title: Transcriptional profiling of turkey muscle satellite cells transfected with MGP-siRNA during proliferation and differentiation

summary: In this study, we directly compared turkey muscle satellite cell gene expression between satellite cells with the gene Matrix Gla Protein (MGP) knocked down by siRNA transfection and those transfected with a lipofectamine control using our 6K Turkey Skeletal Muscle Long Oligo (TSKMLO) microarray (GPL9788).  The MGP gene was previously identified as differentially expressed by genetic line and during development of turkey skeletal muscle (Sporer et al., 2011). Gene expression changes were investigated in satellite cells after 72 h of proliferation and after 48 h of differentiation. We identified novel candidate genes and pathways as playing potentially crucial roles in the MGP-mediated effects on the normal processes of proliferation and differentiation in turkey satellite cells previously identified by Velleman et al. (submitted).

overall_design: This experiment was designed to investigate the role of MGP expression in turkey satellite cells during two crucial processes in muscle development: proliferation and differentiation.  Satellite cells were isolated from 7-week-old turkeys from the RBC2 line.  Cells were transfected with either MGP siRNA or a lipofectamine control; MGP expression was knocked down by over 50% with siRNA transfection (Velleman et al., submitted).  Satellite cells were then induced to proliferate for 72h or differentiate for 48h; culture plates from each stage (n=4) were frozen until RNA extraction.   Microarrays directly compared the MGP -knockdown to control from each of 4 culture plates and utilized a dye swap to equal 8 arrays for each of the cell developmental stages, proliferation and differentiation, and 16 arrays for the overall experiment investigating the role of MGP expression in satellite cell development and function.  Hybridizations were performed in random order.

first: Robert


title: affy_med_2011_06-Analysis of the Medicago noot mutant

status: Public on Jun 01 2012

city: evry

first: stephanie

last: huguet

address: 2 rue gaston cremieux

country: France

institute: inra

summary: affy_med_2011_06 - affy_med_2011_06 - Legume plants establish a symbiotic interaction with soil bacteria called rhizobia. A complex molecular dialogue between the two partners is necessary for the successful infection and organogenesis processes that will ultimately result in the formation of a nitrogen fixing nodule. During a M. truncatula Tnt1 mutant screen, a new class of symbiotic mutant called noot (nodule root) was identified. This original single recessive mutant develops a root in apical position of nodules that are colonized by bacteria and functional for nitrogen fixation. This conversion suggests that the legume nodule morphogenetic pathway may be derived from a root program. We cloned the NOOT gene and showed that it corresponds to Pisum sativum COCH (Ferguson and Reid, 2005, Plant Cell Physiol 46, 1583-1589). The goal of this project is to compare the transcriptomes from wild type nodules and roots to the noot nodule one. This will allow us to unravel the similarity and differences between the wild type and mutant nodule transcriptomes but also to know which developmental pathway is under the control of the NOOT gene. --Seeds of the WT and noot mutant lines (two mutant alleles: Tnk507 and NF2717) were surface sterilized and placed at 4°C for three days on a minimal BNM medium square plate (12cm X 12cm). Seeds were germinated at room temperature and 10 seeds were placed in a row on nitrogen poor (BNM) plate. Seedlings were inoculated using Sinorhizobium meliloti Rm41 for nodule production. Some WT plants were not infected by the bacteria in order to collect roots. Nodules and roots were harvested 18 to 21 days post inoculation. Each experimental repetition (3 WT nodules, 3 WT roots and 2 mutant nodules of each allele) was harvested at a separated day. RNA preparations were done using a Quiagen Kit.

platform_organism:
Sinorhizobium meliloti
Medicago sativa
Medicago truncatula

overall_design: 10 arrays - Medicago; gene knock out,organ comparison

first: Pascal

last: Ratet

first: Samuel

last: Mondy

first: Stephanie

last: Huguet

first: Sandrine

last: Balzergue

first: Marie-Laure

last: Martin-Magniette


title: Characterization and gene expression analysis of the cir multi-gene family of Plasmodium chabaudi chabaudi (AS)

city: Singapore

first: Peter

last: Preiser

address: 60 Nanyang Drive, School of Biological Sciences

country: Singapore

institute: Nanyang Technological University, School of Biological Sciences

summary: The pir genes comprise the largest multi-gene family in Plasmodium, with members found in P. vivax, P. knowlesi and the rodent malaria species. Despite comprising up to 5% of the parasite genome, little is known about the functions of the proteins encoded by pir genes. P. chabaudi causes chronic infection in mice, which may be due antigenic variation. In this model, pir genes are called cirs and may be involved in this mechanism allowing evasion of host immune responses. We have annotated the cir repertoire and performed detailed bioinformatic characterization of the encoded CIR proteins. Two major sub-families were identified: A and B, which display different amino acid motifs, and are thus predicted to have undergone functional divergence. The expression of all cirs was analyzed via RNA sequencing and microarray. Up to 40% of cir genes were expressed in the parasite population during infection, including members of both sub-families. Dominant cir transcripts could also be identified. Finally, specific cir genes were expressed at different time points during the blood stages of infection. Together our data characterizing the cir genes and their expression throughout the intra-erythrocytic cycle of development indicate that CIR proteins are likely to be important for parasite survival in the host.

overall_design: P. chabaudi AS is a highly synchronous parasite for which development in the blood follows its host’s circadian rhythm. Twelve time-points were then collected; one every two hours, to cover the entire 24 h cycle of blood stage development. At the peak of parasitaemia, one mouse was sacrificed at each time point and thin blood films were made and stained with Giemsa for optical microscopy. The pan-rodent microarray was designed using the OligoRankPick program as previously described: Liew, K et al.2010, Defining species specific genome differences in malaria parasites. BMC genomics 11,128. The RNA preparation, Cy-dye coupling to cDNA, hybridization and slide scanning were performed as described by Bozdech and colleagues Bozdech, Z et al 2003, The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum. PLoS Biol 1, E5.

first: Guangan

last: Hu

first: Kingsley

middle: J

last: Liew

first: Sachel

last: Mok

first: Amaladoss

last: Anburaj

first: Onguma

last: Natalang

middle: R

first: Zbynek

last: Bozdech


title: Differentially regulated genes induced in Mycobacterium avium subspecies paratuberculosis by in vitro acid-nitrosative multi-stress

city: Amherst

first: Andrea

last: Cossu

state: MA

address: 102 Holdsworth way

department: Department of Food Science

country: USA

institute: University of Massachusetts, Amherst

summary: Transcriptional profile of Mycobacterium avium subspecies paratuberculosis in in vitro acid-nitrosative multistress, comparing untreated control cells and bacteria under multi-stress.

platform_organism: Mycobacterium avium subsp. paratuberculosis K-10

overall_design: Two-condition experiment, MAP-K vs. MAP-ACID-NO treated. Biological replicates: 3 controls, 3 Acid-NO treated, independently grown and harvested. In controls and Acid-NO treated cells, good quality RNA samples obtained from each pellet were pooled together and used for microarray experiments to get an average of three separate experiments, four replicates per array.

first: Valentina

last: Rosu


title: Transcriptional profiling of equine chondrocyte de-differentiation in culture

city: Lexington

first: Michael

middle: J.

last: Mienaltowski

email: M.Mski@uky.edu, mmienalt@health.usf.edu

state: KY

address: 108 Gluck Equine Research Center

department: Veterinary Science

institute: University of Kentucky

summary:
Monolayer cultures of primary chondrocytes undergo morphological changes that have been broadly characterized as de-differentiation. Transcriptional profiling was used to evaluate changes in gene expression during this process. Articular cartilage was harvested from a single Standardbred horse; the chondrocytes were isolated and then maintained in monolayer culture for up to 14 days. Chondrocytes were collected on Day 1 and Day 14 of culture and snap frozen in liquid nitrogen. Total RNA was isolated, subjected to one round of linear RNA amplification, and then applied to an equine-specific cDNA microarray composed of 9322 elements. Three biological replicates were analyzed at each time point using a dye-swap experimental design. One hundred six transcripts were present at levels greater than or equal to five-fold higher in Day 1 chondrocytes relative to the cells collected at Day 14. Conversely, 68 transcripts were present at levels greater than or equal to five-fold higher in Day 14 chondrocytes. Northern blot hybridization validated the microarray data by confirming the down-regulation of steady state mRNA levels for type II procollagen and aggrecan core protein and the up-regulation of type I procollagen. Gene-by-gene and cluster analyses will be used to compare the process of “de-differentiation” in primary culture to the developmental stages of normal chondrocyte differentiation and to the fibrocartilage repair tissue that forms in osteoarthritic lesions.
Keywords: articular cartilage, de-differentiation, horse, cDNA microarray

overall_design: This is a direct comparison between one and fourteen day cultured chondrocyte transcriptomes. Three sets of technical replicates were compared. For each comparison and its dye-swap, one Day 1 technical replicate was randomly compared to one Day 14 technical replicate.

first: Arnold

last: Stromberg

first: James

middle: N

last: MacLeod


title: Testing the effect of coordinate overexpression of the lovK-lovR two component system on the Caulobacter transcriptome

city: East Lansing

first: Sean

last: Crosson

state: Michigan

address: 567 Wilson Rd

department: Dept. Microbiology and Molecular Genetics

institute: Michigan State University

summary: This experiment is testing the effects of coordinate overexpression of the lovK-lovR two-component system on gene expression in Caulobacter crescentus relative to an empty vector control strain.

overall_design: Transcription in two independent cultures of a lovK-lovR overexpression strain (FC438) are compared to two independent cultures of an empty vector control strain (FC423)


title: Transcriptional profiling of 14 regulators required for Salmonella virulene

status: Public on May 31 2012

city: Rockville

first: Bryan

last: Frank

state: MD

address: 9704 Medical Center Drive

department: Dept of Infectious Diseases

institute: The J. Craig Venter Institute

summary: To cause a systemic infection, Salmonella must respond to many environmental cues during mouse infection and express specific subsets of genes in a temporal and spatial manner, but the regulatory pathways are poorly established. To unravel how micro-environmental signals are processed and integrated into coordinated action, we constructed in-frame non-polar deletions of 83 regulators inferred to play a role in Salmonella enteriditis Typhimurium (STM) virulence and tested them in three virulence assays (intraperitoneal [i.p.], and intragastric [i.g.] infection in BALB/c mice, and persistence in 129X1/SvJ mice). Overall, 35 regulators were identified whose absence attenuated virulence in at least one assay, and of those, 14 regulators were required for systemic mouse infection, the most stringent virulence assay. As a first step towards understanding the interplay between a pathogen and its host from a systems biology standpoint, we focused on these 14 genes. Transcriptional profiles were obtained for deletions of each of these 14 regulators grown under four different environmental conditions. These results, as well as publicly available transcriptional profiles, were analyzed using both network inference and cluster analysis algorithms. The analysis predicts a regulatory network in which all 14 regulators control the same set of genes necessary for Salmonella to cause systemic infection. We tested the regulatory model by expressing a subset of the regulators in trans and monitoring transcription of 7 known virulence factors located within Salmonella pathogenicity island 2 (SPI-2). These experiments validated the regulatory model and showed that the response regulator SsrB and the MarR type regulator, SlyA, are the terminal regulators in a cascade that integrates multiple signals. Furthermore, experiments to demonstrate epistatic relationships showed that SsrB can replace SlyA and, in some cases, SlyA can replace SsrB for expression of SPI-2 encoded virulence factors.

