title: RNA-sequencing reveals the complexities of the transcriptional response to lignocellulosic biofuel substrates in Aspergillus niger.

status: Public on Apr 13 2015

city: Nottingham

first: David

last: Archer

address: University Park

department: School of Life Sciences

institute: University of Nottingham

summary:
Background: Saprobic fungi are the predominant industrial sources of Carbohydrate Active enZymes (CAZymes) used for the saccharification of lignocellulose during the production of second generation biofuels. The production of more effective enzyme cocktails is a key objective for efficient biofuel production. To achieve this objective, it is crucial to understand the response of fungi to lignocellulose substrates. Our previous study used RNA-seq to identify the genes induced in Aspergillus niger in response to wheat straw, a biofuel feedstock, and showed that the range of genes induced was greater than previously seen with simple inducers [GSE33852].
Results: In this work we used RNA-seq to identify the genes induced in A. niger in response to short rotation coppice willow and compared this with the response to wheat straw from our previous study, at the same time-point. The response to willow showed a large increase in expression of genes encoding CAZymes. Genes encoding the major activities required to saccharify lignocellulose were induced on willow such as endoglucanases, cellobiohydrolases and xylanases. The transcriptome response to willow had many similarities with the response to straw with some significant differences in the expression levels of individual genes which are discussed in relation to differences in substrate composition or other factors. Differences in transcript levels include higher levels on wheat straw from genes encoding enzymes classified as members of GH62 (an arabinofuranosidase) and CE1 (a feruloyl esterase) CAZy families whereas two genes encoding endoglucanases classified as members of the GH5 family had higher transcript levels when exposed to willow. There were changes in the cocktail of enzymes secreted by A. niger when cultured with willow or straw. Assays for particular enzymes as well as saccharification assays were used to compare the enzyme activities of the cocktails. Wheat straw induced an enzyme cocktail that saccharified wheat straw to a greater extent than willow. Genes not encoding CAZymes were also induced on willow such as hydrophobins as well as genes of unknown function. Several genes were identified as promising targets for future study.
Conclusions: By comparing this first study of the global transcriptional response of a fungus to willow with the response to straw, we have shown that the inducing lignocellulosic substrate has a marked effect upon the range of transcripts and enzymes expressed by A. niger. The use by industry of complex substrates such as wheat straw or willow could benefit efficient biofuel production.

overall_design: Six samples in total consisting of duplicate shake flask Aspergillus niger cultures from three conditions: glucose 48 h, willow 24 h, willow 24 h + glucose  5 h

first: Steven

last: Pullan

first: Paul

last: Daly

first: Stéphane

last: Delmas

first: Roger

last: Ibbett

first: Matthew

last: Kokolski

first: Almar

last: Neiteler

first: Jolanda

last: van Munster

first: Raymond

last: Wilson

first: Martin

middle: J

last: Blythe

first: Sanyasi

last: Gaddipati

first: Gregory

middle: A

last: Tucker


title: Retinoids induce rapid dynamic changes in the non-coding RNAs and epigenetic profiles of murine Hox clusters

status: Public on Apr 27 2015

city: Kansas City

first: Madelaine

last: Gogol

state: MO

address: 1000 E. 50th Street

department: Computational Biology Core

country: USA

institute: Stowers Institute

type: Expression profiling by genome tiling array

type: Genome binding/occupancy profiling by genome tiling array

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

overall_design: Refer to individual Series


title: Insights into molecular characteristics of anaplastic large cell lymphoma by genome-wide DNA methylation profiling

status: Public on Apr 01 2015

city: Vienna

first: Walter

last: Pulverer

address: Muthgasse 11

department: Health & Environment

country: Austria

institute: AIT - Austrian Institute of Technology GmbH

summary: Aberrant DNA methylation patterns of malignant cells allow for the study of the tumor phenotype and behavior, and can be used for tumor classification. Here, we describe the genome-wide DNA methylation signatures of NPM-ALK positive and negative anaplastic large cell lymphoma (ALCL). Differences in DNA methylation of tumor cells compared to normal T cells concern pathways that are implicated in T cell development and function and reveal a close relationship to distinct developmental stages of thymocytes. We find DNA hypomethylation in regulatory regions that are enriched for conserved transcription factor binding motifs, such as AP1. Our results suggest a direct relationship of oncogenic signaling with epigenetic modifications via transcription factor induction and occupancy.

overall_design: DNA from 15 samples (5 Alk- tumor; 5 Alk+ tumors; 5 CD3 cells) were subjected to genome wide methylation analysis using Illuminas Infinium HumanMethylation450 BeadChip. Findings of the BeadChip analysis have been validated using MSP, COBRA and ChiP analysis.

first: Melanie

middle: R

last: Hassler

first: Ranjani

last: Lakshminarasimhan

first: Elisa

last: Redl

first: Julia

last: Hacker

first: Gavin

middle: D

last: Garland

first: Olaf

last: Merkel

first: Gangning

last: Liang

first: Ana-Iris

last: Schiefer

first: Ingrid

last: Simonitsch-Klupp

first: Lukas

last: Kenner

first: Daniel

last: Weisenberger

first: Andreas

last: Weinhäusel

first: Suzanne

last: Turner

first: Gerda

last: Egger


title: Gene expression analysis of Mycobacterium tuberculosis under arginine conditions

city: Hanover

first: Annegret

last: Hampel

address: Carl-Neuberg-Str. 1

country: Germany

institute: Hannover Medical School

summary: In other bacteria, arginine induces the expression of genes involved in arginine catabolism. This study obtained the identification of genes involved in the arginine metabolism of Mycobacterium tuberculosis.

overall_design: Mycobacterium tuberculosis was cultured with arginine or ammonium chloride as sole nitrogen source. In the log phase of growth, RNA was isolated and whole genome expression was determined. The study contains three biological replicates.


title: Liver samples of Pemt-/- and Pemt+/+ mice under high fat-high-sucrose (HFHS) diet

status: Public on Apr 14 2015

city: Okayama

first: Jun

last: Wada

address: 2-5-1 Shikata-cho, Kita-ku

department: Department of Nephrology, Rheumatology, Endocrinology and Metabolism

country: Japan

institute: Okayama University

type: Methylation profiling by high throughput sequencing


title: Gene expression profiling of oral cancer cell lines with or without AzC treatment

city: Zhunan Miaoli County

first: Chia

middle: Huei

last: Lee

address: 35, Keyan Rd.

