using isoform-specific knockdown techniques, we show that most human diploid fibroblasts, which lack Sp100, rapidly senesce and discuss gene expression changes associated with this rapid senescence.

overall_design: microarray analysis of mRNAs expression in BJV (collected at passage 47) and BJ-S (collected at passage 35). In addition, samples were treated for 24 h with 1000 U/ml IFNB. All RNAs were collected in triplicates of biological samples.

first: Dmitri

middle: G

last: Negorev

first: Olga

last: Vladimirova

first: Andrew

last: Kossenkov

first: Elena

last: Nikonova

first: Renee

last: Demarest

first: Anthony

last: Capobianco

last: Rauscher III


title: Streptococcus mutans growth-phase effects: wild-type(WT) vs. lytS-deficient mutant (lytS)

status: Public on Dec 01 2012

city: Gainesville

first: Sang-Joon

last: Ahn

address: 1395 Center Dr.

department: Department of Oral Biology

institute: University of Florida

summary: Transcriptional profiling of S. mutans cells comparing WT cells with lytS cells at early- and late-exponential growth phase.

overall_design: Four-condition experiment, WT vs. lytS cells and optical density (600nm) 0.2 vs. 0.9. Biological replicates: 4 wild-type, 4 lytS mutant, independently grown and harvested. One replicate per array.

first: Robert

last: Burne


title: Dynamic transcriptional response of Microcoleus vaginatus to hydration and dehydration in a desert biological soil crust

status: Public on Oct 30 2012

first: Lara

last: Rajeev

address: 1 Cyclotron Road

institute: Lawrence Berkeley Lab

summary:
Biological soil crusts (BSCs) are cyanobacteria-dominated microbial communities that cover extensive portions of the world’s arid and semi-arid deserts. The infrequent periods of hydration are often too short to allow for dormancy strategies based on sporulation; consequently, survival is based on the unique capabilities of vegetative cells to resuscitate from and re-enter a stress resistant dormant state, one of which is migration within the crust layers in response to hydration. In this study, we sought to characterize the events that govern the emergence of the dominant cyanobacterium from dormancy, its subsequent growth, and the events triggered by re-desiccation and a transition back to dormant state.
We performed a 48 hour laboratory wetting experiment of a desert BSC and tracked the response of Microcoleus vaginatus using a whole genome transcriptional time-course including night/day periods. This allowed the identification of genes with a diel expression pattern, genes involved uniquely in the signaling after hydration and those that contribute primarily to desiccation preparation.

platform_organism:
Microcoleus vaginatus PCC 9802
Microcoleus vaginatus FGP-2

overall_design: Desert BSC samples collected from Moab, UT, were hydrated over a period of 48 hours followed by drying induced by removal of water. At periodic times soil samples were harvested and used for RNA extraction and whole genome expression analysis using an expression array representing genes from two strains of M. vaginatus (PCC 9802 and FGP-2)

first: Niels

last: Klitgord

first: Ulisses

last: Nunes da Rocha

first: Eric

last: Luning

first: Seth

last: Axen

first: Ben

last: Bowen

first: Cheryl

last: Kerfield

first: Eoin

middle: L

last: Brodie

first: Trent

last: Northen

first: Ferran

last: Garcia-Pichel

first: Aindrila

last: Mukhopadhyay


title: The Methylomes of Six Bacteria

status: Public on Oct 04 2012

city: Menlo Park

first: Tyson

last: Clark

address: 1380 Willow Rd.