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S

overall_design: A total of 55 RNA pools from 14 strains in 4 conditions were prepared. An additional 12 RNA samples were prepared from the parental strain. All were subjected to microarray analysis according to the procedures described  (Porwollik S et al. 2003 Nucleic Acids Res 31: 1869–1876). Genomic DNA from 14028s was isolated and used as reference for hybridization.

first: Hyunjin

last: Yoon

first: Fred

last: Heffron

first: Joshua

last: Adkins

first: Charles

last: Ansong


title: Comparing the transcriptional profiles of a Caulobacter crescentus phyR null mutant to a xylose-inducible phyR overexpression strain

summary:
phyR encodes a general stress regulator protein that is conserved among several alpha-proteobacteria.
This experiment is quantifying transcription in two Caulobacter strains:  one strain is overexpressing phyR (gene CC3477); the other carries a phyR in-frame deletion.  Both strains were cultured in M2 defined medium with xylose as the sole carbon source.  The first strain (FC626) carries a plasmid integrated into the xylX locus; phyR is fused to the xylX promoter in this plasmid, generating a xylose-inducible phyR overexpression strain.  The second strain (FC799) carries an in-frame deletion at the chromosomal phyR locus.

overall_design: Duplicate cultures of: 1) C. crescentus strain CB15 phyR in-frame deletion mutant , and 2) a xylose-inducible phyR overexpression strain, were cultured in M2 xylose defined medium and harvested at OD660=0.3


title: miRNA Expression in AMuLV Cell Lines upon STI571 Treatment

city: BERKELEY

first: Patty

middle: B

last: Garcia

state: CA

address: 439 LSA

institute: UC BERKELEY

summary: We conducted a screen for miRNAs that have a change in expression upon STI571 treatment of AMuLV pro-B cells. We used AMuLV pro-B cells as a model system to identify miRNAs important at the pro-B to pre-B transition in developing B cells in vivo.  Previous groups have shown that miRNAs are necessary for the pro-B to pre-B transition.  We hypothesize that specific miRNAs induced upon STI571 treatment, regulate important developmental programs and pathways to the pre-B stage of B cell development.

overall_design: AMuLV pro-B cells were treated with STI571 (2.5uM) for 12h. Three independently transformed AMuLV pro-B cells were untreated and treated and were analyzed against a reference pool generated with 2ug RNA from each of the samples.


title: Expression data from Shewanella oneidensis MR-1 in time series experiment

status: Public on May 01 2012

city: Boston

first: Qasim

middle: K

last: Beg

address: 44 Cummington St

department: Biomedical Engineering

institute: Boston University

summary: The sumitted data compares gene expression profile of Shewnaella oneidensis MR-1 on two different sets of media conditions (nutritionally rich LB medium and Lactate minimal medium)

overall_design: To explore the effect of various growth phases in Shewanella oneidensis MR-1, the genome-wide transcriptome profiles growth in two sets media was compared to each other. Strain was grown in chemostat at 20% O2 in batch culture. Samples were collected in duplicate from both experiments.

first: Mattia

last: Zampieri

first: Niels

last: Klitgord

first: Sara

last: Collins

first: Claudio

last: Altafini

first: Margrethe

middle: H

last: Serres

first: Daniel

last: Segre


title: shRNA mediated knockdown of TRA2B and SRSF3 in HEK293 cell line

city: Los Angeles

first: Erik

middle: S

last: Anderson

address: 6-567 MRL, 675 Charles E. Young Drive South

department: MBIDP

institute: UCLA

summary: We have independently knocked down TRA2B and SRSF3 in HEK293 cells to identify the sum of alternative splicing changes that results from depletion of each factor.  Each was compared to a control transfection of the hairpin vector alone.

overall_design: In this set, 9 total samples were analyzed.  There were three biological replicates for each of three conditions: knockdown control, TRA2B knockdown and SRSF3 knockdown.  Arrays were analyzed for gene expression using GeneBase and for alternative splicing using MADS+ and OmniViewer software.

first: Chia-Ho

last: Lin

first: Xinshu

last: Xiao

first: Peter

last: Stoilov

first: Christopher

last: Burge

first: Douglas

middle: L

last: Black


title: Transcriptional profiling of abdominal adipose tissue in juvenile broiler chickens divergently selected for abdominal fatness or leanness

status: Public on Apr 27 2012

city: Newark

first: Larry

middle: Albert

last: Cogburn

state: DE

address: 531 South College Ave.

department: Animal and Food Sciences

institute: University of Delaware

summary:
Chickens divergently selected for either high abdominal fat content (fat genotype) or low abdominal fat content (lean genotype) at SRA-INRA, France were used to profile abdominal adipose gene expression during juvenile development (1 to 11 weeks of age) and to identify differentially expressed genes associated with genotype and age. The fat line (FL) and lean line (LL) chickens are different in various phenotypic and metabolic measurements, including abdominal fatness, plasma glycemia and T3. The FL and LL chickens represent unique models for characterizing biomedical and agricultural traits. The Del-Mar 14K Chicken Integrated Systems microarrays were used for a transcriptional scan in abdominal adipose during juvenile development using a balanced block hybridization design. Fluorescence intensities were normalized within array (without background subtraction), and between array (aquantile method) in LIMMA package R [Smyth, G. K. (2004) Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Statistical Applications in Genetics and Molecular Biology, Vol. 3, No. 1, Article 3] producing M-values (log-2 expression ratios) and A-values (average log-2 expression values). Normalized values were analyzed using a two factor ANOVA model. A total of 3,669 unique differentially expressed functional genes were identified (FDR<0.05). Genes were determined to have a significant effect of age (3,222), genotype (344), or an age by genotype interaction (254). The differentially expressed genes include metabolic enzymes, acute phase proteins, growth factors, coagulation factors, immune factors and transcription factors involved in various pathways. Several of the functional genes are also identified as positional candidate genes within QTLs in an F2 population established from an intercross between the FL and LL lines.
Keywords: Divergently selected chickens, fatness, transcriptional profiling, differentially expressed genes

overall_design: A balanced block design was used for microarray hybridizations, where half of the birds of each genotype and age were labeled with Alexa Flour 647 (red) and the other half with Alexa Flour 555 (green). Four biological replicates were used for each genotype (FL or LL) at six different ages (1, 3, 5, 7, 9 and 11 wk).

middle: W

last: Resnyk

first: Jean

last: Simon

middle: A


title: Transcriptional  analysis of epithelial cells in grapefruit peel

status: Public on Apr 19 2012

city: Pullman

first: Siau Sie

last: Voo

state: WA

address: 100 Dairy Road

department: Institute of Biological Chemistry

institute: Washington State University

summary:
Epithelial cells (EC) lining the most inner layers of secretory glands in Citrus peel are hypothesized to be the specialized cells that synthesize citrus essential oil. The major biosynthetic pathway(s) for essential oil are therefore postulated to be specifically and highly active in EC; transcripts that are involved in the pathway(s) are expected to be highly up-regulated in the cells as well.
We performed cell-specific transcriptional analysis using GeneChip Citrus Genome Arrays to probe the global gene expression in EC during initial stage of essential oil biosynthesis and to identify groups of highly expressed genes in the EC.

overall_design: Grapefruits of two different sizes (diameters at 28 mm and 41 mm), at which points where biosynthesis of essential oil entering its active phase, were selected for the purpose of this experiment. For comparison, we selected parenchyma cells (PC), the non-oil-biosynthesizing cells, as the control cell type. Grapefruit peels were fixed, embedded in paraffin, sectioned and mounted on slides prior to cells isolation using laser microdissection and pressure catapulting. RNA was extracted from the isolated cells and then used for microarray hybridization. Transcriptional analysis were carried out by comparing transcript profiles between different cell types of the same time points, and same cell type at the different time points.

first: Siau

first: Derek

last: Pouchnik


title: Transcriptional study of the response of murine bone marrow-derived macrophages to TLR4 stimulation with LPS

status: Public on Mar 23 2012

city: Corvallis

first: Stephen

last: Ramsey

state: OR

address: Dryden Hall 208A

department: Biomedical Sciences

institute: Oregon State University

summary:
Atherosclerosis is a chronic inflammatory disease characterized by the accumulation of lipid-loaded macrophages in the arterial wall. Intimal macrophages internalize modified lipoproteins such as oxidized LDL (oxLDL) through scavenger receptors, leading to storage of excess cholesteryl esters in lipid bodies and a "foam cell" phenotype. In addition, stimulation of macrophage Toll-like receptors (TLRs) has been shown to promote lipid body proliferation. We investigated the possibility that there are transcriptional regulators that are common to both pathways for stimulating foam cell formation (modified lipoproteins and TLR stimulation), and identified the transcription factor ATF3 as a candidate regulator.

In this specific microarray experiment, we studied the transcriptional response of murine macrophages to stimulation with the TLR4 agonist, LPS. Bone marrow-derived macrophages from C57BL/6J mice were incubated in the presence or absence of LPS for 4 h, and then transcriptionally profiled using the Affymetrix Mouse Exon Array 1.0 ST. The goal was to study the pattern of transcript-level differential expression between the unstimulated and LPS-stimulated cells.

overall_design: Three female mice (strain C57BL/6J) were sacrificed at 8-12 weeks of age, and macrophages were derived from the femoral bone marrow using rhM-CSF. On day six, macrophages were divided into two treatment groups per animal, for a total of six samples. LPS was introduced into the medium for three samples (one from each animal) at 10 ng/mL on day seven, and after 4 h of incubation, RNA was isolated using Trizol. Labeled cRNA derived from the RNA samples was hybridized to Affymetrix Mouse Exon Array 1.0 ST GeneChips.  Microarray data were processed using transcript-level probesets, and are in log2 scale.

first: Kathleen

last: Kennedy

middle: E

last: Zak

first: Alan

last: Aderem


title: Distinct perturbation of the translatome by the anti-diabetic drug metformin

status: Public on May 21 2012

city: Stockholm

first: Ola

last: Larsson

department: Department of oncology-pathology

country: Sweden

institute: Karolinska Institutet

summary: Reduced cancer incidence has been reported among type II diabetics treated with metformin. Metformin exhibits anti-proliferative and anti-neoplastic effects associated with inhibition of mTORC1, but the mechanisms are poorly understood. We provide the first genome-wide analysis of translational targets of canonical mTOR inhibitors (rapamycin and PP242) and metformin, revealing that metformin controls gene expression at the level of mRNA translation to an extent comparable to that of canonical mTOR inhibitors. Importantly, metformin's anti-proliferative activity can be explained by selective translational suppression of mRNAs encoding cell cycle regulators via the mTORC1/4E-BP pathway. Thus, metformin selectively inhibits mRNA translation of encoded proteins that promote neoplastic proliferation, motivating further studies of this compound and related biguanides in cancer prevention and treatment.

overall_design: MCF7 cells were treated with rapamycin, metformin or PP242 at concentrations that inhibited proliferation to 50% of control. Both cytoplasmic and polysome-associated mRNA was extracted from treatments and a vehicle treated control and probed with microarrays.

first: Nahum

last: Sonenberg


title: Comparison of microRNA expression using different preservation methods of matched psoriatic skin samples

status: Public on Mar 22 2012

city: Hellerup

first: Marianne

middle: Bengtson

last: Løvendorf

address: Niels Andersens Vej 65

department: Dermato-Allergology

country: Denmark

institute: Gentofte Hospital

summary: MicroRNA expression profiling in matched lesional skin samples from 25 patients with psoriasis using the miRNA analysis platform miRCURY LNATM MicroRNA array (v. 11.0) (Exiqon). Aim: To explore the effect of three different preservation methods (Formalin-fixation paraffin-embedding (FFPE), frozen (FS) and OCT-embedding (OCT)) on miRNA expression levels in matched lesional skin samples from 25 patients with psoriasis.

