title: Pseudomonas pseudoalcaligenes CECT5344 response to cyanide vs. ammonium or nitrogen starvation

status: Public on Jan 27 2016

city: Córdoba

first: Victor M.

last: Luque

address: Edificio Severo Ochoa 1ª planta, Campus de Rabanales

department: Departamento de Bioquímica y Biología Molecular

country: Spain

institute: Universidad de Córdoba

summary: Transcriptional analysis of the cyanotroph Pseudomonas pseudoalcaligenes CECT5344 in response to cyanide present in wastewaters from industrial activities, such as jewelry and electroplating activities

overall_design: Four-conditions experiment, including three different nitrogen sources (ammonium, sodium cyanide or a cyanide-containing wastewater). One experiment without nitrogen added to the media (nitrogen limited condition). Four biological replicates for each condition (added nitrogen source to the media) plus the experiment without nitrogen source added.

first: Víctor

middle: M

last: Luque-Almagro

first: María

last: de la Paz Escribano

first: Isabel

last: Manso

first: Lara

middle: P

last: Sáez

first: Purificación

last: Cabello

first: Conrado

last: Moreno-Vivián

middle: D

last: Roldán


title: Disease-specific modules and potential hub genes for intervention strategies: A co-expression network-based approach for Plasmodium falciparum clinical isolates

status: Public on Jan 30 2016

city: Pilani

first: Ashis

middle: Kumar

last: Das

state: Rajasthan

address: Vidya Vihar

department: Biological Sciences

country: India

institute: Birla Institute of Technology & Science,Pilani (Pilani Campus)

summary: Systems biology approaches that are based on gene expression and bioinformatics analysis have been successful in predicting the functions of many genes in Plasmodium falciparum, a protozoan parasite responsible for most of the deaths due to malaria. However, methods that can provide information about the biological processes that are active in this parasite during complicated malaria conditions have not been employed yet. Here, we report the use of a weighted gene co-expression-based network analysis approach to construct a P. falciparum in vivo systems network. Gene expression profiles of 21 P. falciparum clinical isolates were utilized to construct the same. A total of 20 highly interacting modules were identified post network creation, of which at least 10% members of 12 modules were found to be differentially regulated in complicated isolates compared to uncomplicated isolates. Enrichment analysis identified biological processes like oxidation-reduction, electron transport chain, protein synthesis, ubiquitin-dependent catabolic processes, RNA binding and purine nucleotide metabolic processes to be associated with these modules. Additionally, for each module, highly connected hub genes were identified. Detailed functional analysis of many hub genes with known annotated function underline their importance in parasite development and survival, suggesting that other hub genes with unknown function might be playing crucial roles in parasite biology and are potential candidate for intervention strategies.

overall_design: Plasmodium falciparum isolates were collected from patients (n=21) with differing clinical conditions. The patients exhibited symptoms categorized as uncomplicated (n=5) or complicated malaria (n=16). Criteria for determination of complicated disease were based on World Health Organization year 2000 guidelines. Microarray-based transcriptional profiling was carried out to evaluate the performance of the array.measure expression of genes in each sample.

first: Amit

middle: K

last: Subudhi

first: P

middle: A

last: Boopathi

first: Dhanpat

last: Kochar

first: Sanjay


title: Phenotypic and genomic analysis of multiple myeloma minimal residual disease clonal plasma cells: a new model to understand chemoresistance [CytoScan750K Copy Number, LOH]

status: Public on Jan 28 2016

city: Pamplona

first: Bruno

last: Paiva

address: Av. Pio XII, 55

institute: Clinica Universidad de Navarra

summary: Persistence of chemoresistant minimal residual disease (MRD) plasma cells (PCs) relates to inferior survival in multiple myeloma (MM). MRD PCs are therefore a minor clone able to recapitulate the initial tumor burden at relapse and accordingly, its characterization may represent a unique model to understand chemoresistance; unfortunately, the MRD clone has never been biologically investigated. Here, we compared the antigenic profile of MRD vs. diagnostic clonal PCs in 40 elderly MM patients enrolled in the GEM2010MAS65 study, and showed that the MRD clone is enriched by cells over-expressing integrins (CD11a/CD11c/CD29/CD49d/CD49e), chemokine receptors (CXCR4) and adhesion molecules (CD44/CD54). Genetic profiling of MRD vs. diagnostic PCs showed identical copy number alterations (CNAs) in 3/8 cases, 2 patients with linear acquisition of additional CNAs in MRD clonal PCs, and 3 cases with variable acquisition and loss of CNAs over time. The MRD clone showed significant downregulation of genes particularly related to protein processing in endoplasmic reticulum, as well as novel deregulated genes such as ALCAM that is prognostically relevant in MM and identifies chemoresistant PCs in vitro. Together, we show that therapy-induced clonal selection is already present at the MRD stage, in which chemoresistant PCs show a specific phenotypic signature that may result from the persistence of clones with different genetic and gene expression profiles.

overall_design: Per-protocol, clonal PCs from diagnostic samples were isolated from BM aspirates using CD138+ immunomagnetic beads (Miltenyi Biotech, Bisley, UK). Following induction therapy, BM aspirates were taken to determine patients’ MRD response at cycle 9, and clonal PCs from MRD-positive cases were FACS-sorted (FACSAria II, BDB; purity ≥97%) according to patient-specific aberrant phenotypes. DNA from matched diagnostic and MRD clonal PCs was available in 8 patients. Afterwards, genome-wide detection of copy-number abnormalities (CNAs) and loss of heterozygosity (LOH) were investigated using the standard Affymetrix Cytoscan 750K platform (Affymetrix, Santa Clara, CA, USA). An unpaired analysis was performed using 240 Hapmap files as reference for normal DNA. The complete data set was analyzed by visual inspection using the AGCC and ChAS software programs (Affymetrix). CNAs were reported when the three following criteria were met: ≥25 consecutive imbalanced markers per segment; ≥100Kb minimum genomic size and; <50% overlap with paired control DNA and/or genomic variants of Toronto DB (DGV). Only copy number-neutral LOH (CNN-LOH) larger that 5Mb were considered.

first: Luis

last: Corchete

first: Norma

middle: C

last: Gutierrez

first: Maria-Belen

last: Vidriales

first: Patricia

last: Maiso

first: Idoia

last: Rodriguez

first: Diego

last: Alignani

first: Maria

middle: L

last: Sanchez

first: Paloma

last: Barcena

first: Maria-Asuncion

last: Echeveste

first: Miguel

middle: T

last: Hernandez

first: Ramón

last: García-Sanz

first: Enrique

last: Ocio

first: Albert

last: Oriol

first: Mercedes

last: Gironella

last: Palomera

first: Felipe

last: De Arriba

first: Yolanda

last: Gonzalez

first: Juan-Jose

last: Lahuerta

first: Joan

last: Blade

first: Alberto

last: Orfao

first: Joshua

last: Epstein

first: Bart

last: Barlogie

first: María-Victoria

last: Mateos

first: Jesús

middle: F

last: San Miguel


title: Transcriptome analysis for cellobise-adpative C. glutamicum strains

status: Public on Jan 24 2016

city: Seoul

first: Han

middle: Min

last: Woo

address: Hwarangno 14-gil 5, Seongbuk-gu

department: Clean Energy Research Center

country: South Korea

institute: Korea Institute of Science and Technology

summary: To understrand the altered gene expressions of cellobiose-positive C. glutamicum over cellobiose-negative C. glutamicum

overall_design: Total 7 samples were used to understand the altered gene expressions for C. glutamicum strains grown either on cellobisoe or glucose

first: Jungseok

last: Lee

first: Youngsoon

last: Um


title: Expression analysis of Plasmodium falciparum male and female gametocytes

city: Tampa

first: JUN

last: MIAO

state: Florida

address: 3720 Spectrum Boulevard, MDC84

department: Internal Medicine

country: USA

institute: University of South Florida

summary:
Investigation of whole genome gene expression level in Plasmodium falciparum male and female mature gametocytes, and detection of any transcriptional differences between male and female gametocytes.
The Plasmodium falciparum parasite with green fluorescent protein (GFP) expression under the control of alpha tubulin II promoter facilitated the separation of male and female gametocyte. This engineered parasite strain in this study are further described in Miao J,  Fan Q,  Parker D,  Li X,  Li J,  et al.  (2013) Puf Mediates Translation Repression of Transmission-Blocking Vaccine Candidates in Malaria Parasites. PLoS Pathog 9(4): e1003268.  doi: 10.1371/journal.ppat.1003268

overall_design: A 4 chip study using total RNA recovered from 2 sorted stage V male gametocyte  (3 X 10^ 6) and 2 sorted stage V female gametocyte ( (3 X 10^ 6).  The chip used in this stury was a custom designed microarray by agilent eArray (array name: MALARIAARRAY_JM, Design ID: 048532, Design format: 4 X 44K, Control grid: IS-45220-4-V1_4x44K_GX_EQC_V20060608 )

first: Jun

last: Miao

first: Liwang

last: Cui


title: Expression data from the isolated mouse colonic epithelial cells during colon inflammation induced by DSS

status: Public on Jan 23 2016

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: We used microarray to examine microRNA expression in the mouse colonic epithelial cells changed after DSS treatment

overall_design: Two-condition experiment; the mouse colonic epithelial cells control vs the mouse colonic epithelial cells during colon inflammation induced by DSS

first: Takeshi

last: Yoshikawa

first: Motoyuki

last: Otsuka


title: NOMO-1: A NOVEL GENE ALTERED IN COLORECTAL CANCER, MOSTLY WITHIN THE EARLY-ONSET SUBSET

city: salamanca

first: Juan

middle: Luis

last: Garcia

address: Campus Miguel de Unamuno

institute: Center Cancer Research

type: Genome variation profiling by genome tiling array

summary: aCGH Nimblegen array performed on 146 samples of CRC

first: José

last: Perea

last: García

first: Jessica

last: Pérez

first: Daniel

last: Rueda

first: María

last: Arriba

first: Yolanda

last: Rodríguez

first: Miguel

last: Urioste

first: Rogelio

last: González-Sarmiento


title: microRNA levels in patients receiving CRT

status: Public on Jan 31 2016

city: Boston

first: Saumya

last: Das

state: MA

address: CLS907 330 Brookline Ave

department: Cardiology

institute: Beth Israel Deaconess Medical Center

summary: This is a discovery cohort of six patients who received CRT with significant improvement in ejection fraction (EF), and six who received CRT but did not experience improvement. All patients are male, with left bundle branch block and do not have coronary disease (non-ischemic myopathy). Patients are matched for age and ejection fraction (EF)

overall_design: This is a prospective study. Patients receiving CRT had time zero serum samples drawn. miRNA levels were drawn and screened using low-density array. Responders and non-responders to CRT were compared with the goal of identifying miRNAs important in LV remodeling and response to CRT

first: Yonathan

last: Melman

first: Ravi

last: Shah

first: Kirsty

last: Danielson

first: Junjie

last: Xiao

first: Bridget

last: Simonson

first: Andreas

last: Barth

first: Khalid

last: Chakir

first: Gregory

last: Lewis

first: Quynh

last: Truong

first: Andre

last: Kleber

first: Ranendra

first: Yaoyu

last: Wang

first: David

last: Kass

first: Jagmeet

last: Singh


title: Transcriptional changes associated with the fleshless (flb) somatic variation

city: Ames

first: PLEXdb Curator

middle: Sudhansu

state: IA

address: 1023  Crop Genomes Informatics Lab (Iowa State University)

department: Virtual Reality Application Center

institute: Iowa State University

summary: Genes regulated in the fleshless (flb ) somatic variant identified in grapevine cultivar Ugni Blanc.  Transcriptional changes were analyzed in the flb somatic variant compared to the wild type Ugni Blanc in flowers  (stages 18 according to the modified E-L system, ref: Coombe BG, Aust J Grape Wine Res 1995, 1: 104-110) and 8-day old berries.   ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor,  Lucie Fernandez.  The equivalent experiment is VV35 at PLEXdb.]

