title: Developmental competence

status: Public on Apr 29 2015

city: New York

first: Luke

middle: Mackley

last: Noble

state: NY

address: 12 Waverly Place

institute: New York University

summary: Timecourse of gene expression in vegetative mycelium for wild-type and a precocious mutant

overall_design: Two strains, 5 time points, 22 arrays

middle: M

first: Alex

last: Andrianopoulos


title: microRNA microarray on a cohort study of platinum-sensitive versus platinum-resistant NSCLC patients

status: Public on Apr 15 2015

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

country: Japan

institute: Toray Industries,Inc.

summary: To identify microRNAs that regulate therapeutic resistance, we conducted a high-throughput miRNA microarray on a cohort study of primary NSCLC (non-small cell lung cancer) tissues and adjacent normal tissues. We found some microRNAs related to therapeutic resistance and poor prognosis.

overall_design: In this study, the patients who were diagnosed with resected NSCLC (adenocarcinoma or squamous cell carcinoma) were enrolled. All tumors were reviewed by pathologists and were pathologically diagnosed according to the World Health Organisation Classification of Tumors. Twenty-nine patients who received four or more courses of first-line platinum-based chemotherapy after postoperative recurrence were divided into two groups (responder (n=17) and non-responder group (n=12)). As identified by ANOVA analysis and quantitative RT-PCR (qRT-PCR) of 4 groups, some miRNAs exhibited significant expression changes.

first: Takahiro

last: Ochiya

first: Yu

last: Fujita


title: Yeast Genomic Expression Patterns in Response to glucosylated mycotoxin

status: Public on Apr 01 2015

city: Tukuba

first: Tadahiro

last: Suzuki

state: Ibaraki

address: kan-nondai 2-1-12

department: Applied Microbiology Division

institute: National Food Rsearch Institute

summary: The evaluation of mycotoxicity about glucosylated mycotoxin using yeast gene expression comparison analysis. Yeast BY4743 derivative PDR5 mutant was used for this study.

platform_organism:
Schizosaccharomyces pombe
Saccharomyces cerevisiae

overall_design: Samples were normalized with the three replicates per condition. Yeast strain was grown in YPD medium with 80 μM of deoxynivalenol-3-glucoside. The same volume of DMSO was added into control samples.

first: Yumiko

last: Iwahashi


title: Dynamic mRNA gene expression during a nutritional downshift from glutamine to proline

status: Public on Apr 07 2015

city: Zurich

first: Uwe

last: Sauer

address: Auguste-Piccard-Hof 1

department: Institute of Molecular Systems Biology

country: Switzerland

institute: ETH Zurich

summary: Dynamic mRNA gene expression from the wildtype YSBN6 during a nutritional downshift from glutamine to proline. Glutamine and proline were initially together in the media, with cells consuming exlusively glutamine (proline utilization inhibited due to nitrogen catabolite repression). The concentration of glutamine was frequently evaluated at-line, and the moment at which glutamine was not detected anymore is referred to as the time of the shift.

overall_design:
Given the uncertainty of the exact time of the shift, two samples were taken at steady-state, approximately 10 and 5 minutes before the shift. Once the shift was identified, samples were taken 3, 7, 10, 14, 24, 56 and 120 minutes after the glutamine depletion. Biological triplicate gene expression was measured for samples -10, 7 and 24 minutes after shift, for a total of 15 chips. Changes were generally evaluated relative to the steady-state point (-10 minutes). Biological variability can be assessed from the replicates time points.
Other dynamic omics data are associated with this dataset. Consult the publication for more details.

first: Ana

middle: P

last: Oliveira


title: RNA-Seq reveals an unprecedented complexity of the neuroblastoma transcriptome and is suitable for clinical endpoint prediction [RNA-Seq]

status: Public on May 22 2015

city: Shanghai

first: Leming

last: Shi

address: 2005 Songhu Road

department: School of Life Sciences

country: China

institute: Fudan University

type: Expression profiling by high throughput sequencing

summary:
We generated gene expression profiles from 498 primary neuroblastomas using RNA-Seq and microarrays. We sought to systematically evaluate the capability of RNA deep-sequencing (RNA-Seq)-based classification for clinical endpoint prediction in comparison to microarray-based ones. The neuroblastoma cohort was randomly divided into training and validation sets, and 360 predictive models on six clinical endpoints were generated and evaluated. While prediction performances did not differ considerably between the two technical platforms, the RNA-Seq data processing pipelines, or feature levels (i.e., gene, transcript, and exon junction levels), RNA-Seq models based on the AceView database performed best on most endpoints. Collectively, our study reveals an unprecedented complexity of the neuroblastoma transcriptome, and provides guidelines for the development of gene expression-based predictive classifiers using high-throughput technologies.

Sample clinical characteristics definitions:

dataset: Expression data set used for classification training (1) or validation (2)
Sex: M = male; F= female
age at diagnosis: the age in days at diagnosis
mycn status: Amplification status of the MYCN proto-oncogene (amplified = 1, no amplification = 0; no information = N/A)
high risk: Clinically considered as high-risk neuroblastoma (yes=1, no= 0)
INSS stage: disease stage according to International Neuroblastoma Staging System (INSS) (1, 2, 3, 4 and 4S)
class label: Maximally divergent disease courses - unfavorable (= 1): patient died despite intensive chemotherapy, favorable (=0): patient survived without chemotharapy for at least 1000 days post diagnosis; not applicable (N/A)
progression: Occurrence of a tumor progression event (yes=1; no=0)
death from disease: Occurrence of death from the disease (yes=1; no=0)

overall_design:
Gene expression of 498 neuroblastoma samples was quantified by RNA sequencing as well as by microarray analyses in order to understand the neuroblastoma transcriptome and predict clinical endpoints.

Due to patient privacy issues the raw data was not submitted. The clinical study was done in Germany, and since there are no NIH PI and no US accreditation, the raw data could not be submitted to dbGaP.

first: Wenqian

last: Zhang

first: Danielle

last: Thierry-Mieg

first: Jean

first: Davide

last: Albanese

first: Cesare

last: Furlanello

first: Zhiyu

last: Peng

first: Matthias

last: Fischer


title: Time dynamics of quantitative protein and mRNA levels reveals extensive translational regulation after stress

status: Public on Mar 01 2015

city: Lyngby

first: Federico

last: De Masi

address: Kemitorvet 208

department: Institute of Systems Biology

country: Denmark

institute: Technical University of Denmark

summary: Eukaryotic cells are constantly challenged by the presence of reactive oxygen species, which play an important role in aging and human disease progression. In particular, acute oxidative stress can lead to extensive damage to cellular DNA, proteins, and lipids and can trigger a response that remodels the transcriptional and translational state of the cell. Although a number of previous studies have profiled the relative changes in mRNA and protein and more studies revealing the dynamics of transcription and translation in response to stress are starting to emerge, a quantitative view of this response has been lacking. Here, we have applied quantitative methods to characterize the time dynamics of mRNA and protein levels in the oxidative stress response of the fission yeast Schizosaccharomyces pombe, which has allowed us to perform dynamic modeling of responsive genes in units of copies per cell. Analysis of the resulting time dynamics provided a new genome-wide view of the scale, timing and rates of transcription and translation in the transient response. The majority of dynamic genes were observed to be responsive in their mRNA or protein levels alone implying extensive translational regulation. Nevertheless, modeling of genes with responsive mRNA and protein levels showed that protein levels could, in a majority of these cases, be accurately predicted with constant translation and decay rates while a minority benefited from explicit translation delay parameters. A number of independent features, e.g. measures of codon bias, ribosome occupancy, etc., were found to be less correlated to maximally perturbed protein levels than steady-state levels. Codon bias measures were more correlated than mRNA levels to quantitative protein levels at both perturbed and un-perturbed states. Measures of translation activity, on the other hand, were only significantly correlated at steady state.

overall_design: In total 32 samples: 11 for stressed time series R1, 11 for stressed time series R2, 5 for control time series C1 and 5 for control time series C2

first: Manos

middle: A

last: Papadakis

first: Alexander

last: Schmidt

first: Francesc

middle: X

last: Marsellach

first: Federio

first: Helle

middle: K

last: Pedersen

first: Greg

last: Slodkowicz

first: Andreas

last: Beyer

first: Jürg

last: Bähler

first: Ruedi

last: Aebersold

first: Christopher

middle: T

last: Workman


title: The Plant-Specific RAB5 GTPase ARA6 is Required for Starch and Sugar Homeostasis in Arabidopsis thaliana

status: Public on Feb 18 2015

city: Bunkyo-ku

first: Tomokazu

last: Tsutsui

state: Tokyo

address: Room 02 (BF), Faculty of Science Building 2, 7-3-1 Hongo

department: Biological Sciences

institute: The university of tokyo

summary: Endosomal trafficking plays integral roles in various eukaryotic cell activities. In animal cells, a member of the RAB GTPase family, RAB5, is a key regulator of various endosomal functions. In addition to orthologs of animal RAB5, plants harbor the plant-specific RAB5 group, the ARA6 group, which is conserved in land plant lineages. In Arabidopsis thaliana, ARA6 and conventional RAB5 act in distinct endosomal trafficking pathways; ARA6 mediates trafficking from endosomes to the plasma membrane, whereas conventional RAB5 acts in endocytic and vacuolar trafficking pathways. ARA6 is also required for normal salt and osmotic stress tolerance, although the functional link between ARA6 and stress tolerance remains unclear. In this study, we investigated ARA6 function in stress tolerance by monitoring broad-scale changes in gene expression in the ara6 mutant. A comparison of the expression profiles between wild-type and ara6‐1 plants revealed that the expression of the Qua-Quine Starch (QQS) gene was significantly affected by the ara6‐1 mutation. QQS is involved in starch homeostasis, consistent with the starch content decreasing in the ara6 mutants to approximately 60% of that of the wild-type plant. In contrast, the free and total glucose content increased in the ara6 mutants. Moreover, the proliferation of Pseudomonas syringae pv. tomato DC3000 was repressed in ara6 mutants, which could be attributed to the elevated sugar content. These results suggest that ARA6 is responsible for starch and sugar homeostasis, most probably through the function of QQS.

overall_design: The transcriptional profiling between the wild-type Col. and a RAB5 knock out mutant, ara6-1.

first: Akihiko

last: Nakano

first: Takashi

last: Ueda


title: Evolutionary engineering of a wine yeast strain revealed a key role of inositol and mannoprotein metabolism during low-temperature fermentation

status: Public on Mar 31 2015

city: Paterna

first: Estéfani

last: García-Ríos

state: Valencia

address: Avenue Agustín Escardino, 7

department: Biotechnology

country: Spain

institute: Institute of Agrochemistry and Food Technology (IATA-CSIC)

summary: Wine produced at low temperature is often considered to improve sensory qualities. However, there are certain drawbacks to low temperature fermentations: e.g. low growth rate, long lag phase, and sluggish or stuck fermentations. Selection and development of new Saccharomyces cerevisiae strains well adapted at low temperature is interesting for future biotechnological applications. This study aimed to select and develop wine yeast strains that well adapt to ferment at low temperature through evolutionary engineering, and to decipher the process underlying the obtained phenotypes. To this end, we used a pool of 27 commercial yeast strains and set up batch serial dilution experiments to mimic wine fermentation conditions at 12 ºC. Evolutionary engineering was accomplished by using the natural yeast mutation rate and mutagenesis procedures. One strain (P5) outcompeted the others under both experimental conditions and was able to impose after 200 generations. The evolved strains showed improved growth and low-temperature fermentation performance compared to the ancestral strain. This improvement was acquired only under inositol limitation. The transcriptomic comparison between the evolved and parental strains showed the greatest up-regulation in four mannoprotein coding genes, which belong to the DAN/TIR family (DAN1, TIR1, TIR4 and TIR3).  Genome sequencing of the evolved strain revealed the presence of a SNP in the GAA1 gene and the construction of a site-directed mutant (GAA1Thr108) in a derivative haploid of the ancestral strain resulted in improved fermentation performance. GAA1 encodes a GPI transamidase complex subunit that adds GPI, which is required for inositol synthesis, to newly synthesized proteins, including mannoproteins. Thus we demonstrate the importance of inositol and mannoproteins in yeast adaptation at low temperature and the central role of the GAA1 gene by linking both metabolisms.