institute: Pacific Biosciences

type: Methylation profiling by high throughput sequencing

summary: Six bacterial genomes, Geobacter metallireducens GS-15, Chromohalobacter salexigens, Vibrio breoganii 1C-10, Bacillus cereus ATCC 10987, Campylobacter jejuni subsp. jejuni 81-176 and Campylobacter jejuni NCTC 11168, all of which had previously been sequenced using other platforms were re-sequenced using single-molecule, real-time (SMRT) sequencing specifically to analyze their methylomes.   In every case a number of new N6-methyladenine (m6A) and N4-methylcytosine (m4C) methylation patterns were discovered and the DNA methyltransferases (MTases) responsible for those methylation patterns were assigned.   In 15 cases it was possible to match MTase genes with MTase recognition sequences without further sub-cloning.  Two Type I restriction systems required sub-cloning to differentiate their recognition sequences, while four MTases genes that were not expressed in the native organism were sub-cloned to test for viability and recognition sequences.  No attempt was made to detect 5-methylcytosine (m5C) recognition motifs from the SMRT sequencing data because this modification produces weaker signals using current methods.   However, all predicted m6A and m4C MTases were detected unambiguously.   This study shows that the addition of SMRT sequencing to traditional sequencing approaches gives a wealth of useful functional information about a genome showing not only which MTase genes are active, but also revealing their recognition sequences.

sample_organism:
Campylobacter jejuni
Bacillus cereus
Geobacter metallireducens
Chromohalobacter israelensis
Vibrio breoganii

overall_design: Examination of the methylomes of six different strains of bacteria using kinetic data from single-molecule, real-time (SMRT) sequencing on the PacBio RS.

first: Iain

last: Murray

first: Richard

last: Morgan

first: Matthew

last: Boitano

first: Brian

last: Anton

first: Khai

last: Luong

first: Alexey

last: Fomenkov

first: Stephen

last: Turner

first: Jonas

last: Korlach

last: Roberts


title: Direct measurement of heritable gene expression within single individuals from wild populations.

status: Public on Nov 30 2012

city: Quebec

first: Jukka-Pekka

last: Verta

state: QC

address: 1030 Avenue de la Medecine, Pavillon Charles-Eugene-Marchand, bureau 2225

department: Department of Wood and Forest Sciences

country: Canada

institute: Centre for Forest Research

summary: Heritable variation in gene expression has been largely studied in model organisms by taking advantage of pure and inbred lines. Comparative studies on organisms with contrasting evolutionary history, population size and genome architecture have been hindered by practical considerations, as many of these species are poorly suited for breeding. We have developed a method for determining expression variation in an undomesticated tree species by directly measuring the segregation of gene expression in the haploid meiotic products of a single diploid individual. We show the utility of our approach by identifying expression variation that segregates consistent with one causal variant and identify an unexpectedly large number of these Mendelian expression traits. The megagametophyte approach opens the doors for the application of genetical genomics approaches in a large number of undomesticated plant species.

platform_organism:
Picea glauca
Picea sitchensis

overall_design: Transcriptomics data from 18 megagametophytes of two unrelated mother trees. In tree 80112, all of the 18 megagametophytes were analyzed on to different microarrays with two different dyes. In tree 77111, 16 megagametophytes were replicated as above.

first: Sebastian

last: Caron

first: Isabelle

last: Giguère

first: John

last: MacKay


title: Drosophila melanogaster 2-6hr embryo

status: Public on Aug 10 2012

city: Toronto

first: DCC

last: modENCODE

state: Ontario

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

institute: Ontario Institute for Cancer Research

summary:
modENCODE_submission_752
This submission comes from a modENCODE project of Eric Lai. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We plan to generate a comprehensive catalog of expressed and functional microRNAs, and generate biological evidence for their regulatory activity. We plan also to delineate the primary transcription units of microRNA genes. Finally, we plan to annotate other classes of non-miRNA expressed small RNAs, as least some of which may define novel classes of small RNA genes.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: RNA-seq. BIOLOGICAL SOURCE: Strain: Canton-S; Tissue: embryo; Replicate type: biological; Developmental Stage: embryonic 2-6hr; Sex: NA;  EXPERIMENTAL FACTORS: Strain: Canton-S

first: Eric

last: Lai


title: Drosophila melanogaster 1st Instar Larvae

summary:
modENCODE_submission_762
This submission comes from a modENCODE project of Eric Lai. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We plan to generate a comprehensive catalog of expressed and functional microRNAs, and generate biological evidence for their regulatory activity. We plan also to delineate the primary transcription units of microRNA genes. Finally, we plan to annotate other classes of non-miRNA expressed small RNAs, as least some of which may define novel classes of small RNA genes.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: RNA-seq. BIOLOGICAL SOURCE: Strain: Canton-S; Tissue: L1 larvae; Replicate type: biological; Developmental Stage: 1st Instar Larvae; Sex: NA;  EXPERIMENTAL FACTORS: Strain: Canton-S