overall_design: genotype: flb somatic variant - developmental stage name: Flower(3-replications);  genotype: flb somatic variant - developmental stage name: 8 DAA fruit(3-replications);  genotype: Wild type Ugni Blanc - developmental stage name: Flower(3-replications);  genotype: Wild type Ugni Blanc - developmental stage name: 8 DAA fruit(3-replications)

first: Lucie

last: Fernandez

first: José

last: Martinez-Zapater


title: Mouse fetal liver cells: treated with nanosilver particles (nAg)  vs control.

city: Beijing

first: Zhe

address: 18 Shuangqing Road

country: China

institute: Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences

summary: To investigate the differently expressed genes upon the nanosilver particle (nAg) exposure.

overall_design: Total RNAs were extracted from E14.5 fetal livers in embryos from nAg-treated mice and the control mice. Gene-expression profiling was performed on the CapitalBio 32k mouse Genome Array microchips  (Beijing, China).

first: Sijin

last: Liu

first: Juan

last: Ma


title: Human gut microbiota preservation for functional studies: in-vitro comparison of common cryoprotective agents

status: Public on Jan 29 2016

city: Clermont Ferrand

first: Nadia

last: Gaci

state: Auvergne

address: 28, Place H. Dunant - B.P. 38

department: Pharmacy

country: France

institute: University d Auvergne

summary: The protocol to test the preservation capabilities was based on a standardized procedure using the ECSIM, a chemostat-based fermentation system establishes to maintain microbiota. The initial fresh stool sample (1 g) was first cultivated in 5 mL, then 100 mL and then 1 L of a standard artificial gut medium and then either immediately tested in the P-ECSIM or preserved for 3 and 6 months with cryoprotectants before being next used for inoculation of the P-ECSIM. Three intracellular protecting agents were tested alone and in combinations (i) 10% (v/v) glycerol, the most current one, (ii) 10% (v/v) dimethyl sulfoxide (DMSO), which possesses a much greater penetrating power and (iii) 10% (w/v) polyethylene glycol-4000 (PEG-4000), an emulsifying agent with high molecular weight.

overall_design: Three-condition experiment (0 hour,3 months and 6 months), Control versus 14 different preservation conditions, Biological replicates:1

first: Prem

last: Chaudhary

first: Jean

last: Brugere


title: p38 regulated genes in rat myelinating glia

city: Montreal

first: Guillermina

last: Almazan

state: Quebec

address: 3655 Prom. Sir William Osler

department: Pharmacology and Therapeutics

country: Canada

institute: McGill University

summary:
The objective was to determine the p38-regulated genes in rat primary oligodendrocytes using the p38alpha/beta isoform-selective inhibitor PD169316.
The drug concentration used for all experiments was 5 micromolar; controls were treated with vehicle (DMSO)

overall_design: Oligodendrocyte progenitors were treated for either 1 day or 2 days with PD169316.

first: Stephane

last: Richard

first: Jeffery

last: Haines

first: Debra

last: Fulton


title: Expression analysis of INA6 cells after IL-6 withdrawal using TileShuffle

city: Leipzig

first: Kristin

last: Reiche

address: Perlickstr. 1

department: Diagnostics

country: Germany

institute: Fraunhofer Institute for Cell Therapy and Immunology

type: Expression profiling by genome tiling array

summary: Whole transcriptome expression analysis of INA6 cells on Affymetrix Human Tiling 1.0 array set. IL-6 has been withdrawn for 13 hours which initiates apoptosis. Expression data were processed with our new permutation approach TileShuffle.

overall_design: We analyzed one Affymetrix Human Tiling 1.0R set

first: Antje

last: Kretzschmar

first: Friedemann

last: Horn

first: Jörg

last: Hackermüller

first: Kurt

last: Engeland


title: Expression analysis of colorectal carcinoma cells with overexpressed TP53 using MAT

summary: Whole transcriptome expression analysis of colorectal carcinoma cells with induced expression of TP53 on Affymetrix Human Tiling 1.0 array set. Expression data were processed with MAT.


title: Expression analysis of INA6 cells after IL-6 restimulation using TileShuffle

summary: Whole transcriptome expression analysis of INA6 cells on Affymetrix Human Tiling 1.0 array set. Cells were restimulated with IL-6 for 1 hour after IL-6 has been withdrawn for 13 hours. Expression data were processed with our new permutation approach TileShuffle.


title: Expression analysis of INA6 cells after IL-6 restimulation using MAT

summary: Whole transcriptome expression analysis of INA6 cells on Affymetrix Human Tiling 1.0 array set. Cells were restimulated with IL-6 for 1 hour after IL-6 has been withdrawn for 13 hours. Expression data were processed with MAT (Johnson et al., "Model-based analysis of tiling-arrays for ChIP-chip." Proc Natl Acad Sci USA, 103:12457-62, 2006.).


title: Expression analysis of colorectal carcinoma cells with defunct TP53 using TAS

summary: Whole transcriptome expression analysis of colorectal carcinoma cells with defunct TP53 on Affymetrix Human Tiling 1.0 array set. Expression data were processed with TAS.


title: Expression analysis of colorectal carcinoma cells with defunct TP53 using MAT

summary: Whole transcriptome expression analysis of colorectal carcinoma cells with defunct TP53 on Affymetrix Human Tiling 1.0 array set. Expression data were processed with MAT.


title: Expression analysis of INA6 cells after IL-6 withdrawal using MAT

summary: Whole transcriptome expression analysis of INA6 cells on Affymetrix Human Tiling 1.0 array set. IL-6 has been withdrawn for 13 hours which initiates apoptosis. Expression data were processed with MAT (Johnson et al., "Model-based analysis of tiling-arrays for ChIP-chip." Proc Natl Acad Sci USA, 103:12457-62, 2006.).


title: Expression analysis of colorectal carcinoma cells with overexpressed TP53 using TAS

summary: Whole transcriptome expression analysis of colorectal carcinoma cells with induced expression of TP53 on Affymetrix Human Tiling 1.0 array set. Expression data were processed with TAS.


title: Differential expression analysis of colorectal carcinoma cells (defunct TP53 versus active TP53) using TAS

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

overall_design: Refer to individual Series


title: Differential expression analysis of INA6 cells using TAS


title: Differential expression analysis of INA6 cells using MAT


title: Differential expression analysis of INA6 cells using TileShuffle

overall_design:
Affymetrix Human Tiling 1.0 probes were mapped to human genome assembly hg18 using the corresponding BPMAP files. The expression data were processed with our new permutation approach TileShuffle. TileShuffle was applied using only perfect match (PM) probes, a window size of 200, the arithmetic mean trimmed by maximal and minimal value as scoring function, three GC content bins, 10000 permutations, and a q-value threshold of 0.05. In order to estimate the significance of a window score we repeatedly permute all probe intensities across the array while interchanging only those that belong to the same sequence-specific affinity bin, recompute the window scores, and compare them with the original ones. By counting the number of permuted windows with higher score, we estimate empirical p-values of windows, and report q-values adjusted according to Benjamini and Hochberg ("Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing". Journal of the Royal Statistical Society. Series B (Methodological), 57:289-300, 1995.).

Analysis of differential expression was performed with the same parameters, except of 100000 permutations, aiming at accommodating the more rugged nature of expression difference signal. We provide tow different variants, variant A (i.e. highdiff1 in supplementary file) and variant B (i.e. highdiff3 in supplementary file).

Variant A: Differentially expressed segments are detected by following the same outline as for expression analysis with the exception that two-tailed p-values are estimated in order to regard both regulation directions, up or down. The multiple testing correction is then adjusted to account for these additional comparisons. Here we use a q-value < 0.001.

Variant B: Here it is assumed that entire windows are either up- or downregulated between two conditions and converse behaviour of neighboring probes is a consequence of non-specific hybridization. In order to correct for this bias, the presumed direction of regulation is initially assigned to each window on the basis of the sign of its expression scores. Subsequently, all converse probes, i.e. probes with negative log-fold change within positive windows or vice versa, are ignored and neither permuted nor incorporated into the score calculation for differential expression. Consequently, positive and negative windows are compared to different background distributions. To asses the significance of a window score a one-tailed empirical p-value is estimated (according to the corresponding background distribution) and corrected for multiple testing, similar to the one-state analysis.  Here we use a q-value < 0.01.

To avoid that signal intensity variation at the detection limit is classified as differential expression, we require that differentially expressed intervals must also be significantly expressed in at least one of the investigated conditions, and call these intervals highdiff. Following this definition, TileShuffle takes regions found to be significantly high expressed in at least one of the compared states as input for the two-state analysis, and assesses differential expression solely on the expressed segments.


title: Expression analysis of INA6 cells after IL-6 restimulation using TAS

summary: Whole transcriptome expression analysis of INA6 cells on Affymetrix Human Tiling 1.0 array set. Cells were restimulated with IL-6 for 1 hour after IL-6 has been withdrawn for 13 hours. Expression data were processed with TAS.


title: Differential expression analysis of colorectal carcinoma cells (defunct TP53 versus active TP53) using MAT


title: Expression analysis of INA6 cells after IL-6 withdrawal using TAS

summary: Whole transcriptome expression analysis of INA6 cells on Affymetrix Human Tiling 1.0 array set. IL-6 has been withdrawn for 13 hours which initiates apoptosis. Expression data were processed with TAS.


title: Expression analysis of colorectal carcinoma cells with defunct TP53 using TileShuffle

summary: Whole transcriptome expression analysis of colorectal carcinoma cells with defunct TP53 on Affymetrix Human Tiling 1.0 array set. Expression data were processed with our new permutation approach TileShuffle.


title: Expression analysis of colorectal carcinoma cells with overexpressed TP53 using TileShuffle

summary: Whole transcriptome expression analysis of colorectal carcinoma cells with induced expression of TP53 on Affymetrix Human Tiling 1.0 array set. Expression data were processed with our new permutation approach TileShuffle.


title: Differential expression analysis of colorectal carcinoma cells (defunct TP53 versus active TP53) using TileShuffle


title: Paired copy number analysis of Diffuse Large B Cell Lymphoma [OncoScan]

status: Public on Jan 22 2016

city: Salamanca

first: Elena

last: Sebastián

address: Paseo de San Vicente

department: Hematology

institute: Hospital Universitario de Salamnca

summary: Copy number analysis can be useful for assessing prognosis in diffuse large B cell lymphoma (DLBCL). We analyzed copy number data from tumor samples of 60 patients diagnosed with DLBCL de novo and their matched normal samples. We detected a total of 63 recurrent copy number alterations (CNAs), including 33 gains, 30 losses, and nine recurrent acquired copy number neutral loss of heterozygosity (CNN-LOH). Interestingly, 20% of cases acquired CNN-LOH of 6p21 locus, which involves the HLA region. In normal cells there were no CNAs but we observed CNN-LOH involving some key lymphoma regions such as 6p21 and 9p24.1 (5%) and 17p13.1 (2.5%) in DLBCL patients. Furthermore, a model with some specific CNA was able to predict the subtype of DLBCL, 1p36.32 and 10q23.31 losses being restricted to germinal center B cell-like (GCB) DLBCL. In contrast, 8p23.3 losses and 11q24.3 gains were strongly associated with the non-GCB subtype. A poor prognosis was associated with biallelic inactivation of TP53 or 18p11.32 losses, while prognosis was better in cases carrying 11q24.3 gains, which includes ETS1 and FLI1 genes. In summary, CNA abnormalities identify specific DLBCL groups, and we describe CN-LOH in germline cells from DLBCL patients that are associated with genes that probably play a key role in DLBCL development.

