title: Gene expression profiles of AD 293 cells mediated by Chandipura virus nucleo (N) protein

city: Bangalore

first: Genotypic

last: technology

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

institute: Genotypic Technology

summary: Recombinant adenovirus expressing Chandipura virus nucleo (N) protein (ADN) induces cell lysis in infected cells. In order to find out the pathway involved in cell lysis, we have employed micro array experiment using custom whole genome microarray 4x44k designed by Genotypic Technology private limited, India (AMADID 025085) to identify the genes which involved in apoptotic, cell cycle, signalling etc. AD 293 cells were infected with ADN and the total RNA was purified at 3 and 6 h post infection (PI). In control experiment, the total RNA was purified at 6 h PI from uninfected AD 293cells and cells infected with recombinant adenovirus without N gene. Gene expression profile of these samples was analysed. The data was analyzed using GeneSpring GX Version 11.5 software from Agilent. Normalization of the data was done in GeneSpring GX using the 75th percentile shift. Significant up and down regulated genes showing one fold and above within the group of samples were identified. Genes were classified based on functional category and pathways using Biointerpreter Tool -Biological Analysis Software.

overall_design: Agilent one-color experiment,Organism: Human ,Agilent-025085 Whole Human Genome Microarray 4x44K  Labeling kit: Agilent Quick-Amp labeling Kit (p/n5190-0442)

first: B

last: Anukumar

first: Neena

last: Panicker

first: T

last: Nikhil

first: Nikita

last: Malik


title: Medaka larvae were exposed to HBCD

status: Public on Jul 31 2013

city: xiamen city

first: geng

last: hong

address: School of Life Sciences, Xiamen University,

department: Biology

country: China

institute: School of life sciences

summary: Recently, omics techniques have been widely applied to the discovery of potential bio-markers and explore triggering mechanism. To get a more comprehensive diagnosis of HBCD impacts on marine medaka (Oryzias melastigma), the larvae (within 24 hours post-hatch) were exposed to gradient doses of HBCD. After exposure for 7 days, the profiles of genes expression were examined using a custom-commercial 26, 430-oligonucleotide arrays (4×44K) of Japanese medaka which is shared much genomic information with marine medaka.At the end of the treatment period, 30 larvae/sample were pooled for RNA extraction and labeled by One-Color. A total of twelve independent arrays: three control (DMSO), three low-concentration HBCD (0.2 nM) exposures, three medium-concentration HBCD (2 nM) exposures, and three high-concentration HBCD (20 nM) exposures.

overall_design: The larvae of marine medaka (within 24 hours post-hatch) were exposed to to 0 (control), 0.2nM, 2nM and 20nM of HBCD (dimethyl sulfoxide with a final concentration of 1:30000 v/v water) for 7 days. Each HBCD treatment had three replicates with 100 larvae for each Petri dish. At the end of the treatment period, 30 larvae/sample were pooled for RNA extraction. A total of twelve independent arrays: three control (DMSO), three low-concentration HBCD (0.2 nM) exposures, three medium-concentration HBCD (2 nM) exposures, and three high-concentration HBCD (20 nM) exposures.

first: Zhenghong

last: Zuo

first: Hong

last: Geng


title: Effects of 5α-dihydrotestosterone on male mummichog (Fundulus heteroclitus) testes steroid production and gene expression patterns

city: Gainesville

first: Christopher

middle: Joseph

last: Martyniuk

state: FL

address: CEHT Mowry Road

department: Physiological Sciences

country: USA

institute: UF

summary: To better assess the impact of contaminants on fish reproduction, it is increasingly important to collect data at multiple levels of biological organization.  However, a challenge in ecotoxicology is that three of the most commonly measured reproductive endpoints; gonad histology, ex vivo steroid production, and gene expression, can be difficult to obtain in small-bodied fish (e.g. zebrafish, Japanese medaka, fathead minnow) due to limited tissue availability. Using 5α-dihydrotestosterone (DHT) as a test compound, the objectives of the current study were to assess the feasibility of measuring gene expression in tissues also used for ex vivo steroid production studies.  A portion of the testes was also used for qualitative histological examination. Male mummichog were exposed to 0, 5, and 50 µg/L DHT for 21 days. Following the exposure, testes were collected and separated into three pieces for histology, ex vivo incubation to measure steroidogenic capacity [Testosterone(T), 17β-estradiol (E2), 11-ketotestosterone (11KT)] and gene expression analyses. Testis RNA at time of dissection and testis RNA at end of ex vivo incubation (18 h) was collected and assessed for RNA integrity. The expression of genes coding for estrogen receptor βa (esrba) and estrogen receptor βb (esrbb) as well as the key steroidogenic genes, steroidogenic acute regulatory protein (star), P450 side chain cleavage (p450scc) and 11β-hydroxysteroid dehydrogenase (hsd11b3) were assessed in testis before and after ex vivo incubation. There were no significant differences in RNA quality between the two time points, however the expression of esrba, esrbb and p450scc was significantly lower post-incubation, although star, hsd11b3, and all four reference gene expression levels remained unchanged over time. DHT did not affect the expression of any of the measured genes at either concentration. Histological examination showed that all fish contained mature testes dominated by spermatozoa and spermatids. DHT did not affect T production but significantly decreased 11KT production in the high treatment group. This suggests a role for DHT in androgen regulation, and has

overall_design: Microarray analysis was performed with four biological replicates (4 control and 4 treatment). Male mummichog were exposed to 0, 5, and 50 µg/L DHT for 21 days. Individuals from the high concentration, 50 ug/L DHT, were used for the microarray analysis.

first: Chris

first: Jennifer

last: Ings

first: Meghan

last: Doyle

first: April

last: Feswick

first: Thijs

last: Bosker

first: Kelly

last: Munkittrick


title: Default DNA Methylation is Preceded by Broad, Low-Level Transcription in Fetal Male Germ Cells and Is Inversely Patterned by Dynamic H3K4 Methylation (ChIP-chip and MIRA-chip)

city: Duarte

first: Xiwei

last: Wu

state: CA

address: 1500 E. Duarte Rd.

department: Computational and Quantitative Medicine

institute: City of Hope National Medical Center

type: Genome binding/occupancy profiling by genome tiling array

type: Methylation profiling by genome tiling array

summary: To understand what dictates the emerging patterns of de novo DNA methylation, we mapped DNA methylation, chromatin, and transcription changes in purified fetal mouse germ cells using MIRA-chip, ChIP-chip, and strand-specific RNA-seq, respectively. De novo methylation occurred without any apparent trigger from preexisting repressing chromatin marks but was preceded by broad, low-level transcription along the entire genome in prospermatogonia. Only distinct short sequences remained unmethylated, precisely aligned with constitutive or emerging peaks of H3K4me2. Establishment of methylation at differentially methylated regions (DMRs) of imprinted genes, CpG islands, and IAPs followed these same default rules. Transcription run-through occurred at paternal DMRs with no- or diminishing H3K4me2 peaks. Maternal DMRs remained unmethylated among highly methylated DNA at precisely aligned H3K4me2 peaks with transcription initiating at least in one strand. Our results suggest that the pattern of de novo DNA methylation in prospermatogonia is dictated by opposing actions of broad, low-level transcription and dynamic patterns of active chromatin.

overall_design: ChIP-chip and MIRA-chip were performed to map histone modifications and DNA methylation at different devlopmental time points in germ cells and somatic cells along known imprinted domains and control regions, using custom NimbleGen tiling arrays.

first: Purnima

last: Singh

first: Piroska

middle: E

last: Szabo

first: Diana

middle: A

last: Tran

first: Xuejun

last: Li


title: Expression of PTTG1 is associated with aggressive clear cell renal carcinoma

city: Grand Rapids

first: Karl

last: Dykema

state: MI

address: 333 Bostwick Ave. NE

institute: Van Andel Institute

summary: The pituitary tumor-transforming gene (PTTG1) is a recently discovered oncogene implicated in the malignant progression of a number of neoplasms.  It has been shown to drive both endocrine and non-endocrine malignancies, but has not yet been studied in the context of renal cell carcinoma (RCC).  Clear cell RCC (ccRCC) is cytogenetically characterized by deletion of chromosome 3p, harboring the von-Hippel Lindau tumor suppressor gene, and amplification of chromosome 5q.  The significance of copy number gain of chromosome 5 is not clear, but is presumed to be the location of oncogenes that influence ccRCC development or progression.  The PTTG1 oncogene maps to chromosome 5q, and here we show that PTTG1 is amplified in clear cell RCC, is overexpressed in tumor tissue relative to adjacent normal kidney, and expression is associated with high grade, high stage, and poor prognosis.  Furthermore, we establish a functional role for PTTG1 in ccRCC tumorigenesis and progression.  PTTG1 ablation reduces both the tumorigenic ability of ccRCC cells in vitro and in vivo and the invasive ability of these cells in vitro.  An analysis of genes whose transcription is regulated by PTTG1 was supportive of an association with invasive and metastatic disease.  PTTG1-dependent expression of the Rho-GEF ECT2, another proto-oncogene, is observed in a number of ccRCC cell lines, and ECT2 expression correlates with PTTG1 expression, high stage, high grade, and poor prognosis ccRCC.  As GEF's have been promoted as potential drug targets for targeted cancer therapeutics, the relationship between the PTTG1 and ECT2 oncogenes may be able to be exploited for the treatment of this disease.

overall_design: PTTG1 was knocked down by siRNA.


title: Dysregulation of the colonic mucosally-adherent microbiota associates with HIV disease progression.

status: Public on Jul 10 2013

city: San Francisco

first: Ivan

last: Vujkovic-Cvijin

state: California

address: 1001 Potrero Ave, Bldg 3

institute: University of California, San Francisco

summary:
HIV is known to severely affect the gastrointestinal immune system, in particular compartments of immunity that regulate gut microbial composition. Furthermore, recent studies in mice have shown that dysregulation of the gut microbiome can contribute to chronic inflammation, which is a hallmark of HIV and is thought to fuel disease progression. We sought to understand whether the gut microbial community differs in HIV-infected subjects, and whether such putative differences are associated with disease progression.
We found that dysbiosis in the gut mucosally-adherent bacterial community associates with markers of chronic inflammation and disease progression in HIV-infected subjects, and this dysbiosis remains in many subjects undergiong antiretroviral therapy.

platform_organism: Bacteria Archaea

overall_design: We used G3 PhyloChip microarrays (commercially available from Second Genome, Inc.) to profile gut bacteria in rectosigmoid biopsies from 32 subjects: 6 HIV-infected viremic untreated (VU), 18 HIV-infected subjects on highly active antiretroviral therapy (HAART), 1 HIV-infected long-term non-progressor that is untreated (LTNP), and 9 HIV-uninfected subjects (HIV-).