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

overall_design: Three-condition experiment, FS vs. FFPE, OCT vs. FFPE and FS vs. OCT. Biological replicates: 25 matched samples from patients with psoriasis. One replicate per array.

first: John

last: Zibert

last: Hagedorn

first: Christian

last: Glue

first: Niels

last: Ødum

first: Mads

last: Røpke

first: Lone

last: Skov


title: Expression data from microdissected endosperm transfer cells (ETCs) of barley seeds during different developmental stages

status: Public on Apr 17 2012

city: Gatersleben

first: Johannes

last: Thiel

address: Corrensstrasse 3

country: Germany

institute: IPK-Gatersleben

summary: Endosperm transfer cells (ETCs) of barley grains/seeds are located at the maternal-filial boundary in seeds and fascilitate nutrient transfer from the mother plant into the filial endosperm tissue. Due to the difficult accessibility of ETCs inside the seed, signalling and metabolic pathways involved in differentiation processes of ETCs are poorly understood. To analyse ETC differentiation, we applied laser microdissection pressure catapulting (LMPC) coupled to transcriptome analysis at various developmental stages from cellularization to full functionality and ongoing modifications. ETC-specific transcriptome data identified candidate genes and associated pathways involved in distinct differentiation processes.

overall_design: Barley grains were harvested at 5, 7, 10 and 12 days after flowering/pollination (DAF) and immediately frozen in liquid nitrogen. In a cryostat (-20°C), middle parts were cut by a razor blade, glued onto sample plates by Tissue-Tek® O.C.T™ and 20 µm sections were mounted on PEN membrane slides (PALM, Bernried, Germany). Cryosections were stored for 7 days at -20°C until complete dryness. LMPC-based isolation of ETC tissue from cryosections has been done using the PALM® MicroBeam laser system. For each biological replicate, 50-70 sections from three independent grains were collected. Three biological replicates were generated from each time point (total number of samples = 12).

first: Swetlana

last: Friedel


title: Microarray CGH Profiling Of Serous Ovarian Tumours Identifies Novel Copy Number Alterations Associated with Patient Survival

city: London

first: Christopher

last: Jones

address: Paul O'Gorman Building, 72 Huntley Street

department: Gynaecological Oncology

country: United Kingdom

institute: UCL EGA Institute for Women's Health

type: Genome variation profiling by genome tiling array

summary: We used microarray CGH analysis with a tiling path BAC DNA microarray to profile DNA copy number alterations in 164 serous ovarian adenocarcinomas. Survival probabilities modelled by proportional hazards were used to stratify cases into good, intermediate or poor survival groups. Comparison of aCGH data from these groups was used to identify genomic alterations associated with patient survival.

overall_design:
A total of 984 cases of serous ovarian adenocarcinoma from three different studies were combined and Cox proportional hazards used to model survival using patient age, tumour stage and residual disease status as covariates. Survival probabilities (Pr) were extracted for all cases and used to stratify 384 cases for which microarray CGH data was available. From these, we identified 70 cases with poor survival (Pr>0.784) and 70 cases with good survival (Pr<0.35). aCGH data from these cases was provided to an iterative Support Vector Machine (SVM) routine to detect copy number changes associated with survival. Candidate regions were then validated by survival analysis in all 384 cases for which aCGH data was available.

This series contains aCGH data from 164 tumours from the MALOVA collection.

first: Jones

last: Christopher

first: Morris

last: James

first: Sher

last: Tanya

first: Ghani

last: Sumera

first: Ramus

last: Susan

first: Hogdall

last: Estrid

first: Blaakaer

last: Jan

first: Christensen

last: Lise

last: Clauss

first: Kruger-Kjaer

last: Susanne

first: Mackay

last: Alan

first: Jacobs

last: Ian

first: Gayther

last: Simon


title: How do consumers deal with stoichiometric constraints?

status: Public on Mar 13 2012

city: Notre Dame

first: Jacqueline

last: Lopez

state: Indiana

address: 019 Galvin Life Science Center

department: Biology

institute: University of Notre Dame

summary:
Determine gene expression in daphnia exposed to biotic and abiotic stressors.
Identify in Daphnia pulex unique gene regulatory patterns involved in the regulation of limited phosphorous.

overall_design: One-condition experiment: Exposed Daphnia pulex for 5 days to phosphorous-limited algae. Biological replicates: 4 exposures, 4 nonexposed controls, grown and harvested in groups of 20 daphnia. One replicate per array.

first: Puni

last: Jeyasingh

first: John

last: Colbourne


title: Identification of potential transcripts involved in chicken PGCs development

status: Public on Mar 30 2012

city: Seoul

first: JAE

middle: YONG

last: HAN

address: 1 Gwanak-ro, Gwanak-gu

department: Department of Agricultural Biotechnology

country: South Korea

institute: Seoul National University

summary: From the transcriptomics analysis, this study focused on the genes expressed in PGCs during germline development in early embryogenesis of chickens.

overall_design: Comparision of PGCs and GSCs

first: Bo

last: Lee

first: Jae

middle: Y

last: Han


title: Plant and bird presence strongly influences the microbial communities in soils of Admiralty Bay, Maritime Antarctica

city: Rio de Janeiro

first: Lia

last: Teixeira

state: RJ

address: Av. Carlos Chagas Filho, 373

country: Brazil

institute: Universidade Federal do Rio de Janeiro

summary: Understanding the environmental factors that shape microbial communities is crucial, especially in extreme environments, like Antarctica. Two main forces were reported to influence Antarctic soil microbes: birds and plants. Both birds and plants are currently undergoing unprecedented changes in their distribution and abundance due to global warming. However, we need to clearly understand the relationship between plants, birds and soil microorganisms. We therefore collected rhizosphere and bulk soils from six different sampling sites subjected to different levels of bird influence and colonized by Colobanthus quitensis and Deschampsia antarctica in the Admiralty Bay, King George Island, Maritime Antarctic. Microarray and qPCR assays targeting 16S rRNA genes of specific taxa were used to assess microbial community structure, composition and abundance and analyzed with a range of soil physico-chemical parameters. The results indicated significant rhizosphere effects in four out of the six sites, including areas with different levels of bird influence. Acidobacteria were significantly more abundant in soils with little bird influence (low nitrogen) and in bulk soil. In contrast, Actinobacteria were significantly more abundant in the rhizosphere of both plant species. At two of the sampling sites under strong bird influence (penguin colonies), Firmicutes were significantly more abundant in D. antarctica rhizosphere but not in C. quitensis rhizosphere. The Firmicutes were also positively and significantly correlated to the nitrogen concentrations in the soil. We conclude that the microbial communities in Antarctic soils are driven both by bird and plants, and that the effect is taxa-specific.

platform_organism: Bacteria Archaea

overall_design: The study was carried out at the Brazilian Antarctic Station Comandante Ferraz (EACF, 62°04’S, 58°21’W), located in Martel Inlet, Admiralty Bay, King George Island, Antarctic Peninsula, which is part of the South Shetlands Archipelago in Maritime Antarctica. It is a medium sized research station with a population of 10 to 15 people during the winter months (March to November) and about 60 people during the austral summer months (November to March). During the austral summers of 2006 – 2007 and 2008 – 2009, the vascular plants D. antarctica or C. quitensis were sampled, where both plants were found, in triplicate at six different sites: A – Arctowski (2006 – 2007), Q – Quimica (2006 – 2007), I – Ipanema (2006 – 2007), M – North Mountain (2008 – 2009), D – Demay Point (2008 – 2009), C – Copacabana (2008 – 2009) (Figure 1). Points A, C and D were located inside an environmental protected area. Point A is close to the Arctowski Polish Station and next to a colony of Adelie penguins (Pygoscelis adeliae), point C is next to the USA summer station Copacabana in a Gentoo penguin (P. papua) colony, and point D is near to a Polish refuge next to a colony of Chinstrap penguins (P. antarcticus). At point I, there were no penguin colonies present, but this section was used as a nesting site by local species of flying birds. Point Q was located in the vicinity of the EACF; thus there has been (and continues to be) an intense anthropogenic influence on this spot, which is not the case at the other sampling sites. Point M was located at the top of North Mountain, around 200 m altitude. This site has no influence from penguin colonies and only a few nests of skua (Catharacta sp.) were observed. At each sampling site, triplicate soil samples were taken for chemical and biological analyses, with the exception of the Arctowski site (A) where we only took two replicates. Each vascular plant sample was frozen (-20°C) at the EACF.

middle: C

first: Etienne

last: Yergeau

first: Fabiano

last: Balieiro

first: Marisa

last: Piccolo

first: Raquel

last: Peixoto

first: Alexandre

last: Rosado

first: Charles

last: Greer


title: Detection and mapping of species and strains from the diatom genus Pseudo-nitzchia (Bacillariophyceae) along the Oregon and Washington coast using microarray-based, field-deployable, rapid, high-resolution assay

city: Beaverton

first: Maria

last: Smit

address: 20000 NW Walker Rd

department: Environmental and Biomolecular Systems

institute: Oregon Health and Science University

summary:
DNA oligonucleotide microarrays were designed with 307 probes for 96 internal transcribed spacer (ITS1, located between 18S and 26S rRNA genes) sequences of known  species and strains from the genus Pseudo-nitzschia (Bacillariophyceae). In addition, microarrays also carried 1893 probes targeting ITS1 aequences of marine Crenarchaeota and Alphaproteobacteria of SAR11 clade. In order to assign microarray profiles to Pseudo-nitzschia ribotypes and species and to 'train' the data analysis system, we grew cultures of Pseudo-nitzschia in the laboratory with identities confirmed through rDNA sequence analysis. In total, 9 cultures and 35 environmental water samples were hybridized to microarrays, in some cases, in duplicate or triplicate.
Analysis of microarray data allowed us to identify and map Pseudo-nitzschia spp. in the coastal waters along Washington and Oregon coast of the Eastern Pacific Ocean, and to observe seasonal changes in diatom community composition.

sample_organism:
Pseudo-nitzschia
environmental samples
environmental samples
environmental samples
environmental samples

platform_organism:
Bradyrhizobium
Rhizobium
Skeletonema
Thalassiosira
Pseudo-nitzschia
Mesorhizobium
Roseovarius
uncultured marine crenarchaeote
uncultured Pelagibacterales bacterium

overall_design: Total DNA was isolated from 9 Pseudo-nitzschia laboratory cultures and 35 environmental water samples collected during 7 field campaigns in 2007-2009. The environmental samples were collected at distances of 5 to 55 km from the coast, along the following transects in the Pacific Ocean covering over 300 km of the coastline: La Push (LP), Grays Harbor (GH), Columbia River (CR), and Newport Hydroline (NH). The DNA samples were subjected to PCR amplification with the primers specific for ITS1 sequences. The resultant biotin-labeled target samples were analyzed using microarray hybridization with the CombiMatrix ElectraSense 4X2K format. Out of 44 analyzed samples, 40, 2, and 2 were used for single, duplicate and triplicate hybridizations, respectively.