overall_design: A total of 60 DLBCL cases and paired constitutional DNA from 40 of these patients, were successfully analyzed using copy number arrays. Thirty-eight cases with FFPE DNA available were hybridized on the MIP-assay using Oncoscan FFPE Express custom service (Affymetrix, Santa Clara, CA, USA).Twenty-two cases with HMW DNA from frozen tissue and 40 normal DNAs were analyzed using SNP 6.0 array. Gains and losses were evaluated with visual inspection by 2 different observers using Nexus Biodiscovery software (Biodiscovery, El Segundo, CA, USA).

first: Itziar

last: Salaverria

first: David

last: Martín-García


title: Paired copy number analysis of Diffuse Large B Cell Lymphoma

type:
Genome variation profiling by array
Genome variation profiling by SNP array


title: Paired copy number analysis of DLBCL Diffuse Large B Cell Lymphoma [SNP 6.0 Array]


title: Comparison of isogenic lines differing in vernalization requirement

first: PLEXdb Curator

summary: Gene expression was assyed in seedlings of isogenic barley lines differing in vernalization requirement. Seedlings were harvested after 5 days germination in darkness at 20 degrees. Seedlings were then subjected to 1 day at 4 degrees after 5 days germination in darkness at 20. Genotypes include the winter barley parent Dairokakku, and isogenic lines carrying a deletion of VRN2, active VRN1 allleles (VRN1-10, or VRN1-8) or an active allele of FT1/VRN3.   ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor,  Ben Trevaskis.  The equivalent experiment is BB97 at PLEXdb.]

overall_design: genetic line: +VRN1-10 - temperature: 20 C(3-replications);  genetic line: +VRN1-10 - temperature: 4 C(3-replications);  genetic line: -VRN2 - temperature: 20 C(3-replications);  genetic line: -VRN2 - temperature: 4 C(3-replications);  genetic line: +VRN1-8 - temperature: 20 C(3-replications);  genetic line: +VRN1-8 - temperature: 4 C(3-replications);  genetic line: +FT1/VRN3 - temperature: 20 C(3-replications);  genetic line: +FT1/VRN3 - temperature: 4 C(3-replications);  genetic line: Parent (winter type) - temperature: 20 C(3-replications);  genetic line: Parent (winter type) - temperature: 4 C(3-replications)

first: Ben

last: Trevaskis


title: Hyperglycaemia-induced over-expression of miR-301a promotes the proliferation of prostate cancer cells by repressing Smad4 and p21.

city: guangzhou

first: li

last: jun

state: guangdong

address: Tianhe District Tianhe Road, No. 600

institute: The third affiliated hospital of sun YAT-SEN University

summary: We found a novel molecular link between hyperglycaemia and the increased frequency of aggressive prostate cancer. High glucose was demonstrated to increase the expression of miR-301a which targeted Smad4 and p21, resulted in promoting the proliferation of prostate cancer cells.

overall_design:
male 12-week-old SD rats (weight 230?280 g), obtained from Sun Yat-sen University Experimental Animal Center (Guangzhou, China), were randomly divided into the diabetes and the control groups
Hyperglycaemic and control rats were constructed as described previously by intraperitoneal injection of STZ, which destroys the pancreas and causes hyperglycaemia. Total RNA samples were harvested using Trizol (Invitrogen) and an RNeasy mini kit (Qiagen) according to the manufacturers’ instructions.

first: Jun

last: Li

first: Yi

last: Cai

first: Shubin

last: Peng

first: Xiaojuan

first: Liren

first: Yu

last: Wang

first: Fei

last: Han

first: Yanxiong

last: Chen

first: Yiran

last: Tao

first: Binyuan

last: Yan

first: Zhiqiang

last: Wen

first: Xin

last: Gao

first: Chunhui

last: Shao

first: Xingqiao


title: Comparative early transcriptomic responses to copper and cadmium exposure in rice roots

city: Tainan City

first: Chung-Yi

last: Lin

address: No.1, University Road

country: Taiwan

institute: National Cheng Kung University

summary:
The aim of this study is to do a side-by-side comparison of the transcriptomes that are regulated under Cu and Cd stress at the early stage in rice roots. The comparison of transcriptomes between Cu and Cd treatments and the application of bioinformatics procedures (e.g. regulated gene analysis) are potentially useful approaches for determining the both general and individual early responses triggered by each metal.
Identify genes and pathways that would discriminate among the actions of Cu and Cd.

overall_design: Comparison of mock control and  rice seedlings treated with 5μM Cu and 25μM Cd; Biological replicates: 3 control replicates, 3 Cu-treated replicates, 3 Cd-treated replicates

first: C

first: Y

last: Hsiung

first: L

last: Chia

first: H

last: Huang


title: Arabidopsis Me-0 vs tetraploid Col

status: Public on Jan 14 2016

city: Fukuoka

first: Hiromitsu

last: Araki

address: 744 Motooka Nishi-Ku

institute: Kyushu University

summary: To investigate gene expression differences related to the regulation of stomatal aperture between two Arabidopsis accessions, Me-0 and tetraploid Col, we performed microarray analysis on guard cell protoplasts from these two accessions. We identified 1,777 probes as up-regulated and 1,706 probes as down-regulated differentially expressed genes (DEGs) in Me-0 compared with tetraploid Col (adjusted P-value < 0.001 and log 2 fold change of greater than 1 or less than -1). Using gene set analysis to functionally characterize DEGs, there were eight significant gene sets (at the level of P-value < 0.01) among the up-regulated genes and seven significant gene set among the down-regulated genes. Genes with the lowest P-value among the up-regulated genes were related to “plant-type cell wall loosening”, an essential step in guard cell swelling. Most of the down-regulated genes were related to the defense responses for immunity, hypoxia, and ozone, which also influence stomatal responses or gas exchange. We propose that these gene expression differences may cause the difference in stomatal aperture between Me-0 and tetraploid Col.

overall_design: Four samples from Me-0 and three samples from tetraploid Col are used for a microarray analysis.

first: Keina

last: Monda

first: Satoru

last: Kuhara

first: Koh

last: Iba


title: Target miRNAs of MLL-AF9 as revealed by RNAi

status: Public on Jan 16 2016

city: Munich

first: Katrin

last: Fleischmann

address: Lindwurmstrasse 2a

department: Children’s Research Center

institute: Dr. von Hauner Children’s Hospital, Ludwig-Maximilians-Univeristät München

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

summary: In this study the function of MLL-AF9 was investigated by efficient and specific knockdown via siRNAs in the AML M5 cell line THP1 which harbors the corresponding t(9;11) translocation. MiRNA expression profile analyses revealed 21 differentially expressed miRNAs.

overall_design: 4 samples were analyzed, each corresponding to a pool of five replicate experiments. MLL-AF9 knockdown treatments are represented by 2 samples employing two distinct siRNAs, each targeting MLL-AF9 breakpoint of THP1 cells. Control treatments are represented by 2 samples employing two distinct non-targeting control siRNAs.

first: Philipp

last: Pagel

first: Julia

last: von Frowein

first: Thomas

last: Magg

first: Adelbert

last: Roscher

first: Irene

last: Schmid


title: A Signaling Lipid Associated with Alzheimer’s Disease Promotes Mitochondrial Dysfunction

status: Public on Jan 21 2016

city: Ottawa

first: Linda

middle: J

last: Harris

state: Ontario

address: 960 Carling Ave.

department: Eastern Cereal & Oilseed Research Centre

institute: Agriculture & Agri-Food Canada (AAFC)

summary:
Fundamental changes in the composition and distribution of lipids within the brain are believed to contribute to the cognitive decline associated with Alzheimer’s disease (AD). The mechanisms by which these changes in lipid composition affect cellular function and ultimately cognition are not
well understood. Although “candidate gene” approaches can provide insight into the effects of dysregulated lipid metabolism they require a preexisting understanding of the molecular targets of individual lipid species. In this report we combine unbiased gene expression profiling with a genomewide
chemogenomic screen to identify the mitochondria as an important downstream target of PC(O-16:0/2:0), a neurotoxic lipid species elevated in AD. Further examination revealed that PC(O-16:0/2:0) similarly promotes a global increase in ceramide accumulation in human neurons which was associated with mitochondrial-derived reactive oxygen species (ROS) and toxicity. These findings suggest that PC(O-16:0/2:0)-dependent mitochondrial dysfunction may be an underlying contributing factor to the
ROS production associated with AD.

overall_design: This experiment contains 2 samples, 4 biological reps for each sample were hybridized. Cy3 one-color labelling was used for each sample.

first: Michael

last: Kennedy

first: Tia

last: Moffat

first: Kenneth

last: Gable

first: Suriakarthiga

last: Ganesan

first: Karolina

last: Niewola-Staszkowska

first: Anne

last: Johnston

first: Corey

last: Nislow

first: Guri

last: Giaever

first: Robbie

last: Loewith

first: Vanina

last: Zaremberg

first: Mary-Ellen

last: Harper

first: Teresa

last: Dunn

first: Steffany

last: Bennett

first: Kristin

last: Baetz


title: Global gene expression profiling of L. interrogans serovar Copenhageni in response to UV-C irradiation

city: Sao Paulo

first: Paulo

last: Lee Ho

state: SP

address: 1500 Vital Brazil

department: Centro de Biotecnologia

country: Brazil

institute: Instituto Butantan

summary: The pathogen L. interrogans serovar Copenhageni can be shed in the urine of carrier mammals, and infect humans after weeks on water or mud. This wide range of possible niches implies the bacterium can be exposed to several different genotoxic stresses during its lifecycle.  We assessed the impact of DNA damage in this leptospire, integrating high throughput data from ChIP-seq and DNA microarrays to determine the role of the SOS regulator LexA1. We observed 24 LexA1 binding sites located throughout the chromosome 1 and one in chromosome 2. Analyses of LexA1 ChIP-seq peak sequences revealed the SOS box is an imperfect asymmetric palindrome of 16bp, CTAA[A/T/G]CANNTG[T/A]TTAG. DNA damage caused significant changes of several aspects of bacterial physiology, decreasing expression of genes involved in energy metabolism and translation, in addition to genes related to virulence and motility. On the other hand, post replicative and recombination repair, but not the canonical DNA repair genes, were up regulated. The most striking feature of this response was the massive up-regulation of two prophages. Our findings point to an expression profile shift from cell growth and virulence to mutagenesis and recombination, emphasizing the fundamental role of DNA damage response as a highway for adaptation and evolution.

sample_organism: Leptospira interrogans serovar Copenhageni str. Fiocruz L1-130

overall_design: Cultures of exponential growing cells were irradiated or not with 5 J/m² UV-C and harvested after 12h. RNA isolation was performed by RNEasy mini kit from Qiagen, and cDNA synthesis and labeling with Fairplay III from Agilent. Four biological replicates were hybridized in custom slides of 8x15K from Agilent.