overall_design: The first aim of this study was to assess the most competitive strains that grow under wine fermentation conditions at low temperature. To this end, we performed a growth competition assay with 27 commercial wine strains inoculated at equal population size in synthetic grape must. In spite of the economical and industrial importance of these strains, their phenotypic variation in the main enological traits, particularly those related to optimum growth temperature, and their ability to adapt to low temperature fermentation have been poorly investigated. The second goal was to obtain an improved strain to grow and ferment at low temperature by evolutionary engineering. For this purpose, we maintained growth competition in synthetic grape must during 200 generations to select for the mutations that produce phenotypes with improved growth in this medium. One of these evolved cultures was previously treated with ethyl methanesulfonate (EMS) to increase the mutation rate. Finally, we aimed to decipher the molecular basis underlying this improvement by analyzing the genomic and transcriptional differences between the parental strain and the strain evolved at low temperature.

first: María

last: López-Malo

first: Bruno

last: Melgar

first: Monica

middle: R

last: Sanchez

first: Maitreya

middle: J

last: Dunham

first: José

last: Guillamón


title: Nuclear tRNA sequestering slows aging by a mechanism similar to dietary restriction

status: Public on Feb 03 2015

city: Seattle

first: James

middle: William

last: MacDonald

state: WA

address: 4225 Roosevelt Way NE

department: Environmental and Occupational Health Sciences

country: USA

institute: University of Washington

summary: Dietary restriction (DR) is the best-characterized intervention for slowing aging, and reduced signaling through the target of rapamycin (TOR) kinase is believed to be one of the key mechanisms by which DR extends life span in organisms from yeast to mammals.  Here we describe a role for nuclear sequestration of tRNA in yeast replicative life span (RLS) extension from DR.  DR causes the nuclear tRNA exporter Los1 to become depleted from the nucleus by a mechanism that requires the DNA damage response factor Rad53, and deletion of LOS1 or overexpression of RAD53 is sufficient to extend RLS.  We further report that activation of the nitrogen responsive transcription factor Gln3 is the primary mechanism by which DR extends RLS.  Gln3 is activated by both branches of the DR response and is required for life span extension.  Overexpression of Gln3 extends RLS by approximately 50%.

overall_design: In order to identify potential factors acting to modulate longevity downstream of Los1, we used microarray analysis to compare the gene expression profiles of wild type and LOS1 knockout cells under non-restricted conditions cultured overnight prior to RNA isolation.

middle: W

first: Richard

first: Theodor

last: Bammler

first: Joe

last: Delaney

first: Sylvia

last: Sim

first: Annie

last: Chou

first: Umema

last: Ahmed

first: Daniel

last: Carr

last: Murakami

first: Jennifer

last: Schleit

first: George

middle: L

last: Sutphin

first: Brady

last: Olsen

first: Brian

last: Kennedy

first: Matt

last: Kaeberlein


title: Transcriptional characterization of maize roots in response to urea and nitrate

status: Public on Mar 02 2015

city: Verona

first: Anita

last: Zamboni

address: Strada Le Grazie, 15

country: Italy

institute: University of Verona

summary:
Although urea is the most used nitrogen fertilizer worldwide, little is known on the capacity of crop plants to use urea per se as a nitrogen source for development and growth. To date, the molecular and physiological bases of its transport have been investigated only in a limited number of species.
In particular, up to date only one study reported the transcriptomic modulation induced by urea treatment in the model plant Arabidopsis (Mérigout et al., 2008 doi: 10.1104/pp.108.119339). In maize, one of crops using huge amount of urea, only a physiological characterization of uptake and assimilation of
the N-source has been conducted. General aim of the present work was the comprehension of the molecular basis of urea uptake and assimilation in maize plants, using a transcriptomic approach. In addition, the work focused on the possible interactions between the two main N-sources, conceivably
occurring concomitantly in the soil, urea and nitrate.

overall_design:
5 dd-old maize plants were treated for 8 hours with nutrient solution containing nitrogen in form of urea; nitrate; urea and nitrate; or not exposed to any form of nitrogen.
Three different biological replicates were used for each sample repeating the experiment three times. All samples were obtained pooling roots of six plants.

first: Laura

last: Zanin

first: Nicola

last: Tomasi

first: Zeno

last: Varanini

first: Stefano

last: Cesco

first: Roberto

last: Pinton


title: Expression data from the T-DNA insertion line atpip1;2-1

status: Public on Jan 10 2015

city: Darmstadt

first: Anastassia

last: Boudichevskaia

state: Hessen

address: Schnittspahnstrasse 10

department: FB Biologie

country: Germany

institute: TU Darmstadt

summary:
Some aquaporins do not show a pronounced function as water diffusion facilitators but act as small molecule transport facilitators for substances such as urea, glycerol, boron or gases such as CO2 . Transcriptome analysis provided distinguishable, specific profiles for water stress or for conditions of increased or decreased CO2 concentrations
We used Affymetrix microarray analysis to elucidate the function of the aquaporin AtPIP1;2 gene

overall_design: A T-DNA insertion line  atpip1;2-1 was used for RNA extraction and further microarray analysis based on the Affymetrix platform. The transcriptome of the atpip1;2-1 line was compared to the wild type (N-60000).

first: Marlies

last: Heckwolf

first: Ralf

last: Kaldenhoff


title: Expression data from fission yeast Schizosaccharomyces pombe under nitrosative stress

status: Public on Jan 30 2015

city: Kolkata

first: Sanjay

last: Ghosh

state: West Bengal

address: Dept. of Biochemistry, 35, Ballygunge Circular Road, Kolkata-700019

department: Biochemistry

country: India

institute: University of Calcutta

summary:
Nitric oxide being a versatile molecule inside biological systems, from being both a cell signaling molecule to a potent stress agent, has significant effect in the transcriptional response in fission yeast.
We have used fission yeast microarrays to identify cellular targets of Nitric Oxide (NO) and to further understand the cellular mechanism of NO action. We report the change in the global gene expression profile response to NO in S. pombe cells

overall_design: S. pombe cells were treated with pure NO donor compond detaNONOate for 15 minutes at 30 degrees celcius for both the wild type and pap1 deleted strain, the cells were processed through RNA extraction and hybridization on Affymetrix microarrays. We included pap1 deleted strain of S. pombe alongside wild type strain as we earlier reported that pap1 is important to combat nitrosative stress, so pap1 might control the expression of several genes under nitrosative stress. Wild type control and treated samples as well as Mutant control and treated sets are included in 2 biological replicates for each.

first: Pranjal

last: Biswas


title: Inferring causal metabolic signals that regulate the dynamic TORC1-dependent transcriptome

first: Uwe

last: Sauer

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

overall_design: Refer to individual Series


title: Influence Of Insulin On Oocyte Maturation In Invitro Produced Bovine Embryos

status: Public on Oct 31 2014

city: Uppsala

first: Denise

last: Laskowski

address: Postbox 7054

department: KV

country: Sweden

institute: SLU

summary: Microarray analysis of transcriptome bovine blastocysts Day 8, deriving from oocytes matured under different insulin concentrations as model for metabolic imbalance

overall_design: Three conditions experiment: control, Low Insulin (INS0.1), High Insulin (INS10) treatments.  Biological replicates: 4 for each treatment. One replicate per array.

first: Ylva

last: Sjunnesson

first: Patrice

last: Humblot

first: Marc-André

last: Sirard

first: Göran

last: Andersson

first: Hans

last: Gustafsson

first: Renee

last: Båge


title: HDG1 transcription factor targets

status: Public on Jan 22 2015

city: Wageningen

first: Gabino

last: Sanchez-Perez

address: Droevendaalsesteeg 1

department: Bioscience

country: Netherlands

institute: Wageningen University

summary: The AIL transcription factor BABY BOOM (BBM) is required together with the related PLETHORA proteins for embryo and root meristem development and its expression is sufficient to confer pluripotency and totipotency to somatic tissues. We show that BBM and other AIL proteins interact with multiple members of the L1/epidermal-expressed HD-ZIP class IV / HOMEODOMAIN GLABROUS (HDG) transcription factor family. Ectopic overexpression of HDG1, HDG11 and HDG12 genes induces a reduced growth phenotype, and analysis of HDG1 overexpression lines shows that this growth reduction is due to both root and shoot meristem arrest. To understand how HDG1 controls cell proliferation, as well as its functional relationship with BBM, we performed microarray experiments to identify candidate genes that are directly regulated by HDG1, and compared these to the set of genes that are directly regulated by BBM expression.

overall_design: Transcriptomic profiling was done after 8 hours of dexamethasone induction of 35S::GR-HDG1 and wild-type Col-0 seedlings and significantly differentially expressed genes were identified as HDG1 targets.

first: Anneke

last: Horstman

first: Kim

last: Boutilier

middle: F


title: Comparative analysis of ovine fetal skeletal muscle gene expression:  control and intrauterine growth restriction (IUGR)

status: Public on Dec 31 2014

city: Denver

first: Laura

last: Brown

state: CO

address: Mail Stop C263 12348 East Montview Boulevard

department: Center for Women's Health Research

institute: University of Colorado Anschutz Medical Campus

summary:
Impaired muscle growth as a result of IUGR is a major contributor to lifelong reductions in muscle mass (sarcopenia) and metabolic disease risk. We use an ovine model of chronic placental insufficiency which restricts nutrient supply from mother to fetus and results in intrauterine growth restriction. In our model of placental insufficiency and IUGR, fetal hindlimb muscles weigh less than normally-grown control fetuses and have smaller myofiber diameters.
Given the frequent correlation between functional changes and transcriptional changes, we investigated the effect of chronic placental insufficiency and IUGR on fetal skeletal muscle gene expression. We found that gene expression in the skeletal muscle is significantly altered by chronic placental insufficiency. In gene ontology analysis, we found that genes involved in cell cycle regulation were most significantly affected, with downregulation of several cyclins. These observations may in part account for decreased muscle weight relative to brain weight observed in the late gestation IUGR fetus.

overall_design: Biceps femoris muscle from control and IUGR fetal sheep were excised at 90% of gestation. Total RNA was extracted and biotin-labeled amplified cRNA was hybridized to Affymetrix Bovine Genome Arrays.