department: National Institute of Cancer Research

country: Taiwan

institute: Taiwan National Health Research Institute

summary: To genome-wide screening for the genes whose expression are responsible for the promoter DNA methylation, we performed the cDNA microarray with oral cancer cells before and after a DNA methyltransferase inhibitor, 5-aza-2’-deoxycytidine (AzC), treatment.

overall_design: Total RNA was collected from four oral cancer cell lines before or after AzC treatment.

first: Chia-Huei


title: H3K9 Trimethylation Silences Fas Expression to Confer Colon Carcinoma Immune Escape and 5-Fluorouracil Chemoresistance

city: Augusta

first: Kebin

last: Liu

state: GA

address: 1410 Laney Walker Blvd

department: Biochemistry and Molecular Biology

institute: Medical College of Georgia

summary: We have determined that verticillin A is a histone methyltransfease inhibitor that selectively inhibits human SUV39H1, SUV39H2, G9a and GLP to inhibit H3K9 methylation in human colon cancer cells. The objective here is to identify verticillin A target genes in human colon cancer cells.

overall_design: 5-FU-resistant human colon carcinoma cell lines LS411N-5FU-R was established from the metastatic human colon carcinoma cell line LS411N. LS411N-5FU-R cells were cultured in the absence or presence of verticillin A (50 nM) for 3 days and used for RNA lsolation. DNA microarray analysis was done in replicates in the Georgia Regents University Cancer Center Genomic Core Facility.

first: Amy

middle: V

last: Paschall


title: Established glioma cell lines prove valuable models for tumour heterogeneity - mediated cellular response studies in vitro

status: Public on Apr 08 2015

city: Piran

first: Ana

last: Rotter

address: Fornace 41

department: Marine Biology Station

country: Slovenia

institute: National Institute of BIology

summary: Both established glioma cells lines U87MG and U373 were used for studying their interactions in the indirect co-cultures. Eventhough both being derived from the glioma tissue, those two cell lines prove morphologically and physiologically disctinct. Therefore their intre-cellular interactions were examined on gene exprexssion level in vitro to observe whether those co-cultures could make for a suitable in vitro cell model mimicking the in vivo glioma tumour heterogeneity.

overall_design: Three biological replicates of four cell set-ups were performed: U87MG monoculture, U373 monoculture, U87MG co-cultured with U373 (in Boyden chambers) and U373 co-cultured with U87MG (in Boyden chambers).

first: Helena

last: Motaln

first: Tamara

middle: T

last: Lah

first: Kristina

last: Gruden

first: C

last: van Noorden

first: U

last: Verbovsek


title: The basic helix-loop-helix transcription factor Mist1 overexpression in mouse fetal hepatoblast culture

status: Public on Mar 31 2015

city: Isehara

first: Akihide

last: Kamiya

state: Kanagawa

address: 143 Shimokasuya

institute: Tokai University

summary: To identify the molecular mechanism of Mist1 during hepatoblasts differentiation, we performed gene expression analysis in Mist1 over-expressed cells. Dlk+ hepatoblasts derived from E13 fetal livers were purified. Purification of Dlk+ cells were performed using anti-Dlk antibody after hematopoietic cells were removed. Cells were infected with mock or Mist1-overexpressing retroviruses and cultured for 3days with oncostatin M.

overall_design: Virus infection was performed at the day primary culture was began (day0). Oncostatin M was added at day 1 and the cells were collected at day3. Two independent experiments were performed.

first: Hiromi

last: Chikada


title: Transcriptome Analysis Predicts Clinical Outcome and Sensitivity to Anticancer Drugs of patients with a Pancreatic Adenocarcinoma

status: Public on Apr 09 2015

city: Quebec

first: Ezequiel

middle: L

last: Calvo

state: Quebec

address: 2705 Boul. Laurier

department: Molecular Endocrinilogy

country: Canada

institute: CRCHUL

summary: A major impediment to the effective treatment of patients with PDAC (Pancreatic Ductal Adenocarcinoma) is the molecular heterogeneity of the disease, which is reflected in an equally diverse pattern of clinical responses to therapy. We developed an efficient strategy in which PDAC samples from 17 consecutively patients were obtained by EUS-FNA or surgery, their cells maintained as a primary culture and tumors as breathing tumors by xenografting in immunosuppressed mice. For these patients a clinical follow up was obtained. On the breathing tumors we studied the RNA expression profile by an Affymetrix approach. We observed a significant heterogeneity in their RNA expression profile, however, the transcriptome was able to discriminate patients with long- or short-time survival which correspond to moderately- or poorly-differentiated PDAC tumors respectively. Cells allowed us the possibility to analyze their relative sensitivity to several anticancer drugs in vitro by developing a chimiogram, like an antibiogram for microorganisms, with several anticancer drugs for obtaining an individual profile of drug sensitivity and as expected, the response was patient-dependent. Interestingly, using this approach, we also found that the transcriptome analysis could predict the sensitivity to some anticancer drugs of patients with a PDAC. In conclusion, using this approach, we found that the transcriptome analysis could predict the sensitivity to some anticancer drugs and the clinical outcome of patients with a PDAC.

overall_design: PDAC samples from 17 consecutively patients were obtained by Endoscopic Ultrasound-Guided Fine-Needle Aspiration (EUS-FNA) or surgery. Consents of informed patients were collected, and the ethics review board of the three centers approved the study. All samples were anonymized and obtained in accordance with institutional review boards. EUS-FNA cells were maintained as a primary culture and tumors as breathing tumors by xenografting in immunosuppressed mice.  We characterized 17 PDAC-derived xenografts by duplicate. Total RNA was extracted and hybridized on Human Gene 2.0 (Genechip, Affymetrix) as described previously (Hamidi et al. JCI 122: 2092-2103, 2012).

first: Pauline

last: Duconseil

first: Marine

last: Gilabert

first: Odile

last: Gayet

first: Celine

last: Loncle

first: Vincent

last: Moutardier

first: Olivier

last: Turrini

first: Jacques

last: Ewald

first: Marc

last: Giovannini

first: Mohamed

last: Gasmi

first: Erwan

last: Bories

last: Barthet

first: Mehdi

last: Ouaissi

first: Anthony

last: Goncalves

first: Jean

last: Raoul

first: Veronique

last: Secq

first: Stephane

last: Garcia

first: Patrice

last: Viens

first: Juan

last: Iovanna

first: Nelson

last: Dusetti


title: microRNA expression during tumor-associated macrophage (TAM) differentiation

city: Beijing

first: Yanshuang

last: Li

address: 5 Dong Dan San Tiao

department: National Laboratory of Medical Molecular Biology

country: China

institute: Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College

summary: To further analyze the change of microRNA(miRNA) between normal peritoneal macrophage(PEC) and TAM from early tumor(12 days after 4T1 cell injection) or TAM from late tumor(21 days after 4T1 cell injection) , we employed Agilent mouse microRNA microarray Rel 12.0 as a discovery platform to identify miRNAs

overall_design: Total RNA from peritoneal macrophage and TAM of early tumor (tumor formed for 12days after BALB/c mice injected wth 4T1 cell) or TAM of late tumor(tumor formed for 21days after BALB/c mice injected with 4T1 cell) were extracted and analyzed using Agilent mouse microRNA microarray platform, and changes of miRNA were screened out. Agilent mouse microRNA microarray is designed for the profiling of mouse miRNA .627 mouse miRNA and 39 mouse virus-related miRNA can be detected by our microRNA microarray.