first: Luciane

last: Schons-Fonseca

first: Josefa

middle: B

last: da Silva

first: Juliana

middle: S

last: Milanez

first: Janet

last: Smith

first: Helder

middle: I

last: Nakaya

first: Alan

last: Grossman

last: Ho

first: Renata

last: da Costa


title: miRNA expression profiles of Platelet microparticles (PMPs)

city: shanghai

first: Meiling

last: tang

state: shanghai

address: 536 Chang Le RD, Jiang An district, Shanghai, 200040, China

department: Gynecology

summary: To identify the miRNA expressing profiles of Platelet microparticles（PMPs, we have employed the Agilent Human miRNA 8×60K (Design ID:046064) microarray. Platelet microparticles. The platelets were derived from citrated blood of healthy human donors under an Institutional Review Board-approved protocol. Platelets were isolated after centrifugation of blood (1200r for 30 min at 21℃), then the supernatant (platelet-rich plasma) was centrifuged at 2000r for 30 min at 21℃, and the pellet containing platelets was resuspended in RPMI-1640 medium (HyClone, Logan, UT). Platelets were counted (Clinical Laboratory, Shanghai First Maternity and Infant Hospital, Shanghai) and adjusted to a density of 150 × 106 cells/mL before supplement with 1.5% ACD(sigma ) and stimulated with thrombin (1.0 u/mL; Takeda Austria) for 1 h. PMPs were in the supernatant after centrifugation at 4000r for 10 min at 4℃,then the supernatants were centrifuged at 50,000 × g for 60 min at 4 °C. The pellets containing MPs were resuspended in RPMI-1640 medium and quantified by BCA method.

overall_design: The gene expressions of three independent paired PMPs from platelets stimulated by thrombin or apoptosis.

first: Xipeng

last: Wang

last: Tang

first: Lu

last: Jiang


title: Determination of genes expressed in response to drought in root and shoot of Leucaena leucocephala

status: Public on Jan 13 2016

city: Honolulu

first: Kazue

last: Ishihara

state: HI

address: 1955 East-West Rd AgSci 218

department: Molecular Biosciences and Bioengineering

institute: University of Hawaii at Manoa

summary:
Leucaena leucocephala seedlings were treated with PEG6000 and the shoot and root tissues were collected after 48 hours following the treatment.  The gene expressions were compared between treated and untreated in root and shoot separately.
The differentially expressed genes may be related to drought resistance.

overall_design: RNA from shoot and root from treated and untreated L. leucocephala seedlings were extracted.  Two biological replicates were made for each sample (each replicate represents about 10 individual seedlings).

first: Dulal

last: Borthakur


title: Amniotic fluid cardiomyocytes

status: Public on Jan 20 2016

city: Ann Arbor

first: Guihua

state: MI

address: 109 Zina Pitcher PL

department: Surgery

institute: University of Michigan

summary: Microarray data comparison of amniocytes, amniotic fluid-iPSCs, and cardiomyocyte derivatives

overall_design: Differentiated cardiomyocytes from amniotic fluid and dermal fibroblast controls

first: Shaun

last: Kunisaki


title: Investigation of a Quality Check for Plasma Samples

city: Kyoto

first: Katsutoshi

last: Shoda

address: 465 Kajii-cho, Kamigyo-ku

department: Division of Digestive Surgery, Department of Surgery

institute: Kyoto Prefectural University of Medicine

summary: Plasma samples from healthy volunteers were used for the microarray analysis. The fresh sample and intentionally hemolyzed one due to negative pressure were examined. Microarray analyses were performed using the 3D-Gene microRNA microarray platform, and RNA extraction was conducted according to the manufacturer’s instructions. Only a very small amount of total RNA was present in the plasma samples; therefore 2 out of the 4 µl of total RNA extracted from 300- µl of plasma samples were used in microarray experiments.

overall_design: The purpose of this study is to identify hemolysis related microRNA. Plasma samples from healthy volunteers were used for the microarray analysis. The fresh sample and intentionally hemolyzed one due to negative pressure were examined.

first: Tomohiro

last: Arita

first: Hirotaka

last: Konishi

first: Daisuke

last: Ichikawa

first: Eigo

last: Otsuji


title: Investigation of the molecular mechanisms underlying of herb pair Daji and Gancao with different combination designs acting on hepatocellular carcinoma ascites mice

first: Yanqiong

last: Zhang

address: No 16, Nanxiaojie, Dongzhimennei

institute: Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences

summary: The differentially expressed genes among the blank control, ascites mouse model, Daji (DJ)/ Gancao (GC)-synergistic treatment and DJ/GC-antagonistic treatment groups were identified to investigate the molecular mechanisms underlying the herb pair DJ and GC acting on ascites mice.

overall_design: In the study, 50 male Kunming mice were randomly divided into 5 groups, namely, normal control group, model group, Daji/Gancao-synergy group, Daji/Gancao-antagonism group, Daji group. Normal control group and model group were intragastrically administrated with normal saline, while other 3 groups were intragastrically administrated with corresponding doses.

first: Chen

last: Yan


title: Arabidopsis thaliana Growth is Negatively Regulated by the Class III Peroxidase AtPrx71 during Development and in Response to Cell Wall Damage

status: Public on Jan 06 2016

city: Verona

first: Alberto

last: Ferrarini

state: Veneto

address: Strada le Grazie, 15

department: Scientific and Technological Department

country: Italy

institute: University of Verona

summary: The cell wall is a crucial structure in plant cells, and modifications in its composition often have a major impact on growth and development. However, the molecular mechanisms responsible for the negative effects of cell wall alterations on plant growth are largely unknown. It was previously shown that a reduction in the levels of de-esterified homogalacturonan, a major pectin component of cell walls, in Arabidopsis thaliana plants expressing a fungal polygalacturonase or mutated in the QUASIMODO2 gene (qua2-1 plants), cause severe growth defects. Here we show that the class III peroxidase AtPrx71 is strongly up-regulated in these plants, as well as in response to alterations of other wall structural components, including treatments the cellulose synthase inhibitor isoxaben. Analysis of atprx71 loss-of-function mutants and of plants overexpressing AtPrx71 indicates that this gene negatively affects Arabidopsis growth at different stages of development. Furthermore, lack of AtPrx71 partially suppresses the dwarf phenotype of qua2-1, suggesting that this protein contributes to the growth defects observed in plants undergoing cell wall damage. AtPrx71 appears to promote the production of reactive oxygen species in qua2-1 plants, as well as in plants treated with isoxaben. We propose that production of reactive oxygen species mediated by AtPrx71 negatively regulates Arabidopsis growth both during physiological development and in response to loss of cell wall integrity.

overall_design: Transcriptional profiling of Arabidopsis thaliana wt control plants and PG57 and PG26 transgenic lines overexpressing the AtPrx71 gene.

first: Sara

last: Raggi

first: Massimo

last: Delledonne

first: Christophe

last: Dunand

first: Philippe

last: Ranocha

first: Giulia

last: De Lorenzo

first: Felice

last: Cervone

first: Simone

last: Ferrari


title: Gene expression profiling of adult zebrafish caudal fin and tumor tissues

city: Leiden

first: Herman

middle: Pieter

last: Spaink

address: Einsteinweg 55

department: Institute of Biology

country: Netherlands

institute: Leiden University

summary: Using  Agilent custom made expression microarrays we analyzed the difference of gene expression in caudal fin tissues of wild type fish and transgenic fish that can form melanomas.  For this we used a transgenic line with forced expression of V600EBRAF that resulted in melanocyte hyperplasia, while expression of G12VHRAS resulted in malignant melanocyte neoplasia that initially grows radially (RGP) and then vertically (VGP)

overall_design: This microarray study was designed to determine the gene expression profile of zebrafish caudal fins in wild type or transgenic animals. Total RNA extracted from 3 pools of 10 caudal fins were used for WT, BRAF and RGP samples, whilst for VGP RNA was extracted from 3 pools of 6 caudal fin tumours.

first: H

first: A

last: Hurlstone


title: Identification of candidate targets for Haizao Yuhu Decoction acting on goiter rats

city: Beijing

summary: To predict the different genes, this study compared the gene expression level among the control group, the model group and the treatment groups.

overall_design: In this present study, 20 Wistar rats, weighting 160-180g and as the sex evenly, were randomly divided into five groups: normal control group, model control group , Haizao Yuhu decoction group,  Haizao Yuhu decotion lacking Sargassum fusiforme (DL-S) group, and  Haizao Yuhu decotion lacking Radix Glycyrrhiza (DL-G)  group. Except the rats in control and model groups, the three other groups, which were established as goiter model, were administered appropriate medication  at the dose of 1mL/100g for 28 consecutive days. After all animals sacrificed, thyroids were removed and then put in Trizol for microarray experiments.

first: Yuting

last: Li


title: Transcriptomic analysis of the metabolic impact of higher oligopeptide assimilation mediated by horizontally acquired oligopeptide transporters Fot1/2 in wine strains.

status: Public on Jan 19 2016

city: MONTPELLIER

first: Sylvie

last: Dequin

address: 2 PLACE PIERRE VIALA

institute: INRA

summary: To assess the impact of a higher oligopeptide assimilation mediated by Fot1/2, oligopeptides transporters acquired by HGT on wine yeast cell metabolism in winemaking conditions,we carried out a comparison of transcriptomic profiles of the wine wild type strain 59A and the deletion mutant of FOT1/2 genes during exponential growth.

overall_design: Two strains (59A and 59A FOT-deleted) at 2 released CO2 time point (5g/L and 10g/L) are analyzed. Each condition are in quadriplicate.

first: Souhir

last: Marsit

first: Virginie

last: Galeote

first: Isabelle

last: Sanchez


title: Cell wall-deficient Mycoplasma hominis represses biofilm formation of uropathogenic Escherichia coli.

status: Public on Jan 08 2016

city: Jeonju

first: Younghoon

last: Kim

address: 567 Baekje-Daero, Deokjin-Gu

department: Department of Animal Science

institute: Chonbuk National University

summary:
The features of Mycoplasma in human organ such lung and urinary tract are enigmatic.  Here, the role of M. hominis in regard to biofilm formation of uropathogenic Escherichia coli (UPEC) strain CFT073 was investigated. Although M. hominis were inferred to not impact on UPEC bacterial fitness including growth and productions of signaling molecules as autoinducer-2 (AI-2) and indole, we found that the presence of M. hominis dramatically decreased biofilm formation of UPEC CFT073 as well as slightly repressed attachment and cytotoxicity of that.  Importantly, this activity was observed on UPEC strain specifically, not enterohemorrhagic E. coli (EHEC) strain that exists on intestine.  Whole-transcriptome profiling and quantitative real-time polymerase chain reaction (qRT-PCR) analysis revealed PhoPQ system and anti-termination protein (encoded by ybcQ) participates on the reduction of biofilm formation by M. hominis (corroborated by qRT-PCR). Furthermore, collaborating with previous report that toxin-antitoxin (TA) system involved in biofilm formation, M. hominis increased on the transcriptions of toxin genes including hha (toxin gene in Hha-TomB TA system) and pasT (toxin part in PasT-PasI TA system).  Hence, we propose that one possible role of M. hominis is to influence bacterial biofilm formation in urinary tract.
Only fourteen genes were induced (2.5-fold) by the presence of M. hominis in Uropathogenic Escherichia coli (UPEC) biofilm cells.
Among upregulated genes, ybcQ (encodes anti-termination protein Q homolog) and phoP/phoQ (encode DNA-binding response regulators in two-component regulatory system), were induced by the presence of M. hominis.