first: Holly

middle: M


title: Genomic profiling of colorectal cancer from patients with Lynch syndrome and Familial colorectal cancer type X with comparison to sporadic microsatelite stable and instable colorectal cancer

status: Public on Jun 02 2012

city: Hvidovre

first: Christina

last: Therkildsen

state: Hvidovre

address: Kettegaard Alle 30

department: Clinical Research Centre

institute: Copenhagen University Hospital

summary: Lynch syndrome and Familial colorectal cancer type X (FCCTX) are clinically diagnosed using the same criteria, but genomic differences exist between these two groups and the genomic profiles share similarities with their sporadic counterparts, mismatch repair (MMR) deficient and proficient tumors, respectively.

overall_design: Array-based comparative genomic hybridization was performed on 91 tumors, comprising 23 Lynch syndrome (AH), 23 FCCTX (AA), 23 sporadic MMR deficient (AM) and 22 sporadic MMR proficient tumors, in order to identify differences between Lynch syndrome and FCCTX.

first: Mef

last: Nilbert


title: Congenital hypothryrodism and male rat liver: control vs congenital hypothryoidism

status: Public on Mar 10 2012

city: Las Palmas de Gran Canaria

first: Leandro

last: Fernandez-Perez

state: Las Palmas

address: Dr. Pasteur s/n-Campus of San Cristobal

department: Clinical Sciences

country: Spain

institute: University of Las Palmas de Gran Canaria

summary:
Transcriptional profiling of rat liver comparing male rats with congenital hypothyrodism (CH) vs intact at adulhood. Here we studied how CH influences liver gene expression program in adulthood.
Thyroid hormones are required for normal growth and development in mammals. Congenital-neonatal hypothyroidism (CH) has a profound impact on physiology but its specific influence in liver is less understood. Here we studied how CH influences liver gene expression program in adulthood. Pregnant rats were given anti-thyroid drug methimazole (MMI) from GD12 until PND30 to induce CH in male offspring. Growth defects due to CH were evident as a reduction in body weight and tail length from the second week of life. Once the MMI treatment was discontinued, feed efficiency increased in CH and this was accompanied by significant catch-up growth. On PND80, significant reduction in body mass, tail length, and circulating IGF-I remained in CH rats. On the other hand, mRNA levels of known GH targeted genes were significantly up-regulated. Serum levels of thyroid hormones, cholesterol, and triglycerides showed no significant differences. In contrast, CH rats showed significant changes in expression for hepatic genes involved in lipid metabolism with an increased transcription of PPAR and reduced expression of genes involved in fatty acids and cholesterol uptake, cellular sterol efflux, triglycerides assembly, bile acid synthesis, and lipogenesis. These changes were associated with a decrease of intrahepatic lipids. Finally, CH rats responded to hypothyroidism onset in adulthood with a reduction of serum fatty acids and hepatic cholesteryl esters, and to T3 replacement with enhanced activation of lipogenic transcriptional program. In summary, we provided in vivo evidence that neonatal hypothyroidism causes long-lasting effects on hepatic transcriptional program and tissue sensitivity to hormone treatment. This highlights the critical role that a euthyroid state during development plays on normal liver physiology in adulthood.

overall_design: Two conditions CH vs INTACT male rats. Biological replicates: Four independent hybridizations: 4 controls (age-matched intact rats) vs 4 CH (male rats with congenital hypothyroidism) on postnatal day 80 for a total of four arrays. One replicate per array.

last: Fernández-Pérez


title: miRNA expression profiling of enriched male germ cell populations

status: Public on Mar 17 2012

city: Callaghan

first: Skye

last: McIver

state: NSW

address: University Drive

country: Australia

institute: University of Newcastle

summary: MicroRNA  is essential for the process of spermatogonesis, however analysis of its change in expression within germ cells during this process has been limited. We set out to examine the change in the miRNA expression profile of highly enriched mouse germ cell populations in vairous developmental stages.These inlcuded postnatal gonocytes, day 7-9 spermatogonia as well as pachytene spermatocytes and round spermatids from adult mice

overall_design: Gonocytes (day1) and spermatogonia (day 7-9), pachytene spermatocytes and round spermadits (adult) were enrichged by 2-4% BSA gradient sedementation. Three biological replicates of each cell type were included.

first: S

first: E

last: McLaughlin


title: Genome-wide analysis of Fcγ receptor ligation on dendritic cells from wild-type, FcγRIIb KO or FcR γ chain KO mice

status: Public on May 03 2012

city: Leiden

first: Peter

last: 't Hoen

address: PO Box 9600

department: Center for Human and Clinical Genetics

country: Netherlands

institute: Leiden University Medical Center

summary: Analysis of changes in gene expression after incubation of dendritic cells with immune complexes or medium. Since the dendritic cells are derived from three different mouse strains, either wild type, Fcγ receptor IIb KO (expresses only activating Fcγ receptors) or Fc receptor γ chain KO (expresses only inhibitory Fcγ receptor), the analysis gives important insight into the roles of the activating versus inhibiting Fcγ receptors on dendritic cells.

overall_design: Bone marrow-derived dendritic cells of the three mouse genotypes (see above) were incubated for 4 hours with medium (unstimulated) or OVA-anti OVA immune complexes (IC, stimulated) and changes in gene expression after stimulation with IC were compared between unstimulated vs stimulated with IC and across the three genotypes.

first: Nadine

last: van Montfoort

first: J

last: Verbeek


title: C. elegans: wildtype vs nhr-49-/-; wildtype vs nhr-66-/-; wildtype vs nhr-80-/-

status: Public on Mar 15 2012

city: Seattle

first: Pranali

middle: Prasad

last: Pathare

address: 1100 Fairview Ave. N

department: Basic Sciences

institute: FHCRC

summary: Transcriptional profiling of C. elegans NHR-49, NHR-66 and NHR-80

overall_design: Independent data sets were generated for each mutant vs wildtpe comparison: NHR-49 (N=2), NHR-66 (N=3), NHR-80 (N=4)

first: Alex

last: Lin

first: Stefan

last: Taubert

first: Marc

last: Van Gilst

first: Jeff

last: Delrow

first: Ryan

last: Basom


title: Expression data in the mouse brain following the glucocorticoid receptor overexpression in the forebrain (GRov) during different periods in development

city: ann arbor

first: Qiang

last: Wei

state: MI

address: 205 zina pitcher pl

department: MBNI

institute: University of Michigan

summary:
The glucocorticoid receptor overexpression in early life is sufficient to alter gene expression patterns for the rest of the animal's life.
Hippocampal dentate gyrus (DG) are more responsive than the nucleus accumbens (NAcc) following the glucocorticoid receptor overexpression in the forebrain.

overall_design: Laser capture microdissection was performed. Microdissected areas from the dentate gyrus or nucleus accumbens were collected from serial sections for each animal.

first: Hugh

last: Fentress

first: Huda

last: Akil


title: Cactin is essential for G1 progression in Toxoplasma gondii

status: Public on Mar 14 2012

city: Chestnut Hill

first: Marc-Jan

last: Gubbels

address: 140 Commonwealth Avenue

institute: Boston College

summary: Toxoplasma gondii is an obligate intracellular protozoan parasite whose rapid lytic replication cycles define its pathogenicity. We identified a temperature sensitive growth mutant, FV-P6, which irreversibly arrests before the middle of the G1 stage of the tachyzoite cell cycle. This arrest is caused by a point mutation in a gene conserved across eukaryotes, Cactin, whose product localizes to the nucleus. To elucidate the role of TgCactin we performed genome-wide expression profiling of FV-P6 mutant parasites at 35C and 40C, as well as FV-P6 complemented with a wild-type Cactin encoding cosmid (TOXO93 or comp) and as a pseudo-diploid wild-type line encoding both the wild-type and mutant Cactin locus (S4.2), also at both temperatures. Besides the expected G1 expression profile, many genes associated with the extracellular state as well as with the bradyzoite cyst stage were identified. Consistent with these profiles were the expression of AP2 transcription factors typically associated with extracellular and bradyzoite stage parasites. This suggests a role for TgCactin in control of gene expression. Since TgCactin does not contain any functionally defined domains we reasoned TgCactin exerts its function through interactions with other proteins. In support of this model we demonstrated that TgCactin is present in a protein complex and can oligomerize. Taken together, these results suggest that TgCactin acts as a pivotal protein potentially regulating gene expression at several transition points in parasite development.

overall_design: The role of Cactin in G1 progression of Toxoplasma gondii tachyzoites was assessed by expression profiling a temperature senstive mutant of Cactin at both the permissive (35C) as well as the restrictive (40C) temperature. Controls under the same temperature conditions inlcude the mutant line complemented with a wild-type Cactin allele encoded on a cosmid and a wild-type parasite line expressing an additional, mutant allele of Cactin (pseudo-diploid line).

first: Michael

last: White

first: Jeroen

last: Saeij


title: mRNA expression under alkylating condition in wild-type strain and ttha1564 deletion mutant of Thermus thermophilus HB8

status: Public on Mar 08 2012

city: Toyonaka

first: Hiromasa

last: Ohyama

address: Machikaneyamachou 1-1

country: Japan

institute: Osaka University

summary:
We analyzed the expression profile of wild-type strain and ttha1564 deletion mutant strain of Thermus thermophils HB8 under alkylating condition.  In wild type strain, 107 genes and 96 genes were over 2-fold up- and under 0.5-fold down-regulated by alkylation, respectively. In ttha1564 deletion mutant, 35 genes and 12 genes were over 2-fold up- and under 0.5-fold down-regulated by alkylation, respectively. Keywords: stress response comparison
The T. thermophilus HB8 wild-type and delta ttha1564 strains were cultured in TT medium (0.4%(w/v) polypeptone, 0.2%(w/v) yeast extract, 0.1%(w/v) NaCl, 0.4 mM CaCl2, and 0.4 mM MgCl2, (pH 7.5)) at 70°C until the OD600 reached 0.8. The cultures were then divided into two flasks and an equal volume of TT medium prewarmed at 70°C was added.  One of the media culture of each strain contained 100 micro g/ml MNNG.  We confirmed that the cells can continue to grow in TT medium containing 100 micro g/ml MNNG but DNAs are alkylated sufficiently (Onodera, 2011).  After further cultivation at 70°C for 10 min, the diluted cultures were collected into an equal of 100% ethanol and stored at -80°C.  The procedures used for extraction of crude RNA, synthesis of cDNA, labeling of cDNA fragment, hybridization to a TTHB8401a520105F GeneChip (Affymetrix) and data analysis were basically the same as those described previously (Agari et al., 2008; Shinkai et al., 2007).  To determine the mRNA expression level of each sample, image data for the three independent samples were processed.

overall_design: stress response comparison

first: R

last: Morita

first: H

last: Hishinuma

last: Mega

first: T

last: Ohta

first: K

last: Fukui

first: N

last: Nakagawa

first: Y

last: Agari

first: A

last: Shinkai

first: S

last: Kuramitsu

last: Masui


title: Miscellaneous unmatched samples

city: Heidelberg

first: Ruprecht

last: Kuner

address: Im Neuenheimer Feld 460

department: Molecular Genetics

institute: German Cancer Research Center and National Center of Tumor Diseases

summary: unmatched samples

overall_design: 3 samples


title: Improved resistance to Eimeria acervulina infection in chickens due to dietary supplementation with garlic metabolites

status: Public on Mar 07 2012

city: Beltsville

first: Duk Kyung

last: Kim

address: Bldg. 1043, BARC-East

institute: USDA, ARS

summary: This study utilized comparative global gene expression microarray analysis to evaluate the effects of a compound including garlic-derived secondary metabolites on intestinal immunity of chicken.