title: Genome-wide identification of microRNAs in larch and stage-specific modulation of eleven conserved microRNAs and their targets during somatic embryogenesi

status: Public on Sep 04 2012

first: Liwang

last: Qi

address: Xiang shan Road

department: The Research Institute of Forestry

institute: The Chinese Academy of Forestry

summary: MicroRNAs (miRNAs) are emerging as essential regulators of biological processes. Somatic embryogenesis is one of the most important techniques for gymnosperm breeding programs, but there is little understanding of its underlying mechanism. To investigate the roles of miRNAs during somatic embryogenesis in larch, we constructed a small RNA library from somatic embryos. High-throughput sequencing of the library identified 83 conserved miRNAs from 35 families, 16 novel miRNAs, and 14 plausible miRNA candidates, with a high proportion specific to larch or gymnosperms. qRT-PCR analysis demonstrated that both the conserved and novel or candidate miRNAs were expressed in larch. Several miRNA precursor sequences were obtained via RACE. We predicted 110 target genes using bioinformatics, and validated nine of them by 5’ RACE. Eleven conserved miRNA families including 17 miRNAs with critical functions in plant development and six target mRNAs were detected by qRT-PCR in the larch SE. Stage-specific expression of miRNAs and their targets indicate their possible modulation on SE of larch: miR171a/b might exert function on PEMs, while miR171c acts in the induction process of larch SE; miR397 and miR398 mainly involved in modulation of PEM propagation and transition to single embryo; miR162 and miR168 exert their regulatory function during total SE process, especially during stage 5 to stage 8; miR156, miR159, miR160, miR166, miR167, and miR390 might play regulatory roles during cytoledonary embryo development. These findings indicate that larch and possibly other gymnosperms have complex mechanisms of gene regulation involving specific and common miRNAs operating post-transcriptionally during embryogenesis.

overall_design: Examination of small RNA expression profilings in Larix somatic embryos over seven developmental stages: 1) after 2 and 15 days on sub-culture; 2) 2, 6, and 11 days post-differentiation culture; and 3) somatic embryos at days 33 and 39.

first: Junhong

last: Zhang

first: Shougong


title: Genotoxic alterations of cord blood cells in newborns exposed in utero to a zidovudine-based antiretroviral combination

status: Public on May 03 2012

city: Modena

first: Fabienne

last: Cocchiarella

address: Via G. Gottardi

department: Scienze Biomediche

institute: università di Modena e Reggio Emilia

summary:
Background: Zidovudine remains the cornerstone drug for prophylaxis to prevent mother-to-child HIV-1 transmission. A mild but long-lasting hematological multilineage defect is observed in children exposed in utero.
Objectives: To evaluate the effects of zidovudine-based ARV combinations on newborn cord blood cells.
Methods: Cord blood-derived mononuclear cells from 22 HIV-1-uninfected newborn exposed in utero to a zidovudine-based ARV combination and from 20 healthy unexposed newborn were investigated by immunophenotyping, gene expression analysis, cytogenetic studies and functional capacity testing.

last: Andre-Schmutz

first: Stéphane

last: Blanche


title: Hypothalamic DNA methylation changes during mouse suckling period

status: Public on May 01 2012

city: Houston

first: Robert

last: Waterland

state: TX

address: 1100 Bates St.,

institute: Baylor College of Medicine

type: Methylation profiling by genome tiling array

summary: Investigate the genome-wide DNA methylation changes in the mouse hypothalamus during the suckling period.

overall_design: Hypothalami were collected from new born (P0) mice, or mice of 21 day-old (P21). Two-color experiment was performed as paired comparison of P21 vs. P0 with two biological replicates. Genome-wide DNA methylation changes from P0 to P21 were detected by MSAM. As a brief description of the MSAM: 500ng of genomic DNA was serially digested with SmaI and XmaI followed by an adaptor ligation and adaptor mediated PCR amplification and then cohybridization.

first: Wenjuan