middle: D

first: Kristen

middle: B

last: Barthel

first: Bifeng

last: Gao

first: Tzu

last: Phang

first: Leslie

last: Leinwand


title: Chromium stress response in rice roots: effects on transcriptome proﬁles and signalling pathways responsive

status: Public on Dec 21 2014

city: Tainan

first: Tsai-Lien

last: Huang

state: Taiwan

address: No.1, University Raod,

department: Life Sciences

country: Taiwan

institute: National Cheng Kung University

summary:
Chromium (Cr) is an important environmental contaminant and also a genotoxic metal ion at high concentration, but its molecular mechanisms and signalling pathways of action in plants is still poorly unraveled. To help characterize the mechanism of molecular and signalling of rice, we present the large-scale, transcriptomic analysis of rice root responses to Cr(VI).
We examined the possible involvement of reactive of reactive oxygen species (ROS) and calcium in Cr(VI) signaling transduction pathways, as well as the effect of Cr (VI) on CDPK and MAPK activity. Specially, we used the microarray assay to assess different stage Cr (VI) induced alteration in rice gene expression. This gene discovery effort will help expand our understanding of cellular responses to Cr (VI) treatment, and will identify candidate genes for enhancement of Cr resistance in crop.

overall_design: Two-condition experiment, short exposures and long exposures. Comparison of mock control and rice seedlings treated with 50 μM Cr(VI) during short (pooled from 1- and 3-h treatments), as compared to long (24 h) exposures.; Biological replicates: 3 control replicates (short and long exposures), 3 Cr(VI)-treated replicates (short and long exposures).

first: Shih-Feng

last: Fu

first: Hao-Jen


title: Expression data from Saccharomyces cerevisiae strains deleted for the THSC/TREX-2 subunits Thp1, Sac3 and Sus1

status: Public on Oct 08 2014

city: Seville

first: Andrés

last: Aguilera

address: Av. Américo Vespucio 24

department: Genome BIology

institute: CABIMER, Universidad de Sevilla

summary:
Transcription is a major obstacle for replication fork progression and a cause of genome instability. Such instability increases in mutants with a suboptimal assembly of the nascent messenger ribonucleo-protein particle (mRNP), as THO/TREX and the NPC-associated THSC/TREX-2 complex.
We used microarrays to analyze the global impact of THSC/TREX-2 in gene expression and found that Thp1 and Sac3 depletion has a functional impact in highly-expressed, long and G+C-rich genes regardless of their function

overall_design: S. cerevisiae strains were grown in YPD liquid culture, total RNA was isolated and hybridized on Affymetrix microarrays

first: José

last: Santos-Pereira

first: María

last: García-Rubio

first: Cristina

last: González-Aguilera

first: Rosa

last: Luna


title: Expression data from Saccharomyces cerevisae RNAPII mutant strains

status: Public on Dec 04 2014

summary:
Transcription is a major contributor to genome instability. A main cause of transcription-associated instability relies on the capacity of transcription to stall replication. Such genome instability is increased in RNAPII mutants.
We performed microarrays to analyze the effect of RNAPII mutations on gene expression. The results indicate there is neither a common profile of gene expression nor genes whose gene expression alterations could reasonably explain the genome instability phenotypes of the RNAPII mutants.

first: Irene

last: Felipe-Abrio

first: Juan

last: Lafuente-Barquero

first: Antonio

last: Marín


title: Gene expression by myriocin treatment

status: Public on Sep 22 2014

city: Lexington

first: Jun

last: Liu

state: KY

address: 741 S. Limestone BBSRB B0136

department: Molecular and Cellular Biochemistry

institute: University of Kentucky

summary:
Studies of aging and longevity are revealing how diseases that shorten life can be controlled to improve the quality of life and lifespan itself.  Two strategies under intense study to accomplish this goal are rapamycin treatment and calorie restriction.  New strategies are being discovered including one that uses low-dose myriocin treatment.  Myriocin inhibits the first enzyme in sphingolipid synthesis in all eukaryotes and we showed recently that low-dose myriocin treatment increases yeast lifespan at least in part by down-regulating the sphingolipid-controlled Pkh1/2-Sch9 (ortholog of mammalian S6 kinase) signaling pathway.
Here we show that myriocin treatment has global influences and modulates the evolutionarily conserved Snf1/AMPK, PKA and TORC1 signaling pathways to enhance yeast lifespan.  These extensive affects of myriocin rival those of rapamycin and calorie restriction.  Our studies in yeast along with other studies in mammals reveal the potential of myriocin or related compounds to lower the incidence of age-related diseases in humans.

overall_design: No-myriocin-treated cells and myriocin-treated cells; three biological replicates in each treatment

first: Xinhe

first: Bradley

last: Withers

first: Eric

last: Blalock

first: Ke

first: Robert

middle: C

last: Dickson


title: Genome-wide transcriptome analysis reveals ABA mediated response in Arabidopsis during gold (Aucl4-) treatment

status: Public on Oct 05 2014

city: BOWLING GREEN

first: shivendra

middle: v.

last: sahi

state: KENTUCKY

address: 1906 college heights

department: Biology

institute: western kentucky university

summary: Genome-wide transcriptome analysis was carried out in root tissue of Arabidopsis seedlings treated with gold (Au) as Chloroauric acid (HAuCl4). This study demonstrated remarkable changes in root transcriptome within the 12 h exposure. Most of the genes differentially expressed were related to glutathione binding, methylations, secondary metabolism, sugar metabolism, ABA, ethylene, auxin related signalling, transport and signal-transduction pathways.

overall_design: We analyzed root tissue from 6 samples (3 treated, 3 control) using the Affymetrix Arabidopsis Gene 1.0 ST platform. Array data was processed by Affymetrix Exon Array Computational Tool. No technical replicates were performed.

first: Devesh

last: Shukla

first: Sneha

last: Murthy

first: Shivendra

middle: V

last: Sahi


title: Inactivation of the Budding Yeast Cohesin Loader Scc2 alters Gene Expression both Globally and in Response to a Single DNA Double Strand Break [expression array]

status: Public on Oct 16 2014

city: Stockholm

first: Lena

last: Ström

address: Berzelius väg 35

department: Cell and Molecular Biology

institute: Karolinska Institutet

summary: Genome integrity is fundamental for cell survival and cell cycle progression. Important mechanisms for keeping the genome intact are proper sister chromatid segregation, correct gene regulation and efficient repair of damaged DNA. Cohesin and its DNA loader, the Scc2/4 complex have been implicated in all these cellular actions. The gene regulation role has been described in several organisms. In yeast it has been suggested that the proteins in the cohesin network would effect transcription based on its role as insulator. More recently, data are emerging indicating direct roles for gene regulation also in yeast. Here we extend these studies by investigating whether the cohesin loader Scc2 is involved in regulation of gene expression. We performed global gene expression profiling in the absence and presence of DNA damage, in wild type and Scc2 deficient G2/M arrested cells, when it is known that Scc2 is important for DNA double strand break repair and formation of damage induced cohesion. We found that not only the DNA damage specific transcriptional response is distorted after inactivation of Scc2, but also the overall transcription profile. Interestingly, these alterations did not correlate with changes in cohesin binding.

overall_design: We investigated the gene transcription profiles using GeneChip Yeast Genome 2.0 Array  in WT and Scc2 deficient cells in the absence and presence of DNA damage.

first: Emma

last: Lindgren

first: Sara

last: Hägg

first: Fosco

last: Giordano

first: Johan

last: Björkegren


title: Molecular mechanism of flocculation self-recognition in yeast and its role in mating and survival

status: Public on Dec 24 2014

city: Brussel

first: Katty

last: Goossens

address: Pleinlaan 2

department: DBIT

country: Belgium

institute: Vrije Universiteit Brussel

summary: Saccharomyces cerevisiae flocculation occurs when fermentable sugars are limiting and is therefore considered as a way to enhance the survival chance of Flo-expressing yeast cells. In this paper, the role of Flo1p in mating was demonstrated by showing that the mating efficiency, which contributes to the increased survival rate as well by generating genetic variability, is increased when cells flocculate. This was revealed by liquid growth experiments in a low shear environment and differential transcriptome analysis of FLO1 expressing cells compared to the non-flocculent wild-type cells. The results show that a floc provides a uniquely organized multicellular ultrastructure that provides a suitable microenvironment to induce and perform cell conjugation.

overall_design: S. cerevisiae strains BY4742 WT, BY4742::FLO8 and BY4742 [FLO1] were grown in microgravity and 1-g.  A transcriptomic analysis was performed and the transcriptome data were integrated with the high quality protein-protein interaction networks. The identified high score sub-networks (qvalue < 0.001) were considered and further evaluated concerning their GO enrichment using a hypogeometric test.

first: Francesco

middle: S

last: Ielasi

first: Intawat

last: Nookaew

first: Ingeborg

last: Stals

first: Livan

last: Alonso-Sarduy

first: Luc

last: Daenen

first: Sebastiaan

middle: E

last: Van Mulders

first: Rudy

middle: G

last: van Eijsden

first: Catherine

last: Stassen

first: Verena

last: Siewers

first: Freddy

last: Delvaux

first: Sandor

last: Kasas

first: Jens

last: Nielsen

first: Bart

last: Devreese

first: Ronnie

last: Willaert


title: Expression data from yeast heterologously expressing αENaC, CFTR or Kir2.1 [Kir2.1]

status: Public on Sep 10 2014

city: Pittsburgh

first: Teresa

last: Buck

state: PA

address: 4200 5th Ave

institute: University of Pittsburgh

summary: Misfolded membrane proteins are retained in the endoplasmic reticulum (ER) and are subject to the ER associated degradation pathway, which clears the secretory pathway of potentially toxic species.  While the transcriptional response to environmental stressors has been extensively studied, limited data exist describing the cellular response to misfolded membrane proteins.  To this end, we expressed and then compared the transcriptional profiles elicited by the synthesis of three ER retained, misfolded ion channels: The α subunit of the epithelial sodium channel, ENaC, the cystic fibrosis transmembrane conductance regulator, CFTR, and an inwardly rectifying potassium channel, Kir2.1, which vary in their mass, membrane topologies, and quaternary structures.  To examine transcriptional profiles in a null background, the proteins were expressed in yeast, which was previously used to examine the degradation requirements for each substrate.  Surprisingly, the proteins failed to induce a canonical unfolded protein response or heat shock response, although messages encoding several cytosolic and ER lumenal protein folding factors rose when αENaC or CFTR were expressed. In contrast, the levels of these genes were unaltered by Kir2.1 expression; instead, the yeast iron regulon was activated.  Nevertheless, a significant number of genes that respond to various environmental stressors were upregulated by all three substrates, and when compared to previous microarray data we deduced the existence of a group of genes that reflect a novel misfolded membrane protein response. These data indicate that aberrant proteins in the ER elicit profound yet unique cellular responses.

overall_design: Yeast heterologously expressing αENaC, CFTR, Kir2.1 or harboring a vector control were grown under identical conditions (at least 3 biological replicates) and subject to gene expression analysis.