first: Joseph

middle: M

last: McCune

first: Susan

middle: V

last: Lynch


title: Tight coordination of protein translation and heat shock factor 1 activation supports the anabolic malignant state [Gene Expression Data]

status: Public on Jul 21 2013

city: Cambridge

first: Marc

last: Mendillo

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

summary:
A unifying characteristic of aggressive cancers is a profound anabolic shift in metabolism to enable sustained proliferation and biomass expansion.  The ribosome is centrally situated to sense metabolic states but whether it impacts systems that promote cellular survival is unknown.   Here, through integrated chemical-genetic analyses, we find that a dominant transcriptional effect of blocking protein translation in cancer cells is complete inactivation of heat shock factor 1 (HSF1), a multifaceted transcriptional regulator of the heat-shock response and many other cellular processes essential for tumorigenesis.  Translational flux through the ribosome reshapes the transcriptional landscape and links the fundamental anabolic processes of protein production and energy metabolism with HSF1 activity.  Targeting this link deprives cancer cells of their energy and chaperone armamentarium thereby rendering the malignant phenotype unsustainable.
Gene Expression Data

overall_design: We used microarrays to examine affect of rocaglates on gene expression in cancer cell lines.  MCF7 breast cancer cells were treated with either 200 nM Rocaglamide A or DMSO, as a control. Two biological replicates for all samples.

first: Sandro

last: Santagata

middle: L

first: Yun-chi

last: Tang

first: Aravind

last: Subramanian

first: Casey

middle: C

last: Perley

first: Stéphane

middle: P

last: Roche

first: Bang

last: Wong

first: Hyoungtae

last: Kwon

first: Martina

last: Koeva

first: Angelika

last: Amon

first: Todd

middle: R

last: Golub

first: John

last: Porco

first: Luke

last: Whitesell

last: Lindquist


title: PGC methylome analysis revealed large, germline-specific mouse hypomethylated DNA domains with unique genomic and epigenomic features [ChIP-chip_NimbleGen]

status: Public on Jul 01 2013

city: Tsukuba

first: Rieko

last: Ikeda

state: Ibaraki

address: 3-1-1 Koyadai

department: BioResource Center

country: Japan

institute: RIKEN

summary:
With the goal of understanding the epigenetic regulation required for germ cell-specific gene expression, we devised a method of DNA methylation analysis adapted for a small number of developing germ cells. This microarray-based method provides the genome-wide assay of DNA methylation using a sub-nanogram quantity of genomic DNA. Using this technique, we obtained DNA methylation profiles for mouse germ cells in various developmental stages including primordial germ cells (PGC) and for stem cells derived from embryos or germ cells.
Cluster analysis of the data revealed that each cell type possesses its own characteristic DNA methylation profile, enabling classification of the cell types. This classification is generally consistent with that based on gene expression profiles except for primordial germ cells, whose genome is globally hypomethylated. Among the differentially methylated sites thus identified, we focused on a group of genomic sequences hypomethylated specifically in germline cells. These hypomethylated sequences tend to be clustered, forming large (10 kb to ~9 Mb) genomic domains. Most of these hypomethylated regions designated here as Large Hypomethylated Domain (LoD) correspond to segmentally duplicated regions that contain gene families showing germ cell-specific expression. These include mouse orthologues of human cancer testis antigen genes. Most LoDs appear to be enriched with H3 lysine 9 dimethylation (H3K9me2), usually regarded as a repressive histone modification. It thus appears t  hat such a unique epigenomic state (i.e., DNA hypomethylation with H3K9me2 enrichment) may be a prerequisite for the expression of genes contained in these genomic domains.

overall_design: H3K9me2 of GS cells and cumulus

first: Kuniya

last: Abe


title: MicroRNAs as potential biomarkers for APE

status: Public on Aug 08 2013

city: Shanghai

first: junjie

last: xiao

address: 150 Ji Mo Road

institute: Key Laboratory of Arrhythmias, Ministry of Education, China (Tongji University School of Medicine)

summary: Acute pulmonary embolism (APE) remains among the most formidable challenges facing public health practice in the 21st century. Accurate diagnosis of APE is severely hindered by the lack of biomarkers with both high sensitivity and specificity. MicroRNAs (miRNAs) involve various pathophysiologic processes underlying multitudinous diseases. Accmulating evidences point to the fact that miRNAs may serve as ideal biomarkers.The aim of the present study was to explore the potential of plasma miRNAs as biomarkers for diagnosis of APE.

overall_design: Two TaqMan miRNA arrays were performed on plasma of 10 APE patients and 10 healthy controls.


title: PGC methylome analysis revealed large, germline-specific mouse hypomethylated DNA domains with unique genomic and epigenomic features

summary:
With the goal of understanding the epigenetic regulation required for germ cell-specific gene expression, we devised a method of DNA methylation analysis adapted for a small number of developing germ cells. This microarray-based method provides the genome-wide assay of DNA methylation using a sub-nanogram quantity of genomic DNA. Using this technique, we obtained DNA methylation profiles for mouse germ cells in various developmental stages including primordial germ cells (PGC) and for stem cells derived from embryos or germ cells.

Cluster analysis of the data revealed that each cell type possesses its own characteristic DNA methylation profile, enabling classification of the cell types. This classification is generally consistent with that based on gene expression profiles except for primordial germ cells, whose genome is globally hypomethylated. Among the differentially methylated sites thus identified, we focused on a group of genomic sequences hypomethylated specifically in germline cells. These hypomethylated sequences tend to be clustered, forming large (10 kb to ~9 Mb) genomic domains. Most of these hypomethylated regions designated here as Large Hypomethylated Domain (LoD) correspond to segmentally duplicated regions that contain gene families showing germ cell-specific expression. These include mouse orthologues of human cancer testis antigen genes. Most LoDs appear to be enriched with H3 lysine 9 dimethylation (H3K9me2), usually regarded as a repressive histone modification. It thus appears t  hat such a unique epigenomic state (i.e., DNA hypomethylation with H3K9me2 enrichment) may be a prerequisite for the expression of genes contained in these genomic domains.

This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: TAL1 regulated miRNAs

status: Public on Jun 15 2013

city: Boston

last: Mansour

address: 450 Brookline Avenue

department: Pediatric Oncology

institute: Dana-Farber Cancer Institute

summary: miRNA profiling of Jurkat T-ALL cells after knockdown with two control shRNAs and two shRNAs targeting TAL1 to identify miRNAs that are regulated by TAL1

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

overall_design: miRNA profiling using Exiqon arrays 48hrs after transduction of Jurkat cells with two control shRNAs (pLKO1-GFP and pLKO1-LUCIFERASE) vs two shRNAs targeting TAL1 (pLKO1-shRNA1 and pLKO1-shRNA2). Biological duplicates per shRNA. One replicate per array.Total of 8 arrays.

first: Takaomi

last: Sanda


title: PGC methylome analysis revealed large, germline-specific mouse hypomethylated DNA domains with unique genomic and epigenomic features [DNA methylation_NimbleGen]

overall_design: DNA methylation data sets from early developmenatal stage of mouse, cultured cell, and somatic tissue cells.


title: Transcriptional effect of CRH on MCF7 estrogen receptor signalling

status: Public on Jul 02 2013

city: coventry

first: dimtiris

last: grammatopoulos

address: gibbet hill road

country: United Kingdom

institute: warwick medical school

summary: MCF7 cells were stimulated with vehicle or 100nM corticotropin releasing hormone (CRH) for 24h. The effect of CRH on the expression of genes relevant to estrogen signalling was investigated by using the Human Estrogen Receptor Signaling RT² Profiler™ PCR Array (SABioscience Corp).

overall_design: qPCR gene expression profiling. MCF7 cells were treated separately in triplicate. Equal amount total RNA was processed further for gene expression analysis.

first: D

middle: K

last: Grammatopoulos

first: S

last: Lal


title: Human STAV cells from AB and FCS sublines grown in cell culture or as xenografts

status: Public on Jun 18 2013

city: Stockholm

first: Gustav

last: Nilsonne

state: None/Not Applicable

address: Retzius väg 8 A2:3

country: Sweden

institute: Karolinska Institutet

summary: Array comparative genomic hybridization (aCGH) analysis of chromosome 3 in human mesothelioma cells grown in cell culture or as xenografts

overall_design: Comparison between cell sublines and cell culture vs xenograft. 1 biological sample for each condition, 5 replicate measures.

first: Eva

last: Darai-Ramqvist

first: Carmen

last: Flores-Staino

first: Anders

last: Hjerpe

first: Katalin

last: Dobra


title: MicroRNA profiling of benign and malignant adrenocortical tumors reveals potential biomarkers of recurrence

status: Public on Jun 30 2013

city: Grenoble Cedex 09

first: Nadia

last: Cherradi

address: 17 Rue des Martyrs

department: iRTSV/CEA

country: France

institute: INSERM U1036

summary: MicroRNAs are small, non-coding RNAs that regulate gene expression at post-transcriptional levels. There is increasing evidence to suggest that miRNAs could be useful in cancer diagnosis, prognosis, and therapy. The aim of our study was to  identify miRNAs predictors of poor prognosis in adrenocortical cancer. miRNA microarray expression profiling was performed on a cohort of 6 adenomas, 6 non-recurrent carcinomas (Carc_B) and 6 recurrent carcinomas (Carc_A). We identified several miRNAs that were differentially expressed between adenomas and carcinomas as well as between Carc_A and Carc_B. We found that the best discriminatory miRNAs between carcinomas and adenomas were miR-195 and miR-335 which were down-regulated in carcinomas. MiR-139-5p was the most powerful discriminatory miRNA between Carc_A and Carc_B subtypes with consistent up-regulation in the recurrent carcinoma subgroup (Carc_A). Target prediction analysis showed that predicted targets of these miRNAs could be involved in biological processes and pathways that enhance tumor progression. Our data suggest that adrenocortical cancer cells progressively switch from a high miR-195 and miR-335 status to a low miR-195 and miR-335 phenotype. MiR-139-5P is a potential prognostic biomarker of recurrent adrenocortical carcinomas.

sample_organism:
Homo sapiens
synthetic construct

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

overall_design: Six tumor samples from patients with adrenocortical adenomas (Adenoma_1 to Adenoma_6), six tumor samples from patients with aggressive carcinomas (Carc_A1 to Carc_A6) and six tumor samples from patients with non-aggressive carcinoma (Carc_B1 to Carc_B6) were used to prepare total RNA for microarray analysis using MiRXploreTM Microarrays. miRXplore Universal Reference was used as control. One tumor sample was used per array.

first: Dirk

last: Dietrich

first: Silvia

last: Ruberg

first: Olivier

last: Chabre

first: Jean-Jacques

last: Feige


title: Global transcriptomic response of serum-resistant Neisseria meningitidis

city: Marcy l'Etoile

first: Bachra

last: Rokbi

address: 1541 Av M Mérieux

institute: sanofi pasteur

summary: Neisseria meningitidis remains an important cause of septicemia and meningitis. One of its major virulence traits is its ability to avoid killing by human serum. In the present work, the effect of growth phase (exponential versus stationary) and growth medium (THB versus Catlin) on normal human serum (NHS) sensitivity was assessed on two N. meningitidis serogroup B strains (MC58 and M982). Both strains were found to be dramatically more resistant to 20% NHS killing at early exponential phase than at stationary phase (73-100% survival after 1 to 2 hours of growth compared to less than 10% survival after 7 hours of growth). This growth phase effect was detected only when a rich medium (THB) was used while no such effect was observed using Catlin medium. KDO (2-Keto-3-deoxyoctulosonic acid) and sialic acid content were measured on serum-resistant and serum-sensitive bacteria and were found comparable, indicating that differences in LPS and capsule expression were not at the origin of the observed phenotypes. Transcriptome profiling using a PCR-array was used to compare serum-resistant and serum-sensitive bacteria. A set of 255 genes was found to be differentially expressed with 159 genes up-regulated in serum-resistant bacteria, among them 12 genes involved in glucose catabolism and 22 are known virulence factors. Overall, this study shows that serum-resistant phenotype of N. meningitidis could be obtained through modulating growth conditions. The nature of growth media and growth phases have a major impact on the ability of N. meningitidis to resist to NHS killing. Consequently, the present work underlines the critical importance of carefully controlling those parameters in any studies aimed at investigating the mechanisms and factors involved in N. meningitidis serum-resistance.