last: Shi

first: Dexian

last: Zheng


title: Coronary Artery Disease Associated Transcription Factor TCF21 Regulates Smooth Muscle Precursor Cells that Contribute to the Fibrous Cap

status: Public on Mar 19 2015

city: Philadelphia

first: Sylvia

last: Nurnberg

state: PA

address: 3400 Civic Center Blvd

department: Medicine

institute: University of Pennsylvania

type: Expression profiling by high throughput sequencing

summary: Recent genome wide association studies have identified a number of genes that contribute to the risk for coronary heart disease. One such gene, TCF21, encodes a basic-helix-loop-helix transcription factor believed to serve a critical role in the development of epicardial progenitor cells that give rise to coronary artery smooth muscle cells (SMC) and cardiac fibroblasts. Using reporter gene and immunolocalization studies with mouse and human tissues we have found that vascular TCF21 expression in the adult is restricted primarily to adventitial cells associated with coronary arteries and also medial SMC in the proximal aorta of mouse. Genome wide RNA-Seq studies in human coronary artery SMC (HCASMC) with siRNA knockdown found a number of putative TCF21 downstream pathways identified by enrichment of terms related to CAD, including “vascular disease,” “disorder of artery,” and “occlusion of artery” as well as disease-related cellular functions including “cellular movement,” and “cellular growth and proliferation.” In vitro studies in HCASMC demonstrated that TCF21 expression promotes proliferation and migration and inhibits SMC lineage marker expression. Detailed in situ expression studies with reporter gene and lineage tracing revealed that vascular wall cells expressing Tcf21 before disease initiation migrate into vascular lesions of ApoE-/- and Ldlr-/- mice. While Tcf21 lineage traced cells are distributed throughout the early lesions, in mature lesions they contribute to the formation of a subcapsular layer of cells, and others become associated with the fibrous cap. The lineage traced fibrous cap cells activate expression of SMC markers and growth factor receptor genes. Taken together, these data suggest that TCF21 may have a role regulating the differentiation state of SMC precursor cells that migrate into vascular lesions and contribute to the fibrous cap and more broadly, in view of the association of this gene with human CAD, provide evidence that these processes may be a mechanism for CAD risk attributable to the vascular wall.

overall_design: RNA-Seq: 3 versus 3 technical replicates, siControl versus siTCF21

first: Karen

last: Cheng

first: Azad

last: Raiesdana

first: Ramendra

last: Kundu

first: Clint

last: Miller

first: Juyong

middle: B

last: Kim

first: Komal

last: Arora

first: Ivan

last: Carcamo-Oribe

first: Yiqin

last: Xiong

first: Nikhil

last: Tellakula

first: Vivek

last: Nanda

first: Nikitha

last: Murthy

first: William

last: Boisvert

first: Ulf

last: Hedin

first: Ljubica

last: Perisic

first: Silvia

last: Aldi

first: Lars

last: Maegdefessel

first: Milos

last: Pjanic

first: Gary

middle: K

last: Owens

first: Michelle

last: Tallquist

first: Thomas

last: Quertermous


title: In vivo and in vitro Genome wide binding (ChIP-Seq) of Bapx1 and Sox9

city: Potsdam

last: Lufkin

state: NY

address: 8 Clarkson Avenue

department: Biology

institute: Clarkson University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Bapx1 was endogenously tagged with S-Peptide and dissected vertebral columns from these tagged embryos at E12.5 were subjected to immunoprecipitation by S-peptide antibody. Simultaneously V5 tagged Bapx1 was also over expressed in NIH_3T3 cells and immunoprecipitated with V5 antibody. Concurrently vertebral column fro E12.5 mouse embryos were subjected to immunoprecipitation with Sox9 antobody to compare binding sites of Sox9 and BApx1 in the vertebral column of developing mouse embryo

overall_design: Bapx1 was tagged with S-peptide tag by homologous recombination in mESC and stable mouse lines were generated. Similarly Bapx1 cDNA was cloned into the pCDNA 6 vector containing a n-terminal V5 tag and overexpressed in NIH_3T3 cells. Both these were used for immunoprecipitation with either V5 or S-pepetide to determine overall genome wide binding of Bapx1 and genome wide binding of Bapx1 in E12.5 vertebral column. For Sox9, endogenous Sox9 antibody was used to pull down Sox9 in veretebral column of E12.5 mouse embryo

first: Sumantra

last: Chatterjee


title: Methylation profiling of oral squamous cell carcinoma (OSCC)

first: Chia

last: Lee

summary: According to epidemiological studies, a vast majority, approximately 80%~90% of male OSCC patients in Taiwan habitually drink alcohol (A), and chew betel quid (B), and use cigarette (C). To assess the impact of these dietary factors on the epigenome, we conduct a high-throughput screen survey in an oral cancer cohort with exposure of A, B, and C. Results indicate aberrent methylation patterns are prevalent in OSCC patients with ABC risk factors.

overall_design: Genomic DNA was collected from tumor and non-tumor pair-wise samples. These biopsies were obtained from 40 male OSCC patients who regularly drink alcohol, chew areca nut and smoking.

first: Chia-Huei

first: Chun-Yen

last: Chang

first: Jenn-Ren

last: Hsiao


title: Epigenome analysis of first trimester CVS samples from normal and Trisomy 13,18,21 pregnancies, and maternal whole blood samples.