overall_design: Two-condition experiment, UPEC CFT073 alone vs. UPEC CFT073 with Mycoplasma hominis PG21 (10^5 ccu/ml). For preparing the total RNA, UPEC CFT073 cells were grown at 37°C in biofilm cells on glass wool with or without M. hominis for 24 h.

first: Sangnam

last: Oh

first: Nag-Jin

last: Choi


title: Effects on transcriptional regulation and lipid droplet characteristics in the liver of female juvenile pigs after early postnatal feed restriction and refeeding are dependent on birth weight

city: Dummerstorf

first: Constance

last: Nebendahl

address: Wilhelm-Stahl Allee 2

institute: Leibniz Institute for Farm Animal Biology

summary:
Low (U) and normal (N) birth weight female porcine offspring were used to study molecular and physiological changes in the liver before and after postnatal feed restriction (R, 50% of controls) and after subsequent refeeding period in comparison to non-restricted control animals (K). Overall, the following questions were addressed at the transcriptional, epigenomic and metabolic level: 1) Are there differences in the hepatic transcriptional profile between U and normal birth weight 2) Are these effects reflected on the metabolic level? 3) Could the possible birth weight-dependent effects be modified through feed restriction intervention? 4) Are these effects persistent and, moreover, can improvements with regard to lipid homeostasis be observed?
Microarrays were used to study the effects of birth weight and/or feed restriction on the transcriptional level.

overall_design: For whole genome expression analysis, RNA was isolated from liver samples of three randomly chosen animals per group  (NK, NR, UK, UR) and time point. Liver tissue was harvested at the age of 75 days (before feed restriction, T1), at the age of 98 days (after 3 wk feed restriction, T2) and at the age of 131 days (after 5 wk refeeding period, T3), resulting in a total of 10 experimental groups.

first: Ricarda

last: Krüger

first: Solvig

last: Görs

first: Karen

last: Martens

first: Elke

last: Albrecht

first: Steffen

last: Hennig

first: Niels

last: Storm

first: Wolfgang

last: Höppner

first: Ralf

last: Pfuhl

first: Barbara

middle: U

last: Metzler-Zebeli

first: Harald

middle: M

last: Hammon

first: Cornelia

last: Metges


title: Transcriptional response of yellow perch to changes in ambient metal concentrations - a reciprocal field transplantation experiment

status: Public on Jan 11 2016

city: Québec

first: Berenice

last: BOUGAS

state: QC

address: 1030 avenue de la médecine, IBIS, Pavillon Marchand

department: Biology

institute: Laval university

summary:
Our main objectives wereto investigate the molecular mechanisms involved in metal toxicity and detoxification in the field using juvenile yellow perch subjected to differents levels of this metal exposure.
Recent local adaptation to pollution has been evidenced in several organisms inhabiting environments heavily contaminated by metals. Nevertheless, the molecular mechanisms underlying adaptation to high metal concentrations are poorly understood, especially in fishes. Yellow perch (Perca flavescens) populations from lakes in the mining area of Rouyn-Noranda (QC, Canada) have been faced with metal contamination for about 90 years. Here, we examine gene transcription patterns of fish reciprocally transplanted between a reference and a metal-contaminated lake and also fish caged in their native lake. After four weeks, 111 genes were differentially transcribed in metal-naïve fish transferred to the metal-contaminated lake, revealing a plastic response to metal exposure. Genes involved in the citric cycle and beta-oxidation pathways were under-transcribed, suggesting a potential strategy to mitigate the effects of metal stress by reducing energy turnover. However, metal-contaminated fish transplanted to the reference lake did not show any transcriptomic response, indicating a reduced plastic response capability to sudden reduction in metal concentrations. Moreover, the transcription of other genes, especially ones involved in energy metabolism, was affected by caging. Overall, our results highlight environmental stress response mechanisms in yellow perch at the transcriptomic level and support a rapid adaptive response to metal exposure through genetic assimilation.

overall_design: Comparison between fish Op and Op→Op using a pairwise design corresponding to the cage experiment in the reference lake Opasatica (Op), comparison between fish Du and Du→Du using a pairwise design corresponding to the cage experiment in the metal contaminated lake Dufault (Du), comparison between fish from reference lake transplanted to the metal contaminated lake (Op→Du) and fish from reference lake caged in their own lake (Op→Op) using pairwise design corresponding to the experiment of metal contamination, comparison between fish from metal contaminated lake transplanted to the reference lake (Du→Op) and fish from the metal contaminated lake caged in their own lake (Du→Du) using pairwise design corresponding to the depuration experiment.

last: Bougas

first: Eric

last: Normandeau

first: Julie

last: Grasset

first: Michel

last: Defo

first: Peter

middle: G

last: Campbell

first: Patrice

last: Couture

first: Louis

last: Bernatchez


title: Root transcriptional profile of tomato Fe-deficient plants in response to supply with natural chelating agents.

first: Anita

last: Zamboni

address: Strada Le Grazie, 15

department: Biotechnology

summary: Tomato, a Strategy I model plant for Fe deficiency, is an important economical crop. The transcriptional responses induced by Fe deficiency in tomato roots were previously described (Zamboni et al., 2012). The changes in trascriptome caused by the supply of Fe to plants starved fro 1 week were described in relation to the different nature of chelating agents (Fe-WEHS, Fe-CITRATE and Fe-PS).

overall_design: Transcriptional profile obtained by roots (27-d) of 21-d-old tomato plants starved of iron (0 μM Fe-EDTA) for 1 week and supplied for 1 h with 1 μM of Fe as Fe-WEHS (supply_Fe_WEHS), Fe citrate (supply_Fe_CITRATE) and Fe-PS (supply_Fe_PS). Tomato plants were hydroponically grown in all three case of Fe supply. Three different biological replicates were used for each sample repeating the experiment three times. All samples were obtained pooling roots of six plants (27-d-old).

first: Laura

last: Zanin

first: Nicola

last: Tomasi

first: Mario

last: Pezzotti

first: Roberto

last: Pinton

first: Zeno

last: Varanini

first: Stefano

last: Cesco


title: Characterization of microRNA Expression Profiles in Intestinal Mucosa of HIV-infected treatment-naive Individuals

status: Public on Jan 15 2016

city: Kunming

first: Kunhua

last: Wang

state: Yunnan

address: #295 Xichang Road

department: Department of Gastrointestinal and Hernia Surgery

institute: First affiliated Hospital of Kunming Medical University

summary: Differentially expressed miRNAs between HIV-infected treatment-naïve individuals and HIV-negative individuals were found, and the altered signaling pathways were predicted using these differentially expressed miRNAs.

overall_design: In the study presented here, RNA from three HIV-infected antiretroviral therapy-naive individuals and three HIV-negative healthy individuals was used to detect the expression levels of miRNAs with 3,100 miRNA probes.


title: Comparison of Chamelea gallina gene expression profiles among different season and collection sites

city: Legnaro

first: Massimo

last: Milan

state: PD

address: Viale dell'Università 16

department: Dept. of Department of Public Health, Comparative Pathology,and Veterinary Hygiene

institute: University of Padova

summary: A C. gallina microarray platform was developed to assess variations on transcritpomic profiles between different seasons and sampling sites

overall_design: A comparative analysis of gene expression was conducted in Chamelea gallina  collected in two different areas along Abruzzi coasts subjected to different mortality events. In particular sampling activities have been performed in collaboration with fishing cooperatives along Abruzzi coasts, Chamelea gallina clams have been  collected from two sites (T4 and T7) at 0.25 mi (ca. 0.4 km) at commercial size (25 mm) and harvested by hydraulic dredge. The harvesting has been conducted in three periods of 2014 (July, August and September). The time of sampling has been obliged by a dramatic reduction of harvesting in T4 that has been reported by fishing cooperatives during spring. After sampling, clams have been kept with ice till their arrival in laboratory, within 6 hours. From each sampling site and each period, the digestive gland of 30 clams has been dissected and frozen at -21°C, for a total of 150 clams divided in 5 pools for each period and each site of sampling.  During  the clam sampling, from the same sites, the upper layer of bed sediments (0–10 cm) was collected by a small grab sampler in July and September. Composite sediment samples have been refrigerated during transport and stored at − 20 °C within a few hours from sampling, until analysis. Briefly, about 400 g of sediment have been suitably homogenized and dried in an oven at 40 ° C for 24 hours, then crushed, ground and sieved to 2 mm. A portion of about 100 g for each sample has been further ground and screened to 0.2 mm for heavy metal analysis.   The content of cadmium (Cd), lead (Pb) and arsenic (As) have been performed, after extraction by aqua regia, by Inductively Coupled Plasma-Optical Emission Spectrometer ( ICP-OES…..) the analysis have been recorded as means triplicate measurements. The determination of Hg have been done in Atomic Adsorption with Hydride System. Ten grams (accuracy ± 0.0001 g) of dry and homogenized sediment of 0.2 mm has been put into a clean centrifuge tube, and a 1:1 (v/v) acetone/n-hexane (5 mL), and surrogate standard mixture (2-fluorobiphenyl and 4-terphenyl-d14) solutions were then added, after extraction and clean-up processes, the  samples were analyzed with a gas chromatographer–electron capture detector (GM-ECD) to evaluate concentrations of Polycyclic aromatic hydrocarbons (PAHs) and organophosphate pesticides (OPPs).  Organochloride pesticides (OCPs) have been analysed, after purification, with static headspace GC   Gene expression profiling was performed using an Chamelea gallina-specific oligo-DNA microarray of15,019 probes representing 12,064 transcripts based on single-colour detection (Cyanine-3 only). Microarrays were scanned with Agilent scanner G2565BA (barcode on the left, DNA on the back surface, scanned through the glass) at a resolution of 5 microns; all slides were scanned twice at two different sensitivity settings (XDRHi 100% and XDRLo 10%); the scanner software created a unique ID for each pair of XDR scans and saved it to both scan image files. Feature Extraction (FE) 9.5 used XDR ID to link the pairs of scans together automatically when extracting data. The signal left after all the FE processing steps have been completed is ProcessedSignal that contains the Multiplicatively Detrended, Background-Subtracted Signal.

first: Chiara

last: Papetti

first: Fiorentina

last: Palazzo


title: Sweet corn: low- vs. high-yielding hybrids

status: Public on Jan 05 2016

city: Urbana

first: Eunsoo

last: Choe

state: Illinois

address: s-306 Turner hall 1102 S. Goodwin Ave.

institute: USDA-ARS

summary:
Transcriptional profiling of sweet corn plant density (crowding stress) tolerance influencing yield.
Tolerance to crowding stress has played a crucial role in improving agronomic productivity in field corn; however, commercial sweet corn hybrids vary greatly in crowding stress tolerance. The experiment was conducted to 1) explore transcriptional changes among sweet corn hybrids with differential yield under crowding stress, 2) identify relationships between phenotypic responses and gene expression patterns, and 3) identify groups of genes associated with yield and crowding stress tolerance. Under conditions of crowding stress, three high-yielding and three low-yielding sweet corn hybrids were grouped for transcriptional and phenotypic analyses. Transcriptional analyses identified from 372 to 859 common differentially expressed genes (DEGs) for each hybrid. Large gene expression pattern variation among hybrids and only 26 common DEGs across all hybrid comparisons were identified, suggesting each hybrid has a unique response to crowding stress. Over-represented biological functions of DEGs also differed among hybrids. Strong correlation was observed between: 1) modules with up-regulation in high-yielding hybrids and yield traits, and 2) modules with up-regulation in low-yielding hybrids and plant/ear traits. Modules linked with yield traits may be important crowding stress response mechanisms influencing crop yield. Functional analysis of the modules and common DEGs identified candidate crowding stress tolerant processes in photosynthesis, glycolysis, cell wall, carbohydrate/nitrogen metabolic process, chromatin, and transcription regulation. Moreover, these biological functions were greatly inter-connected, indicating the importance of improving the mechanisms as a network.