middle: M

first: Rick

last: Jordan

first: James

last: Lyons-Weiler

first: Patrick

last: Needham

first: Thomas

last: Kleyman

first: Jeffrey

last: Brodsky


title: Functional genomic analysis reveals overlapping and distinct features of chronologically long-lived yeast populations

status: Public on Sep 12 2014

city: Charlottesville

last: Smith

email: jss5y@virginia.edu, sb3de@virginia.edu

state: VA

address: 1340 Jefferson Park Avenue

department: Biochemistry and Molecular Genetics

institute: University of Virginia

summary: The chronological lifespan (CLS) of Saccharomyces cerevisiae is defined as the number days that non-dividing cells remain viable, typically in stationary phase cultures or in water. CLS is extended by restricting glucose in the starting cultures, and is considered a form of caloric restriction (CR). Through a previous genetic screen our lab determined that deleting components of the de novo purine biosynthesis pathway also significantly increased CLS. Significant similarities in gene expression profiles between calorie restricted WT cells and a non-restricted ade4∆ mutant suggested the possibility of common gene expression biomarkers of all chronologically long lived cells that could also provide insights into general mechanisms of lifespan extension. We have identified additional growth conditions that extend CLS of WT cells, including supplementation of the media with isonicotinamide (INAM), a known sirtuin activator, or by supplementation with a concentrate collected from the expired media of a calorie restricted yeast culture, presumably due to an as yet unidentified longevity factor. Using these varied methods to extend CLS, we compared gene expression profiles in the aging cells (at day 8) to identify functionally relevant biomarkers of longevity. Nineteen genes were differentially regulated in all 4 of the long-lived populations relative to wild type. Of these 19 genes, viable haploid deletion mutants were available for 16 of them, and 12 were found to have a significant impact on CLS.

overall_design: Duplicate cultures were grown to saturation in SC media cultures, aged, and then harvested on day 8. The deletion mutant ade4∆ as well as WT cells treated with 25 mM isonicotinamide, calorie restricted (0.5% glucose), or treated with expired media concentrate from previously calorie restricted cultures. These 4 conditions were then compared to a wild-type (WT) strain. Total RNA was isolated and used for microarray hybridizations onto Affymetrix Yeast 2.0 Gene arrrays.

first: Margaret

last: Wierman

first: Mirela

last: Matecic

first: Veena

last: Valsakumar

first: Daniel

first: Stefan

last: Bekiranov


title: Expression data from yeast heterologously expressing αENaC, CFTR or Kir2.1 [CFTR]


title: Microarray and ChIP-chip analyses of the THSC/TREX-2 complex

first: Andrés

last: Aguilera

type: Genome binding/occupancy profiling by genome tiling array


title: Expression data from yeast heterologously expressing αENaC, CFTR or Kir2.1 [αENaC]


title: Expression data from yeast heterologously expressing αENaC, CFTR or Kir2.1


title: Diurnal cycle effect on whole leaf, mesophyll and vasculature: time course

city: Kyoto

first: Motomu

last: Endo

state: Kyoto

address: Sakyo-Ku, Yoshida-Konoe-Cho

department: Biostudies

institute: Kyoto University

summary: Many organisms acquired circadian clock system to adapt daily and seasonal environmental changes. Mammals have the master clock in the brains’ suprachiasmatic nucleus (SCN) that synchronizes other circadian clocks in the peripheral tissues or organs. Plants also have circadian clock in their bodies, but the presence of the tissue-specific functions of circadian clock is remained elusive. The aim of this experiment is to compare tissue-specific gene expression profile using gene expression Microarray.

overall_design: The study was designed to compare the tissue-specific regulation of gene expression between tissues and between day lengths.  All experiments were performed in 9-day-old wild type (Col-0) grown under long day and short day conditions. Whole leaf, mesophyll and vasculature were isolated every four hours over two days. The total numbers of used arrays were 72 Affymetrix Arabidopsis Gene 1.0 ST arrays.  We detected cyclling genes with an FDR<3% using HAYSTACK (http://haystack.mocklerlab.org).


title: Genomic Microarray of Rat Alveolar Type 2 cells Following Chronic Ethanol Ingestion

status: Public on Jul 02 2014

city: Atlanta

first: Gregory

last: Doho

state: GA

address: 1365B Clifton Rd NE

institute: Emory University

summary: Chronic alcohol ingestion changes the alveolar landscape.  We used microarrays to characterize the change in mRNA expression following chronic alcohol ingestion in male Sprague Dawley rates (EtOH 36% of calories)

overall_design: We used microarrays to characterize the change in mRNA expression following chronic alcohol ingestion in male Sprague Dawley rats (EtOH 36% of calories for 6 weeks).  Control animals were given an isocaloric substitution for EtOH for 6 weeks. Alveolar type 2 cells were isolated using an immuno-absorption /technique and RNA was extracted by Trizol. Four control animals and three EtOH treated animals were used for this study.

first: My

middle: N

last: Helms

first: Lou

middle: A

last: Brown


title: The Scc2NIPBL/Scc4MAU2 complex acts in sister chromatid cohesion and transcriptional regulation by maintaining nucleosome-free regions [microarray]

status: Public on Aug 01 2014

city: London

first: Lidia

last: Lopez-Serra

address: 44 Lincoln's Inn Fields

department: Chromosome segregation

country: United Kingdom

institute: Canser Research UK

summary: The Scc2/Scc4 complex binds to broad nucleosome-free regions in the promoters of highly expressed genes. The cohesin loader is recruited to these sites by the RSC chromatin remodeling complex

overall_design: Total RNA was isolated from wt, scc2-4 and sth1-3 cells at 25°C and 37°C. dscDNA was obtained using the IVT system (Invitrogen) and hybridized to Affymetrix Yeast Genome 2.0 Arrays to analyze the expression profile of wt, scc2-4 and sth1-3 cells.

first: Gavin

last: Kelly

first: Harshil

last: Patel

first: Aengus

last: Stewart

first: Frank

last: Uhlmann


title: Transcriptional data from yeast expressing mammalian PIK3CA

status: Public on Jul 19 2014

city: MADRID

first: Teresa

last: Fernandez-Acero

address: PLAZA DE RAMÓN Y CAJAL S/N

department: Departamento de Microbiología II

institute: Facultad de Farmacia UCM

summary: We studied the transcriptional profile in response to acute PtdIns-4,5P2 depletion induced by heterologous expression of a plasma membrane-directed version of mammalian PI3K catalytic subunit (p110α-CAAX).

overall_design: Three biological samples were analyzed for samples expressing for 4 hours p110α-CAAX (PI3K) versus the kinase dead mutant p110α-CAAX K802R (KD), and one microarray experiment was carried out for each sample.


title: Gene expression analysis of S. cerevisiae treated with the histone deacetylase inhibitor CG-1521

status: Public on Jun 02 2014

city: Rensselaer

first: Sridar

last: Chittur

address: One Discovery Drive, CRC 342G

department: Center for Functional Genomics

institute: SUNY-University at Albany

summary: We set out to identify early changes in gene expression in S. cerevisiae after treatment with the histone deacetylase inhibitor CG-1521.

overall_design: Exponentially growing yeast cells were treated with 50 μM CG-1521 or vehicle control for 1h. The experiment was performed in two independent biological replicates.

first: Ann-Christin

last: Gaupel

first: Martin

last: Tenniswood

first: Thomas

last: Begley


title: Transcriptomic changes in response to mercury toxicity in rice roots

status: Public on May 28 2014

first: Wen-Chang

last: Chi

address: No.1, University Road, Tainan City

department: Life Science

summary:
To gain more insight into cellular responses to mercury, we have undertaken a large-scale analysis of the rice transcriptome during mercury stress.More transcripts were responsive to mercury during short (pooled from 1- and 3-h treatments) , as compared to long (24 h) exposures. After short exposures, these induced genes can be divided into different functional categories, mainly on the basis of cell wall formation, chemical detoxification, secondary metabolism, signal transduction and abiotic stress response.
Molecular mechanisms for the mercury toxicity in rice roots.

overall_design: Two-condition experiment, short exposures and long exposures. Comparison of mock control and rice seedlings treated with 25mM Hg during short (pooled from 1- and 3-h treatments), as compared to long (24 h) exposures.; Biological replicates: 3 control replicates (short and long exposures), 3 Hg-treated replicates (short and long exposures).

first: Yun-An

last: Chen

first: Hao-Jen

last: Huang


title: Chemostat expression data of amylase producing yeast Saccharomyces cerevisiae

status: Public on Jun 14 2014

city: Gothenburg

first: Zihe

last: Liu

address: Kemivägen 10

institute: Chalmers University of Technology

summary:
In this study we focus on two Saccharomyces cerevisiae (CEN. PK series) strains producing either insulin precursor or amylase and we compare the transcriptional regulation at different dilution rates, in particular with the objective to identify the relationship between cell metabolism and recombinant protein production.
We found that anaerobic conditions showed high amount of amylase productions when comparing to aerobic conditions and the genome-scale transcriptional analysis suggested that genes related to the endoplasmic reticulum (ER), lipid synthesis and stress responses were generally up-regulated at anaerobic conditions. Moreover, we proposed a model for the electron transfer from ER to the final electron acceptor, fumarate under anaerobic conditions.

overall_design: Two Saccharomyces cerevisiae strains producing either insulin precursor or amylase were selected at different dilution rates in chemostat cultivation for RNA extraction and hybridization on Affymetrix microarrays. Biological triplicates were applied.

first: Jin

last: Hou


title: Expression data from Saccharomyces cerevisiae WT, WT(hsf1), hac1∆ and hac1∆(hsf1)

status: Public on Jul 01 2014

city: Göteborg

first: Tobias

last: Österlund

department: Dept. of Chemical and Biological Engineering

summary:
In the yeast Saccharomyces cerevisiae, accumulation of misfolded proteins in the endoplasmic reticulum (ER) causes ER stress and activates the unfolded protein response (UPR) mediated by Hac1p, whereas the heat shock response (HSR) mediated by Hsf1p mainly regulates cytosolic processes and protects the cell from different stresses. In this study, we find that a constitutive activation of the HSR by over-expression of a mutant HSF1 gene could relieve ER stress in both wild type and hac1∆ UPR-deficient cells.
We studied the genome-wide transcriptional response in order to identify regulatory mechanisms that govern the interplay between UPR and HSR responses. Interestingly, we find that the regulation of ER stress via HSR is mainly through facilitation of protein folding and secretion and not via the induction of Rpn4-dependent proteasomal activity.

overall_design: Four Saccharomyces cerevisiae strains, WT, WT(hsf1), hac1∆ and hac1∆(hsf1), were grown in SD-URA medium and treated with 2.5 mM DTT. After two hours induction, samples were taken for RNA extraction and hybridization on Affymetrix microarrays. Biological triplicates were applied.


title: Integration of growth and patterning during vascular tissue formation in Arabidopsis

status: Public on Aug 15 2014

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

summary: Coordination of cell division and pattern formation is central to tissue and organ development, and is particularly important in plants where walls prevent cell migration. Auxin and cytokinin are both critical for division and patterning, but it is unknown how these hormones converge to control tissue development. Here, we identify a genetic network that reinforces an early embryonic bias in auxin distribution to create a local, non-responding cytokinin source within the root vascular tissue. We provide experimental and theoretical evidence that these cells act as a local tissue organizer by positioning the domain of oriented cell divisions. We further demonstrate that the auxin-cytokinin interaction acts as a spatial incoherent feed forward loop, which is essential to generate distinct hormonal response zones, thus establishing a stable pattern within a growing vascular tissue.