city: Vejle

first: Anders

last: Bojesen

address: Kabbeltoft 25

department: Department of Clinical Genetics

country: Denmark

institute: Vejle Hospital

type: Methylation profiling by genome tiling array

summary: Genome wide DNA methylation profiling of normal and trisomic placentas, and maternal blood cell DNA. The aim of this study was to search for methylation differences between maternal and fetal(placenta) cell free DNA, and between normal and trisomic placentas for an optimized methylation based noninvasive prenatal diagnosis of fetal chromosomal aberations.   The Illumina Infinium 450k Human DNA methylation Beadchip was used to obtain DNA methylation profiles across approximately 450,000 CpGs in DNA samples from Chorionic villus samples(CVS)  and DNA samples from whole blood. Samples included 12 Maternal blood cell samples from normal pregnancies, 12 normal CVS, 12 Trisomy 21 CVS, 12 trisomy 18 CVS and 6  trisomy 13 CVS samples.

overall_design: Bisulphite converted DNA from the 54 samples were hybridized to the Illumina Infinium 450k Human Methylation Beadchip.

first: Mads

middle: M

last: Aagaard

first: Jesper

last: Graakjaer

first: Lotte

last: Hatt

first: Steen

last: Kolvraa

first: Cathrine

last: Bach

first: Steffen

last: Sommer

first: Inge

last: Agerholm


title: Porphyromonas gingivalis 33277 wild-type vs Fur orthologue Har isogenic mutant ECR455

city: Carlton

first: Catherine

last: Butler

state: VIC

address: 720 Swanston St

department: The Melbourne Dental School

country: Australia

institute: The University of Melbourne

summary: Porphyromonas gingivalis is a major pathogen associated with the microbial biofilm-mediated disease chronic periodontitis. P. gingivalis has an obligate requirement for iron and protoporphyrin IX which it satisfies by transporting heme and iron liberated from the human host. The level of cellular iron in P. gingivalis affects the expression of a distinct iron-associated regulon of 64 genes and low iron invokes an iron sparing response. Iron homeostasis is usually mediated in Gram-negative bacteria at the transcriptional level by the Ferric Uptake Regulator (Fur). There is a single predicted P. gingivalis Fur superfamily orthologue named Har (heme associated regulator) that lacks the conserved metal binding residues found in other Fur orthologues. We show that Har binds both heme and ferrous iron resulting in a conformational change in the protein. Har was unable to complement the Escherichia coli H1780 fur mutant and there was no change in cellular metal content in a P. gingivalis Har mutant compared with the wild-type. The Har regulon of 44 genes is not predicted to play a role in iron homeostasis. Together these data indicated that Har does not regulate iron homeostasis in P. gingivalis. However, Har was required for heme-responsive biofilm development and its regulon overlapped P. gingivalis regulons previously identified after growth in heme limitation or as a homotypic biofilm. P. gingivalis is unique as an iron-dependent Gram-negative bacterium with a single heme-binding Fur superfamily orthologue, Har, that does not regulate iron homeostasis.

overall_design: Paired samples were compared on the same microarray using a two-colour system. A total of 6 paired microarray hybridizations were performed representing 6 biological replicates, where a balanced dye design was used, with the overall analysis including three microarrays where P. gingivalis 33277 samples were labeled with Cy3 and the paired ECR455 samples were labeled with Cy5 and three other microarrays where samples were labeled with the opposite combination of fluorophores.

first: Helen

last: Mitchell

first: Stuart

middle: G

last: Dashper

first: Eric

middle: C

last: Reynolds


title: Identification of Tox chromatin binding properties and of its downstream targets by DamID

status: Public on Mar 16 2015

city: Dresden

first: Federico

last: Calegari

address: Fetscherstr. 105

department: Center for Molecular and Cellular Bioengineering (CMCB)

institute: TU Dresden

summary:
Purpose: The goal of this study was to characterize the chromatin binding features and the transcriptional target genes of a new key player during corticogenesis, the transcription factor Tox
Methods: DamID was performed using two cell lines, the Neuro-2a and the HEK-293T cells. Experiments were performed in duplicates for each cell line by infecting them with pLgwV5Eco-ToxDam lentiviruses and using the pLgxV5Dam viruses as control. DamID was performed as described in Vogel et al., 2006.
Results: Our analysis identifyed ca. 13,000 Tox chromatin binding regions

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

first: Benedetta

last: Artegiani

first: Antonio

last: de Jesus Domingues

first: Andreas

last: Dahl


title: Water limitation and rootstock genotype interact to alter grape berry metabolism through transcriptome reprogramming

first: Christian

last: Kappel

address: Karl-Liebknecht-Str. 24-25, Haus 26

department: Institut für Biochemie und Biologie

institute: Universität Potsdam

summary: Grapevine is a perennial crop often cultivated by grafting a scion cultivar on a suitable rootstock. Rootstocks influence scions, particularly with regard to water uptake and vigor. Therefore, one of the possibilities to adapt viticulture to the extended drought stress periods is to select rootstocks conferring increased tolerance to drought. However, the molecular mechanisms associated with the ability of rootstock/scion combination to influence grape berry metabolism under drought stress are still poorly understood. The transcriptomic changes induced by drought stress in grape berries (cv. Pinot noir) from vines grafted on either 110R (drought tolerant) or 125AA (drought sensitive) rootstock were compared. The experiments were conducted in the vineyard for two years and two grape berry developmental stages (50% and 100 % veraison. The genome-wide microarray approach showed that water stress strongly impacts gene expression in the berries, through ontology categories that cover cell wall metabolism, primary and secondary metabolism, signalling, stress, and hormones, and that some of these effects strongly depend on the rootstock genotype. Indeed, under drought stress, berries from vines grafted on 110R displayed a different transcriptional response compared to 125AA concerning genes related to jasmonate, phenylpropanoid metabolism and PR-proteins. The data also suggests a link between jasmonate and secondary metabolism in water-stressed berries. Overall, genes related to secondary metabolism and jasmonate are more induced and/or less repressed by drought stress in the berries grafted on the drought-sensitive rootstock 125AA. These rootstock-dependent gene expression changes are relevant for berry composition and sensory properties.

overall_design: 48 samples, three replicates for each rootstock-stage-treatment-year combination.

first: Mariam

last: Berdeja

first: Philippe

last: Nicolas

first: Zhan

middle: W

last: Dai

first: Ghislaine

last: Hilbert

first: Anthony

last: Peccoux

first: Magali

last: Lafontaine

first: Nathalie

last: Ollat

last: Gomès

first: Serge

last: Delrot


title: MiRNAs in the genomes of Bombus terrestris and Bombus impatiens

status: Public on Mar 06 2015

city: Norwich

first: Matthew

last: Beckers

state: Norfolk

address: Norwich Research Park

country: United Kingdom

institute: University of East Anglia

type: Non-coding RNA profiling by high throughput sequencing

summary: Our aims in this study were: 1) to identify the miRNAs of the bumble bees Bombus terrestris and B. impatiens; 2) to compare the total numbers of miRNAs between both bumble bee species and between them and the honey bee, Apis mellifera; and 3) to test whether the sequences and expression patterns of miRNAs were conserved between species. To investigate each of these aims we used miRNA-seq (deep sequencing of miRNA-enriched libraries) in B. terrestris, and bioinformatics prediction programs to identify miRNAs in both Bombus species. We identified 131 miRNAs in B. terrestris, and 114 in B. impatiens; of these, 17 were new miRNAs that had not previously been sequenced in any species. We found a striking level of difference in the miRNAs present between Bombus and A. mellifera, with 103 miRNAs in A. mellifera not being present in the genomes of the two bumble bees.

overall_design:
miRNA profiles of Bombus terrestris at two developmental stages in larvae.