sample_organism:
Neisseria meningitidis
Neisseria meningitidis MC58

overall_design: All experiments were performed in dye swap. These experiments were performed with 2 strains of N. meningitidis serogroup B.  In one set of experiments, the gene expression profile of bacteria cultured in THB medium during 7h was compared with the corresponding profile of bacteria cultured during 1h in the same medium. In a second set of experiments, the gene expression profile of 1 strain cultured in THB medium during 7h was compared with the corresponding profile of the same strain cultured in Catlin medium during 7h. 3 biological replicates were performed for each comparison.

first: Olivia

last: Fratantonio

first: Philippe

last: Lhéritier

first: Noëlle

last: Mistretta

first: Nadège

last: Arnaud-Barbe

first: Renauld

last: Geneviève


title: A temperature-responsive network links cell shape and virulence traits in a primary fungal pathogen -- ChIP-chip

status: Public on Jun 14 2013

first: Mark

last: Voorhies

address: 513 Parnassus, S472

department: Microbiology and Immunology

institute: University of California

summary:
The ability to grow at host temperature is a critical trait for most pathogenic microbes of humans. Thermally dimorphic fungal pathogens, including Histoplasma capsulatum, are a class of soil fungi that undergo a dramatic change in cell shape and virulence gene expression in response to host temperature. Here we elucidate a complex temperature-responsive network in H. capsulatum, which switches from an environmental filamentous form to a pathogenic yeast form. We dissect the circuit driven by three regulators that control yeast-phase growth, and demonstrate that these factors, including two deeply conserved Velvet family proteins of unknown function, associate with DNA. We identify and characterize a fourth regulator of this pathway, and define cis-acting motifs that recruit these transcription factors to a tightly interwoven network of temperature-responsive target genes. Our results provide the first comprehensive analysis of the complex transcriptional network that links temperature to morphology and virulence in thermally dimorphic fungi.

This submission gives the chromatin immunoprecipitation results.

overall_design: For each of the four Ryp proteins, ChIP vs. input hybridizations were performed for three replicate immunoprecipitations from the wild-type strain and two negative control replicates from the corresponding mutant strain.

first: Sinem

last: Beyhan

first: Anita

last: Sil


title: The effect of alcohol on the expression of miroRNAs in rat nucleus accumbens

status: Public on Aug 01 2013

city: Elmhurst

first: Chunxiang

last: Zhang

state: United States

address: 438 E May St

department: Pharmacology

institute: Rush University Medical Center

summary:
MicroRNAs (miRNAs) are small non-coding RNAs with strong biological functions.  However, the roles of miRNAs in alcohol addiction are still unclear. In this study, we analyzed miRNA profile of in the nucleus accumbens (NAc) of rats treated with alcohol.
The results demonstrated, among the 300 detected miRNAs in NAc, multiple miRNAs were aberrantly expressed after treatment with alcohol.

overall_design: To perform the experiment, 18 male rats (weighing 150-180 g) were divided into two treatment groups: vehicle (500 ul saline, ip bid) or alcohol (1 g/kg, ip bid). Seven days later, the animals were sacrificed and their NAc were isolated for miRNA microarray analysis. The miRNA expressions were determined using miRNA microarrays for rat (LC Sciences).  Data were normalized using cyclic method and statistically analyzed using Ttest.

first: Jingyuan

last: Li


title: PGC methylome analysis revealed large, germline-specific mouse hypomethylated DNA domains with unique genomic and epigenomic features [DNA methylation_Agilent]

first: Rieko

last: Ikeda

overall_design: DNA methylation data sets from cumulus cells.

first: Kuniya

last: Abe


title: Interaction of Phenotypic Plasticity and Natural Selection on Gene Expression

status: Public on Jul 30 2013

city: Miami

first: David

middle: I

last: Dayan

state: Florida

address: 4600 Rickenbacker CSWY

institute: University of Miami

summary: Temperature profoundly affects biological systems across all levels of organization. Over generations, species become evolutionarily adapted to specific thermal environments. In addition to evolved adaptive differences, individuals may reversibly modify their phenotype within their lifetimes in response to different thermal environments in a process termed phenotypic plasticity. The interaction between, evolutionary adaptation and phenotypic plasticity is complex and contentious. We utilize Fundulus glycolytic muscle physiology to address this interaction. We conducted a microarray analysis of muscle gene expression using three populations of Fundulus acclimated to three different temperatures. A phylogenetic comparative analysis among populations from different thermal environments demonstrates adaptive variation in mRNA expression for 186 genes. Sixty-seven genes had significant differences in mRNA expression in response to thermal acclimation. Interestingly, evolutionary adaptation and phenotypic plasticity appear to operate primarily orthogonally: few genes (although more than expected by chance alone) exhibit both adaptive variation and phenotypic plasticity. The magnitude and function of the adaptive variation in gene expression is dependent on acclimation temperature (e.g., more genes have adaptive differences at 12° and 28°C than at 20°C), demonstrating the importance of gene-by-environment interactions. Finally, a functional analysis of gene expression provides novel, testable hypotheses regarding adaptation of muscle physiology.

sample_organism:
Fundulus heteroclitus
Fundulus grandis

overall_design: A loop design was used for the microarray hybridizations. The loop consisted of 56 individual labeled with Cy3 and Cy5 aRNAs for three populations acclimated to three temperatures (12°C, 20°C 28°C). The loop formed was MA→GA→Fg→ME..., where each arrow represents a separate hybridization (array) with the biological sample at the base of the arrow labeled with Cy3 and the biological sample at the head of the arrow labeled with Cy5. ME are F. heteroclitus individuals from Maine, GA are F. heteroclitus individuals from Georgia, and Fg are F. grandis individuals from Florida. Acclimation temperatures and individuals randomized within this loop. Slides were scanned using a ScanArray Express with 5um resolution at half speed. Images were quantitated using ImaGene software.

first: Marjorie

middle: F

last: Oleksiak

first: Douglas

last: Crawford


title: A temperature-responsive network links cell shape and virulence traits in a primary fungal pathogen -- T-DNA mutants (2)

summary:
The ability to grow at host temperature is a critical trait for most pathogenic microbes of humans. Thermally dimorphic fungal pathogens, including Histoplasma capsulatum, are a class of soil fungi that undergo a dramatic change in cell shape and virulence gene expression in response to host temperature. Here we elucidate a complex temperature-responsive network in H. capsulatum, which switches from an environmental filamentous form to a pathogenic yeast form. We dissect the circuit driven by three regulators that control yeast-phase growth, and demonstrate that these factors, including two deeply conserved Velvet family proteins of unknown function, associate with DNA. We identify and characterize a fourth regulator of this pathway, and define cis-acting motifs that recruit these transcription factors to a tightly interwoven network of temperature-responsive target genes. Our results provide the first comprehensive analysis of the complex transcriptional network that links temperature to morphology and virulence in thermally dimorphic fungi.

This submission gives the expression profiling results.

overall_design: cDNA from each ryp mutants and wild-type controls was labeled with Cy5 and competitively hybridized against the Cy3-labeled pooled reference sample using  H. capsulatum whole-genome 70-mer oligonucleotide microarray. For the experiments with ryp T-DNA mutants, there were 4 to 6 replicates for each strain and condition, and for the experiments with ryp knockdown strains, there were 3 to 12 replicates for each strain and condition.  The T-DNA and knockdown experiments are being submitted as separate series, with samples further divided based on G217B platform version.


title: A temperature-responsive network links cell shape and virulence traits in a primary fungal pathogen -- RNAi mutants (2)


title: A temperature-responsive network links cell shape and virulence traits in a primary fungal pathogen -- T-DNA mutants (1)


title: A temperature-responsive network links cell shape and virulence traits in a primary fungal pathogen

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


title: PGC methylome analysis revealed large, germline-specific mouse hypomethylated DNA domains with unique genomic and epigenomic features [Agilent 44Kx4 Array Expression]

overall_design: Gene expression data sets from early developmenatal stage of mouse, cultured cell, and somatic tissue cells.


title: PGC methylome analysis revealed large, germline-specific mouse hypomethylated DNA domains with unique genomic and epigenomic features [Agilent 44Kx1 Array Expression]

overall_design: Gene expression data sets from somatic tissue cells.


title: Distinct translational control in CD4+ T-cell subsets

status: Public on Jun 01 2013

first: Ola

last: Larsson

department: Department of oncology-pathology

summary: Regulatory T cells expressing the transcription factor Foxp3 play indispensable roles for the induction and maintenance of immunological self-tolerance and immune homeostasis. Genome-wide mRNA expression-studies have defined canonical signatures of T-cell subsets. Changes in steady-state mRNA levels do, however, often not reflect those of corresponding proteins due to post-transcriptional mechanisms including mRNA translation. Here, we unveil a unique translational signature, contrasting CD4+Foxp3+ regulatory T (TFoxp3+) and CD4+Foxp3- non-regulatory T (TFoxp3-) cells, which imprints subset-specific protein expression. We further show that translation of eukaryotic translation initiation factor 4E (eIF4E) is induced during T-cell activation and, in turn, regulates translation of cell cycle related mRNAs and proliferation in both TFoxp3- and TFoxp3+ cells. Unexpectedly, eIF4E also affects Foxp3 expression and thereby lineage identity. Thus, mRNA-specific translational control directs both common and distinct cellular processes in CD4+ T-cell subset.

overall_design: CD4+/Foxp3+ and CD4+Foxp3- cells were studied ex vivo or activated in vitro for 36h. Both polysome-associated and cytoplasmic RNA was isolated to enables studies of translational control


title: A temperature-responsive network links cell shape and virulence traits in a primary fungal pathogen -- RNAi mutants (1)


title: Integrated analyses of genome-wide DNA occupancy and expression profiling identify key genes and pathways involved in cellular transformation by Marek's disease oncoprotein, Meq

status: Public on May 31 2013

city: East Lansing

first: sugalesini

last: Subramaniam

address: 3606 E Mount Hope Rd

department: CMIB

institute: Michigan State University

summary: Marek’s disease (MD) is an economically significant disease in chickens caused by the highly oncogenic Marek’s disease virus (MDV). A major unanswered question is the mechanism of MDV-induced tumor formation. Meq, a bZIP transcription factor discovered in the 1990s, is critically involved in viral oncogenicity but only a few of its host target genes have been described impeding our understanding of MDV-induced tumorigenesis. Using ChIP-seq and microarray analysis, a high confidence list of Meq-binding sites in the chicken genome and a global transcriptome of Meq-responsive genes was generated. Meq binding sites were found to be enriched in the promoter regions of up-regulated genes, but not in those of down-regulated genes. ChIP-seq was also performed for c-Jun, a known heterodimeric partner of Meq. Close location of binding sites of Meq and c-Jun was noted, suggesting cooperativity between these two factors in modulating transcription. Pathway analysis indicated that Meq transcriptionally regulates many genes that are part of several signaling pathways include the ERK/MAPK, Jak-STAT, and ErbB pathways that are critical for oncogenesis and/or include signaling mediators involved in apoptosis. Meq activates oncogenic signaling cascades by transcriptionally activating major kinases in the ERK/MAPK pathway and simultaneously repressing phosphatases, as verified using inhibitors of MEK and ERK1/2 in a cell proliferation assay. This study provides significant insights into the mechanistic basis of Meq-dependent cell transformation.