overall_design: Two-condition experiment, Garlic metabolites-fed chickens vs. Non-treated control chickens. Biological replicates: 2 control replicates, 2 Garlic metabolites-fed replicates with dye-switching.

first: Duk-Kyung

first: Hyun

last: Lillehoj


title: Genome wide analysis of Circulating Tumor Cells from Patients with Metastatic Prostate Cancer Reveals Clinically Relevant Aberrations Associated with Castration Resistance

city: San Francisco

first: Mark

last: Magbanua

address: 1450 3rd Street, PO Box 589001

department: HemOnc

institute: UCSF/Helen Diller Familiy Comprehensive Cancer Center

summary:
The number of circulating tumor cells (CTCs) in metastatic prostate cancer patients provides prognostic and predictive information. However, it is the molecular characterization of CTCs that offers insight into the biology of these tumor cells in the context of personalized treatment. We performed a pilot study to evaluate the feasibility of isolation and genomic profiling of CTCs in castration-resistant prostate cancer.
CTCs in 7.5 mLs of blood in 20 castration-resistant metastatic prostate cancer patients were enumerated using CellSearch. Additional 10-20 mLs of blood from 12 patients positive for CTCs were subjected to immunomagnetic enrichment and fluorescence activated cell sorting (IE/FACS) to isolate pools of ~20 CTCs. Genomic DNA of CTCs was subjected to whole genome amplification followed by gene copy number analysis via array comparative genomic hybridization (aCGH). Archival primary tumor biopsy samples available from 2 patients were also subjected to aCGH.

overall_design: Enumeration of CTCs revealed 15 patients with >=5 CTCs per 7.5 mLs. Of these, 12 samples were subjected to IE/FACS for CTC isolation, and 9 (75%) were successfully analyzed for copy number aberrations. Genomic profiling of CTCs revealed numerous copy number aberrations commonly observed in primary prostate tumors including gains in 8q and losses in 8p. High level copy number gains at the androgen receptor (AR) locus were observed in 7 (78%) of cases. Comparison of genomic profiles between CTCs and their matched tumors revealed a common lineage. Consistent with previous observations high-level gains in the AR were only observed in CTCs but not in the matched primary tumors. This is consistent with CTCs representing progressive disease that has adapted to hormone therapy.

middle: J

first: Eduardo

middle: V

last: Sosa

first: Janet

last: Scott

first: Jeff

last: Simko

first: Colin

last: Collins

first: Dan

last: Pinkel

first: Charles

last: Ryan

first: John

last: Park


title: Effect of sexual recombination on population diversity in aflatoxin production by Aspergillus flavus and evidence for cryptic heterokaryosis

city: Raleigh

first: Ignazio

last: Carbone

state: NC

address: 851 Main Campus Drive, Suite 233

department: Plant Pathology

institute: North Carolina State University - Center for Integrated Fungal Research

summary: Aspergillus flavus is the major producer of carcinogenic aflatoxins in crops worldwide.  Natural populations of A. flavus show tremendous variation in aflatoxin production some of which can be attributed to extreme environmental conditions (e.g., drought), differential regulation of the aflatoxin biosynthetic pathway, missing cluster genes or loss-of-function mutations.  Understanding the evolutionary processes that generate genetic diversity in A. flavus may also explain quantitative and qualitative differences in aflatoxigenicity.  Several population studies provide indirect evidence of recombination in the aflatoxin gene cluster and genome-wide, using multilocus genealogical approaches.  More recently A. flavus has been shown to be functionally heterothallic and capable of sexual reproduction in laboratory crosses.  In the present study, we characterize the progeny from nine A. flavus crosses and show that crossovers in the aflatoxin cluster coincide with inferred recombination blocks and hotspots in natural populations, which suggests that recombination in the cluster is primarily driven by sex.  Moreover, we show that a single crossover event in the cluster can restore aflatoxigenicity, which is significant as mycotoxin production in A. flavus is highly heritable.  aCGH was used to corroborate inferences from cluster-based MLSTs and to possibly identify additional crosovers within the cluster.

platform_organism:
Zea mays
Aspergillus flavus
Aspergillus oryzae

overall_design: aCGH comparison between 3 strains of A. flavus:  2 parental (P) and 1 progeny (F1) analyzed at the probe level.  A total of 9 trio comparisons were made from a total of 18 isolates analyzed by aCGH.  Trio comparisons are as follows:  IC278 (P), IC1179 (P) and IC1650 (F1); IC201 (P), IC310 (P) and IC1719 (F1); IC307 (P), IC308 (P) and IC1751 (F1); IC277 (P), IC311 (P) and IC1766 (F1); IC277 (P), IC311 (P) and IC1775 (F1); IC244 (P), IC277 (P) and IC2205 (F1); IC244 (P), IC277 (P) and IC2207 (F1); IC301 (P), IC1179 (P) and IC2171 (F1); and finally IC244 (P), IC277 (P) and IC2209 (F1).

first: Rodrigo

last: Olarte

first: Bruce

last: Horn

first: Joe

last: Dorner

first: James

middle: T

last: Monacell

first: Rakhi

last: Singh

first: Eric

last: Stone


title: Analysis of transcriptome in moss Physcomitrella patens CNGCb null mutant at 25 and 34 degrees C for 30 minutes [Unpublished data]

status: Public on Mar 06 2012

city: Lausanne

first: Andrija

last: Finka

address: Batiment Biophore

department: Department of Plant Molecular Biology

country: Switzerland

institute: University of Lausanne

summary:
Analysis of transcriptome in moss Physcomitrella patens CNGCb null mutant  at 25  and 34 degrees C for 30 minutes. Results provide insight into role of CNGCb in acquired thermotolerance induced by non-lethal heat treatment.
Typically at dawn of a hot summer day, land plants need precise molecular thermometers to  sense harmless increments in the ambient temperature to timely develop a heat-shock  response (HSR) and accumulate protective heat shock proteins (Hsps), in anticipation of  upcoming harmful temperatures at mid-day. Here, we found that the CNGCb gene from  Physcomitrella patens and its Arabidopsis ortholog CNGC2, encode for a component of  cyclic nucleotide gated Ca2+ channels acting as the primary thermosensors of land plant cells.  Disruption of CNGCb or CNGC2 produced a hyper-thermosensitive phenotype, giving rise to  a HSR and acquired thermotolerance at significantly milder heat-priming treatments than in  wild type plants. In an aequorin-expressing moss, CNGCb loss-of-function caused altered  Ca2+ signaling and a sustained Ca2+ influx. Patch clamp recordings on moss protoplasts  showed the presence of three distinct thermo-responsive Ca2+-channels in wild type cells.  Deletion of CNGCb led to a total absence of one, and it increased the open probability of the  remaining two thermo-responsive Ca2+ channels. Thus, both in Arabidopsis and moss,  CNGC2 and CNGCb are expected to form with other related CNGCs, heteromeric Ca2+  channels in the plasma membrane that respond to mild increments in the ambient temperature  by triggering an optimal HSR, leading to the onset of plant acquired thermotolerance.

overall_design: The WT moss tissues were heat-shocked for a half an hour at 34°C and 38°C and CNGCb at 25and 34°C followed by liquid nitrogen  freezing. Total RNA was isolated using RNeasy Mini Kit (QIAGEN, Hilden, Germany) and  two biological replicate samples for each treatment, were extracted. An Agilent-certified  microarray service lab (MOgene, LC, St. Louis, MO, USA) was used to verify the integrity of  the RNA and perform the microarray experiments. Two biological replicates were performed.

first: Pierre

last: Goloubinoff


title: miRNA profiling array and analysis in mouse hippocampal neurons

status: Public on Mar 02 2012

city: Baltimore

first: Claudia

middle: Roxana

last: Ruiz

address: 725 N. Wolfe St

department: Neuroscience

institute: The Johns Hopkins School of Medicine

summary: We addressed the potential for global regulation of miRNA biogenesis by BDNF using miRNA arrays that selectively measure mature miRNA, as opposed to pre-miRNA.  Hippocampal neurons were treated with BDNF for 30 min in the presence of Actinomycin-D to assess changes due to processing of existing pre-miRNAs rather than new pre-miRNA production.  We used Applied Biosystems 7900HT Fast Real-Time PCR system using Taqman Rodent MicroRNA Array A.  Data is from three paired BDNF and Mock experiments (1,2,3).

overall_design: Each array (TaqMan) contained 375 rodent miRNA targets of which 195 were detectable in hippocampus in three independent paired experiments.


title: Characterization of Neurospora crassa ghh (NCU06095) mutant strains

status: Public on Mar 01 2012

city: New York

first: Adam

last: Paré

state: NY

address: 1275 York Avenue

department: Developmental Biology

institute: Memorial Sloan Kettering Cancer Center

summary: To determine the genes directly and indirectly under the control of the Grainy-head homolog (GHH) transcription factor in Neurospora crassa

overall_design: Three different sample types (Aerial Hyphae & Conidia; Mycelia; or Whole Colonies) of both wild-type (FGSC #2489) and grainy-head homolog (FGSC #13563) strains of Neurospora crassa were subjected to transcriptome analyses to determine the genes differentially expressed in the ghh background compared to wild type.

last: Pare

first: William

last: McGinnis


title: Comparison of transcript abundance in aerial mycelium of the Magnaporthe oryzae TRA1-deleted mutant and its parental strain

status: Public on Mar 03 2012

city: Kaiserslautern

first: Karsten

last: Andresen

address: Erwin-Schroedinger-Str. 56

institute: IBWF

summary: In order to understand the function of the Tra1p transcription factor we identified potentially Tra1p-regulated genes by comparison of transcript abundance in aerial mycelium of the tra1- mutant and the parental strain 70-15.

overall_design: Two-condition experiment, wild-type vs. TRA1-deleted mutant. 4 biological replicates with dye-swaps. Each microarry slide had 2 arrays with 44k spots (22k spots printed twice). Thus, rep1 and rep2 are technical replicates of the same biological sample (derived from one raw data file).

first: B

last: Breth

first: D

last: Odenbach

first: M

last: Schroeder

last: Bode

first: E

last: Thines

first: L

last: Antelo

first: K

first: A

last: Yemelin

first: N

last: Schlink

last: Foster


title: Expression analysis of RCc3:OsNAC9 and GOS2:OsNAC9 transgenic rice plants

city: Yongin

first: Jin

middle: Seo

last: Jeong

state: Gyeonggido

address: San 38-2 Namdong, Cheoin-gu

institute: Myongji University

type: Expression profiling by genome tiling array

summary: For identification of genes up-regulated in RCc3:OsNAC1, GOS2:OsNAC1 plants, total RNA (100 μg) was prepared from root tissues of 14-d-old transgenic and non-transgenic rice seedlings (Oryza sativa cv Nipponbare) grown under normal growth conditions.