This submission represents 'Bombus terrestris' component of study.

first: David

middle: H

last: Collins

first: Andrew

middle: F

last: Bourke

first: Tamas

last: Dalmay


title: Microarray analysis of the gene expression profile and lipid metabolism in fat-1 transgenic cattle

status: Public on Mar 10 2015

city: Hohhot

first: Xinfeng

last: Liu

address: 24 Zhaojun Road

institute: Inner Mongolia University

summary: The aim of this study was to analyze the gene expression profile and the mechanism of lipid metabolism in fat-1 transgenic cattle, and accumulate important basic data required to obtain more efficient fat-1 transgenic cattle. Using data obtained from microarray analysis, transcriptome profiling of fat-1 transgenic and wild type cattle identified differentially expressed genes involved in 90 biological pathways, eight of which were related to lipid metabolism processes, which included 36 genes related to lipid metabolism. This analysis also identified 11 significantly enriched genes that were involved in the peroxisome proliferator-activated receptor signaling pathway. These findings were verified by quantitative polymerase chain reaction. The information obtained in this study indicated that the introduction of an exogenous fat-1 gene into cattle affects the gene expression profile and the process of lipid metabolism in these animals.

overall_design: Three transgenic and three wild type cattle were selected for the microarray analysis, and then this results were validated by real-time PCR.

first: Chunling

last: Bai

first: Xiangbin

last: Ding

first: Zhuying

last: Wei

first: Hong

last: Guo

first: Guangpeng

last: Li


title: miRNA-seq expression profiling of Huntington's Disease and neurologically normal human post-mortem prefrontal cortex (BA9) brain samples

status: Public on Mar 12 2015

city: Boston

first: Richard

last: Myers

state: Massachusetts

address: 72 E Concord St, E301

department: Neurology

institute: Boston University School of Medicine

summary:
BACKGROUND MicroRNAs (miRNAs) are small non-coding RNAs that recognize sites of complementarity of target messenger RNAs, resulting in transcriptional regulation and translational repression of target genes. In Huntington’s disease (HD), a neurodegenerative disease caused by a trinucleotide repeat expansion, miRNA dyregulation has been reported, which may impact gene expression and modify the progression and severity of HD.
METHODS: We performed next-generation miRNA sequence analysis in prefrontal cortex (Brodmann Area 9) from 26 HD, 2 asymptomatic HD, and 36 control brains. Neuropathological information was available for all HD brains, including age at disease onset, CAG-repeat size, Vonsattel grade, and Hadzi-Vonsattel striatal and cortical scores, a continuous measure of the extent of neurodegeneration. Linear models were performed to examine the relationship of miRNA expression to these clinical features, and messenger RNA targets of associated miRNAs were tested for gene ontology term enrichment.
RESULTS: We identified 75 miRNAs differentially expressed in HD brain (FDR q-value <0.05). Among the HD brains, nine miRNAs were significantly associated with Vonsattel grade of neuropathological involvement and three of these, miR-10b-5p, miR-10b-3p, and miR-302a-3p, significantly related to the Hadzi-Vonsattel striatal score (a continuous measure of striatal involvement) after adjustment for CAG length.  Five miRNAs (miR-10b-5p, miR-196a-5p, miR-196b-5p, miR-10b-3p, and miR-106a-5p) were identified as having a significant relationship to CAG length-adjusted age of onset including miR-10b-5p, the mostly strongly over-expressed miRNA in HD cases. Although prefrontal cortex was the source of tissue profiled in these studies, the relationship of miR-10b-5p expression to striatal involvement in the disease was independent of cortical involvement. Correlation of miRNAs to the clinical features clustered by direction of effect and the gene targets of the observed miRNAs showed association to processes relating to nervous system development and transcriptional regulation.
CONCLUSIONS: These results demonstrate that miRNA expression in cortical BA9 provides insight into striatal involvement and support a role for these miRNAs, particularly miR-10b-5p, in HD pathogenicity. The miRNAs identified in our studies of postmortem brain tissue may be detectable in peripheral fluids and thus warrant consideration as accessible biomarkers for disease stage, rate of progression, and other important clinical characteristics of HD.

overall_design: 26 Huntington's disease, 2 asymptomatic HD gene positive and 49 neurologically normal control prefrontal cortex samples. Adapter sequence: TGGAATTCTCGGGTGCCAAGG

last: Hoss

first: Adam

last: Labadorf

first: Jeanne

last: Latourelle


title: Genome-wide analysis of translational efficiency reveals distinct but overlapping functions of yeast DEAD-box RNA helicases Ded1 and eIF4A

status: Public on Mar 02 2015

city: Bethesda

first: Alan

last: Hinnebusch

state: MD

address: 6 CENTER DR Room 230, MSC 0609

institute: NICHD

summary: DEAD-box RNA helicases eIF4A and Ded1 are believed to promote translation initiation by resolving mRNA secondary structures that impede ribosome attachment at the mRNA 5’ end or subsequent scanning of the 5’UTR, but whether they perform distinct functions or act redundantly in vivo is poorly understood. We compared the effects of mutations in Ded1 or eIF4A on global translational efficiencies (TEs) in yeast by ribosome footprint profiling. Despite similar reductions in bulk translation, inactivation of a cold-sensitive Ded1 mutant substantially reduced the TEs of >600 mRNAs, whereas inactivation of a temperature-sensitive eIF4A mutant yielded <40 similarly impaired mRNAs. The broader requirement for Ded1 did not reflect more pervasive secondary structures at low temperature, as inactivation of temperature-sensitive and cold-sensitive ded1 mutants gave highly correlated results. Interestingly, Ded1-dependent mRNAs exhibit greater than average 5’UTR length and propensity for secondary structure, implicating Ded1 in scanning though structured 5' UTRs. Reporter assays confirmed that cap- distal stem-loop insertions increase dependence on Ded1 but not eIF4A for efficient translation. While only a small fraction of mRNAs is strongly dependent on eIF4A, this dependence is significantly correlated with requirements for Ded1 and 5’UTR features characteristic of Ded1- dependent mRNAs. Our findings suggest that Ded1 is critically required to promote scanning through secondary structures within 5’UTRs; and while eIF4A cooperates with Ded1 in this function, it also promotes a step of initiation common to virtually all yeast mRNAs.