overall_design: Transcript profiling of DF-1 (a chicken embryo fibroblast cell line) and Meq-DF-1 clone 5G (DF-1 stably expressing Meq driven by the CMV promoter) using Affymetrix chicken GeneChips

first: Sugalesini

first: John

last: Johnston

first: Likit

last: Preeyanon

first: C

middle: T

last: Brown

first: Hsing-Jien

last: Kung

first: Hans

middle: H

last: Cheng


title: Expression analysis of Candida glabrata CBS138 delta-cnb1, delta-crz1, delta-slt2, and delta-ire1 mutants in response to tunicamycin exposure (Transcriptional response of Candida glabrata to tunicamycin exposure)

city: Suzuka

first: Hironobu

last: Nakayama

state: Mie

address: 3500-3 Minami-Tamagaki Cho

department: Phamaceutical Science

institute: Suzuka University of Medical Science

summary:
Investigation of whole genome gene expression level changes in response to tunicamycin, an inhibitor of protein N-glycosylation, in Candida glabrata CBS138 delta-cnb1, delta-crz1, delta-slt2, and delta-ire1 mutants, compared to the wild-type strain. The mutations engineered into these strains render them hypersusceptible to tunicamycin.
The mutants analyzed in this study are further described in Miyazaki, T. et al. (2010) Antimicrob Agents Chemother. 54(4):1639-1643 (PMID: 20100876) and Miyazaki, T. et al. (2010) FEMS Yeast Res 10(3):343-352, 2010 (PMID: 20214686).

overall_design: A fifteen chip study using total RNA isolated from Candida glabrata wild-type control and four mutant strains, in which the entire ORFs of CNB1 (XP_448800), CRZ1 (XP_449644), SLT2 (XP_447735), or IRE1 (XP_446111) are deleted. Each chip measures the expression level of 5,217 genes from Candida glabrata CBS138 with six 60-mer-probe pairs per gene, with two-fold technical redundancy.

first: Taiga

last: Miyazaki


title: Undomesticated Bacillus subtilis RemA regulon

status: Public on May 29 2013

city: New York

first: Patrick

last: Eichenberger

email: pe19@nyu.edu, arb401@nyu.edu

state: New York

address: 12 Waverly Place

department: Center for Genomics and Systems Biology

institute: New York University

summary: Transcriptional profiling of Bacillus subtilis str 3610 cells comparing sinR-/epsH- cells to sinR-/epsH-/remA- cells in MSgg Medium at optical density (600nm) of 1.0

overall_design: remA+ vs remA- (epsH-, sinR- background).  Biological replicates 3

first: Ashley

last: Bate

first: Daniel

last: Kearns


title: miR-1915 and miR-1225-5p Regulate The Expression of CD133, PAX-2 and TLR2 in Adult Renal Progenitor Cells

status: Public on May 30 2013

city: Bari

first: Fabio

last: Sallustio

state: Bari

address: Piazza G. Cesare N°11

country: Italy

institute: University of Bari

summary: Adult renal stem/progenitor cells (ARPCs), first identified in the Bowman’s capsule, were recently identified also in the tubular compartment and it was demonstrated that renal progenitors from both locations were positive for PAX-2, CD133 and CD24 and exhibited multipotent differentiation ability. Recent studies indicated that microRNAs (miRNAs), a class of noncoding small RNAs that participate in the regulation of gene expression, may play a key role in stem cell self-renewal and differentiation. Distinct sets of miRNAs are specifically expressed in pluripotent stem cells but not in adult tissues, suggesting a role for miRNAs in stem cell self-renewal. We compared miRNA expression profiles of renal progenitors with that of renal proximal tubular cells (RPTECs) and of mesenchymal stem cells (MSC) and found distinct sets of miRNAs that were specifically expressed both in tubular and glomerular ARPCs. In particular, the miR-1915 and miR-1225-5p regulated the expression of important markers of renal progenitors, such as CD133 and PAX-2, and important genes involved in the repair mechanisms of ARPCs, such as TLR2. We demonstrated that the expression of  both the renal stem cell markers CD133 and PAX-2 depends, at least in part, on lower miR-1915 levels and showed that the increase of miR-1915 levels improved capacity of ARPCs to  differentiate into adipocyte-like and epithelial-like cells. Finally, we found that the low levels of miR-1225-5p were responsible for high TLR2 expression in ARPCs. Therefore, together, the miR-1915 and the miR-1225-5p seems to regulate important trait of ARPCs: the stemness and the repair capacity.

overall_design: Sixteen samples consisting of 5 glomerular and tubular ARPCs each, 3 MSCs, and 3 RPTECS.

first: Grazia

last: Serino


title: Lymph node CD4+ T cell and thioglycollate-elicited peritoneal macrophage expression data from naïve young and old SJL/J and SJL-ChrY^B10.S male mice

status: Public on May 28 2013

city: Burlington

first: Laure

last: Case

address: 89 Beaumont Ave

institute: University of Vermont

summary: Understanding the DNA elements that constitute and control the regulatory genome is critical for the appropriate therapeutic management of complex diseases. Here, using chromosome Y (ChrY) consomic mouse strains on the C57BL/6J background, we show that susceptibility to two diverse animal models of autoimmune disease, including experimental allergic encephalomyelitis (EAE) and experimental myocarditis, correlates with the natural variation in copy number of Sly and Rbmy multicopy ChrY genes. In the B6 background, ChrY possesses gene regulatory properties that impact both genome-wide gene expression and the presence of alternative splice variants in pathogenic CD4+ T cells. Using a ChrY consomic strain on the SJL background, we discovered a preference for ChrY-mediated gene regulation in macrophages, the immune cell subset underlying the EAE sexual dimorphism in SJL mice, rather than CD4+ T cells. Importantly, in both genetic backgrounds, an inverse correlation exists between the number of Sly and Rbmy ChrY gene copies and the number of significantly upregulated genes in immune cells, thereby supporting a link between copy number variation of Sly and Rbmy with the ChrY genetic element exerting regulatory properties. Moreover, in humans, an analysis of the CD4+ T cell transcriptome from male multiple sclerosis patients versus healthy controls provides further evidence for an evolutionarily conserved mechanism of gene regulation by ChrY. Thus, these data establish ChrY as a member of the regulatory genome in mammals due to its ability to regulate gene expression and alternative splicing in immune cells linked to disease.

overall_design: Three biological replicates from young (≤4 weeks) and old (≥ 6 months) mice from each strain were pooled from 5 mice for each replicate. RNA was isolated from CD4+TCRB+ FAC sorted cells and from thioglycollate-elicited peritoneal macrophages.

first: Emma

last: Wall

first: Julie

last: Dragon

first: Naresha

last: Saligrama

first: Dimitry

middle: N

last: Krementsov

first: Mohamad

last: Moussawi

first: James

last: Zachary

first: Sally

last: Huber

first: Elizabeth

last: Blankenhorn

first: Cory

last: Teuscher


title: Changes in gene expression in porcine lungs following infection with Zaire ebolavirus

city: Winnipeg

first: Charles

last: Nfon

state: Manitoba

address: 1015Arlington Street

department: Science Branch

country: Canada

institute: Canadian Food Inspection Agency

summary: To elucidate the mechanisms involved in pulmonary inflammation in Zaire ebolavirus-infected pigs, lung sections infected pigs were used for a porcine microarray to analyse changes in gene expression with particular interest in proinflammatory cytokine and chemokine transcription.

overall_design: Pigs were given inhalation anaesthesia and then inoculated with 106 plaque forming units of Zaire ebolavirus in sterile PBS per pig via the intranasal, intraocular and oral routes. Three control pigs were mock inoculated with PBS and housed separately.

first: Gary

last: Kobinger

first: Anders

last: Leung

first: Greg

last: Smith

first: Carissa

last: Embury-Hyatt

first: Hana

last: Weingartl


title: Circulating microRNAs predict biochemical recurrence in prostate cancer patients

status: Public on May 22 2013

city: Bedford Park

first: Luke

last: Selth

state: SA

address: Flinders Drive

department: College of Medicine and Public Health

country: Australia

institute: Flinders University

summary: Comparison of circulating miRNA levels in patients who experienced rapid biochemical recurrence or no recurrence following radical prostatectomy

overall_design: qRT-PCR miRNA expression profiling of patient serum


title: Legionella pneumophila transcriptomic response of hfq mutant during post-exponential phase

status: Public on May 21 2013

city: St-Anne-de-Bellevue

first: Sebastien

last: Faucher

state: QC

address: 21,111 Lakeshore

department: Natural Resource Sciences

institute: McGill University

summary: Legionella pneumophila wild-type and hfq mutant were grown to post-exponential. The wild-type strain is used as the control.

platform_organism: Legionella pneumophila subsp. pneumophila str. Philadelphia 1

overall_design: Two strains: wild-type (control) and hfq mutant (test). Three biological replicates.  Ch1 is gDNA, use as a reference channel (Talaat, 2002, NAR)

last: Trigui

first: Paulina

last: Dudyk

first: Janet

last: Sum

first: Howard

last: Shuman


title: HeLa Cells infected with Shigella in the presence/absence of Staurosporin

city: Bethesda

first: Douglas Scott

last: Merrell

state: MD

address: 4301 Jones Bridge Road

department: Dept. of Microbiology and Immunology

institute: Uniformed Services University

summary:
Question Addressed: What is the host response (specifically apoptosis pathways) to Shigella infection and what is the contribution of MxiE to the host response? The arrays are apoptosis Exon hit arrays, thus splice variation can be determined.  Array data from HeLa cells that remained Uninfected or were infected with wildtype S. flexneri serotype 2a strain 2457T or an isogenic mixE mutant. These groupings are further divided such that Uninfected or Infected cells remained untreated or were treated with the apopotosis inducer staurosporine (STS). The design of the experiment was a time course and samples were harvested at the indicated time points (hr). All hybridizations were conducted against a common reference sample that was made from pooled samples of normal uninfected healthy HeLa cells.
Infection: HeLa cells were infected with wt Shigella (wt), mxiE mutant (mixE) or were left uninfected (uninfected)
Compound Based Treatment: Cultures were treated with Staurosporin (STS) or were left untreated (untreated)
Infection time: Cells were harvested at the indicated time after treatment

overall_design: 20 Samples

first: Douglas

middle: S


title: MCF7 breast cancer cells treated with mesenchymal stem cell-derived exosomes

status: Public on May 20 2013

city: beijing

first: shihua

last: wang

address: dongdan santiao 5#

institute: peking union medical college

summary: Human mesenchymal stem cell (MSC)-conditioned medium (CM) was previously reported to affect the biology of tumor cells; however, the precise mechanisms remain unclear. Here, we show that MSCs secreted 40- to 100-nm particles, which have the typical characteristics of exosomes, and these MSC-derived exosomes promoted migration of the breast cancer cell line MCF7. To further investigate the effect of MSC-exosomes on MCF7, we analyzed the gene expression profiles of MCF7 treated with or without MSC-exosomes for 24 h.