overall_design: 4-day-old plants grown on MS were treated with the indicated compounds for the indicated time, whereafter roots were harvested and total RNA was isolated. Alternatively, roots were protoplasted and cell sorted for GFP+ cells followed by total RNA extraction.

first: Bert

last: De Rybel

first: Mark

last: Boekschoten

first: Dolf

last: Weijers


title: Expression data from aged wild-type, met15Δ and rtg3Δ met15Δ yeast

status: Public on Apr 10 2014

city: Philadelphia

first: Jay

last: Johnson

address: 422 Curie Blvd

department: Pathology and Laboratory Medicine

institute: University of Pennsylvania

summary: To explore putative connections between genetic methionine restriction and the retrograde response, we asked whether the altered transcriptional program of methionine-restricted cells required RTG3 (which is indispensible for retrograde signaling in yeast).

overall_design: Towards this end, we used Affymetrix GeneChip Yeast Genome 2.0 arrays to perform expression profiling of aged (Day 3) wild-type, met15Δ and rtg3Δ met15Δ yeast.

first: J

first: F


title: Microarray analysis comparing yeast Eco1 mutant W216G to mutants of FOB1 and RAD61

status: Public on Apr 03 2014

city: Kansas City

first: Chris

last: Seidel

state: MO

department: Genomics

institute: Stowers Institute

summary: Eco1 is an acetyltransferase subunit of the cohesin complex and acts during DNA replication to establish cohesion between sister chromatids. However, cohesin has additional functions in gene expression, DNA damage repair, and higher-order organization of chromosomes. The eco1 mutant W216G disrupts acetyltansferase activity, and causes genome-wide transcriptional defects which can be suppressed by deletion of FOB1, a gene also involved in DNA replication. This experiment investigates gene expression differences between the eco1-W216G mutant, and mutants in FOB1, and RAD61 a gene involved in inhibition of cohesion establishment but mutation of which is able to suppress temperature sensitivity of the eco1-W216G mutant.

overall_design: Wt and mutant strains of yeast were grown to mid log phase in liquid culture in triplicate and harvested for comparison on Affymetrix microarrays. The following strains were compared: 1) eco1-W216G, 2) eco1-W216G fob1Δ, 3) eco1-W216G rad61Δ, 4) fob1Δ, 5) rad61Δ, and 6) WT.

first: Shuai

last: Lu

first: Bo

last: Xiong

first: Jennifer

last: Gerton


title: Transcript analyses of cisplatin and Sky1 effects in Saccharomyces cerevisiae

city: A Coruña

first: M Esperanza

last: Cerdan

state: A Coruña

address: Campus de A Zapateira

department: Biología Celular y Molecular

institute: Universidad de A Coruña

summary: Sky1 is a Saccharomyces cerevisiae rich serine-arginine (SR) protein-specific kinase and its enzymatic activity is essential in the cytotoxicity caused by cisplatin, although the molecular mechanisms supporting this function are not understood. We present a transcriptome analysis discriminating between RNA changes induced by cisplatin which are dependent or independent of the Sky1 function.

overall_design:
The S. cerevisiae strain W303 (MATa ade2-1 can1-100 leu2-3,112 trp1-100 ura3- 52) and its derivative W303-Δsky1 previously described (Rodríguez- Lombardero et al., 2012) have been used in these analyses. Biological replicates of cultures and treatments were run in triplicate.  The yeast cells were pre-cultured over night in 10mL of complete synthetic medium (SD) prepared as previously described (Zitomer and Hall, 1976). The following day the cells were inoculated at initial OD600 of 0.4 in 70 mL SD and grown in 250 mL Erlenmeyer flasks at 30 ºC and with agitation at 250 rpm. When cells reached OD600 of 0.6, the cultures from each strain were divided in two aliquots of 25 mL (control and cisplatin treatment). A stock solution of cisplatin 6 mM in dimethyl sulfoxide (DMSO) was prepared and the drug was added to the treated cultures at a final concentration of 600 microM. An equivalent volume of DMSO was added to the control cultures. The treatment was done at 30ºC and with agitation at 250 rpm during four hours in darkness. RNA was extracted from a number of cells corresponding to OD600 of 3 with the AurumTM Total RNA Mini Kit (Bio-Rad) and following the manufacturer’s instructions. The RIN parameter (RNA Integrity Number) evaluated with the 2100 was near to the value 9 in all the samples.
Three different RMA analyses were performed:
Analysis 1: GSM1008483-GSM1008488
Analysis 2: GSM1008489-GSM1008494
Analysis 3: GSM1008495-GSM1008500

first: Silvia

last: Rodríguez-Lombardero

first: Angel

last: Vizoso-Vázquez

first: Manuel

last: Becerra

first: M

last: Cerdán


title: Expression data from Saccharomyces cerevisiae strains carrying the rna14-1 or the rna15-1 allele

status: Public on Mar 31 2014

city: Seville

first: Andrés

last: Aguilera

address: Av. Américo Vespucio 24

summary: In the yeast Saccharomyces cerevisiae, cleavage factor I (CFI) and cleavage and polyadenylation factor (CPF) build the core of the transcription termination machinery. CFI comprises the Rna14, Rna15, Pcf11, and Clp1 proteins, as well as the associated Hrp5 RNA-binding protein. We found that CFI participates in the DNA damage response and that rna14-1 shows synthetic growth defects with mutants of different repair pathways, including homologous recombination, non-homologous end joining, post replicative repair, mismatch repair, and nucleotide excision repair, implicating that impaired RNAPII termination and 3’-end processing decreases the cellular tolerance for DNA damage. Beyond replication progression defects, we found that bypass of the G1/S checkpoint in rna14-1 cells leads to synthetic sickness, accumulation of phosphorylated H2A, as well as increase in Rad52-foci and in recombination. Our data provide evidence that CFI dysfunction impairs RNAPII turnover, leading to replication hindrance and lower tolerance to exogenous DNA damage. These findings underscore the importance of coordination between transcription termination, DNA repair and replication in the maintenance of genomic stability.

overall_design: S. cerevisiae strains were grown in YPAD liquid culture at 30°C, total RNA was isolated and hybridized on Affymetrix microarrays.

first: Hélène

last: Gaillard


title: Expression data from yeast wild type (WT) and sod1Δ strains after treatment with hydrogen peroxide (H2O2)

status: Public on Mar 18 2014

city: Guangzhou

first: Chi Kwan

last: Tsang

address: Building #3, 613 Huangpu avenue west

department: Clinical Neuroscience Institute

institute: Jinan University

summary:
An important cellular defense mechanism against oxidative stress is the induction of genes involved in ROS resistance and DNA damage repair. Under normal conditions, Sod1 is localized mainly in the cytosol. However, we found that Sod1 translocates into the nucleus after oxidative stress.
To address the physiological role of Sod1, we performed DNA microarray analysis of global gene expression in wild type (WT) and sod1Δ cells before and after treatment with H2O2.

overall_design: Early log phase WT and sod1Δ cells were treated with or without H2O2 for 20 min and RNA samples were extracted and subjected to hybridization on Affymetrix microarrays. We then compared the dataset of WT +/- H2O2 with SOD1 deleted cells +/- H2O2 to identify the H2O2-responsive genes whose induction was attenuated in sod1Δ cells by more than 50%.

first: Chi

middle: K

first: Steven

middle: X

last: Zheng


title: Expression data from Saccharomyces cerevisiae strains carrying the spt16-11 or the pob3-7 allele

status: Public on Mar 17 2014

department: Genome BIology

institute: CABIMER, Universidad de Sevilla

summary: The conserved FACT (FAcilitates Chromatin Transcription) complex is a chromatin-reorganizing complex that promotes RNAPII transcription through chromatin templates by interacting with histones. It facilitates promoter activation by nucleosome eviction, and transcription elongation by nucleosome disruption and reassembly ahead and behind the RNAP. It also has a role in replication not fully understood yet. Genome-wide microarray analyses in spt16-11 and pob3-7 strains revealed a set of genes whose mRNA levels were altered with respect to the WT levels. These include 48 up-regulated and 80 down-regulated genes that are common to both strains. The up-regulated genes were longer and expressed at lower levels than the genome average whereas the down-regulated genes were more similar to the average of the genome.

overall_design: S. cerevisiae strains were grown in YEPD  liquid culture 4 h after a 26-to-30ºC temperature shift, total RNA was isolated and hybridized on Affymetrix microarrays.

first: Emilia

last: Herrera-Moyano

first: Xénia

last: Mergui

first: María

last: García-Rubio

first: Sonia

last: Barroso


title: Chronological Aging of Yeast in SD medium

status: Public on Mar 04 2014

first: Dina

last: Petranovic

address: Kemivagen 10

department: Chemical and Biological Engineering

summary:
Yeast grown in synthetic complete medium (SD) until glucose depletion is aged chronologically. Cells are stressed by lacking of nutrients and accumulating toxic substances, and thus undergo gene expression changes in response to those.
We performed microarray experiments to capture gene expression profiles of yeast cultured at 4 different time points.

overall_design: Saccharomyces cerevisiae CENPK 113-7D strain was grown in SD medium (2% glucose). Yeast cells were harvested at Log phase, 2 days, 6 days and 10 days of cultivation for microarray analysis.  Each time point was perfromed in triplicate and prepared according to the manufacturer's instructions.

first: Kwanjeera

last: Wanichthanarak

first: Arastoo

last: Badoei


title: Gene expression data from yeast exposure to pyrimethanil

status: Public on May 23 2014

city: Lisboa

first: Cristina

middle: Anjinho

last: Viegas

address: Av Rovisco Pais

department: Bioengineering

country: Portugal

institute: Instituto Superior Técnico

summary:
Pyrimethanil (PYR) is a world-wide used fungicide approved for use in plant protection products in Agriculture, and with some (eco)toxicological concerns.We aimed at finding molecular biomarkers in the model yeast Saccharomyces cerevisiae that may be used to predict potential cytotoxic effects of this xenobiotic while providing mechanistic clues possibly relevant for experimentally less accessible non-target eukaryotes.
We used microarrays to carry out a gene expression profiling analysis in S. cereviseae strain BY4741 upon 2 hours exposure to PYR at concentrations exerting moderate to median levels of phenotypic effects (inhibition of yeast growth rate). Two exposure scenarios were analysed, namely the 20% and 50%-inhibitory concentrations of PYR (IC20 and IC50, respectively), compared to control cells not exposed to the fungicide (CT02).

overall_design: Exponential standardized cell suspensions of S. cerevisiae BY4741 in minimal growth medium were incubated in the presence of 20 and 110 mg/L of PYR (corresponding to the PYR IC20 and IC50, respectively), or in medium non-supplemented with the fungicide (control cells, CT02) during 2 h, and used for total RNA isolation and hybridization on Affymetrix microarrays. Exposure experiments with both concentrations of PYR and with control cells were carried out together. For each exposure condition, independent biological triplicates were processed and analysed.

first: Jörg

last: Becker

first: Fátima

last: Gil


title: Expression data from Saccharomyces cerevisiae histone H2A mutants

status: Public on Mar 01 2014

city: Los Angeles

first: Siavash

last: Kurdistani

state: CA

address: 615 Charles E Young Dr South

department: Biological Chemistry

institute: UCLA

summary:
The N-terminal tail of histone H2A shows evolutionary changes that parallel genome size and aid chromatin compaction. As genome size increases, so does the number of arginines. In contrast, serines corellate with small genomes. Examples for such changes are arginine in position 11 and serine in position 15.
To test if these residues affect mRNA levels, we analysed gene expression profiles of S.cerevisiae strains containing either WT or mutant H2A.