overall_design: We compared the effects of mutations in Ded1 or eIF4A on global translational efficiencies (TEs) in yeast by ribosome footprint profiling.The study includes 32 samples, comprised of 16 mRNA-Seq samples and 16 ribosome footprint profiling samples, derived from biological replicates of 3 mutant strains, ded1-cs, ded1-ts and tif1-ts, and the corresponding wild-type strains. The tif1-ts mutant and its wild-type counterpart were analyzed at 30°C and 37°C.

first: Neelam

last: Sen

first: Fujun

last: Zhou

first: Nicholas

last: Ingolia


title: microRNA expression signatures for human primary NK cells

status: Public on Feb 27 2015

city: Hefei

first: Fang

last: Ni

address: Huang shan Road

institute: University of Science and Technology of China

summary: We examined miRNA profiles of human NK cells from different cell compartments (peripheral blood, cord blood, and uterine deciduas) and of NKT and T cells from peripheral blood, and identified distinct classes of up-regulated microRNAs in different human NK cells.

overall_design: For the microarray assay, RNAs from 6 donors with equal amount were pooled together to get each cell sample.


title: Gene expression profile in myeloproliferative neoplasms

status: Public on Mar 14 2015

city: Belgrade

first: Vladan

middle: Predrag

last: Cokic

address: Dr Subotica 4

country: Serbia

institute: Institute for Medical Research

summary: Myeloproliferative neoplasms (MPN) are clonal hematopoietic diseases that include essential thrombocytosis (ET), polycythemia vera (PV) and primary myelofibrosis (PMF) as well as BCR-ABL+ chronic myelogenous leukemia (CML). In the past several years, studies with cDNA microarrays have defined patterns of gene expression corresponding to specific molecular abnormalities, oncologic phenotypes, and clinical outcomes in hematologic malignancies. This study was aimed at the description of a gene expression signature in MPN which would eventually present a new pathogenetic approaching and also diagnostic as well as prognostic information. Using cDNA microarray analysis, involving 25,100 unique genes, we studied the gene expression profile of the pluripotent hematopoietic CD34+ stem cells and mature granulocytes obtained from peripheral blood of ET, PV, PMF and CML patients compared with healthy individuals. The average number of CD34+ cells (cells/µl) in peripheral blood was approximately 6 in PV and ET, 111 in PMF and 2880 in CML as measured by flow cytometry. A somatic point mutation JAK2V617F was detected in 93% of PV, 73% of PMF and 55% of ET patients within genetically homogenous population. The homozigosity for JAK2V617F mutation was the highest in PV (60%), less prominent in PMF (42%) and low in ET (11%) patients. The JAK2V617F mutation negative patients were also negative for exon 12 mutations. Approximately 420, 680 and 1130 genes had unique expression among CD34+ cells of ET, PV and PMF patients, respectively. In addition comparing to healthy controls, ET, PV, PMF and CML patients showed difference in 840, 1180, 1160 and 2050 expressed genes, respectively.  Furthermore, we studied EPO and JAK-STAT signaling pathways related genes expression in MPN. The FOS, RAF1 and JAK2 gene expression, related to EPO signaling pathway, was elevated in ET, PV, PMF and reduced in CML comparing to healthy controls. Related to these genes, the JAK2V617F mutation homozygous and heterozygous patients generally displayed more significant differences comparing to patients with no mutation. STAT5 gene expression was decreased in all MPN patients. CSF3R, STAT1 and STAT3 gene expression, related to JAK-STAT signaling pathway, was elevated in ET, PV, PMF and reduced in CML comparing to healthy controls. CREBBP gene expression was reduced in CD34+ cells of ET, PV and PMF patients, but during maturation it enhanced expression in granulocytes.  In conclusion, molecular profiling of CD34+ cells and granulocytes revealed a certain number of genes with changed expression that, beyond their recognized function in disease pathogenesis, can be related to patients’ clinical characteristics and may have an imminent prognostic relevance.

overall_design: All study de novo patients were subjects to 30 ml of peripheral blood draw on one occasion, collected in 10% sodium citrate. The maximum time interval between venepuncture and arrival in the laboratory was 2 hours. Each 30 ml of diluted lymphocytes and other mononuclear cells (1:1,2 with Ca2+/Mg2+-free PBS) was then layered gently on top of 15 ml lymphocyte separation medium (LSM, PAA Laboratories GmbH, Pasching, Austria). After centrifugation (400g, 30 min, 20C), the interface of containing mononuclear cells was collected and washed with PBS. The CD34+ progenitor cells were isolated from the collected mononuclear cells using a magnetic separation column (Super Macs II, Miltenyi Biotec, Bergisch Gladbach, Germany) and a mixture of magnetic microbeads conjugated with antibody against CD34 (Miltenyi Biotec) according to the manufacturer's instructions. The pellet which is formed, during centrifugation with LSM, is comprised mostly of erythrocytes and granulocytes that migrated through the gradient. Contaminating erythrocytes were removed by using lysing solution (0.15 M NH4Cl,  0.1 mM Na2EDTA, 12 mM NaHCO3). High quality of purified granulocytes was confirmed by cytospin preparations and Wright–Giemsa staining. The viable CD34+ cell and granulocyte counts were performed with the use of a trypan-blue exclusion technique (BioWhittaker). The purity of recovered cells was determined by flow cytometry using PE–anti-CD34 mAb (BD Biosciences, San Jose, CA, USA) and was over 80% in samples for microarray analysis. Karyotype analysis did not show any chromosome aberrations in samples for microarray analysis.

middle: P

first: Raj

last: Puri

first: Jing

last: Han


title: Transcriptional profiling of host gene expression in chicken embryo fibroblasts infected with Reticuloendotheliosis virus strain HA1101

city: Yangzhou

first: Ji

last: Miao

state: Jiangsu

address: No.12, Wenhui East Road

department: College of Veterinary Medicine

institute: Yangzhou University

summary: Reticuloendotheliosis virus (REV), a member of the Gammaretrovirus genus in the Retroviridae family, causes an immunosuppressive, oncogenic and runting-stunting syndrome in multiple avian hosts. To better understand the host interactions at the transcriptional level, microarray data analysis was performed in chicken embryo fibroblast (CEF) cells at 1, 3, 5, and 7 days after infection with REV. This study identified numerous differentially expressed genes that were classified into several functional groups. Significant differences were mainly observed in the expression of genes involved in the immune response, especially during the later post-infection time points. These results revealed that differentially expressed genes play important roles in the pathogenicity of REV infection. Our study is the first to use microarray analysis to investigate REV, and these findings provide insights into the underlying mechanisms of the host antiviral response and the molecular basis of viral pathogenesis.