overall_design: 3 high-and 3 low-yielding hybrids with 2-3 biological replications grown under high population density (crowding stress)

first: Martin

last: Williams II


title: Genomic Run On (GRO): determination of the nascent transcriptional rates in a spt16 mutant

city: Burjassot

first: Jose

middle: E.

last: Perez-Ortin

state: Valencia

address: Dr. Moliner 50

department: Bioquimica y Biologia Molecular

institute: Universitat de Valencia

summary: We analyzed the effect of SPT16 on the transcription rates, mRNA stabilities and mRNA levels by doing GRO experiments in a thermosensitive spt16 point mutant (G132D) mutant at 35 ºC comparing with permisive temperature (30 ºC) and a wt treated in the same way.

overall_design: Cells (wt or spt16 mutant) were grown in SC-ura at 30 ºC to 0.25 OD600. At that time α factor was added and let to stand for 160 min in the same conditions. Then each sample (wt or mutant) was separated in two aliquots. One of them remain at 30ºC and the other was incubated at 35ºC. Both aliquots in the presence of α factor for 1h more. Finally, samples were processed for GRO experiment as described in Garcia-Marinez et al (2004). Three replicates of the whole experiment were done.

first: José

middle: E

last: Pérez-Ortín

first: Douglas

last: Maya

first: Daniel

last: Medina

last: García-Martínez

first: Sebastían

last: Chávez


title: WB001A: Genome-wide analysis reveals NRP1 as a critical HIF1-E2F7 target gene in the regulation of motor neuron guidance in vivo

status: Public on Jan 04 2016

city: Utrecht

first: Marian

last: Groot Koerkamp

state: Utrecht

address: Heidelberglaan 25

department: Research

institute: Princess Maxima Center for Pediatric Oncology

summary: In this study, we explored the existence of a transcriptional network co-regulated by E2F7 and HIF1α, as we show that expression of E2F7, like HIF1α, is induced in hypoxia, and because of the previously reported ability of E2F7 to interact with HIF1α. Our genome-wide analysis uncovers a transcriptional network that is directly controlled by HIF1α and E2F7, and demonstrates both stimulatory and repressive functions of the HIF1α -E2F7 complex. Among this network we reveal Neuropilin 1 (NRP1) as a HIF1α-E2F7 repressed gene. By performing in vitro and in vivo reporter assays we demonstrate that the HIF1α-E2F7 mediated NRP1 repression depends on a 41 base pairs 'E2F-binding site hub', providing a molecular mechanism for a previously unanticipated role for HIF1α in transcriptional repression. To explore the biological significance of this regulation we performed in situ hybridizations and observed enhanced nrp1a expression in spinal motorneurons (MN) of zebrafish embryos, upon morpholino-inhibition of e2f7/8 or hif1α. Consistent with the chemo-repellent role of nrp1a, morpholino-inhibition of e2f7/8 or hif1α caused MN truncations, which was rescued in TALEN-induced nrp1a(hu10012) mutants, and phenocopied in e2f7/8 mutant zebrafish. Therefore, we conclude that repression of NRP1 by the HIF1α-E2F7 complex regulates MN axon guidance in vivo.

overall_design: The following samples were analyzed by microarrays: RNA isolated from HeLa cells transfected with either control (scr), E2F7, HIF1a, E2F7 and E2F8, or E2F7 and HIF1a siRNAs. Cells were harvested 48h after transfection, and were grown the last 16h in hypoxia. RNA isolated from scr-transfected, normoxic HeLa cells was used as common reference RNA. Within each group of two biological replicates, sample versus common reference hybridisations were performed in balanced dye-swap. Microarrays used were human whole genome gene expression microarrays V1 (Agilent, Belgium).

first: Alain

last: de Bruin

first: Peter

middle: W

last: Cornelissen

first: Bettina

middle: C

last: Kirchmaier

first: Michal

last: Mokry

first: Elhadi

last: Iich

first: Ella

last: Nirmala

first: Kuo

middle: H

last: Liang

first: Annemarie

last: Végh

first: Koen

last: Scholman

first: Frank

last: Holstege

first: Edwin

last: Cuppen

first: Jeroen

last: den Hertog

first: Stefan

last: Schulte-Merker

first: Walbert

last: Bakker


title: Orbital Cavernous Hemangioma Tissues: Control vs. Benign Lymphoepithelial Lesions of the Lacrimal Gland tissues

first: Jing

last: Li

address: Dongjiaominxiang 1#, Dongcheng District

department: Ophthalmology

institute: Beijing Tongren Hospital, Capital Medical University

summary: Aim to investigate the pathogenesis of BLEL of the lacrimal gland, which is a kind of IgG4 related disease.

overall_design: A prospective study. Orbital Cavernous Hemangioma Tissues (nine continuous cases) vs. Benign Lymphoepithelial Lesions of the Lacrimal Gland tissues (nine continuous cases). Duplicate chips were used for each RNA sample.

first: Jianmin

last: Ma


title: Identification of novel type 2 diabetes candidate genes involved in the crosstalk between the mitochondrial and the insulin signaling systems: chronic insulin treatment

city: Barcelona

first: Josep M

last: Mercader

state: Catalunya

address: C/Jordi Girona 29 08034

department: Life Science Department

institute: Barcelona Supercomputing Center

summary: Type 2 diabetes (T2D) is a highly prevalent chronic metabolic disease with strong co-morbidity with obesity and cardiovascular diseases. There is growing evidence supporting that a crosstalk between mitochondria and the insulin-signaling cascade could be involved in the etiology of TD2 and insulin resistance. In this study, we investigated the molecular basis of this crosstalk by using systems biology approaches. We combined, filtered and interrogated different types of functional interaction data, such as direct protein-protein interactions, co-expression analyses and metabolic and signaling dependencies. As a result, we constructed the mitochondria-insulin (MITIN) network, which highlights 286 genes as candidate functional linkers between these two systems. The results of internal gene expression analysis of three independent experimental models of mitochondria and insulin signaling perturbations further support the connecting roles of these genes. In addition, we further assessed whether these genes are involved in the etiology of T2D using the largest genome-wide meta-analysis from the DIAGRAM consortium, involving 8,130 T2D cases and 38,987 controls. We found significant enrichment of T2D-associated SNPs in the genomic context of our linker genes, including four already confirmed and 14 additional SNPs, which when combined were also associated with increased fasting glucose levels according to MAGIC genome-wide meta-analysis (p = 2.8 x 10-7). This study highlights the potential of combining systems biology, experimental, and genome-wide meta-analyses mining for identifying novel genetic variants that increase vulnerability to complex diseases.

overall_design:
Three biological replicates of chronic insulin treatment and three biological controls were analyzed.

Contributors:
DIAGRAM Consortium
MITIN Consortium

first: Josep

first: Montserrat

last: Puiggros

first: Ayellet

middle: V

last: Segrè

first: Evarist

last: Planet

first: Eleonora

last: Sorianello

first: David

last: Sebastian

first: Sergio

last: Rodriguez-Cuenca

first: Vicent

last: Ribas

first: Sílvia

last: Bonàs-Guarch

first: Sorin

last: Draghici

first: Chenjing

last: Yang

last: Mora

first: Antoni

last: Vidal-Puig

first: Josée

last: Dupuis

first: Jose

last: Florez

first: Antonio

last: Zorzano

last: Torrents


title: MDM33 overexpression suppressor screen

status: Public on Jan 12 2016

city: Bayreuth

first: Alfons

middle: R

last: Weig

address: Universitaetsstrasse 30

department: Genomics and Bioinformatics

institute: University of Bayreuth

summary: We performed a genome-wide screen for genetic MDM33 interaction partners. Using the opposite approach of the well known synthetic dosage lethality (screening for deletion strains in which a non-toxic overexpression is associated with a synthetic growth arrest) we screened the whole genome for genes that are essential for the growth arrest associated with MDM33 overexpression. In a pooled collection of viable haploid gene deletion mutants, of which each is tagged with a unique identifying molecular ‘‘bar-code’’ sequence, the overexpression of MDM33 was induced using a galactose responsive promotor. While overexpression resulted in a growth arrest in almost all strains a small fraction of deletion mutants was able to grow under inductive conditions. We identified these strains using a microarray DNA hybridization technique that quantifies the abundance of the molecular barcodes. We propose that the affected genes are possible functional genetic interaction partners of MDM33.

overall_design: Replicate set 1: knockout strains transformed with empty vector and MDM33 overexpression vector; each transformation plated on glucose and galactose media; uptags and downtags were labelled and detected independently; Replicate set 2: same as replicate set 1, plus dye-swap;

first: Till

last: Klecker

first: Benedikt

last: Westermann


title: Identify gene expression signatures in the niche cells (CD45 negative) during proliferation of Hematopoietic stem cells (LSK)

status: Public on Jan 01 2016

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

institute: Genotypic Technology

summary: To further identify gene expression signatures in the niche cells (CD45 negative) during proliferation of Hematopoietic stem cells (LSK), we employed mice whole genome (60K) microarray expression profiling as a discovery platform to identify the up-regulated and down-regulated genes of the niche.

overall_design:
[Samples A-D] In this experiment a physiological stress model was created where the recipient mice were subjected to sub lethal radiation (700 CGy) following a transplantation of 30,000 LSK cells (HSCs). Bone marrow cells were isolated on day 0 (before transplantation) and day 10 (post transplantation of 30,000 LSK cells when maximum proliferation of HSCs was observed). Donor HSCs was sorted by FACS following RNA isolation and cDNA synthesis followed by single color global gene expression analysis.
Agilent one-color experiment,Organism:Mouse, Agilent Whole Genome Mouse 8x60k (AMADID: 26986)  , Labeling kit: Agilent Quick-Amp labeling Kit (p/n5190-0442)

first: Asok

last: Mukhopadhyay

first: Roy

last: Sushmita


title: MeDIP-on-Chip for the Ciliary derived stem/progenitor cells and their differentiated progeny.

status: Public on Jan 02 2016

type: Methylation profiling by genome tiling array

summary: Whole genome profiling of DNA methylation in Ciliary derived stem/progenitor cells and differentiated cells

overall_design: 6 samples total, 3 with CPE derived neurospheres and 3 with CPE derived differentiated progeny.

first: Srilatha

last: Jasty

first: S

last: Krishnakumar


title: Non-coding RNA expression in colorectal cancer

city: Aarhus

first: Morten

middle: Muhlig

last: Nielsen

address: Palle Juul-Jensens Bouleward 99

department: Department of Molecular Medicine

country: Denmark

institute: Aarhus University

type: Non-coding RNA profiling by genome tiling array

summary: Expression was measured in 113 colorectal cancer samples using a costumized array.

overall_design: Expression was measured in 113 human colorectal cancer samples using a custom-designed array containing 26,910 non-coding RNA features and a set of 6,856 protein-coding genes.

first: Claus

middle: L

last: Andersen

first: Torben

middle: F

last: Ørntoft

first: Anders

last: Lund

first: Jakob

last: Pedersen


title: The differentially expressed genes of A. ferrooxidans ATCC 23270 at different time after introduced fluoride

city: Changsha

first: Liyuan

last: Ma

address: 932 S. Lushan Rd.