overall_design: Expression profiling was conducted using a Rice 3’-Tiling Microarray. Information on the microarray can be found at http://www.ggbio.com (GreenGene Biotech). The Rice 3’-Tiling Microarray was designed from 27,448 genes deposited at IRGSP, RAP1 database (http://rapdb.lab.nig.ac.jp). Among these, 20,507 genes were from representative RAP1 sequences with cDNA/EST supports and 6,941 genes were predicted without cDNA/EST supports. Ten 60-nt long probes were designed from each gene starting 60 bp ahead the end of stop codon with 10 bp shifts in position so that 10 probes covered 150 bp in the 3' region of the gene. In total, 270,000 probes were designed (average size, 60-nt) to have Tm values of 75 to 85 °C. The microarray was manufactured by NimbleGen Inc. (http://www.nimblegen.com/). Random GC probes (38,000) were used to monitor the hybridization efficiency and fiducial markers at the four corners (225) were included to assist with overlaying the grid on the image. The microarray was used to profile gene expression in RCc3:OsNAC1, GOS2:OsNAC1 and Non-transgenic plants. Cy3-labeled target cDNA fragments were synthesized using a Cy3-9mer primer. For normalization, data were processed with cubic alpine normalization using quartiles to adjust signal variation between chips and with Rubust Multi-Chip Analysis using a median polish algorithm implemented in NimbleScan (Workman et al., 2002; Irizarry et al., 2003). To assess the reproducibility of the microarray analysis, we repeated the experiment three times with independently prepared total RNAs.

first: Mark

last: Redillas

first: Youn

last: Kim

first: Yang

middle: D

last: Choi

first: Christophe

last: Reuzeau

first: Ju-Kon


title: Rap1 Turnover Galactose Induction Time Course

status: Public on Mar 05 2012

city: Chapel Hill

first: Jason

last: Lieb

address: 408 Fordham Hal, CB#3280

institute: UNC-Chapel Hill

type: Genome binding/occupancy profiling by array

summary: A strain harboring two copies of RAP1 is used for a competition-ChIP experiment.  One copy of RAP1 is expressed from the endogenous RAP1 promoter and a c-terminal 3X FLAG epitiope tag and the other is  expressed from a weakened Galactose inducible promoter and a c-terminal 9X MYC tag.  Following induction by  2% galactose Rap1-Myc and Rap1-Flag levels are determined genome wide using ChIP-chip.

overall_design: Time Course ChIP-ChIP experiment, Rap1-Flag IP and Rap1-Myc IP. 13 Time Points (0, 10, 20, 30, 40, 50, 60, 90, 120, 150, 180, 210, 240 Minutes) 2 Biological Replicates.  Total Rap1 Occupancy at times 0 and 60 minutes in the time course; 2 Biological Replicates. mRNA expression levels at times 0 and 60 minutes in the time course; 2 biological Replicates. ChIPs comparing the occupancy of Rap1 in a strain containing two copies of Rap1, one with a Flag tag and one with a Myc tag, and expressed from an identical promoter.

first: Colin

middle: R

last: Lickwar


title: Characterization of late-stage Drosophila grainy head IM-allele (grhIM) mutant embryos

first: Adam

last: Paré

summary: To determine the genes directly and indirectly under the control of the Grainy head transcription factor during late stages of Drosophila embryogenesis.

overall_design: Total RNA from pre-larval (late stage 16 and early stage 17) grhIM homozygous (+; cn, grhIM, bw, sp; +) and wild-type (y; cn, bw, sp; +) embryos were compared.

last: Pare

first: William

last: McGinnis


title: Expression diversity in Phytophthora ramorum

city: Davis

first: Takao

last: Kasuga

address: 382 Huchison Hall

institute: USDA-ARS

summary: Expression diversity of P. ramorum isolates belonging to the NA1 clonal lineage growing on solid CV8 was examined.  It was found that although all the analyzed isolates belonged to a single clonal lineage, expression patterns were distinctive between isolates originating from coast live oak and California bay laurel.

overall_design: Global expression patterns of 13 isolates originating from coastal live oak and California bay laurel was investigated.  No biological replicates were generated.  The sequenced strain Pr102 was included.  Gene models Phytophthora ramorum v1.0 were used to construct NimbleGen 72K x4 custom arrays.

first: Melina

last: Kozanitas

first: Mai

last: Bui

first: Daniel

last: Huberli

first: David

last: Rizzo

first: Matteo

last: Garbelotto


title: Transcriptome profiling and methyl homeostasis of an Arabidopsis mutant deficient in S-adenosylhomocysteine hydrolase1 (SAHH1)

status: Public on Feb 14 2012

city: Saskatoon

first: Ed

last: Tsang

address: 110 Gymnasium Place

department: Plant Bioinformatics Institute

country: Canada

institute: National Research Council of Canada

summary: Transcriptome profiling was conducted to detect genes whose expression is significantly changed in an Arabidopsis mutant deficient in S-adenosylhomocysteine hydrolase1 (SAHH1) during early seedling development when mutant phenotypes could be clearly observed. A total of 2,040 differentially expressed genes were identified, representing approximately 6.7% of the 30,385 DNA oligonucleotide targets on the microarray. Among these differential expressed genes, many were mapped to pathways essential to plant growth and development including those of primary, secondary and hormone metabolisms. A significant proportion of up-regulated genes encoded transposable elements which were mapped to the centromeric and pericentromeric regions of the Arabidopsis chromosomes.  A number of down-regulated genes were found to be involved in root hair formation, which might have contributed to the root hair defective phenotype of the mutant. Supplement of homocysteine in the growth medium promoted root cell growth and root hair formation in the sahh1 mutant seedlings.  Despite SAHH1 deficient, the expression of genes encoding methyltransferase remained largely unchanged in the sahh1 mutant. Bisulfite sequencing analysis of transposons revealed that their sequences were deficient of 5-methylcytosines in the mutant. Analysis of mutant genomic DNA using restriction endonucleases that were unable to cut methylated DNA suggested a genome-wide hypomethylation had occurred. These results indicated that SAHH1 plays a critical role in methyl homeostasis, and its deficiency is a major contributing factor to the change of global gene expression, metabolic pathways and activation of transposons in the sahh1 mutant.

overall_design: transcriptome profiles between wild type and sahh1 mutant at four different seedling stages (1, 4, 7, 10 days) were compared.

first: Bo

last: Ouyang

first: Zhangjun

last: Fei

first: Je-Gun

last: Joung

first: Allan

last: Kolenovsky

last: Caplan

first: Wilfred

last: Keller

first: Yuhai

last: Cui

first: Adrian

last: Cutler

first: Edward


title: Integrative genome-wide analysis reveals cooperative regulation of alternative splicing by hnRNP proteins (splicing arrays)

status: Public on Feb 20 2012

city: La Jolla

first: Gene

last: Yeo

address: 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab

institute: UCSD

summary: Understanding how RNA binding proteins control the splicing code is fundamental to human biology and disease. Here we present a comprehensive study to elucidate how heterogeneous nuclear ribonucleoparticle (hnRNP) proteins, among the most abundant RNA binding proteins, coordinate to regulate alternative pre-mRNA splicing (AS) in human cells. Using splicing-sensitive microarrays, cross-linking and immunoprecipitation coupled with high-throughput sequencing, and cDNA sequencing, we find that more than half of all AS events are regulated by multiple hnRNP proteins, and that some combinations of hnRNP proteins exhibit significant synergy, whereas others act antagonistically. Our analyses reveal position-dependent RNA splicing maps, in vivo consensus binding sites, a surprising level of cross- and auto-regulation among hnRNP proteins, and the coordinated regulation by hnRNP proteins of dozens of other RNA binding proteins and genes associated with cancer. Our findings define an unprecedented degree of complexity and compensatory relationships among hnRNP proteins and their splicing targets that likely confer robustness to cells.

overall_design: In triplicate, polyA-selected RNA was extracted from control, hnRNP A1, hnRNP A2/B1, hnRNP H1, hnRNP F, hnRNP M, and hnRNP U siRNA treated human 293T cells, and hybridized to custom splice-junction arrays

first: Stephanie

last: Huelga


title: Comparison of transcript abundance in ungerminated spores of the Magnaporthe oryzae TRA1-deleted mutant and its parental strain

first: Karsten

last: Andresen

summary: In order to understand the function of the Tra1p transcription factor we identified potentially Tra1p-regulated genes by comparison of transcript abundance in conidia of the tra1- mutant and the parental strain 70-15.

overall_design: Two-condition experiment, wild-type vs. mutant. 3 biological replicates

first: B

last: Breth

first: D

last: Odenbach

first: M

last: Schroeder

last: Bode

first: E

last: Thines

first: L

last: Antelo

first: K

first: A

last: Yemelin

first: N

last: Schlink

last: Foster


title: Acute depletion of Tet1-dependent 5-hydroxymethylcytosine levels impairs LIF/Stat3 signaling and results in loss of embryonic stem cell identity [expression profiling]

status: Public on Jan 06 2012

city: RTP

first: Raja

last: Jothi

address: 111 TW Alexander Drive; A314

department: National Institute of Environmental Health Sciences

institute: National Institutes of Health

summary: The TET family of FE(II) and 2-oxoglutarate-dependent enzymes (Tet1/2/3) promote DNA demethylation by converting 5-methylcytosine to 5-hydroxymethylcytosine (5hmC), which they further oxidize into 5-formylcytosine and 5-carboxylcytosine. Tet1 is robustly expressed in mouse embryonic stem cells (mESCs) and has been implicated in mESC maintenance. Here we demonstrate that, unlike genetic deletion, RNAi-mediated depletion of Tet1 in mESCs led to a significant reduction in 5hmC and loss of mESC identity. The differentiation phenotype due to Tet1 depletion positively correlated with the extent of 5hmC loss. Meta-analyses of genomic datasets suggested interaction between Tet1 and leukemia inhibitory factor (LIF) signaling. LIF signaling is known to promote self-renewal and pluripo-tency in mESCs partly by opposing MAPK/ERK mediated differentiation. Withdrawal of LIF leads to differentiation of mESCs. We discovered that Tet1 depletion impaired LIF-dependent Stat3-mediated gene activation by affecting Stat3's ability to bind to its target sites on chromatin. Nanog overexpression or inhibition of MAPK/ERK signaling, both known to maintain mESCs in the absence of LIF, rescued Tet1 depletion, further supporting the dependence of LIF/Stat3 signaling on Tet1. These data support the conclusion that analysis of mESCs in the hours/days immediately following efficient Tet1 depletion reveals Tet1’s normal physiological role in maintaining the pluripotent state that may be subject to homeostatic compensation in genetic models.

overall_design: Genome-wide mapping of 5hmC and microarray gene expression profiling in E14Tg2a mESCs after transfection with indicated siRNAs: Tet1 siRNA #1 (Invitrogen, MSS284895), Tet1 siRNA #2 (Invitrogen, MSS284897), and Control siRNA duplex targeting firefly luciferase.

first: Guang

last: Hu

first: Johannes

last: Freudenberg


title: Genome-wide expression profiling reveals transcriptional reprogramming in Fusarium graminearum by FgV1-DK21 virus infection

city: Seoul

first: Won

middle: Kyong

last: Cho

address: 5103-ho, 200-dong, Daehak-dong, Kwanak-gu

department: Department of Agricultural Biotechnology and Center for Fungal Pathogenesis

institute: Seoul National University

summary:
Using a 3′-tiling microarray covering the whole F. graminearum genes, we carried out genome-wide expression analyses of F. graminearum infected with FgV-DK21 (Mycovirus) at two different time stages (36 h and 120 h).
Our study is the first report which elucidated the global alternation of the prominent cellular pathways in fungal host by FgV1-DK21 virus infection.