overall_design:
Investigation of whole genome gene expression level changes in breast cancer cell line MCF7 which were treated with or without mesenchymal stem cell-derived exosomes.
This study uses total RNA recovered from two samples. One sample is MCF7 treated with PBS for 24 hours and another one is MCF7 treated with mesenchymal stem cell-derived exosomes for 24hours. The ultimate concentration of  mesenchymal stem cell-derived exosomes used in this experiment was 400ng/ul.

first: Chunhua

last: Zhao

first: Ruizhu

last: Lin

first: Shihua

last: Wang


title: Vibrio cholerae Freezing Study

status: Public on May 23 2013

summary:
Question Addressed: Does gene expression in V. cholerae change when samples are frozen at -80 degrees? An in vitro grown culture of O1 Inaba ICDDR,B (strain DSM-V999 described in Nature. 2002 Jun 6;417(6889):642-5) that had been grown to exponential phase (OD600 + 0.2) was placed in a 15 ml conical and then placed in a -80 degree freezer.  A portion of the starting culture was harvested prior to freezing to serve as the control/reference for downstream hybridizations. RNA was recovered from the non-frozen sample as well as by prepping material directly from frozen samples.  Labeling reactions were performed in quadruplicate for each sample.
A replicate experimental design type is where a series of replicates are performed to evaluate reproducibility or as a pilot study to determine the appropriate number of replicates for a subsequent experiments.


title: Characterization of the transcriptomes Actinobacillus pleuropneumoniae drip flow biofilm  dripflow biofilm

city: St-Hyacinthe

first: Yannick

last: Tremblay

state: Quebec

address: 3200, rue Sicotte

department: Microbiologie et Pathologie

institute: Université de Montréal

summary: The transcriptome of Actinobacillus pleuropneumoniae dripbiofilm biofilms was compared to the transcriptome of effluent cells

platform_organism: Actinobacillus pleuropneumoniae serovar 5b str. L20

overall_design: 4 samples were analyzed which included 3 biological replicate,  1 technical replicate and 1 dye swap

middle: D

first: Vincent

last: Deslandes

first: Mario

last: Jacques


title: Transcriptome of 6h static biofilm Actinobacillus pleuropneumoniae

summary: The transcriptome of Actinobacillus pleuropneumoniae biofilms was compared to the transcriptome of planktonic bacteria


title: Analysis of the effect of acid stress in Lactococcus lactis MG1363

status: Public on May 17 2013

city: Groningen

first: Ana

last: Solopova

address: Nijenborgh 7

department: MolGen

country: Netherlands

institute: RUG

summary: To understand the system response to pH changes in the environment, the expression of genes during the pH shift was investigated. Pre-adaptation effects were examined by comparing the effects seen with cells pre-grown in pH 5.1 or pH 6.5 to those occuring after a sudden pH change (pre-grown in pH 6.5, and suspended in buffer of pH 5.1).

sample_organism: Lactococcus cremoris subsp. cremoris MG1363

overall_design: mRNA of L. lactis MG1363 cells grown at pH 6.5 and suspended in 50 mM KPi buffer, pH 5.1 and of those grown at pH 5.1 and suspended in 50 mM KPi buffer, pH 5.1 were compared. Control experiment was performed with mRNA of cells grown at pH 6.5 and suspended in buffer of pH 6.5 compared to that of cells grown in pH 5.1 and suspended in buffer of 5.1.

last: Lúcia Carvalho

first: David

last: Turner

first: Luís

last: Fonseca

first: Teresa

last: Catarino

first: Oscar

last: Kuipers

first: Eberhard

middle: O

last: Voit

last: Rute Neves

first: Helena

last: Santos


title: Comparison between the transcriptomes of 4h static biofilm and a 6h static biofilm of Actinobacillus pleuropneumoniae

summary: The transcriptome of Actinobacillus pleuropneumoniae 4h static biofilms was compared to the transcriptome of 6h static biofilm


title: Responses of maize source leaf metabolism to low temperature, low nitrogen and low phosphorus stress

status: Public on May 15 2013

city: Erlangen

first: Urte

last: Schluter

address: Staudtstr. 5

department: Biology

country: Germany

institute: FA University Erlangen

summary: Abiotic stress causes disturbances in the cellular homeostasis. Re-adjustment of balance in carbon, nitrogen and phosphorus metabolism therefore plays a central role in stress adaptation. However, it is currently unknown which parts of the primary cell metabolism follow common patterns under different stress conditions and which represent specific responses. To address these questions, changes in transcriptome, metabolome and ionome were analyzed in maize source leaves from plants suffering low temperature, low nitrogen (N) and low phosphorus (P) stress. The selection of maize as study object provided data directly from an important crop species and the so far underexplored C4 metabolism. Growth retardation was comparable under all tested stress conditions. The only primary metabolic pathway responding similar to all stresses was nitrate assimilation, which was down-regulated. The largest group of commonly regulated transcripts followed the expression pattern: down under low temperature and low N, but up under low P. Several members of this transcript cluster could be connected to P metabolism and correlated negatively to different phosphate concentration in the leaf tissue. Accumulation of starch under low temperature and low N stress, but decrease in starch levels under low under low P conditions indicated that only low P treated leaves suffered carbon starvation. In conclusion, maize employs very different strategies for management of nitrogen and phosphorus metabolism under stress. While nitrate assimilation was regulated depending on demand by growth processes, phosphate concentrations changed depending on availability, thus building up reserves under excess conditions. Carbon and energy metabolism of the C4 maize leaves were particularly sensitive to P starvation.

overall_design: Responses of maize source leaves to low temperature, low nitrogen and low phosphorus conditions were tested in independent single-stress experiments. Seedlings were cultivated in pots containing nutrient-poor peat soil under the controlled conditions of a growth chamber. The plants were fertilized with modified Hoagland solutions, containing 15mM KNO3 and 0.5mM KH2PO4 for control conditions; for low N and low P treatment, the nutrient concentrations were reduced to 0.15mM KNO3 and 0.1mM KH2PO4, respectively. Low temperature treated plants were always supplied with control nutrient solution. Plants from the nitrogen and phosphorus experiment as well as the control temperature plants were exposed to 28°C during the day and 20°C during the night. Low temperature treatment was limited to the night period and was reduced to 4°C for the 10h dark period. Source leaf lamina were harvested at day 20 (low temperature experiment) or day 30 after start of germination (low nitrogen and low phosphorus experiment) for parallel analysis of transcriptome, metabolome and ion profiles. The molecular data is further supplemented by phenotypic characterization of the maize seedlings under investigation.

first: U

last: Schlüter

last: Sonnewald


title: Transcriptome of A. pleuropneumoniae biofilms cultured under different growth conditions

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

overall_design: Refer to individual Series


title: Functional Characterization of Fission Yeast Transcription Factors by Overexpression Analysis

status: Public on May 11 2013

city: Calgary

first: Gordon

last: Chua

state: Alberta

address: 2500 University Drive NW

department: Biological Sciences

institute: University of Calgary

summary: In Schizosaccharomyces pombe, over 90% of transcription factor genes are nonessential. Moreover, the majority do not exhibit significant growth defects under optimal conditions when deleted, complicating their functional characterization and target gene identification. Here, we systematically overexpressed 99 transcription factor genes with the nmt1 promoter. Screening the overexpression array revealed that 64 transcription factor genes exhibited reduced fitness when ectopically expressed.  Cell cycle defects were also often observed. We further investigated three uncharacterized transcription factor genes (toe1+-toe3+) which displayed cell elongation when overexpressed. Ectopic expression of toe1+ resulted in a G1 delay while toe2+ and toe3+ overexpression produced an accumulation of septated cells with abnormalities in septum formation and nuclear segregation, respectively. Transcriptome profiling and ChIP-chip analysis of the transcription factor overexpression strains indicated that Toe1 activates target genes of the pyrimidine-salvage pathway, while Toe3 regulates target genes involved in polyamine synthesis. We also found that ectopic expression of the putative target genes SPBC3H7.05c, and dad5+ and SPAC11D3.06 could recapitulate the cell cycle phenotypes of toe2+ and toe3+ overexpression, respectively.  Furthermore, the phenotypes of toe1+and toe2+ overexpression could be suppressed by deletion of the putative target genes urg2+ and SPAC1399.04c, and SPBC3H7.05c, SPACUNK4.15 and rds1+, respectively. This study implicates new transcription factors and metabolism genes in cell cycle regulation and demonstrates the potential of systematic overexpression analysis to elucidate the function and target genes of transcription factors in S. pombe.

overall_design: We generated 3 overexpression microarrays and 2 deletion microarray with dye swaps, 3 deletion microarrays with drug treatments with dye swaps, 1 deletion single replicate microarray experiment, and 3 single replicate chIP-chip experiments. The effect of the mutant strains were all compared to wild type or empyty vector strains except for two experiments one that looked at the toe1 mutant with and without chlorpromazine and another that looked at wild type with and without chlorpromazine.

first: Lianne

last: Vachon

first: Justin

last: Wood

first: Eun-Joo

middle: G

last: Kwon

first: Amy

last: Laderoute

first: Kate

last: Chatfield-Reed

first: Jim

last: Karagiannis


title: Transcriptional analysis of exogenously supplied and transgenic of senescence-induced cytokinin for broccoli postharvest yellowing improvement

status: Public on May 01 2013

city: Taipei

first: Mao-Sen

last: Liu

address: 128 Academia Road, Section 2, Nankang, Taipei 115, Taiwan

country: Taiwan

institute: Institute of Plant and Microbial Biology, Academia Sinica, Taiwan

summary: Both exogenously supplied and transgenic induced cytokinin production can effectively delay senescence of broccoli florets during postharvest storage. However, a substantial comparison between the mechanisms of these two treatments on delaying broccoli florets senescence was absent. Here, we conduct microarray analysis on broccoli florets of N6-benzylaminopurine treated and ipt-transgenic broccoli that harbor a senescence-associated-gene promoter triggering isopentenyltransferase gene expression during postharvest storage.

overall_design: Analysis used RNA of Green King inbred line 104 as control sample for comparison to the experimental samples of ipt-transgenic line 102, 103 and parental line Green King as well as 10 ppm BA treated Green King at harvest and after postharvest storage at 25 centigrade in the dark for 4 days.

first: Long-Fang

last: Chen


title: Transcriptomic profiling of Salmonella Typhimurium upon desiccation on stainless steel and subsequent rehydration

status: Public on May 09 2013

city: Dublin

first: Sarah

last: Finn

address: University College Dublin

department: School of Public Health, Physiotherapy and Population Science

country: Ireland

institute: Centre for Food Safety

summary: Transcriptional profiles of Salmonella Typhimurium str. ST4/74 air-dried onto stainless steel for 4 h was compared to an early stationary phase (ESP) culture control.  Cells that had been air-dried for 4 h were then subsequently rehydrated with water for a 30 min period, after which the transcriptional profile was compared to an ESP control.