institute: Central South University

summary: The deleterious fluoride ions, which released from fluoride in uranium during its bioleaching, strongly influenced microbial growth, energy intake, enzyme activity and relative metabolism. Whole-genome microarrays were used to obtain a comprehensive description of the molecular response by A. ferrooxidans ATCC 23270 at 4.8 mM fluoride stress.

sample_organism: Acidithiobacillus ferrooxidans ATCC 23270

overall_design: The experimental group was introduced 4mM fluoride at the mid-log phase. RNA from control samples were compared to the experimental samples taken at 10, 30, 60, 120 and 240 min after fluoride added. It was used to analyze the genome-wide expression profiling at different time after fluoride was introduced.

first: Qian

last: Li


title: Expression data from 9-day-old and 21-day-old rat Sertoli cell.

city: Shanghai

first: Xiaoqin

last: Yin

state: Shanghai

address: No. 355 Luding Road, Shanghai 200062, P.R.China.

department: Shanghai Children’s Hospital

institute: School of medicine, Shanghai Jiao Tong University

type: Genome binding/occupancy profiling by array

summary:
9-day-old Sertoli cells have a stronger proliferative activity compared with 21-day-old Sertoli cells.
We used microarrays to detail the global programme of gene expression underlying cellularisation and identified distinct classes of up-regulated and down-regulated genes during this process.

overall_design: Rat Sertoli cell were selected at postnatal day 9 and postnatal day 21 for RNA extraction and hybridization on Affymetrix microarrays. We sought to obtain the differentially expressed genes that were involved in cell proliferation, cell cycle, and cell death which were associated with the function of Sertoli cell.

first: Dongmei


title: Gene Expression Profiles of tumor sorted fractions demarcating cancer stem cell heirarchy using PKH dye in ovarian cancer xenograft tumor

city: Pune

first: Sharmila

last: Bapat

address: NCCS Complex, Ganeshkhind

institute: National Centre for Cell Science

summary: Our earlier report states isolation of ovarian cancer stem cell heirarchy using membrane labeling PKH26/67 dyes (Kusumbe and Bapat Cancer Research. 2009) in a xenograft model. We earlier reported that ovarian cancer is a stem cell disease with isolation of cell line (A4T) from a patient with Grade IV serous adenocarcinoma (Bapat et al. Cancer Research. 2005). A4T cells were labelled with PKH26 membrane labeling dye, flourescence intensity was quantified and set as 100% dye retaining cells (PKHhi) with flow cytometery. 2.5x10^6 P65 A4PKH26 labeled cells were injected s.c in NOD/SCID mice, while unlabeled cells were also injected for generation of control tumors .  Mice were observed for tumor formation and tumors were harvested at day 28 (4 weeks) and processed  for collagenase digestion for preparation of single cell suspension. Tumor cells were acquired on BD FACS Aria II across PE channel of blue laser. Cells retaining dye intensity as that of preinjected cells were gated as PKHhi while cells exhibiting complete dye depletion were gated as PKHneg using unlabeled tumor cells as control;  while cells showing intermediate label intensity were gated as PKHlo. Details of the flow cytometry analysis and sorting are published in our earlier reports (Kusumbe and Bapat Cancer Research. 2009).

overall_design: PKHhi  PKHlo and  PKHneg were sorted with 99% purity and 1x10^5 cells from each fraction was subjected to RNA isolation, labeling and microarray analysis. RNA of each fraction was labeled with Cy3 and designated as A4PKHhi, A4PKHlo and A4PKHneg. Three samples of each were chosen for hybridization. Custom Agilent Human whole Gene Expression Microarray 8x60K designed by Genotypic Technology Private Limited.(AMADID: 27114);Labeling kit: Agilent Quick-Amp labeling Kit (p/n5190-0442)

middle: A

first: R

last: Naik


title: Microarray analysis of the deletion of transcription regulator SurR in the hyperthermophilic archaeon Thermococcus kodakarensis

city: Sanda

first: Ryota

last: Hidese

state: Hyogo

address: Gakuen 2-1

department: School of Science and Technology

institute: Kwansei-Gakuin University

summary: Thermococcus kodakarensis preferentially utilizes amino acids as carbon and energy sources in the presence of elemental sulfur as a terminal electron acceptor, while it can assimilate and grow on starch or pyruvate using proton as a terminal acceptor, generating hydrogen in the absence of elemental sulfur. SurR is a transcriptional regulator controlling hydrogen and elemental sulfur metabolism. To identify the genes that are under the regulation of Tk-SurR, we investigated the transcriptional profiling of Tk-SurR deletion strain grown in the presence of elemental sulfur at 85˚C by comparing with the host strain, KU216.

overall_design: One-condition experiment, KU216 vs. DTS cells. Technical replicates: 2 DTS grown in the presence of elemental sulfur at 85˚C, independently measured. One replicate per array.

first: Keita

last: Yamashita

first: Shinsuke

last: Fujiwara

first: Tamotsu

last: Kanai

first: Haruyuki

last: Atomi

first: Tadayuki

last: Imanaka


title: Gene expression analysis of tumor sorted fractions demarcating cancer stem cell hierarchy and DNA content based ploidy

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

overall_design: Refer to individual Series


title: Genome wide host gene expression analysis in duck lungs infected with highly or low pathogenic H5N1 avian influenza virus

city: bhopal

first: Anamika

last: Mishra

state: Madhya Pradesh

address: Anand Nagar

department: Animal Genetics

institute: NIHSAD

summary: The underlying molecular mechanisms of pathogenesis and outcome of disease to different pathotypes of H5N1 influenza infection in ducks remain unclear. For that, we studied genome wide host gene expression of lung tissues infected with A/duck/India/02CA10/2011(AD2011) H5N1 virus and A/duck/Tripura/103597/2008 (AD2008) H5N1 virus in ducks using custom designed microarray.  AD2011 is highly pathogenic whereas AD2008 is low pathogenic to ducks. Comparative analysis of differentially expressed genes revealed that 688 genes were commonly expressed, 877 and 1556 genes are uniquely expressed to infection with AD2011 and AD2008 virus isolate, respectively. The up-regulation of cytokines genes OAS, IL1B, IL17, IFITM2, CCL4, CXCR4, STAT3, TGFB1 and TGFB2 in the lungs tissues may cause high mortality in ducks infected with AD2011 virus.  The expression of important antiviral immune genes IFIT5, IFITM5, RSAD2, EIF2AK2 (PKR), Mx, β-defensins, TRIM23 and SLC16A3 to AD2008 infection, but not in AD2011 infection, cause the host may fine-tune their innate immune responses and prevent from cytokines storms and tissue damage. Several immune related Gene ontology (GO) terms and immune pathways activated were qualitatively similar but quantitatively different to both virus infections.  Based on these findings, we conclude that subtle differences in host immune responses may determine the different outcome of H5N1 infection in ducks.

overall_design: Agilent Custom Duck  Gene Expression 8X60k (AMADID: G4102A_059612) designed by Genotypic Technology Private Limited , Labeling kit: Agilent Quick-Amp labeling Kit (p/n5190-0442)

first: Pradip

middle: B

last: Ranaware

first: Ashwin

last: Raut

first: Diwakar

middle: D

last: Kulkarni

first: Periyasamy

last: Vijayakumar

first: Avneesh

last: Kumar


title: Expression profiling of PEG induced water stress responsive genes in Eucalyptus grandis

first: Genotypic

last: technology

summary: The study was conducted to identify differentially expressed polyethylene glycol (PEG) induced water stress responsive genes in E. grandis. Forty day old rooted cutting of E. grandis was subjected to -0.225 MPa PEG treatment and total RNA was isolated from leaves of water treated control and PEG treated samples after three hours of treatment. The differential expression of water stress responsive genes was analyzed using microarray technique.

overall_design: Agilent two-color experiment, Organism: Eucalyptus,Custom Agilent  Eucalyptus 8x60k Microarray Gene expression  (AMADID: 59849 ) designed by Genotypic Technology Pvt.Ltd.

first: Modhumita

last: Dasgupta

first: Veeramuthu

last: Dharanishanthi


title: Molecular Characterization of Spontaneously Transformed Epithelial Murine Colon Cell Lines as a Model of Human Colorectal Neoplasia (CGH)

city: Bethesda

first: Hesed

middle: Maria

last: Padilla-Nash

state: MD

address: 50 South Drive

department: Genetics Branch

institute: NCI

summary:
To characterize a series of mouse colon cells that have become spontaneously transformed over time in order to identify the chromosomal and genomic alterations that take place during the development of tumorigenesis.
Colorectal cancer is the third common malignancy in the United States. The stepwise progression from adenoma to carcinoma is accompanied by specific genomic alterations.  Existing mouse models of human colon cancer have been induced by chemicals, viruses, or through genetic manipulation.   Presented here is a unique mouse model of spontaneous transformation designed to identify the sequential steps of tumorigenesis.     Normal epithelial colon cells were selectively isolated from the large intestine from eight different isogenic five-six week old C57BL/6 mice.  Primary colon cells were grown in vitro with reduced serum concentration. The cells were sequentially recovered from culture based on distinct morphological changes: first, when the cells were in the pre-immortal stage and established as adherent cultures; second, as the cells bypassed crisis, increased their mitotic activity and became immortal; third, at early transformation, as the cells first formed foci; fourth, mid-transformed where the cells had higher proliferation rates in later passages; and finally, late transformed with  rapid proliferation, contact inhibition, and multiple foci. The cells within each stage were analyzed using the molecular cytogenetic techniques of spectral karyotyping (SKY) and array comparative genomic hybridization (aCGH), and gene expression profiling.  The late transformed cells were injected into nude mice to assess their tumorigenic potential.      Spectral karyotyping revealed many recurrent structural and numerical aberrations, specifically in the late transformed cells.  Loss of chromosome 4 is a consistent chromosomal aberration observed in all stages of the transformed colon cells, as well as in other tissues during the process of spontaneous transformation. Array CGH identified a pattern of gains and losses, and showed deletions of APC and Trp53 as well as a gain of Kras similar that observed in human colorectal cancer.  Gene expression profiling identified the deregulation of several genes known to be involved in the progression of human colon cancer.   Tumors resulted from three of the eight late transformed cultures confirming tumorigenic potential. Ultimately, the molecular characterization of spontaneously transformed murine epithelial colon cells indeed recapitulated the step wise progression of human colon cancer, and will prove to be an invaluable system in which to test potential rational intervention strategies.

overall_design: Mouse colon epithelial cells were isolated from the colon of 8 isogenic C57BL\6 mice. These cells were grown in reduced serum and over time spontaneously became immortal and transformed. Our objective is to compare these changes to those that occur during human colon cancer development.

first: Nicole

last: McNeil


title: Genome-wide expression analysis of xylogenesis -related genes in Eucalyptus tereticornis

summary: The expression pattern of transcripts involved in secondary development was determined in four genotypes of E. tereticornis using 8x60K Gene chip. The genome-wide expression data was used to develop a gene co-expression network for xylogenesis.

overall_design: Agilent one-color experiment, Organism: Eucalyptus,Custom Agilent  Eucalyptus 8x60k Microarray Gene expression  (AMADID: 59849 ) designed by Genotypic Technology Pvt.Ltd.