overall_design: Yeast strains have endogenous histone H2A genes deleted and express plasmid born WT or mutant H2A. PolyA RNA of these strains was analyzed by single channel microarray hybridization. Three WT biological replicates provide the control. Two biological  replicates of each of the mutants containing either R11, K11, carrying a deletion in S15 and the double mutant carrying both the deletion of S15 and an insertion of R11 are analysed.

first: Benjamin

middle: R

last: Macadangdang

first: Amit

last: Oberai

first: Tanya

last: Spektor

first: Oscar

last: Campos

first: Fang

last: Sheng

first: Maria

last: Vogelauer

first: Michael

last: Carey


title: Expression data from 26972c yeast ± bHLHm1 (SAT1)

status: Public on Mar 12 2014

city: Urrbrae

first: Brent

last: Kaiser

state: SA

address: Waite Campus

department: School of Agriculture Food and Wine

country: Australia

institute: The University of Adelaide

summary: 26972c yeast cells were transformed with either empty vector (pYES3) or pYES3:Gm:bHLHm1. Cells were grown on low ammonium concentrations to observe transcriptional changes in the yeast genome in response to the soybean bHLHm1 transcription factor.

overall_design: The ammonium transport mutant (26972c) was transformed with either a empty vector control (pYES3) or pYES3 containing GmbHLHm1.Independent replicates (3) for each treatment were grown for 12 hours in the presence of 1 mM ammonium and 2 % w/vol galactose to activate the Gal promoter located on pYES3.  Cells were harvested and total RNA extracted. Quantified RNA was analaysed using microarray analysis using the [Yeast_2] Affymetrix Yeast Genome 2.0 Array.


title: Time-course expression data during assurance of the chronological longevity by caloric restriction in budding yeast

status: Public on Dec 31 2013

city: Seoul

first: Cheol-Koo

last: Lee

address: Korea University, Biotechnology #318 West building, Anam-dong, Seongbuk-gu

department: Biotechnology

country: South Korea

institute: Korea University

summary:
Caloric restriction (CR) is the only non-genetic intervention to retard aging and increase longevity in a variety of species. It is important to understand the fundamental mechanism by which CR extends lifespan that remains elusive. Owing to well-established genomic tools and convenience of culture system, we used a single cell organism, Saccharomyces cerevisiae, to clarify the mechanisms of CR.
In order to identify genes responsible for CR-mediated longevity, we performed microarray experiments across the longevity assurance time-points.

overall_design: Since the CR-treated cells obtained the longevity potential around 12 hours after inoculation and the strength of potential gradually increased up to 48 hours, we concluded that the changes across these time-points must be a critical need for assurance of longevity by CR. For preparation of total RNA, yeast cells under control (2% glucose) and CR (0.5% glucose) conditions were harvested at 12h, 18h, 24h and 48h after inoculation. After total RNA extraction, we performed Affymetrix Yeast GeneChip 2.0 array for biological triplicate repeats according to the manufacturer's instructions.

first: Kyung-Mi

last: Choi


title: Isp7 is a novel regulator of amino acid uptake in the TOR signaling pathway

status: Public on Feb 05 2014

city: Tel Aviv

first: Metsada

last: Pasmanik-Chor

address: Ramat Aviv

department: Biology

country: Israel

institute: Tel Aviv University

summary:
We show that the sensitivity of tsc mutant cells to rapamycin is mediated by TORC1 and can be suppressed by overexpression of the 2-oxoglutarate-Fe(II) dependent oxygenase, Isp7. We show that Isp7 is a novel regulator of amino acids uptake that acts via regulation of gene expression, both upstream and downstream of TOR signaling.   suppressed by overexpression of the putative 2-oxoglutarate-Fe(II) dependent oxygenase, Isp7.   We show that Isp7 is a novel master regulator of amino acids uptake  that acts via regulation of gene expression, both upstream and downstream of TOR signaling.
TOR proteins reside in two distinct complexes, TOR complex 1 and 2 (TORC1 and TORC2) that are central for the regulation of cellular growth, proliferation and survival. TOR is also the target for the immunosuppressive and anti-cancer drug rapamycin. In Schizosaccharaomyces pombe, disruption of the TSC complex, mutations in which can lead to the Tuberous Sclerosis syndrome in humans, results in a rapamycin sensitive phenotype under poor nitrogen conditions. We show here that the sensitivity to rapamycin is mediated via inhibition of TORC1 and suppressed by overexpression of isp7+, a member of the family of 2-oxoglutarate-Fe(II) dependent oxygenases. The transcript level of isp7+ is negatively regulated by TORC1 but positively regulated by TORC2. Yet, we find extensive similarity between the transcriptome of cells disrupted for isp7+ and cells mutated in the catalytic subunit of TORC1. Moreover, Isp7 regulates amino acid permease expression similarly to TORC1 and in contrast to TORC2. Overexpression of isp7+ induces TORC1-dependent phosphorylation of ribosomal protein Rps6, while inhibiting TORC2-dependent phosphorylation and activation of the AGC-like kinase Gad8. Taken together, our findings suggest a central role for Isp7 in amino acid homeostasis and the presence of isp7+-dependent regulatory loops that affect both TORC1 and TORC2.

overall_design: 6 Samples (arrays) were performed. We generated pairwise comparison between DISP7 and WT, using Partek Genomics Suite. Genes with p≤5%[FDR] and a fold-change difference of  ≥2\1.5 or <-2\-1.5 were selected.

first: Dana

last: Laor

first: Adiel

last: Cohen

first: Varda

last: Oron-Karni

first: Martin

last: Kupiec

first: Ronit

last: Weisman


title: Response of Saccharomyces cerevisiae (Dal80Δ) to linoleic acid hydroperoxide

status: Public on Feb 13 2014

city: Sydney

first: Patrick

middle: John

last: O'Doherty

state: NSW

address: Goldsmith Ave

institute: University of Western Sydney

summary:
Oxidative stress is experienced by all aerobic organisms and results in cellular damage. The damage caused during oxidative stress is particular to the oxidant challenge faced, and so too is the induced stress response. The eukaryote Saccharomyces cerevisiae is sensitive to low concentrations of the lipid hydroperoxide - linoleic acid hydroperoxide (LoaOOH) - and its response is unique relative to other peroxide treatments. Part of the yeast response to LoaOOH includes a change in the cellular requirement for nutrients, such as sulfur, nitrogen and various metal ions. The metabolism of sulfur is involved in antioxidant defence, although the role nitrogen during oxidative stress is not well understood. Investigating the response induced by yeast to overcome LoaOOH exposure, with a particular focus on nitrogen metabolism, will lead to greater understanding of how eukaryotes survive lipid hydroperoxide-induced stress, and associated lipid peroxidation, which occurs in the presence of polyunsaturated fatty acids.
We used genome-wide microarrays to investigate the changes in gene expression of S. cerevisiae (Dal80Δ) to LoaOOH-induced oxidative stress.

overall_design: S. cerevisiae (Dal80Δ) were exposed to an arresting concentration of LoaOOH (75 µM) for 1 hr to induce oxidative stress. Yeast treated with an equivalent volume of solvent (methanol) were used as a control. Following treatment conditions, total RNA was extracted from LoaOOH-treated or control yeast and hybridised onto Affymetrix microarrays.

middle: J

last: O’Doherty

first: Victoria

last: Lyons

first: Nay

last: Tun

first: Peter

last: Rogers

first: Trevor

last: Bailey

first: Ming

last: Wu


title: Population Structure and Comparative Genome Hybridization of European flor yeast reveal a unique group of Saccharomyces cerevisiae strains with few gene duplications in their genome

status: Public on Jun 01 2014

city: Montpellier cedex1

first: Jean-Luc

last: Legras

address: 2, place Viala

department: UMR1083, Science pour l'Oenologie

country: France

institute: INRA

summary: Wine biological aging is a wine making process used to produce specific beverages in several countries in Europe, including Spain, Italy, France, and Hungary. This process involves the formation of a velum at the surface of the wine. Here, we present the first large scale comparison of all European flor strains involved in this process. We inferred the population structure of these European flor strains from their microsatellite genotype diversity and analyzed their ploidy. We show that almost all of these flor strains belong to the same cluster and are diploid, except for a few Spanish strains. Comparison of the array hybridization profile of six flor strains originating from these four countries, with that of three wine strains did not reveal any large segmental amplification. Nonetheless, some genes, including YKL221W/MCH2 and YKL222C, were amplified in the genome of four out of six flor strains. Finally, we correlated ICR1 ncRNA and FLO11 polymorphisms with flor yeast population structure, and associate the presence of wild type ICR1 and a long Flo11p with thin velum formation in a cluster of Jura strains. These results provide new insight into the diversity of flor yeast and show that combinations of different adaptive changes can lead to an increase of hydrophobicity and affect velum formation.

sample_organism: Saccharomyces cerevisiae x Saccharomyces kudriavzevii

overall_design: Each strain is compared to S288C and is hybridized in duplicate or triplicate

first: Jean-luc

first: Claude

last: Erny

first: Claudne

last: Charpentier


title: Saccharomyces cerevisiae stress responses to HMF and furfural (xylose and glucose)  Oct

status: Public on Nov 25 2013

first: Magnus

last: Ask

summary: HMF and furfural were pulse added to xylose-utilizing Saccharomyces cerevisiae during either the glucose consumption phase or the xylose consumption phase. Transcriptome samples were collected before and one hour after pulsing of inhibitors.

overall_design: Three biological replicates from each conditions analyzed.

first: Maurizio

last: Bettiga

first: Lisbeth

last: Olsson


title: Expression data from the Schizosaccharomyces pombe opi10- strain.

status: Public on Nov 12 2013

city: Wako

first: Makoto

last: Kimura

state: Saitama

address: 2-1 Hirosawa

country: Japan

institute: RIKEN

summary:
Opi10 is the S. pombe homolog of human Hikeshi, which imports Hsp70s into the nucei during the heat shock.
We compared the gene expression of the S. pombe opi10+ and opi10- strains before, during and after the heat shock.

overall_design: RNA were extracted from the S. pombe opi10+ and opi10- strains cultured at 30C, heat treated for 1 h at 43C, and then cultred for 1 and 3 h at 30C, and analyzed using Affymerix DNA microarrays.