overall_design: A total of 12 chips were used for microarray. At 36 h and 120 h, total RNAs were extracted from virus free Fusarium and virus infected Fusarium with three biological replicates.

first: Won-Kyong

first: Jisuk

last: Yu

first: Kyung-Mi

last: Lee

first: Moonil

last: Son

first: Kook-Hyung

last: Kim


title: Sarcolipin is a potential biomarker for dystrophy and is involved in inflammatory processes in skeletal muscles

status: Public on Dec 09 2011

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

summary: Myopathies and muscular dystrophies are devastating diseases sharing characteristic symp-toms. Little is known about common aetiopathology and biomarkers are rare.   We studied skeletal muscle gene expression in mouse models of myopathies. As dystrophic processes in muscles are characterised by inflammatory processes, we expanded our analy-sis on a rat model of sepsis.  We find 25 commonly dysregulated genes. Sarcolipin was upregulated most, exhibiting in-creased protein levels in different muscles as well as in rats treated with an inflammatory agent. Upregulation strongly correlated with disease status.  Our findings suggest Sarcolipin as a potential biomarker and imply a new function in inflam-matory response.

overall_design: Comparison of the expression profile of quadriceps in 2 B6C3Fe a/a-Ttnmdm/J mice with Titin-mutation versus the expression profile  of 2 mice without the mutation in Titin [Ttn].

first: Christine

middle: H

last: Kohl

first: Charalambos

last: Tsagogiorgas

first: Dittmar

last: Labeit

first: Christian

last: Witt


title: Expression analysis of the AdnA regulon in Pseudomonas fluorescens Pf0-1

status: Public on Nov 30 2011

city: Boston

first: Matthew

last: Mastropaolo

state: MA

address: 136 Harrison Ave

department: Molecular Biology and Microbiology

institute: Tufts Universicty School of Medicine

summary:
Investigation of whole genome gene expression

AdnA in Pseudomonas fluorescens, an ortholog of FleQ in P. aeruginosa, regulates both motility and flagella-mediated attachment to various surfaces.  A whole genome microarray determined the AdnA transcriptome by comparing the gene expression pattern of wild-type Pf0-1 to that of Pf0-2x (adnA-) in broth culture.  In the absence of AdnA, expression of 92 genes was decreased, while 11 genes showed increased expression.  Analysis of 16 of these genes fused to lacZ confirmed the microarray results.  Several genes were further evaluated for their role in motility and biofilm formation.  Two genes, Pfl01_1508 and Pfl01_1517, affected motility and had different effects on biofilm formation in Pf0-1.  These two genes are predicted to encode proteins similar to the glycosyl transferases FgtA1 and FgtA2, which have been shown to be involved in virulence and motility in P. syringae.  Three other genes, Pfl01_1516, Pfl01_1572, and Pfl01_1573, not previously associated with motility and biofilm formation in Pseudomonas had similar affects on biofilm formation in Pf0-1.  Deletion of each of these genes led to different motility defects.  Our data revealed an additional level of complexity in the control of flagella function beyond the core genes known to be required, and may yield insights into processes important for environmental persistence of P. fluorescens Pf0-1.

sample_organism:
Pseudomonas fluorescens
Pseudomonas fluorescens Pf0-1

overall_design: Catalog design for Pseudomonas fluorescens Pf0-1 (Taxonomy Id: 205922) covering NC_007492. Probes selected for 5736/5736 sequences. Median number of probes/sequence is 13 with an average of 13.00. Each probe will be replicated 5 times on the chip. Probes are randomly distributed over the surface of the array. Unused features have been filled with randomly generated probes of comparable GC content.

first: Mark

last: Silby


title: Salmonella Typhimurium stbC mutant

status: Public on Dec 25 2011

city: Taipei

first: Ke-Chuan

last: Wang

address: 250 Wu-Hsing Street

country: Taiwan

institute: Taipei medical university

summary:
Salmonella enterica serotype Typhimurium produces a variety of fimbrial appendages, among which the type 1 fimbriae is the most common type.  In vitro static broth culture favors S. Typhimurium to produce type 1 fimbriae, while solid agar inhibits its expression.  A transposon inserted in the stbC gene, which would encode an usher protein for Stb fimbriae of a non-flagellar S. Typhimurium LB5010 strain, conferred it to agglutinate yeast cells on both cultures, and was mannose-sensitive.  Reverse transcription polymerase chain reaction (RT-PCR) revealed that the expression of the fimbrial major subunit gene fimA, and fimZ, a positive regulator gene of fimA, were both increased in the stbC mutant strain when grown on LB agar; fimW, a repressor gene of fimA, exhibited lower expression.  Flagella were observed in the stbC mutant and this phenotype was correlated with the motile phenotype detected by MSRV agar medium and reaction with flagella antiserum.  Microarray data and RT-PCR also indicated that the expression of three genes, motA, motB, and cheM, was enhanced in the stbC mutant.  The S. Typhimurium stbC mutant was resistant to a variety of antibiotics, consistent with the finding that expression of yhcQ and ramA, two genes involved in multidrug resistance, was enhanced.  A complementation test revealed that transforming a recombinant plasmid possessing the coding sequence of the stbC gene restored the mannose-sensitive agglutination phenotype to the stbC mutant much as that in the parental S. Typhimurium LB5010 strain, indicating the possibility of an interplay of different fimbrial systems in coordinating their expression.
Key Words: Salmonella enterica serotype Typhimurium, fimbriae, type 1 fimbriae, stbC, transposon, multidrug resistant, flagella

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2

overall_design:
RNA transcript of Salmonella Typhimurium LB5010 strain comparing wild-type with stbC mutant.
Two-cindition experiment, wild-type vs. stbC mutant strain.

first: Kuang-Sheng

last: Yeh


title: DNA hypermethylation in breast cancer: breast cancer tissues vs. normal breast tissues

status: Public on Nov 11 2011

city: Beijing

first: wang

last: liang

address: 7A North Yongchang Road BDA

country: China

institute: BioChainBJ

summary: To screen candidate methylation markers for early detection of breast cancer, we performed methylated-CpG island recovery assay combined with CpG island array on 61982 CpG sites across 4162 genes in 10 breast tumor tissues and 10 non-tumor breast tissues. We detected 70 significantly hypermethylated genes in breast tumor tissues, including many novel hypermethylated genes such as ITGA4, NFIX, OTX2 and FGF12. Direct bisulfite sequencing showed widespread methylations occurred in intragenic regions of WT1, PAX6 and ITGA4 genes and promoter region of OTX2 in breast cancer tissue. COBRA assay in independent tumor and non-tumor samples confirmed that WT1, OTX2 and PAX6 genes were hypermethylated in breast cancer tissues. To explore the relationship between methylation and gene expression, gene expression profiling analysis was performed in 8 breast tumor tissues and 8 non-tumor breast tissues. We found that some hypermethylated genes in breast cancer were not expressed in breast tissues. RT-PCR assay showed that WT1 and PITX2 were only weakly expressed in the breast tumor tissues and weren’t expressed in most non-tumor breast tissues. OTX2 and PAX6 weren’t expressed in both breast tumor tissues and non-tumor tissues.

overall_design: Unpaired experiments, breast cancer tissue vs. normal cancer tissue. Biological replicates: 10 breast cancer tissue replicates, 10 normal breast tissue replicates.

first: Zhen-qiang

last: Lian

first: Qi

first: Wen-ping

last: Li

first: An-qin

last: Zhang

first: Ling

last: Wu


title: Daphnia ecotypes fed lab versus natural resources

status: Public on Jan 01 2012

city: Columbia

first: Jeffry

middle: L.

last: Dudycha

state: SC

address: 715 Sumter Street

department: Biological Sciences

institute: University of South Carolina

summary: Consumer-resource interactions are a central issue in evolutionary and community ecology because they play important roles in selection and population regulation.  Most consumers encounter resource variation at multiple scales, and respond through phenotypic plasticity in the short term or evolutionary divergence in the long term.  The key traits for these responses may influence resource acquisition, assimilation and/or allocation.  To identify candidate genes, we experimentally assayed genome-wide gene expression in pond and lake Daphnia ecotypes exposed to alternate resource environments.  One was a simple, high-quality laboratory diet, Ankistrodesmus falcatus.  The other was the complex natural seston from a large lake.  In temporary ponds, Daphnia generally experience high-quality, abundant resources, whereas lakes provide low-quality, seasonally shifting resources that are chronically limiting.  For both ecotypes, we used replicate clones drawn from a number of separate populations.

sample_organism:
Daphnia pulex
Daphnia pulicaria

overall_design: We compared gene expression in whole Daphnia pulex that had been raised in the lab for 10 days, and then exposed to alternate resource environments for 24 hours.  One resource environment was a 24 hour continuation of the lab resource, a satiating level of Ankistrodesmus falcatus.  The alternate environment was the natural seston present in the epilimnion of Lake Murray, South Carolina.  Two ecotypes were analyzed, one adapted to large lakes, and one adapted to temporary ponds.  For each ecotype, eight replicate clones were used.  Clones of the lake ecotype were isolated from eight independent lakes, clones of the pond ecotype were isolated from six different ponds.  The total number of arrays is 16 (8 replicate clones x 2 ecotypes) x 2 resource environments). Total RNA was extracted from eight whole organisms pooled together. Pools were then converted to cDNA and labelled with a single round of amplification.  For array hybridizations, samples from the two resource environments were paired for each clone, and dyes were swapped across clones.

middle: L

first: Kevin

last: Deitz

first: Christopher

middle: S

last: Brandon


title: Dengue virus inhibits immune responses in Aedes aegypti cells

status: Public on Oct 31 2011

first: George

last: Dimopoulos

address: 615 N. Wolfe Street

department: Molecular Microbiology and Immunology

institute: Johns Hopkins School of Public Health

summary: The ability of many viruses to manipulate the host antiviral immune response often results in complex host-pathogen interactions. In order to study the interaction of dengue virus (DENV) with the Aedes aegypti immune response, we have characterized the DENV infection-responsive transcriptome of the immune-competent A. aegypti cell line Aag2. As in mosquitoes, DENV infection transcriptionally activated the cell line Toll pathway and a variety of cellular physiological systems. Most notably, however, DENV infection down-regulated the expression levels of numerous immune signaling molecules and antimicrobial peptides (AMPs). Functional assays showed that transcriptional induction of AMPs from the Toll and IMD pathways in response to bacterial challenge is impaired in DENV-infected cells. In addition, Escherichia coli, a gram-negative bacteria species, grew better when co-cultured with DENV-infected cells than with uninfected cells, suggesting a decreased production of AMPs from the IMD pathway in virus-infected cells. Pre-stimulation of the cell line with gram-positive bacteria prior to DENV infection had no effect on DENV titers, while pre-stimulation with gram-negative bacteria resulted in an increase in DENV titers. These results indicate that DENV is capable of actively suppressing immune responses in the cells it infects, a phenomenon that may have important consequences for virus transmission and insect physiology.

overall_design: Infected (dengue virus or heat-inactivated dengue virus) vs. naive cells. 3 replicates each.


title: Expression data from FCA-csRRM2 transgenic B. napus

status: Public on Nov 01 2011

city: Shanghai

first: weiwei

last: qi

address: 220#Handan road

institute: Fudan university

summary: Over-expression of a conserved RRM domain (csRRM2) improves Brassica napus yield components by regulating cell size

overall_design: Leaf tissues of one-month-stage transgenic and nontransgenic seedlings (3 plants each),respectively,were selected.