title: Lasting effects of early exposure to temperature on the gonadal transcriptome at the time of sex differentiation in the European sea bass, a fish with mixed genetic and environmental sex determination

status: Public on Jan 17 2016

first: Noelia

middle: T

last: Díaz Blanco

state: Barcelona

address: Passeig Marítim de la Barceloneta 37-49

department: Marine Renewable Resources

institute: Institute of Marine Sciences (ICM-CSIC)

summary:
Background: Sex in fish is plastic and in several species can be influenced by environmental factors. In sensitive
species, elevated temperatures have a masculinizing effect. Previous studies on the effects of temperature on gene
expression have been restricted to a few cognate genes, mostly related to testis or ovarian development, and analyzed
in gonads once they had completed the process of sex differentiation. However, studies on the effect of temperature
at the whole gonadal transcriptomic level are scarce in fish and, in addition, temperature effects at the time of sex
differentiation at the transcriptomic level are also unknown. Here, we used the European sea bass, a gonochoristic
teleost with a polygenic sex determination system influenced by temperature, and exposed larvae to elevated
temperature during the period of early gonad formation. Transcriptomic analysis of the gonads was carried out about
three months after the end of temperature exposure, shortly after the beginning of the process of sex differentiation.
Results: Elevated temperature doubled the number of males with respect to untreated controls. Transcriptomic
analysis of early differentiating female gonads showed how heat caused: 1) an up-regulation of genes related to
cholesterol transport (star), the stress response (nr3c1) and testis differentiation (amh, dmrt, etc.), 2) a decrease in the
expression of genes related to ovarian differentiation such as cyp19a1a, and 3) an increase in the expression of several
genes related to epigenetic regulatory mechanisms (hdac11, dicer1, ehmt2, jarid2a, pcgf2, suz12, mettl22).
Conclusions: Taken together, the results of this study contribute to the understanding of how the early environment
sets permanent changes that result in long-lasting consequences, in this case in the sexual phenotype. Results also
show the usefulness of comparing the effects of heat on the behavior of cognate genes related to sex differentiation
as well as that of genes involved in establishing and maintaining cell identity through epigenetic mechanisms.

overall_design: Whole gonad transcriptome analysis from 10 individuals: 5 individuals early reared at a low temperature (15°C) and 5 individuals early reared at high temperature (21°C).

last: Díaz

first: Francesc

last: Piferrer


title: Gene Expression Profiles of tumor sorted fractions demarcating genetic instability using DNA-RNA content based cell cycle analysis in ovarian cancer xenograft tumor

first: Sharmila

last: Bapat

summary: Our earlier report states role of genetic instability and aneuploid cells in drug resistance and tumor recurrence. Hence segregating tumor based on DNA content is a good model to study genetic in stability. We have earlier reported isolation of cell line  (A4T) from a patient with Grade IV serous adenocarcinoma (Bapat et al. Cancer Research. 2005). Xenograft generated  by injecting A4T cells in NOD/SCID mice exhibited genetic instability (Kusumbe and Bapat Cancer Research. 2009; Naik et.al Oncogene 2015).  We generated xenograft by injecting 2.5x106 A4T P65 s.c in NOD/SCID mice. Mice were observed for tumor formation and tumors were harvested at day 28 (4 weeks) and processed  for collagenase digestion for preparation of single cell suspension. Further cells were subjected to staining with Hoechst (33342) for 45min at 37˚C followed by pyronin Y for  45min at 37˚C and processed for FACS sorting. Staining profile was acquired on BD FACS Aria II across UV laser for Hoechst and PE channel for PyroninY with linear scale. Details of the Hoechst pyronin Y based ploidy and cell cycle analysis are published in our earlier reports (Kusumbe and Bapat Cancer Research. 2009; Naik et.al Oncogene 2015). DNA content of cell line injected is considered as euploid while the higher genetic content is called as aneuploid.

overall_design: Euploid and  aneuploid were sorted with 99% purity and 1x105 cells from each fraction was subjected to RNA isolation, labeling and microarray analysis. RNA of each fraction was labeled with Cy3 and designated as A4Euploid and A4Aneuploid. Three samples of each were chosen for hybridization.

first: S

first: R

last: Naik


title: Transcriptional analysis of apoptotic cerebellar granule neurons following rescue by Gip, Sp, Pacap and Igf1

city: Catania

first: Sebastiano

last: Cavallaro

state: Catania

address: Via Paolo Gaifami 18

institute: CNR-ISN

summary: Primary cultures of Cerebellar Granule Neurons (CGNs) have been extensively utilized to examine the signal transduction mechanisms underlying neuronal apoptosis. We conducted whole-genome expression profiling to decipher the transcriptional program controlling the apoptotic/survival switch in cerebellar granule neurons (CGNs) following the induction of apoptosis by serum and potassium deprivation and their rescue by gastric inhibitory polypeptide (Gip), substance p (Sp), insulin-like growth factor-1 (Igf1) or pituitary adenylyl cyclase-activating polypeptide (Pacap). Our results reveal the transcriptional changes intersecting neuronal apoptosis and survival and form the basis for further functional analyses and pharmacological exploitation to identify neuroprotective drugs.

overall_design: After six days “in vitro” (DIV), extracellular KCl of CGNs was shifted from 25 to 5 mM for neuronal apoptotic death induction. After two washes with serum-free BME containing 5 mM KCl, neurons were incubated with the same medium for 6 h (K5), while control neurons were incubated with serum free medium supplemented with 25 mM KCl (K25). K5 neurons were also treated with a maximal effective dose of Gip, Sp, Igf1 and Pacap.  Four biological replicates (derived from the same litter) for each of the experimental conditions (K25, K5, K5 + Gip; K25, K5, K5 + Sp; K25, K5, K5 + Igf1; K25, K5, K5 + Pacap) were analyzed.

middle: S


title: Silica-mediated airway chronic inflammation promotes lung carcinogenesis through the activation of preneoplastic lesions in the context of an immunosuppressive microenvirontment

status: Public on Jan 03 2016

city: Pamplona

first: Daniel

last: Ajona

address: Pio XII, 55

institute: CIMA

summary:
Basic studies on preneoplastic lesions are important to determine the molecular alterations that take place in early steps of lung carcinogenesis. Little is known about the molecular events preceding the development of lung cancer in the context of an inflammatory environment. In this study we report the generation of a chemical-induced lung carcinogenesis mouse model in the presence of silicotic chronic inflammation. Silica-induced lung inflammation, strongly promoted incidence of lung cancer in mice treated with NDMA, a carcinogen found in tobacco smoke.
Histological and molecular analysis revealed that permanent inflammation contributed to lung tumorigenesis through the adquisition of preneoplastic changes in lung epithelial cells. Inflammatory milieu increased the expression of PDCD1, TGFβ-1, MCP-1, LAG3, and Foxp3 and the presence of regulatory T cells within preneoplastic lesions. In addition concomitant chronic inflammation changed the K-ras mutational profile of the generated tumors from Q61R to G12D transition. In summary, these data identify early molecular mechanisms underlying lung carcinogenesis in an inflammatory context at different steps, providing a novel approach for the identification of drivers from preneoplastic to neoplastic lesions

overall_design: Gene expression profile was analyzed in 11 individual lesions (8 adenomas and 3 adenocarcinomas) from the NDMA-silica treated mice and 5 lesions (2 adenomas, and 3 adenocarcinomas) from NDMA-only treated mice

first: Freire

last: Javier

first: Ruben

last: Pio

first: Luis

middle: M

last: Montuenga


title: Cytokeratin-19 positivity is acquired along cancer progression and does not predict cell origin in rat hepatocarcinogenesis (I)

city: CAGLIARI

first: AMEDEO

last: COLUMBANO

state: CA

address: VIA PORVELL 4

department: DIPARTIMENTO DI SCIENZE BIOMEDICHE

institute: UNIVERSITA' DEGLI STUDI DI CAGLIARI

summary: Analysis of early changes in the R-H model of carcinogenesis in order to investigate the relationship between oval cell proliferation and preneoplastic foci

overall_design: 2 controls, 6 Oval cells, 5 Preneoplastic foci

first: Pia

last: Sulas


title: ChIP-on-Chip for the Ciliary derived stem/progenitor cells and their differentiated progeny.

first: Genotypic

last: technology

type: Genome binding/occupancy profiling by genome tiling array

summary: Whole genome profiling of histone methylation (H3K4me3, H3K27me3 and RNA Pol II) in Ciliary derived stem/progenitor cells and differentiated cells. In the present study we focus on the cellular differentiation that involves loss of pluripotency and gain of lineage and cell type-specific characteristics and we show developments from adult ciliary derived stem/progenitor cells to differentiated retinal neurons/glial cells of human cadaveric eyes in vitro.

overall_design: Ciliary pigment epithelial cells isolated from human cadaveric eye balls were cultured in the presence of mitogens like Epidermal Growth Factor (EGF) and Fibroblast Growth Factors (FGF) to generate neurospheres (Stem/progenitor population). The generated neurospheres were plated on laminin and poly-D-lysine-coated cover slips in the presence of the Brain derived neurotrophic factor (BDNF), Retinoic acid (RA) and 10% FBS for the differentiation (Retinal neuron/glial cells). Global Methylation patterns of histone H3K4me3, RNA Pol II and H3K27me3 were analysed in the present study. This work would provide an outline of epigenetic modifications in ciliary derived stem/progenitor cells and the progeny that underwent differentiation into retinal neurons/glial cells and present that specific histone methylations are involved in gene expression reprogramming during the process of differentiation.

first: Srilatha

last: Jasty

last: Krishnakumar


title: HT-project: Expression profiling after prolonged experimental febrile seizures suggests structural remodeling in the hippocampus

first: Marian

last: Groot Koerkamp

summary: Febrile seizures are the most prevalent type of seizures among children up to 5 years of age (2-4% of Western-European children). Complex febrile seizures are associated with an increased risk to develop temporal lobe epilepsy. To investigate short- and long-term effects of experimental febrile seizures (eFS), we induced eFS in highly febrile convulsion-susceptible C57BL/6J mice at post-natal day 10 by exposure to hyperthermia (HT) and compared them to normotherm-exposed (NT) mice. We detected structural re-organization in the hippocampus 14 days after eFS. To identify molecular candidates, which entrain this structural re-organization, we investigated temporal changes in mRNA expression profiles eFS 1 hour to 56 days after eFS. We identified 931 regulated genes and profiled several candidates using in situ hybridization and histology at 3 and 14 days after eFS. This is the first study to report genome-wide transcriptome analysis after eFS in mice. We identify temporal regulation of multiple processes, such as stress-, immune- and inflammatory responses, glia activation, glutamate-glutamine cycle and myelination. Identification of the short- and long-term changes after eFS is important to elucidate the mechanisms contributing to epileptogenesis.

overall_design: Acute, short-, and long-term effects of prolonged febrile seizures on gene expression were investigated in whole hippocampal samples. Samples were taken from C57BL/6J animals one hour (HT n = 8, NT n = 8), three days (HT n = 6, NT n = 6), fourteen days (HT n = 6, NT n = 6), and fifty-six days (HT n = 6, NT n = 6) after HT. Two-channel oligonucleotide microarray analysis was performed with an NT and HT sample on the same chip, including a dye-swap (technical replicate). 3 failed hybridizations were omitted from further analysis.

first: Bart

last: Jongbloets

first: Koen

last: van Gassen

first: Anne

last: Kan

first: Anneke

last: Olde Engberink

first: Marina

last: de Wit

first: Inge

middle: G

last: Wolterink-Donselaar

middle: J

first: Onno

last: van Nieuwenhuizen

first: Frank

last: Holstege

first: Pierre

middle: N

last: de Graan