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium str. ST4/74

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

overall_design: Carried out using 2 biological replicates for each sample; hybridised in a two-channel hybridization against Salmonella genomic DNA as the comparator/reference.

first: Kristian

last: Händler

first: Orla

last: Condell

first: Aoife

last: Colgan

first: Shane

last: Cooney

first: Peter

last: McClure

first: Alejandro

last: Amézquita

first: Jay

last: Hinton

first: Séamus

last: Fanning


title: Stability selection for regression-based models of transcription factor-DNA binding specificity

city: Durham

first: Raluca

last: Gordan

state: NC

address: 101 Science Dr, CIEMAS 2179

department: Center for Genomic and Computational Biology

institute: Duke University

type: Genome binding/occupancy profiling by array

summary:
Motivation: The DNA binding specificity of a transcription factor (TF) is typically represented using a position weight matrix (PWM) model, which implicitly assumes that individual bases in a TF binding site contribute independently to the binding affinity, an assumption that does not always hold. For this reason, more complex models of binding specificity have been developed. However, these models have their own caveats: they typically have a large number of parameters, which makes them hard to learn and interpret.
Results: We propose novel regression-based models of TF-DNA binding specificity, trained using high resolution in vitro data from custom protein binding microarray (PBM) experiments. Our PBMs are specifically designed to cover a large number of putative DNA binding sites for the TFs of interest (yeast TFs Cbf1 and Tye7, and human TFs c-Myc, Max, and Mad2) in their native genomic context. These high-throughput, quantitative data are well suited for training complex models that take into account not only independent contributions from individual bases, but also contributions from di- and trinucleotides at various positions within or near the binding sites. To ensure that our models remain interpretable, we use feature selection to identify a small number of sequence features that accurately predict TF-DNA binding specificity. To further illustrate the accuracy of our regression models, we show that even in the case of paralogous TF with highly similar PWMs, our new models can distinguish the specificities of individual factors. Thus, our work represents an important step towards better sequence-based models of individual TF-DNA binding specificity.

overall_design: Four protein binding microarray (PBM) experiments of human transcription factors were performed. Briefly, the PBMs involved binding GST-tagged transcription factors c-Myc, Max, and Mad2(Mxi1) to double-stranded 180K Agilent microarrays in order to determine their binding specificity for putative DNA binding sites in native genomic context. Briefly, we represent three categories of 36-bp sequences: 1) bound probes, 2) unbound probes (or negative controls), and 3) test probes. Bound probes corresponded to genomic regions bound in vivo by c-Myc, Max, or Mad2 (ChIP-seq P < 10^(-10) in HeLaS3 or K562 celld (ENCODE)) that contain at least two consecutive 8-mers with universal PBM E-score > 0.4 (Munteanu and Gordan, LNCS 2013). All putative binding sites occurr at the same position within the probes on the array. “Unbound” probes corresponded to genomic regions with ChIP-seq P < 10^(-10) and a maximum 8-mer E-score < 0.2. We also designed test probes that contain, within constant flanking regions, all nnCACGTGnn 10-mers and 18 nnnCACGTGnnn 12-mers (where n = A, C, G, or T). Each DNA sequence represented on the array is present in 6 replicate spots. We report the PBM signal intensity for each spot. The PBM protocol is described in Berger et al., Nature Biotechnology 2006 (PMID 16998473).


title: Gene expression profile of response to auxin at 3 h after treatment in rice root tips: IR64 vs Dro1-NIL

status: Public on May 07 2013

city: Tsukuba

first: Yusaku

last: Uga

address: 2-1-2, Kannondai

institute: National Institute of Agrobiological Sciences

summary: Gene expression profile of response to auxin at 3 h after treatment in rice root tips: IR64 (loss-of-function of DRO1 type) vs Near-isogenic line homozygous for the Kinandang Patong allele of DRO1 in an IR64 genetic background (Dro1-NIL; gain-of-function of DRO1 type)

overall_design: We used two rice varieties, IR64 and near-isogenic line homozygous for the Kinandang Patong allele of DRO1 in an IR64 genetic background (Dro1-NIL). We performed comprehensive microarray analysis of rice root tips with auxin treatment (3h) and pre-treatment (0h) in IR64 and Dro1-NIL. Seedling root tips of IR64 and Dro1-NIL were treated with 10 µM 2,4-D. n = 3 biological repeats (15 seedlings per repeat).


title: The pre-ovulatory LH surge elicits different effects on the granulosa- and theca-specific expression profiles in bovine follicles

city: Kansas City

first: Sumedha

last: Gunewardena

state: Kansas

address: 3901 Rainbow Boulevard

institute: University of Kansas Medical Center

summary: The molecular mechanisms that regulate the pivotal transformation processes observed in the follicular wall following the pre-ovulatory LH-surge, are still not established, particularly for cells of the thecal layer. To elucidate thecal and granulosa cell type-specific biological functions and signaling pathways, large dominant bovine follicles were collected before and 21 hrs after an exogenous GnRH induced LH surge. Because LH receptor density varies within the granulosa cell populations, antral granulosa (aGC; those aspirated by follicular puncture) and membrane associated granulosa (mGC; those scraped from the follicular wall) were compared to thecal cell expression profiles determined by mRNA microarrays. Thecal cell gene expression was less affected in the peri-ovulatory follicle when compared to granulosa cells, as evidenced by only 2% versus 25% of the ~11,000 genes expressed changing in response to the LH surge, respectively. The majority of the 203 LH-regulated thecal genes were also LH regulated in granulosa cells, leaving a total of 58 genes as LH-regulated theca cell specific genes. Most of the 58 genes (i.e., 74%) thecal specific genes including several known thecal markers (CYP17A1, NR5A1) were downregulated, while most genes identified are new to theca. Many of the newly identified upregulated thecal genes (e.g., PTX3, RND3, PPP4R4) were also upregulated in granulosa. Minimal expression differences were observed between aGC and mGC, however, transcripts encoding extracellular proteins (NID2) and matrix modulators (ADAMTS1, SASH1) predominated these differences. We also identified large numbers of unknown LH-regulated granulosa cell genes and discuss their putative roles in ovarian function.

overall_design: The single dominant ovarian follicle was collected from each cow before the LH surge or 22 hours after GnRH (used to induce LH surge).  RNA was extracted from three independent cells within each follicle and there were hybridized on Affymetrix microarrays.

first: Lane

last: Christenson

first: Jens

last: Vanselow


title: MicroRNA expression profiling of skeletal muscle from PPARalpha- and PPARbeta-overexpressing mice

city: Orlando

first: Zhenji

last: Gan

state: FL

address: 6400 Sanger Rd

institute: SBMRI

summary:
This experiment was conducted to identify target microRNAs of the peroxisome proliferator-activated receptor (PPAR) in skeletal muscle of transgenic mice that overexpressed PPARalpha or PPARbeta.

We have recently demonstrated that skeletal muscle-specific PPARb transgenic (MCK-PPARb) mice exhibit increased exercise endurance, whereas MCK-PPARa mice have reduced exercise performance. Accordingly, we sought to determine whether PPARb and PPARa drive distinct programs involved in muscle fiber type determination. Myosin heavy chain (MHC) immunohistochemical staining of soleus muscle revealed a marked increase in type 1 fibers in the MCK-PPARb muscle compared to non-transgenic (NTG) littermates but a profound reduction in MCK-PPARa muscle. miRNA profiling revealed that levels of miR-208b and miR-499 were increased in MCK-PPARb muscle but reduced in MCK-PPARa muscle. miR-208b and miR-499, which are embedded in the Myh7 and Myh7b genes, respectively, have been shown previously to regulate slow-twitch muscle genes. Lastly, combined inhibition of miR-208b and miR-499 abolished the enhancing effects of PPARb on MHC1 expression in skeletal myotubes, while forced expression of miR-499 in MCK-PPARa muscle completely reversed the type 1 fiber program and exercise capacity. Taken together, these findings demonstrate that miR-208b and miR-499 are necessary to mediate the effects of PPARb and PPARa on muscle fiber type determination.

platform_organism:
Mus musculus
Rattus norvegicus

overall_design: Comparison of microRNA expression from soleus muscles isolated from wild-type (non-transgenic (NTG)) and PPARalpha-overexpressing (MCK-PPARa) mice, and comparison of microRNA expression from soleus muscles isolated from wild-type (NTG) and PPARbeta-overexpressing (MCK-PPARb) mice. Three replicates of each are analyzed.

first: Daniel

last: Kelly


title: Expression data of multiple sclerosis patients receiving Interferon-beta therapy [TaqMan(r) Array Human MicroRNA B Cards v2.0]

status: Public on Apr 24 2013

city: Rostock

first: Michael

last: Hecker

address: Gehlsheimer Str. 20

department: Department of Neurology

institute: University of Rostock

summary:
The purpose of this study was to investigate the expression dynamics of mRNAs and microRNAs in response to subcutaneous IFN-beta-1b treatment (Betaferon, 250 µg every other day) in patients with clinically isolated syndrome (CIS) suggestive of multiple sclerosis (MS) or relapsing-remitting type of the disease (RRMS).
By using TaqMan Array MicroRNA Cards, we obtained microRNA expression profiles of peripheral blood mononuclear cells from 6 patients within the first month of IFN-beta treatment.

overall_design:
EDTA blood samples were taken from all patients immediately before first, second and third IFN-beta injection as well as after 1 month.
Total RNA of Ficoll-isolated peripheral blood mononuclear cells from each sample was extracted. Real-time PCR measurements were performed in 384-well plates with TaqMan assay reagents to quantify the microRNA expression levels.
This GEO entry provides the data of the TaqMan Array Human MicroRNA B Cards v2.0.

first: Dirk

last: Koczan

first: Uwe

last: Zettl


title: Transcriptome of 4h static biofilm Actinobacillus pleuropneumoniae

first: Yannick

last: Tremblay

first: Vincent

last: Deslandes

first: Mario

last: Jacques


title: Expression data of multiple sclerosis patients receiving Interferon-beta therapy [HG-U133_Plus_2]

summary:
The purpose of this study was to investigate the expression dynamics of mRNAs and microRNAs in response to subcutaneous IFN-beta-1b treatment (Betaferon, 250 µg every other day) in patients with clinically isolated syndrome (CIS) suggestive of multiple sclerosis (MS) or relapsing-remitting type of the disease (RRMS).
By using Affymetrix microarrays, we obtained gene expression profiles of peripheral blood mononuclear cells from 6 patients within the first month of IFN-beta treatment.

overall_design:
EDTA blood samples were taken from all patients immediately before first, second and third IFN-beta injection as well as after 1 month.
Total RNA of Ficoll-isolated peripheral blood mononuclear cells from each sample was extracted, labeled and hybridized to Affymetrix Human Genome U133 Plus 2.0 arrays to quantify the mRNA levels.
This GEO entry provides the U133 Plus 2.0 microarray data.


title: Characterization of the microbial community structure in Candidatus Liberibacter asiaticus-infected Citrus plants treated with antibiotics in the field

city: Fort Pierce

first: muqing

last: zhang

address: 2199 South Rock Road

institute: University of Florida

summary:
Huanglongbing (HLB) is a worldwide devastating disease of citrus. There are no effective control measures for this newly emerging but century-old disease. Previously, we reported a combination of Penicillin G and Streptomycin was effective in eliminating or suppressing the associated bacterium, ‘Candidatus Liberibacter asiaticus’ (Las).
Here we report the bacterial composition and community structure in HLB-affected citrus plants during a growing season and while being treated with antibiotic combinations PS (Penicillin G and Streptomycin) and KO (Kasugamycin and Oxytetracycline) using the Phylochip™ G3 array.