overall_design: Infection of Reticuloendotheliosis virus induced gene expression in chicken fibroblasts was measured at 1, 3, 5, and 7 days post-infection after exposure to a multiplicity of infection of 1.  Both infection group and non-infection group experiments were performed for 3 independent replicates at each time point.

first: Aijian

last: Qin


title: RNA-seq Analysis Identifies New Genes Regulated by the Histone-like Nucleoid Structuring Protein (H-NS) Affecting Vibrio cholerae Virulence, Stress Response and Chemotaxis

status: Public on Feb 16 2015

city: Atlanta

first: Julio

middle: C.

last: Ayala

state: Georgia

address: 1600 Clifton Rd NE Rm 3-642

department: Division of STD Prevention

institute: Centers for Disease Control and Prevention

summary: Cholera is a diarrheal disease caused by Vibrio cholerae of serogroups O1 and O139 that affects impoverished populations worldwide. The histone-like nucleoid structuring protein (H-NS) is a global regulator of environmentally-regulated gene expression that plays a fundamental role in V. cholerae adaptation to disparate ecological niches. We used RNA-seq to characterize the hns transcriptome of El Tor biotype V. cholerae. H-NS affected the expression of 18% of all predicted genes in a growth phase-dependent manner. It silenced the transcription of genes encoding virulence regulators and cytotoxic factors such as the VieSAB regulatory system, the repeat in toxin (RTX) and hemolysin. H-NS was 10 times more effective in silencing the vieSAB promoter in El Tor compared to classical biotype V. cholerae. In the El Tor biotype hns mutant, VieSAB significantly enhanced the expression of cholera toxin genes.  For the RTX and hemolysin, we found that overexpression of the transcription activator HlyU diminished H-NS occupancy at the hlyA promoter but not at the rtxCA and rtxBDE promoters. H-NS had a significant impact on the cell envelope and the mutant expressed elevated rpoE encoding the extracytoplamic sigma factor E (sE), though this effect was indirect. A remarkable feature of the hns transcriptome was the down-regulation of numerous methyl-accepting chemotaxis proteins in early stationary phase that translated into diminished chemotaxis toward the amino acids glycine and serine. Our study suggests that H-NS transcriptional silencing can contribute to multiple phenotypic differences observed between V. cholerae biotypes, mainly by differentially repressing the VieSAB sensory pathway.

overall_design: Transcriptome profiles of wild type and Δhns mutant cells of the V. cholerae strain C7258 grown in LB medium were generated by Next Generation Sequencing using the Illumina HiSeq2000 platform. Samples from mid-exponential phase (OD600 0.5) and early stationary phase (OD600 2.0) were analyzed in duplicate

first: Hongxia

last: Wang

first: Jorge

middle: A

last: Benitez

first: Anisia

middle: J

last: Silva


title: Elucidating the Sigmulome of P.aeruginosa PA14 by ChIP-Seq and RNA-Seq approaches

status: Public on Feb 12 2015

city: Braunschweig

first: Denitsa

last: Eckweiler

state: Lower Saxony

address: Spielmannstr. 7

department: Institute of Microbiology

institute: Technische Universität Braunschweig

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

overall_design: Refer to individual Series


title: Intratracheally Instilled Titanium Dioxide Nanoparticles Translocate to Heart and liver and Activate Complement Cascade in the Heart of C57BL/6 Mice (Heart)

city: Ottawa

first: Mainul

last: Husain

address: 50 Colombine Driveway

institute: Health Canada

summary:
An estimated 1% or less of the nanoparticles (NPs) deposited in lungs translocate to systemic circulation and enter other organs; however this estimation may not be accurate considering the low sensitivity of the existing in vivo NP detection methods. Moreover, the biological outcomes of such low levels of translocation are not elucidated. The objectives of the present study were to employ a Nano-scale Hyperspectral Microscope to spatially observe and spectrally profile NPs in tissues, and characterize the effects of NPs in blood, liver and heart following pulmonary deposition and subsequent translocation from lungs. Adult female C57BL/6 mice were exposed via intratracheal instillation to 18 and 162 µg per mouse of industrially relevant non-doped titanium dioxide nanoparticles (nano-TiO2). Using the Nano-scale Hyperspectral Microscope translocation to heart and liver was confirmed at both doses and to blood at the highest dose at 24 hours post-exposure time-point. The analysis of biological effects using DNA microarrays, RT-qPCR and ELISA revealed activation of complement cascade and inflammatory process in heart and specific activation of complement factor 3 in blood, potentially suggestive of activation of early innate immune response essential for particle opsonisation and clearance. The liver showed subtle response with changes in the expression of few genes associated with acute phase genes. This study establishes a direct link between particle translocation and systemic effects.
An estimated 1% or less of the nanoparticles (NPs) deposited in lungs translocate to systemic circulation and enter other organs; however this estimation may not be accurate considering the low sensitivity of the existing in vivo NP detection methods. Moreover, the biological outcomes of such low levels of translocation are not elucidated. The objectives of the present study were to employ a Nano-scale Hyperspectral Microscope to spatially observe and spectrally profile NPs in tissues, and characterize the effects of NPs in blood, liver and heart following pulmonary deposition and subsequent translocation from lungs. Adult female C57BL/6 mice were exposed via intratracheal instillation to 18 and 162 µg per mouse of industrially relevant non-doped titanium dioxide nanoparticles (nano-TiO2). Using the Nano-scale Hyperspectral Microscope translocation to heart and liver was confirmed at both doses and to blood at the highest dose at 24 hours post-exposure time-point. The analysis of biological effects using DNA microarrays, RT-qPCR and ELISA revealed activation of complement cascade and inflammatory process in heart and specific activation of complement factor 3 in blood, potentially suggestive of activation of early innate immune response essential for particle opsonisation and clearance. The liver showed subtle response with changes in the expression of few genes associated with acute phase genes. This study establishes a direct link between particle translocation and systemic effects.