first: Weiwei

last: Qi

first: Jinshui

last: Yang


title: Response to bile of Lactobacillus casei BL23

status: Public on Oct 20 2011

city: Paterna

first: Manuel

last: Zúñiga

state: Valencia

address: Avda. Profesor Agustín Escardino 7

department: Biotecnología

institute: Instituto de Agroquímica y Tecnología de Alimentos

summary: The response to bile of Lactobacillus casei BL23 was investigated.

overall_design: Lactobacillus casei BL23 was grown in MRS medium at 37C without shaking until O.D. 595 nm. reached 0.5. The cultures were then two fold diluted with prewarmed MRS medium (control) or MRS supplemented with 0.2% bovine bile (treatment) and incubation continued for 45 min. Cells were then harvested and total RNA purified.

first: Cristina

last: Alcántara


title: Oncogenic ETS proteins regulate a Ras/MAPK gene expression program in the absence of MAPK signaling

status: Public on Oct 19 2011

city: Notre Dame

first: Jacqueline

last: Lopez

address: 019 Galvin Life Science Center

department: Biology

institute: University of Notre Dame

summary: Approximately 50% of prostate cancers have chromosomal translocations resulting in the over-expression one of four ETS family transcription factors. However, it is not known why these four four family members are selected for oncogenic roles, while other ETS proteins are not.  We found that the four oncogenic ETS family members have a specific role in prostate cell migration.  Using chromatin immunoprecipitation coupled with next-generation sequencing, this specific biological function was matched to a specific set of genomic targets highlighted by the presence of an AP-1 binding site.  ETS/AP-1 binding sites are prototypical Ras-responsive elements, but oncogenic ETS proteins could activate a Ras/MAPK transcriptional program in the absence of MAPK activation.  These findings indicate that the specific function of ETS proteins over-expressed in prostate cancer is the activation of a Ras/MAPK gene expression program in the absence of signaling pathway mutations.

overall_design: 16 samples were analyzed, comprised of four replicates each of four different biological conditions.  RNA from U0126 treated RWPE-1 empty vector cell RNA serves as a control for each experiment. Cell lines have retroviral expression constructs expressing either empty vector, Flag-ERG, or Flag-ETV1.

first: Peter

last: Hollenhorst

first: Mary

middle: W

last: Ferris


title: Maize gene expression during infection with Colletotrichum graminicola

status: Public on Aug 04 2011

city: Erlangen

first: Lars

middle: Matthias

last: Voll

address: Staudtstrasse 5

department: Division of Biochemistry

summary: The hemibiotrophic fungal pathogen Colletotrichum graminicola is the causal agent of anthracnose disease on maize stalks and leaves. After the formation of appressoria the host cell wall is penetrated by the conversion of appressorial turgor pressure into forceful ejection of a penetration peg. Subsequently, C. graminicola establishes biotrophic hyphae in the penetrated epidermis cell at around 36 hours post inoculation (hpi) until a switch of hyphal morphology and lifestyle takes place during the colonization of neighboring host cells at around 72 hpi. During the ensuing necrotrophic growth, dark necrotic lesions are formed that are visible as anthracnose symptoms. We used microarrays to detail the global programme of gene expression during the infection process of Colletotrichum graminicola in its host plant to get insight into the defense response of this compatible interaction and into the metabolic reprogramming needed to supply the fungus with nutrients.

overall_design: In three independent experiments, maize plants were infected with conidia of the Colletotrichum graminicola strain CgM2 by spray inoculation of leaves. Samples from infected leaves were taken at 36 and 96 hours post infection, corresponding to initial biotrophic and necrotrophic phase, respectively. Samples from uninfected control plants were taken at the same time points.

first: B

last: Samans

first: S

last: Münch

first: A

last: Voitsik

first: R

last: Wahl

first: G

last: Doehlemann

last: Kahmann

first: U

last: Sonnewald

first: H

middle: B

last: Deising

first: L


title: Global gene expression of Ruegeria pomeroyi strain DSS3 in response to glucose, ammonium, phosphate, or sulfate limitation

status: Public on Oct 01 2011

city: Athens

first: Shalabh

last: Sharma

state: GA

address: Department of Marine Science

department: Marine Science

institute: UGA

summary: We used the previously designed oligonucleotide-based microarray (Burgmann et al. Environmental Microbiology 2007, 9: 2742-2755) to detect the transcripts of R. pomeroyi DSS-3 genes when the cells were cultured under steady-state carbon (glucose), nitrogen (ammonium), phosphorus (phosphate), or sulfur (sulfate) limitation.

overall_design: A total of 14 mRNA samples were hybridized to the arrays (three biological replicates from glucose, ammonium, phosphate, or sulfate limitation and one technical replicate each for ammonium or sulfate limitation)

middle: A

last: Moran

first: Leong-Keat

last: Chan

first: Ryan

last: Newton


title: P. pacificus : Dauers and Dauer-Exit at 12 hour time-point vs. Mix-stage worms

status: Public on Sep 03 2011

city: Ipswich

first: Amit

last: Sinha

address: 240 County Road

institute: New England Biolabs

summary: Transcriptional profiling of P. pacificus worms from (1) dauer stage, or (2) dauer-exit at 12 hours stage, compared to mix-stage worms as a common reference. The goal was to determine genes regulated during dauer development and recovery or exit from dauer stage. This data was then compared to data generated for corresponding developmental stages in the C. elegans (see NCBI GEO series GSE30977) , to study evolution of developmental pathways regulating dauer development.

overall_design: Two-condition experiments.  Experiment 1 = Dauers vs. Mix-stage worms. 4 biological replicates for each condition, including 2 dye-swaps.   Experiment 2 = Dauer-Exit at 12 hour time-point s vs. Mix-stage worms. 3 biological replicates for each condition, including 1 dye-swaps.   Total samples from both experiments 1 and 2 = 7.

first: Christoph

last: Dieterich

first: Ralf

last: Sommer


title: Identification of calcineurin- and Crz1-dependent targets in Candida glabrata

status: Public on Sep 01 2011

city: Durham

first: Ying-Lien

last: Chen

address: Dept. of Molecular Genetics and Microbiology, Duke University Medical Center

department: Molecular Genetics and Microbiology

institute: Duke University

summary: In order to identify calcineurin pathway-regulated genes, we compared the genome-wide expression profile of wild-type with FK506-treated wild-type, cna1, and crz1 mutants. We expect that FK506-treated wild-type will have similar expression profile with that of the cna1 mutant. In response to calcineurin inhibitor FK506, the up- and down-regulated by FK506 were 113 and 87 genes, respectively (cutoff q < 0.001). The genes regulated by FK506 are largely overlapped (90%, 180/200) with those of cna1 mutant. Interestingly, FK506 induced 20 distinct genes other than that of the cna1 mutant. These genes encode proteins involved in plasma membrane ATP-bindding cassette (ABC) multidrug transporters (PDR15, PDR5, and YOR1), amino acid transporters (ALP1 and YBT1), and transcription factors (CUP2 and INO2). We also identified 34 genes regulated by calcineurin and Crz1. These genes encode proteins involved in cell wall biosynthesis (YPS5, YPS1, YSR3, YPC1, PIR1, HOR7, and NTE1), heat shock protein responses (SBA1 and GRE2), regulator of calcineurin (RCN2), and other functions.

overall_design: 5 sample wheel hybridization design with dye swaps totaling 10 arrays replicated 2 times to include an additional set of biological replicates. 20 arrays total.

first: Jay

last: Konieczka


title: Response of Chlamydomonas reinhardtii to different oxidative and electrophilic stress conditions

status: Public on Jul 15 2011

city: Dübendorf

first: Beat

last: Fischer

address: Ueberlandstr. 133

department: Department of Environmental Toxicology

institute: Eawag

summary: Acclimation to singlet oxygen was shown to induce various oxidative stress response genes of which some were also strongly overexpressed in the singlet oxygen resistant mutant sor1. Because sor1 was also more tolerant to other oxidative and electrophilic stress conditions, and because many of the sor1 overexpressed genes are known to be involved in the detoxification of reactive electrophile species, the response of the C. reinhardtii wild-type strain to various oxidative and electrophilic stress conditions was determined. Therefore, cultures were exposed to the reactive oxygen species-producing photosensitizer neutral red, the organic hydroperoxide tert-butylhydroperoxide, the photosynthetic herbicide 2,5-dibromo-3-methyl-6-isopropyl-p-benzoquinone (DBMIB) and the lipophilic electrophile 2(E)-Hexenal for two hours and the global genetic response was analyzed. Cluster analysis revealed the most similar expression pattern between DBMIB and 2(E)-Hexenal and to a lower degree between NR and tBOOH. Still, there were many common induced genes including several of the oxidative stress response and detoxification genes overexpressed in the sor1 mutant.

overall_design: The 4A+ wild-type strain was grown mixotrophically in a Tris-acetate phosphate to a density of 2x10^6 cells/ml. Then cultures were split into 20 ml subcultures, and exposed to either of the four chemicals DBMIB (2 µM), 2(E)-Hexenal (0.3 mM), neutral red (NR, 3 µM), tert-butylhydroperoxide (tBOOH, 100 µM) or no chemical (control) for 2 hours, in three independent biological replicates. The cells of each replicate were harvested by centrifugation and total RNA was isolated using the RNeasy Mini Kit (Qiagen). DNA microarrays were performed using the ‘One-Color Microarray-Based Gene Expression Analysis’ system and a custom made 4 × 44 K ‘Chlamydomonas Whole Genome DNA Microarrays’ (Agilent Technologies) containing 15143 specific probes designed based on the Chlamydomonas version 4.0 transcript models provided by the DOE Joint Genome Institute (JGI), with an average of three replicates for each probe

first: Krishna

middle: K

last: Niyogi


title: Gene expression analysis of neural crest in zebrafish to identify novel downstream targets of Twist1

status: Public on Sep 23 2011

city: Los Angeles

first: Ankita

last: Das

email: ankita23@gmail.com, gcrump@usc.edu

address: 1425 San Pablo Street

department: Broad CIRM Center

institute: University of Southern California

summary: sox10:GFP transgenic embryos were used to FACS sort neural crest and microarray analysis was done to compare genes expressed differentially between GFP positive and negative and fold changes were compared to differentially expressed genes in embryos treated with morpholino oligonucleotides to knockdown function of Twist1

overall_design: A Nimblegen catalog design microarray study done in biological triplicates to analyze expression of genes in neural crest and regulated by Twist1

first: Gage

last: Crump


title: Regulation of Human Dendritic Cell Apoptosis and IL-12 Production by MiR-221and MiR-155 through targeting of p27kip1, KPC1 and SOCS1

status: Public on Jun 30 2011

city: Minneapolis

first: Xiaoxiao

last: Zhang

address: 312 Church St. SE

institute: University of Minnesota

summary: We systematically analyzed miRNA profiling from human monocyte, immature DCs (imDCs) and mature DCs(mDCs) using miRNA microarray . miR-155 and miR-221 expression correlated with p27kip1 accumulation in DCs.

platform_organism:
Caenorhabditis elegans
Drosophila melanogaster
Danio rerio
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: 2 replicates for each of 3 cell types (monocyte, imDCs, DCs)

first: Yan

last: Zeng

first: Changming

last: Lu

first: Xianzheng

last: Zhou