overall_design: The antibiotic treatments were conducted on the randomized complete block design with four replicates. For each replicate, five HLB-affected, 7-year-old citrus trees (a unique hybrid, 10c-5-58, which is an open-pollinated seedling from the combination of Lee mandarin × Orlando tangelo) at the USHRL farm, 10 cm in diameter, were injected with either 100 ml of the antibiotic combination treatment PS (5 g of penicillin G potassium + 0.5 g of Streptomycin per tree) or the antibiotic treatment KO (2 g of oxytetracycline + 1.0 g of kasugamycin per tree). Five trees were injected with water as injection controls (CK). Injections were made using an Avo-Ject syringe injector (a catheter-tipped 60 ml syringe; Aongatete Coolstores Ltd., NZ) beginning in August of 2010. The tapered tip was firmly fitted into a 19/64-in (7.5 mm) diameter hole, ≈3 cm deep, drilled into the tree. The injector was kept in the tree and the treatment lasted for one week in each injection-trunk. Treatments were repeated every 2 months for one year and ceased in August of 2011. Before and during treatment more than 30 leaf samples per tree were taken from different positions around the tree canopies for qPCR assays at 2 month intervals.DNA for the PhyloChip™ G3 analysis, which was extracted from 20 samples of the same treatment, was pooled in equal amounts and quantified by the PicoGreen® method. The PhyloChipTM G3 analysis was conducted by Second Genome Inc. (San Francisco, CA).

first: Muqing

last: Zhang

first: Charles

middle: A

last: Powell

first: Ying

last: Guo

first: Lesley

last: Benyon

first: Yongping

last: Duan


title: Physiological and transcriptional response of Bacillus cereus treated with low-temperature nitrogen gas plasma

status: Public on May 06 2013

first: Maarten

last: Mols

institute: University of Groningen

summary: Aims: To investigate the inactivation kinetics of Bacillus cereus vegetative cells upon exposure to low-temperature nitrogen gas plasma and to reveal the mode of inactivation by transcriptome profiling.  Methods and results:  Exponentially growing B. cereus cells were filtered and put on agar plates. The plates, carrying the filters with the vegetative cells, were placed into nitrogen gas plasma at atmospheric pressure and cold temperature (~37°C). After different exposure times the cells were harvested for RNA extraction and enumeration. The RNA was used to perform whole transcriptome profiling using DNA microarrays. The transcriptome profile showed a large overlap with profiles obtained from conditions generating reactive oxygen species inside B. cereus. However, excess radicals such as peroxynitrite, hydroxyl and or superoxide were not found.  Conclusions:  Antibacterial activity of nitrogen gas plasmas is not based on UV radiation but on the formation of reactive oxygen or nitrogen species in the plasma jet rather than inside the targeted cells.  Significance and impact of the study:  This study represents the ﬁrst investigation of differential gene expression on a genome-wide scale in B. cereus following nitrogen gas plasma exposure. This study may help to design cheap, safe, and effective plasma decontamination devices.

overall_design: Plasma treated sampes compared with nitrogen gas flow treated samples and plasma treated samples compared to untreated control samples. Nitrogen flow samples in duplicate, plasma treated samples 4 replicates. Replicates hybridized with dyes swapped.

first: Tjakko

last: Abee


title: Transcription networks responsible for early regulation of Salmonella-induced inflammation in the jejunum of pigs.

status: Public on Apr 17 2013

city: Lelystad

first: Marcel

last: Hulst

state: Flevoland

address: Edelhertweg 15

department: Livestock research

institute: Animal Sciences Group

summary: The early interaction of Salmonella enterica serovar typhimurium DT104 with intact small intestinal mucosa was studied in a Small Intestinal Segment Perfusion (SISP) model. Intestinal segments were infected with or without Salmonella. Scrapings from jejunal segments were collected after perfusion for 0, 2, 4, or 8 hours. Details of the SISP experiment are described in: Niewold TA, Veldhuizen EJ, van der Meulen J, Haagsman HP, de Wit AA, Smits MA, Tersteeg MH, Hulst MM. Using the Operon 13K pig oligonucleotide array differences in host gene expression were recorded between infected and uninfected segments within a single pig (isogenic comparisons), and between identical treated segments collected from 3 individual SISP pigs, all responding markedly different to infection with Salmonella (inter-animal comparisons).

overall_design:
A Small Intestinal Segment Perfusion (SISP) test was performed with 3 pigs (pig no. 2, 3, and 4) (cross-bred Yorkshire×(Large White×Landrace)). Two adjacent segments prepared in the mid-jejunum of each pig were perfused for 1 hour with Salmonella enterica serovar typhimurium DT104 suspended in peptone solution (10E-09 CFU/ml) or with peptone solution alone (mock infected segment) respectively. Subsequently, segments were perfused with peptone solution alone for a maximum period of 8 hours. At 2, 4, and 8 hours a part of the infected segment was dissected to obtain mucosal scrappings. The same was done at 0 and 8 hours for the uninfected (mock) control segment. RNA isolated from scrappings was used for microarray comparisons using the Operon 13K pig oligonucleotide array. 9 comparisons were done. For each of the 3 SISP pigs, expression in the 8 hours perfused infected segment, perfused for 8 hours, was compared to expression in its adjacent mock infected segment (3 isogenic comparisons, 8 hpi.). Expression in the infected segment of each SISP pig, dissected after 2 or 4 hours of perfusion, was compared to expression in an infected segment dissected from another SISP pig (2 versus 3, 2 versus 4, and 3 versus 4 / 3 comparisons at 2 hpi., and 3 comparisons at 4 hpi.). Dye-swaps were performed for each comparison.
jejunum pig, host-microbe interaction, Salmonella enterica serovar typhimurium DT104.

middle: M

first: Mari

last: Smits

first: Stephanie

last: Vastenhouw

first: Agnes

last: de Wit

first: Theo

last: Niewold

first: Jan

last: van der Meulen


title: Expression data of multiple sclerosis patients receiving Interferon-beta therapy [TaqMan(r) Array Human MicroRNA A Cards v2.0]

first: Michael

last: Hecker

overall_design:
EDTA blood samples were taken from all patients immediately before first, second and third IFN-beta injection as well as after 1 month.
Total RNA of Ficoll-isolated peripheral blood mononuclear cells from each sample was extracted. Real-time PCR measurements were performed in 384-well plates with TaqMan assay reagents to quantify the microRNA expression levels.
This GEO entry provides the data of the TaqMan Array Human MicroRNA A Cards v2.0.

first: Dirk

last: Koczan

first: Uwe

last: Zettl


title: Expression data from wild-type Vibrio fischeri and a flrA deletion mutant.

status: Public on Apr 05 2013

city: Madison

first: Caitlin

middle: Aran

last: Brennan

state: WI

address: 1550 Linden Drive

department: MMI

institute: University of Wisconsin

summary:
The marine bacterium Vibrio fischeri requires flagellar motility to undergo symbiotic initiation with its host, the Hawaiian bobtail squid Euprymna scolopes.
We sought to identify the genes activated by the sigma54-dependent flagellar master regulator, FlrA, in V. fischeri, thereby determining the flagellar regulon in this model symbiont.

overall_design: We performed microarray analysis on wild-type Vibrio fischeri ES114 and a flrA deletion mutant, DM159, grown to mid-log phase in seawater tryptone, a condition in which cells are highly motile (two biological replicates per condition).

first: Amy

last: Schaefer


title: Transcriptome-based characterization of the interactions between Saccharomyces cerevisiae and Lactobacillus delbrueckii subsp. bulgaricus in lactose-grown chemostat co-cultures

status: Public on Apr 01 2013

city: Brabrand

first: Sander

last: Sieuwerts

address: rørdrumvej 2

department: Arla Scientific Innovation Centre

country: Denmark

institute: Arla Foods

summary:
The present study aims to explore chemostat-based transcriptome analysis of mixed cultures by investigating interactions between the yeast S. cerevisiae and the lactic acid bacterium L. bulgaricus . S. cerevisiae and L. bulgaricus are both frequently encountered in kefir, a fermented dairy product. In the context of this study, this binary culture serves as a model for the many traditional food and beverage fermentation processes in which yeasts and lactic acid bacteria occur together. The design of the cultivation conditions was based on the observation that L. bulgaricus, but not S. cerevisiae, can use lactose as a carbon source for growth and that S. cerevisiae, but not L. bulgaricus, can grow on galactose that is released upon hydrolysis of lactose by the bacterial β-galactosidase.
Mixed populations of yeasts and lactic acid bacteria occur in many dairy, food and beverage fermentations, but knowledge about their interactions is incomplete. In the present study, interactions between Saccharomyces cerevisiae and Lactobacillus delbrueckii subsp. bulgaricus, two microorganisms that co-occur in kefir fermentations, were studied during anaerobic growth on lactose. By combining physiological and transcriptome analysis of the two strains in the co-cultures, five mechanisms of interaction were identified. 1. L. bulgaricus hydrolyses lactose, which cannot be metabolized by S. cerevisiae, to galactose and glucose. Subsequently, galactose, which cannot be metabolized by L. bulgaricus, is excreted and provides a carbon source for yeast. 2. In pure cultures, L. bulgaricus only grows at increased CO2 concentrations. In anaerobic mixed cultures, the yeast provides this CO2 via alcoholic fermentation. 3. Analysis of amino acid consumption from the defined medium indicated that S. cerevisiae supplied alanine to the bacteria. 4. A mild but significant low-iron response in the yeast transcriptome, identified by DNA microarray analysis, was consistent with the chelation of iron by the lactate produced by L. bulgaricus.  5. Transcriptome analysis of L. bulgaricus in mixed cultures showed an overrepresentation of transcripts involved in lipids metabolism suggesting either a competition of the two microorganisms for fatty acids, or a response to the ethanol produced by S. cerevisiae.

platform_organism: Lactobacillus delbrueckii subsp. bulgaricus ATCC BAA-365

overall_design: To investigate the impact of of co-cultivation with S. cerevisiae on L. bulgaricus, a DNA microarray-based transcriptome analysis of L. bulgaricus response was performed on anaerobic, lactose-limited chemostat cultures grown in the presence and absence of S. cerevisae.

first: Filipa

last: Mendes

first: Erik

last: de Hulster

first: Marinka

middle: J

last: Almering

first: Marijke

last: Luttik

first: Jack

last: Pronk

first: Eddy

last: Smid

first: Peter

last: Bron

first: Pascale

last: Daran-Lapujade


title: Genome-wide search for exonic variants affecting translational efficiency

status: Public on Apr 18 2013

city: Houston

first: Hui-Qi

last: Qu

state: TX

address: 1200 Herman Pressler

department: Division of Epidemiology, Human Genetics and Environmental Sciences

institute: The University of Texas School of Public Health

summary: To date, the search for expression quantitative trait loci (eQTL) has centered entirely on transcription; variants with effects on mRNA translation have not been systematically studied. We tested the use of ribosomal association as proxy for translational efficiency of polymorphic mRNAs to develop a novel high throughput approach for translational cis-regulation in the human genome.