first: Yuumi

last: Oda

first: Naoko

last: Imamoto


title: Expression data from Saccharomyces cerevisae strains deleted for the RNA-binding hnRNP Npl3

status: Public on Nov 15 2013

first: Andrés

last: Aguilera

summary:
Transcription is a major obstacle for replication fork progression and a cause of genome instability. Such instability increases in mutants with a suboptimal assembly of the nascent messenger ribonucleo-protein particle (mRNP), as THO/TREX and some heterogeneous nuclear ribonucleoproteins (hnRNPs) mutants.
We used microarrays to the global impact of Npl3 in gene expression and found that Npl3 deletion has a functional impact in highly-expressed, long and G+C rich genes regardless of gene function

overall_design: S. cerevisiae strains were grown in YPD liquid culture, total RNA was isolated and hybridized on Affymetrix microarrays

first: José

last: Santos-Pereira

first: Ana

last: Herrero

first: María

middle: L

last: García-Rubio

first: Antonio

last: Marín

first: Sergio

last: Moreno


title: Expression data from fission yeast deletion mutant of Klf1, a C2H2 zinc finger-transcription factor, in G0 and VE phases

status: Public on Dec 01 2013

city: Onna-son

first: Mizuki

last: Shimanuki

state: Okinawa

department: Research Support Division

institute: Okinawa Institute of Science and Technology Graduate University

summary: Fission yeast Schizosaccharomyces pombe is a model for studying cellular quiescence. Shifting to medium without a nitrogen-source induces proliferative cells to enter long-term G0 quiescence. Klf1 is a Kruppel-like transcription factor with a 7-amino acid-spaced C2H2-type zinc finger motif. The deletion mutant ∆klf1 normally divides in vegetative medium, but proliferation is not restored after long-term G0 quiescence. Cell biologic, transcriptomic, and metabolomic analyses revealed a unique phenotype of the ∆klf1 mutant in quiescence. Mutant cells had diminished transcripts related to signaling molecules for switching to differentiation. In contrast, proliferative metabolites for cell-wall assembly and antioxidants significantly increased. Further, the size of the ∆klf1 cells is markedly increased during quiescence due to the aberrant accumulation of calcofluor-positive chitin-like materials beneath the cell wall. After 4 weeks quiescence, the ability for reversible proliferation is lost, but energy metabolism is maintained. Klf1 thus plays a role in G0 phase longevity through enhancing the differentiation signal and suppressing metabolism for growth. If Klf1 is lost, S. pombe fails to maintain a constant cell size during quiescence.

overall_design:
Gene expression profile of fission yeast wild type cells and klf1-gene disruptant cells in proliferating state and in quiescent state.
Type of experiment: Comparing between wild type cells and klf1-gene disruptant cells in proliferating condition and in quiescent condition.
Experimental factor: Exponentially proliferating state in synthetic medium, EMM2, and quiescent G0 state in nitrogen-depleted synthetic medium, EMM2-N.
Quality control steps taken: All experiments were repeated twice in each condition.

first: Lisa

last: Uehara

first: Tomáš

last: Pluskal

first: Tomoko

last: Yoshida

first: Aya

last: Kokubu

first: Yosuke

last: Kawasaki

first: Mitsuhiro

last: Yanagida


title: Integrated analysis, transcriptome-lipidome, reveals the effects of INO-level (INO2 and INO4) on lipid metabolism in yeast

status: Public on Dec 23 2013

first: Pramote

last: Chumnanpuen

summary: Characterize the transcriptional response to INO2 and INO4 expression level (INO-level) and efficient factor

overall_design: We used microarrays to capture the global responses of INO-level in Carbon and Nitrogen limited growth.

first: Intawat

last: Nookaew

first: Jens

last: Nielsen


title: Expression data from wild-type and rph1-deleted yeasts

status: Public on Nov 06 2013

city: Taipei

first: Wan-Sheng

last: Lo

address: 128 Academia Road, Section 2, Nankang

department: IPMB

institute: Academia Sinica

summary: Cells respond to environmental signals by alteration of gene expression through action of transcription factors. A JmjC-domain-containing protein Rph1 belongs to the C2H2 zinc finger protein family and functions to repress transcription of PHR1 via histone demethylation. However, additional targets of Rph1 remain largely unknown. Here, we investigate the regulatory network of Rph1 by microarray analyses. More than 75% of Rph1-regulated genes showed increased expression in rph1Δ, suggesting Rph1 serves as a transcriptional repressor under physiological conditions. The binding motif of Rph1 resembling the STress Response Element (STRE) was over-represented in the promoters of Rph1-repressed genes. In addition, significant proportions of Rph1-regulated genes responded to DNA damage and environmental stress, implying a repressive role of Rph1 in the cross-protection of stress responses.

overall_design:
We used expression microarray to identify Rph1-regulated genes and established Rph1 functioned as a transcriptional repressor to link DNA damage signaling and general stress response.
We compared gene expression in wild-type and rph1-deleted strains cultured in rich medium (YPD) during exponential growth. 3 biological samples were analyzed.

first: Chung

middle: Y

last: Liang


title: Microarray and ChIP-chip of Rrm3-Flag in wild-type and npl3 cells, and ChIP-chip of Npl3-Myc in wild type cells

first: Andrés

last: Aguilera

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

overall_design: Refer to individual Series

first: José

last: Santos-Pereira

middle: B


title: Expression Data from the Riesling grape must fermentation by industrial M2 and M2 nsf1∆  S. cerevisiae  strains for functional characterization of the NSF1 (YPL230W) gene via Correlation Clustering-based method

status: Public on Oct 16 2013

city: Guelph

first: Kyrylo

last: Bessonov

state: ON

address: 50 Stone Rd East

department: Molecular Biology

country: Canada

institute: University of Guelph

summary:
The main objectives of this study were to expand our understanding of NSF1 gene function in industrial S. cerevisiae  M2 strain during fermentation by finding the largest maximal clique of co-expressed genes (i.e. Interdependent Correlation Cluster), and to establish the impact of Nsf1p on genome-wide gene expression during the fermentation  process with possible implications related to wine quality and S. cerevisiae adapation to stressful fermentation conditions
The Affymetrix Yeast 2.0 microarrays were used to capture the global gene expression profile of M2 and M2 nsf1∆ grown under fermentation conditions in Riesling grape must at 18°C with no shaking at various time points. The analysis of this microarray dataset expanded our understanding of the mechanism of action and the roles of NSF1 under fermentation stress conditions.

overall_design: The overall experimental setup consisted of 2 stains (M2 and M2 nsf1∆) and 3 sample time points (24h post-innoculation, 20% and 85% of total glucose fermented)  .

first: George

last: van der Merwe


title: Expression data from Saccharomyces cerevisiae and Saccharomyces pastorianus var. carlsbergensis

status: Public on Sep 11 2013

city: Freising

first: Susanne

last: Procopio

address: Weihenstephanersteig 20

department: Lehrstuhl für Brau- und Getränketechnologie

institute: Technische Universität München

summary: During fermentation Saccharomyces yeast produces various aroma-active metabolites determining the different characteristics of aroma and taste in fermented beverages. Amino acid utilization by yeast during brewer´s wort fermentation is seen as linked to flavour profile. To better understand the relationship between the biosynthesis of aroma relevant metabolites and the importance of amino acids, DNA microarrays were performed for Saccharomyces cerevisiae strain S81 and Saccharomyces pastorianus var. carlsbergensis strain S23, respectively. Thereby, changes in transcription of genes were measured, which are associated with amino acid assimilation and its derived aroma-active compounds during fermentation.

sample_organism:
Saccharomyces cerevisiae
Saccharomyces pastorianus

overall_design: 48 samples were used in this experiment

first: Thomas

last: Becker


title: Glucocorticoid-Dependent Hippocampal Transcriptome in Male Rats: Pathway-Specific Alterations with Aging

status: Public on Jul 22 2013

city: Lexington

first: Eric

last: Blalock

address: 800 Rose St.

department: Molecular and Biomedical Pharmacology

institute: University of Kentucky

summary: Although glucocorticoids (GCs) are known to exert numerous effects in the hippocampus, their chronic regulatory functions remain poorly understood. Moreover, evidence is inconsistent regarding the longstanding hypothesis that chronic GC exposure promotes brain aging/Alzheimer's disease. Here, we adrenalectomized male F344 rats at 15-months-of-age, maintained them for 3 months with implanted corticosterone (CORT) pellets producing low or intermediate (glucocorticoid-receptor (GR)-activating) blood levels of CORT, and performed microarray/pathway analyses in hippocampal CA1. We defined the chronic GC-dependent transcriptome as 393 genes that exhibited differential expression between Intermediate- and Low-CORT groups. Short-term CORT (4 days) did not recapitulate this transcriptome. Functional processes/pathways overrepresented by chronic CORT-upregulated genes included learning/plasticity, differentiation, glucose metabolism and cholesterol biosynthesis, whereas processes overrepresented by CORT-downregulated genes included inflammatory/immune/glial responses and extracellular structure. These profiles indicate that GCs chronically activate neuronal/metabolic processes while coordinately repressing a glial axis of reactivity/inflammation. We then compared the GC-transcriptome with a previously-defined hippocampal aging transcriptome, revealing a high proportion of common genes. Although CORT and aging moved expression of some common genes in the same-direction, the majority were shifted in opposite directions by CORT and aging (e.g., glial inflammatory genes downregulated by CORT are upregulated with aging). These results contradict the hypothesis that GCs simply promote brain aging, and also suggest that the opposite-direction shifts during aging reflect resistance to CORT regulation. Therefore, we propose a new model in which aging-related GC resistance develops in some target pathways while GC overstimulation develops in others, together generating much of the brain aging phenotype.

overall_design: Forty male Fischer 344 rats aged 14-15 months (late mid-age) were either sham operated (n=10) or adrenalectomized (n=30) at Harlan, Inc. (Indianapolis) and shipped to University of Kentucky 7-10 d after surgery.  Animals were allowed to acclimate for 2 weeks after receipt prior to pellet-implant and were provided with food and water ad lib. Adrenalectomized (ADX) animals were maintained on drinking water containing isotonic saline with 1% sucrose, and also given supplemental feed mash (standard chow mixed with water and warmed) and apple chunks, as well as subcutaneous injections of 1.25 mg corticosterone sulfate (Solu-DeltaCort, Pfizer). During pellet-implant surgery, subjects were anesthetized with isoflurane, placed on a warming pad, and a 3 cm2 area on the animal's flank was shaved and sterilized. A 1-cm incision was made through the skin to form a subcutaneous pocket. Each sham animal received an inert pellet. ADX animals were divided into two groups, low-dose animals (n = 20) received one 25 mg CORT pellet and intermediate-dose animals (n = 10) received one 200 mg CORT pellet (slow release pellets, Innovative Research of America, Sarasota, FL). Incisions were closed with wound clips (removed after 7-10 days). Following implant surgery, subjects were housed singly for 3 months prior to euthanasia at age 18 months. Low-dose animals continued to receive saline/ sucrose drinking water, but other supplementation (food mash, Solu-Delta CORT, apple chunks) was discontinued. One ADX animal was removed from the study for declining health. During the twelfth week, just prior to study termination, half of the ADX low-dose CORT subjects were given a short-term, high-dose regimen consisting of 4 daily IP injections of 5mg/d CORT (considered a relatively high dose- Makino et al., 1995). All animals were killed between 8 and 10 AM on the last two days of the study. After deep CO2 anesthesia and decapitation, trunk blood was collected for CORT radioimmunoassay and hippocampal CA1 brain tissue was dissected as described previously (Blalock et al., 2003) for microarray analysis (see below). Final treatment groups consisted of: 1) Sham (intact) control, 2) Low-CORT (ADX), 3) Intermediate-CORT (ADX), and 4) Low-CORT (ADX) + short-term high-dose injected (n=9-10/group).