overall_design:
Cell lysates of lymphoblastoid cell lines (LCL) from 38 parents of the European HapMap set (CEU) were subjected to ultracentrifugal fractionation to separate polysomal/nonpolysomal mRNA. The ratio of polysomal/nonpolysomal mRNA level  was taken as a proxy for translational efficiency and tested as a quantitative trait for association with single-nucleotide polymorphisms (SNPs) on the same mRNA transcript.
Supplementary file “logTIfolds38CEUparents.txt” lists the polysomal/nonpolysomal mRNA level ratios, ready for QTL testing. Genotyping information is available on the HapMap or 1000 Genome websites.
Besides the 38 parents of the European HapMap set, a few other samples were included for QC purposes. These other samples include one child, and three samples from the CEPH (PLATE II).

first: Constantin

last: Polychronakos


title: The development of microRNA expression profile of human umbilical vein endothelial cells (HUVECs) after exposed to HCCLM3 cells

status: Public on Feb 22 2013

city: Shanghai

first: Kai

last: Zhu

address: 136 Yi Xue Yuan Road

institute: liver cancer institute, Fudan University

summary: we have employed whole microRNA microarray to see the microRNA expression changes of HUVECs after exposed to HCCLM3 cells

overall_design: examine the microRNA expression profile of HUVECs in the absence or presence of human HCC cells

first: Jian

last: Zhou


title: Molecular profiling of cutaneous squamous cell carcinomas and actinic keratoses from organ transplant recipients

status: Public on Feb 06 2013

city: Leiden

first: Harry

last: Vrieling

address: Einthovenweg 20

department: Toxicogenetics, S4-P

institute: Leiden University Medical Center

summary: The risk of developing cutaneous squamous cell carcinoma (SCC) is markedly increased in organ transplant recipients (OTRs) compared to the normal population. Next to sun exposure, the immunosuppressive regimen is an important risk factor for the development of SCC in OTRs. Various gene mutations (e.g. TP53) and genetic alterations (e.g. loss of CDKN2A, amplification of RAS) have been found in SCCs. The aim of this genome-wide study was to identify pathways that are consistently involved in the formation of SCCs and their precursor lesions, actinic keratoses (AKs). To perform the analysis in an isogenic background, RNA and DNA were isolated from normal (unexposed) epidermis, benign  AK, and SCC from each of 15 OTRs. Hierarchical cluster analysis of mRNA expression profiles showed SCC, AK and epidermal samples to separate into three distinct groups. Several thousand genes were differentially expressed between epidermis, AK and SCC; most upregulated in SCCs were genes related to hyperproliferation and stress markers, such as keratin 6 (KRT6), KRT16 and KRT17. Matching to oncogenic pathways revealed activation of downstream targets of RAS and cMYC in SCCs and of NFkappaB and TNF already in AKs.

overall_design: Patients were selected from the group of OTRs that are regularly seen at the dermatology clinic of the Leiden University Medical Center. Patients with clinically suspected SCC were informed on the study and after informed consent was obtained, fresh frozen samples were obtained from SCCs (n=15), AKs (n=14) and NS (n=13). RNA was isolated and gene expression profiles were obtained using HumanWG-6 v2 Expression BeadChips (Illumina). The normalized expression data was analyzed for differences in expression between SCC, AK and NS, at single-gene level but also at geneset level.

first: Liesbeth

last: Hameetman

first: Suzan

last: Commandeur

first: Jan

last: Bouwes Bavinck

first: Hermina

middle: C

last: Wisgerhof

first: Frank

last: de Gruijl

first: Rein

last: Willemze

first: Leon

last: Mullenders

first: Cornelis

last: Tensen


title: Identification of thalidomide modulation related genes in  mesenchymal stem cells

status: Public on Mar 12 2013

city: Jinan

first: Ji

last: Ma

state: Shandong

address: West Wen Hua Road 107

department: Department of Hematology

institute: Qilu Hospital, Shandong University

summary: Comparison of gene expression data from thalidomide modulated- and unmodulated-MSCs from patients with idiopathic thrombocytopenic purpura (ITP).

overall_design: This experiment consists of 3 arrays.

first: Yun-na

last: Ning

first: Miao

last: Xu

first: Jun

last: Peng

first: Ming

last: Hou


title: C. elegans nasp-1 / btr-1 mutant versus wild-type N2, exposed to pathogen Bacillus thuringiensis DB27

status: Public on Jan 31 2013

city: Ipswich

first: Amit

last: Sinha

state: MA

address: 240 County Road

institute: New England Biolabs

summary: Transcriptional profiling of C. elegans nasp-1 / btr-1 mutant worms versus wild type N2 strain, both exposed to the bacterial pathogen Bacillus thuringiensis DB27.

overall_design:
One-condition experiment.
C. elegans nasp-1 / btr-1 mutant versus N2, exposed to Bacillus thuringiensis DB27. 3 biological replicates, including 1 dye-swaps.

first: Igor

last: Iatsenko

first: Ralf

last: Sommer


title: Functional Comparison of Chronological and In Vitro Aging: Differential Role of the Cytoskeleton and Mitochondria in Mesenchymal Stromal Cells

status: Public on Jan 05 2013

city: Berlin

first: Sven

last: Geissler

state: Berlin

address: Augustenburger Platz 1

department: Julius Wolff Institute and BCRT

institute: Charite - Universitaetsmedizin Berlin

summary: Mesenchymal stromal cells (MSCs) are of high relevance for the regeneration of mesenchymal tissues such as bone and cartilage. The promising role of MSCs in cell-based therapies and tissue engineering appears to be limited due to a decline of their regenerative potential with increasing donor age, their limited availability in human tissues and the need of in vitro expansion prior to treatment. We therefore aimed to determine to which degree in vitro aging and chronological aging may be similar processes or if in vitro culture-related changes at the cellular and molecular level are at least altered as a function of donor age. For that purpose we established MSCs cultures from young (yMSCs) and aged (aMSCs) rats that were cultured for more than 100 passages. These long-term MSCs cultures were non-tumorigenic and exhibited similar surface marker patterns as primary MSCs of passage 2. During in vitro expansion, but not during chronological aging, MSCs progressively lose their progenitor characteristics, e.g., complete loss of osteogenic differentiation potential, diminished adipogenic differentiation, altered cell morphology and increased susceptibility towards senescence. Transcriptome analysis revealed that long-term in vitro MSCs cultivation leads to down-regulation of genes involved in cell differentiation, focal adhesion organization, cytoskeleton turnover and mitochondria function. Accordingly, functional analysis demonstrated altered mitochondrial morphology, decreased antioxidant capacities and elevated ROS levels in long-term cultivated yMSCs as well as aMSCs. Notably, only the MSC migration potential and their antioxidative capacity were altered by in vitro as well as chronological aging. Based on specific differences observed between the impact of chronological and in vitro MSC aging we conclude that both are distinct processes.

overall_design: Total mRNA obtained from MSCs from 12 month and three week old Sprague Dawley rats of passage 2, 30 and 100. Total RNA was isolated using Trizol® (Invitrogen) reagent as describes previously and purified using Qiagen RNeasy® mini kit (Qiagen, Germany, www.qiagen.com) according to manufacturers instruction. Illumina® BeadChip hybridization: Biotinylated cRNA was produced from 500ng total RNA using llumina® TotalPrep™ RNA amplification kit (Invitrogen). Illumina® RatRef-12 Expression BeadChips hybridization, washing, Cy3 streptavidin staining, and scanning were performed using Illumina® BeadStation 500 platform.

last: Geißler

first: Martin

last: Textor

first: Jirko

last: Kühnisch

first: Delia

last: Könnig

first: Oilver

last: Klein

first: Andrea

last: Ode

first: Tilman

last: Pfitzner

first: James

last: Adjaye

first: Grit

last: Kasper

first: Georg

last: Duda


title: Identification and Comparative Analyses of Myocardial miRNAs Involved in Fetal Response to Maternal Obesity

status: Public on Feb 01 2013

city: Portland

first: Alina

last: Maloyan

state: OR

address: 3181 SW Sam Jackson Park Rd

department: Medicine

institute: Oregon Health and Science University

summary: Maternal obesity programs the offspring to cardiovascular disease, insulin resistance, and obesity. We sequenced and profiled the cardiac miRNAs that were dysregulated in the hearts of baboon fetuses born to a high fat / high fructose diet fed mothers compared to a regular diet fed mothers.

overall_design: Fetal hearts were collected from baboon fetuses born to obese and lean mothers, total RNA was isolated, and fetal cardiac miRNA were sequenced and profiled

first: Peter

middle: W

last: Nathanielsz

first: Leslie

last: Myatt


title: Functional genomic and phenotypic responses to desiccation in natural populations of a desert drosophilid.

status: Public on Jan 15 2013

city: Las Vegas

first: Allen

middle: G.

last: Gibbs

state: Nevada

address: 4505 S Maryland Parkway

department: School of Life Sciences

institute: University of Nevada

summary: Investigation of whole genome transcription expression level changes in Drosophila mojavensis wild-type populations (1. Punta Onah:PO; 2. Organ Pipe National Manument:OPNM; 3. Punta Prieta:PP; & 4. San Quintin:SQ). The experiment was designed to investigate effects of desiccation exposure (0, 9 & 18 hr) and host plant (diet) on transcriptome.

overall_design: A total of  95 hybridizations were performed in this entire experiment. We used 135K 12-plex NimbleGen arrays. Total RNA was recovered from each sample listed below. The experimental design consisted a total of four populations (1. Punta Onah:PO; 2. Organ Pipe National Manument:OPNM; 3. Punta Prieta:PP; & 4. San Quintin:SQ),  two host diets (Agria and Organ pipe) and three desiccation treatments (0, 9 and 18 hours). Each chip measures the expression level of 15528 transcripts. Four to 5 replicates were used for each type (R-1, R-2, R-3 etc.)

first: William

last: Etges

first: Subhash

last: Rajpurohit

first: Cassia

last: de Oliveira


title: Comparison of Apis mellifera workers and queens brain development at fourth instar larvae

status: Public on Dec 31 2012

city: Alfenas

first: Joseana

last: Vieira

state: Minas Gerais

address: Rua Gabriel Monteiro da Silva, 700

country: Brazil

institute: Unifal-MG

summary: In Apis mellifera, the female eggs can develop into workers or queen depending on the diet offered during early development. The outputs of the developed honeybee females are two morphs with particular morphological traits and related physiology. The differential feeding regime experienced by the queen and the worker larvae of the honeybee Apis mellifera shapes a complex endocrine response cascade that ultimately sets up differences in brain morphologies. Herein we report on aspects of  brain morphogenesis during larval development and the brain gene expression signature of fourth instar larvae (L4) of both castes, a developmental stage characterized by the greatest differences in juvenile hormone (JH) titers between castes Using results from the hybridization of whole genome-based oligonucleotide arrays with RNA samples from brain of  fourth instar larvae  honeybees of both castes we present a list of differentially expressed genes.

overall_design: Analysis used one dye-swap combination to compare workers and queens brain development at fourth instar larvae when juvenile hormone titers is  higher in queens.

first: Anna

last: Freire

first: Ana

last: Bomtorin

first: Livia

last: Moda

first: Angel

middle: R

last: Barchuk

first: Zilá

middle: L

last: Simoes