first: Kuey-Chu

last: Chen

first: Nada

last: Porter

first: Meredith

last: Curran-Rauhut

first: Susan

first: Jeanise

last: Staton

first: Allison

last: Secrest-Walters

first: Philip

middle: W

last: Landfield


title: Gene expression profile in yeast under physiological changes of stress adaptation and stress recovery

city: Huddinge

first: Anthony

last: Wright

address: Blickagången 6

institute: Karolinska Institute

summary: The data provide information expression profile in yeast  for 5 different physioloigcal conditions during stress adpatation and stress recovery  (normal growth, during stress adaptation, after stress adaptation, under stress recovery, after stress recovery) in yeast. The purpose of the study is to understand how histone acetyltransferase HATs (Gcn5) apply it is function in gene regulation by changing global or local histone acetylation level under different physiological conditions.

overall_design: Gene expression levels measured for at 5 different time points of physiological changes under stress adaptation and stress recovery.

first: Yongtao

last: Xue-Franzén


title: CD8+ T-cell memory bears the transcriptional imprint of progressive differentiation

status: Public on Aug 01 2013

city: Cleveland

first: Peter

last: Wilkinson

state: Ohio

address: 2103 Cornell Road

department: Pathology / Systems Biology & Bioinformatics

institute: Case Western Reserve University

summary: The generation of CD8+ T-cell memory is an important aim of immunization. While several distinct subsets of CD8+ T-cell memory have been described, the lineage relationships between effector (EFF), effector memory (EM) and central memory (CM) T cells remain contentious. Specifically, there is contradictory experimental evidence to support both the linear (Naive>EFF>EM>CM) and progressive differentiation (Naive>CM>EM>EFF) models. In this study, we applied a systems biology approach to examine global transcriptional relationships between the three major CD8+ T cell subsets arising endogenously as a result of vaccination with three different prime-boost vaccine regimens. Differential gene expression analysis and principle component analysis revealed that central memory cells were more closely related to naive T cells than both effector memory and effector cells. When the transcriptional relationships between subsets were enriched in an unbiased fashion with known global transcriptional changes that result when T-cells repeatedly encounter antigen, our analysis favored a model whereby cumulative antigenic stimulation drives differentiation specifically from Naive > CM > EM > EFF. These findings provide an insight into the lineage relationship between mature CD8+ T-cell subsets and will help in the rational design of vaccines aimed at generating effective immune responses against infections and cancer.

overall_design: Effector (EFF), effector memory (EM), central memory (CM) and naive CD8+ T cells from mice spleen. Memory subset arise endogenously as a result of vaccination with three different prime-boost vaccine regimens: DNA-rAd5, rAd5-rAd5 and rAd5-rLCMV.

first: Rahul

last: Roychoudhuri

first: Francois

last: Lefebvre

first: Mitsuo

last: Honda

first: Christopher

last: Klebanoff

first: Madhusudhanan

last: Sukumar

first: Li

last: Pan

first: Jean-Philippe

last: Goulet

first: Nadia

last: Kettaf

first: Elias

last: Haddad

first: Luca

last: Gattinoni

first: Gary

last: Nabel

first: Nicholas

middle: P

last: Restifo

first: Rafick

last: Sékaly

first: Lukas

last: Flatz


title: Expression data from Saccharomyces cerevisiae with Rnase H overexpression

status: Public on Sep 01 2013

city: Vancouver

first: Yujia Alina

last: Chan

state: British Columbia

address: 2185 East Mall

institute: University of British Columbia

summary: Transcripts up- or down-regulated comparing a strain where Rnase H is ectopically overexpressed versus wild type (empty vector); assessing the effect of DNA:RNA hybrid degradation on the transcriptome.

overall_design: Strains harboring the RNase H1 over-expression plasmid (p425-GPD-RNase H1) or control plasmid (p425-GPD) were grown in SC-Leucine at 30°C. For both sets of microarray experiments, duplicate cultures were analyzed. Total RNA was isolated from 1 unit of A600 mid-log phase cells using a RiboPure Yeast kit (A&B Applied Biosystems), amplified, labeled and fragmented using a Message Apm III RNA Amplification Kit (A&B Applied Biosystems) and hybridized to a GeneChIP Yeast Genome 2.0 array using the GeneChip Hybridization, Wash, and Stain Kit (Affymetrix). Arrays were scanned by the Gene Chip Scanner 3000 7G and expression data was extracted using Expression Console™ Software (Affymetrix) with the MAS5.0 statistical algorithm.

first: Yujia-Alina

first: Zongli

last: Luo


title: Expression data from polysomal, nonpolysomal, and total RNAs in the S. cerevisiae tRNA trafficking mutants, msn5 and mtr10

city: Columbus

first: Hui-Yi

last: Chu

state: OH

department: Molecular Genetics

institute: The Ohio State University

summary:
tRNAs are transcribed and partially processed in the nucleus before they are exported to the cytoplasm where they have an essential role in protein synthesis. Surprisingly, mature cytoplasmic tRNAs shuttle between nucleus and cytoplasm and its distribution is nutrient-dependent. At least three members of β-importin family, Los1, Mtr10, and Msn5, function in tRNA nuclear-cytoplasmic intracellular movement. To test the hypothesis that the tRNA retrograde pathway regulates translation of particular transcripts
We compared individual translation activity index (P/NP), obtained from the ratio of polysome-associated (P) to not associated (non-polysomal, NP) mRNAs, in the msn5Δ, mtr10Δ, and wild-type cells under fed or acute amino acid depletion conditions

overall_design: Polysome associated (P), not associated (non-polysomal, NP), and total (T) RNAs were isolated from yeast cells, including wild-type (BY4742), msn5 deletion, mtr10 deletion, grown in fed and 30-min amino acid starvation conditions

first: Anita

last: Hopper


title: Gene expression changes of Saccharomyces cerevisiae to linoleic acid hydroperoxide

status: Public on Jun 12 2013

first: Patrick

last: O'Doherty

summary:
Reactive oxygen species, generated in vivo or exogenously encountered, constantly challenge living organisms. Oxidation of polyunsaturated fatty acids (PUFA), which are susceptible to oxidant attack, can lead to initiation of lipid peroxidation and in turn rapid production of toxic lipid hydroperoxides. Eukaryotic microorganisms such as Saccharomyces cerevisiae can survive harsh industrial conditions that contain high levels of the PUFA linoleic acid and its oxidised derivative, linoleic acid hydroperoxide (LoaOOH). The precise signalling and response mechanisms induced by yeast to overcome lipid hydroperoxide stress are ill understood.
We used genome-wide microarrays to investigate the changes in gene expression of S. cerevisiae to LoaOOH-induced oxidative stress.

overall_design: S. cerevisiae (BY4743) were exposed to an arresting concentration of LoaOOH (75 µM) for 1 hr to induce oxidative stress. Yeast treated with an equivalent volume of solvent (methanol) were used as a control. Following treatment conditions, total RNA was extracted from LoaOOH-treated or control yeast and hybridised onto Affymetrix microarrays.

last: O’Doherty

first: Victoria

last: Lyons

first: Vincent

last: Higgins

first: Peter

last: Rogers

first: Trevor

middle: D

last: Bailey

first: Ming

last: Wu


title: Functional studies of the Yeast Mediator Tail Module Subunits

status: Public on Jun 07 2013

city: Bedford Park

first: Luke

last: Selth

address: Flinders Drive

department: College of Medicine and Public Health

institute: Flinders University

summary: The yeast Mediator complex can be divided into three modules, designated Head, Middle and Tail. Tail comprises the Med2, Med3, Med5, Med15 and Med16 protein subunits, which are all encoded by genes that are individually non-essential for viability. In cells lacking Med16, Tail is displaced from Head and Middle. However, inactivation of MED5/MED15 and MED15/MED16 are synthetically lethal, indicating that Tail performs essential functions as a separate complex even when it is not bound to Middle and Head. We have used the N-Degron method to create temperature sensitive (ts) mutants in the Mediator tail subunits Med5, Med15 and Med16 to study the immediate effects on global gene expression when each subunit is individually inactivated, and when MED5/15 or MED15/16 are inactivated together.

overall_design: All Degron constructs were expressed from their normal chromosomal location under the control of their respective endogenous promoters. We isolated RNA from each strain as early as 45 minutes after changing from the permissive to the restrictive growth conditions to minimize possible secondary effects on gene expression that are not directly caused by the Degron construct(s).

first: Miriam

last: Larsson

first: Hanna

last: Uvell

first: Stefan

last: Bjorklund


title: Expression data from S. cerevisiae following tRNA gene deletion

status: Public on May 17 2013

city: Rehovot

first: Zohar

last: Bloom-Ackermann

address: Hertzl

institute: Weizmann Institute of Science

summary: We created a comprehensive tRNA deletion library in yeast and characterized the phenotypic and further characterized the molecular changes in a subset of deletion strains

overall_design: Each tRNA deletion strain was created using homologous recombination by introduction of an antibiotic cassette. Each strain was grown at 30°C in rich medium to mid log phase from which mRNA was extracted

first: Sivan

last: Navon

first: Hila

last: Gingold

first: Ruth

last: Towers

first: Yitzhak

last: Pilpel

first: Orna

last: Dahan


title: Yeast under physiological changes of stress adaptation and stress recovery

first: Anthony

last: Wright

summary:
Background
Gcn5 belongs to a family of histone acetyltransferases (HATs) that regulate protein function by acetylation. Gcn5 plays several different roles in gene transcription throughout the genome but their characterisation by classical mutation approaches is hampered by the high degree of apparent functional redundancy between HAT proteins.

Results
Here we utilise the reduced redundancy associated with the transiently high levels of genomic reprogramming during stress adaptation as a complementary approach to understand the functions of redundant protein families like HATs. We show genome-wide evidence for two functionally distinct roles of Gcn5. First, Gcn5 transiently re-localises to the ORFs of long genes during stress adaptation. Taken together with earlier mechanistic studies, our data suggests that Gcn5 plays a genome- wide role in specifically increasing the transcriptional elongation of long genes, thus increasing the production efficiency of complete long transcripts. Second, we suggest that Gcn5 transiently interacts with histones close to the transcription start site of the many genes that it activates during stress adaptation by acetylation of histone H3K18, leading to histone depletion, probably as a result of nucleosome loss as has been described previously.

Conclusions
We show that stress adaptation can be used to elucidate the functions of otherwise redundant proteins, like Gcn5, in gene transcription. Further, we show that normalization of chromatin-associated protein levels in ChIP experiments in relation to the histone levels may provide a useful complement to standard approaches. In the present study analysis of data in this way provides an alternative explanation for previously indicated repressive role of Gcn5 in gene transcription.

Keywords: Gcn5; Gene length; Transcription elongation; Histone acetyltransferase; Stress; Genome-wide association study

overall_design:
HATs family proteins are highly redundant at normal growth conditions. Here we utilize a KCl stress model so that Gcn5 performs its specific function. To study the transient regulation of Gcn5 during stress, and adaptation and recovery growth regime, samples are collected at 5 different time points, which represent different growth phases. For each sample, gene expression changes are measured by expression microarray. In parallel, genome-wide localisation of Gcn5, histone H3 density, as well as acetylation level of relevant histone marks (H3K18 and acH4K16) are measured by ChIP-on-chip tiling array.
This SuperSeries is composed of The super data series include gene expression data and ChIP-on-chip tiling array data.
Direct link to the expression data:  http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE36599
Direct link to the ChIP-on-chip tiling array data: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE36600