overall_design: This experiment consists of one dose of nano-TiO2 (162 ug) and one control. There are 2 time points for each treatment and control group, e.g., day 1 and day 28. Each dose or time point has 5-6 biological replicates. There are total 22 samples (arrays)

first: Pallavi

last: Gupta

first: Dongmei

last: Wu

first: A

last: Saber

first: N

middle: R

last: Jacobsen

first: Andrew

last: Williams

first: Carole

last: Yauk

first: H

last: Wallin

first: U

last: Vogel

first: Sabina

last: Halappanavar


title: Effects of GDM involves alterations in gene specific DNA methylation

status: Public on Feb 10 2015

city: beijing

first: Huixia

last: Yang

address: No.8 xishiku street,Xicheng District

institute: Peking Unversity First Hospital

summary: Gestational diabetes mellitus(GDM) will bring health issues for offspring. The offspring of diabetic mothers often reveal high birth weight and are prone to have obesity, hypertension and dyslipidemia. It was implied that the phenotype of offspring might be influenced by intrauterine environment and planned in utero already in addition to the genetic influences.‘Programming’ refers to the process whereby a stimulus at a critical window of development has long-term effects. A large body of studies investigated the adverse intrauterine environment was correlated with poor fetal growth and increased risk of Type 2 diabetes in the adulthood. Epigenetic mechanism has been proposed to involve in the link between environmental and nutritional factors and gene expression regulation. DNA methylation is one of the major epigenetic modifications. We hypothesized that DNA methylation changes could participate in the gene expression related to glucose intolerance in the offspring. Furthermore, DNA methylation might also determine the transgenerational disease transmission.

overall_design: comparison of intrauterine hyperglycemia exposed rats vs. control rats for genome-wide DNA methylation changes

first: Rina

last: Su

first: Jie

last: Yan


title: Intratracheally Instilled Titanium Dioxide Nanoparticles Translocate to Heart and liver and Activate Complement Cascade in the Heart of C57BL/6 Mice (Liver)


title: Imporatance of substantial weight loss for altering gene expression during intensive cardiovascular lifestyle modification

status: Public on Feb 21 2015

city: Windber

first: Darrell

last: Ellsworth

address: 620 Seventh St.

institute: Windber Research Institute

summary:
The objective of this study was to examine relationships between weight loss through changes in lifestyle and peripheral blood gene expression profiles. Substantial weight loss (-15.2+3.8%) in lifestyle participants was associated with improvement in selected cardiovascular risk factors and significant changes in peripheral blood gene expression from pre- to post-intervention: 132 unique genes showed significant expression changes related to immune function and inflammatory responses involving endothelial activation.
In contrast, participants losing minimal weight (-3.1+2.5%) showed only minor changes in cardiovascular risk factors and markers of inflammation, and no changes in gene expression compared to non-intervention controls after 1 year. Weight loss (>10%) during lifestyle modification is associated with down-regulation of genetic pathways governing interactions between circulating immune cells and the vascular endothelium and may be required to successfully reduce CVD risk.

overall_design: A prospective nonrandomized trail was conducted over 1 year in participants undergoing intensive lifestyle modification to reverse or stabilize progression of coronary artery disease. Cardiovascular risk factors, inflammatory biomarkers, and gene expression as a function of weight loss were assessed in 89 lifestyle participants and 71 retrospectively matched controls undergoing usual care.

first: Kimberly

last: Mamula

first: Heather

last: Blackburn

first: Fionnuala

last: McDyer

first: Gera

last: Jellema

first: Ryan

last: van Laar

first: Nicholas

middle: S

last: Costantino

first: Renata

last: Engler

first: Marina

middle: N

last: Vernalis


title: Comparative transcriptome profiles of cotton (G. hirsutum L. cv. Bikaneri narma) during boll development stages under bollworm infested biotic stress

status: Public on Mar 01 2015

city: New Delhi

first: Mogilicherla

last: Kanakachari

state: Delhi

address: LBS Building, PUSA Campus

department: Molecular Biology and Biotechnology

country: India

institute: National Research Centre on Plant Biotechnology

summary:
Comparative transcriptome profiles of cotton (G. hirsutum L. cv. Bikaneri narma) during boll development stages (0, 2, 5 and 10 dpa) under bollworm infested biotic stress.
Cotton is one of the most commercially important fibre crops in the world and used as a source for natural textile fibre and cottonseed oil. The biotic stress is one of the major constraints for crop production. Cotton bollworm (Helicoverpa armigera) is one the major insect pest in cotton and drastically damages the cotton boll. To decipher the molecular mechanisms involved in cotton boll/fibre cell development, transcriptome analysis has been carried out by comparing G. hirsutum L cv. Bikaneri narma cotton boll samples induced by biotic stress (bollworm infested) and that their respective control cotton bolls collected under field conditions. Cotton bolls were collected at fibre initiation (0, 2 dpa/days post anthesis) and elongation (5, 10 dpa) stages for both control and biotic stress condition and gene expression profiles were analyzed by Affymetrix cotton GeneChip Genome array.

platform_organism:
Gossypium barbadense
Gossypium hirsutum
Gossypium arboreum
Gossypium raimondii

overall_design: Cotton plants (G. hirsutum L. cv. Bikaneri narma) were grown under field condition. Helicoverpa armigera (cotton bollworm) second instar larvae was released at the time of flower opening and covered with polythene bag to prevent insect escape and tagged. The infested flowers were collected after 8 hrs infestations and labeled as 0 dpa. Likewise after two and five day’s infestation the bolls were collected and labelled as 2 and 5 dpa, respectively.  After five days the insect was removed from bolls and left the bolls for up to 10 days and collected then labeled as 10 dpa. Meanwhile respective control samples also tagged and collected. Total RNA was isolated from control (WT) and biotic stress (bollworm infested) induced samples collected at 0, 2, 5 and 10 dpa boll development stages using SpectrumTM Plant Total RNA kit (Sigma, USA) according to the manufacturer’s protocol. Affymetrix cotton GeneChip Genome array (Affymetrix, USA) having 23,977 probe sets representing 21,854 cotton transcripts was used for transcriptome analysis. Three biological replicates were maintained to test the reproducibility and quality of the chip hybridization. cDNA labeling, array hybridization, staining and washing procedures were carried out as described in the Affymetrix protocols. CEL files having estimated probe intensity values were analyzed with GeneSpring GX-11.5 software (Agilent Technologies, USA) to get differentially expressed transcripts. The Robust Multiarray Average (RMA) algorithm was used for the back ground correction, quantile normalization and median polished probe set summarization to generate single expression value for each probe set. Normalized expression values were log2 transformed and differential expression analysis was performed using unpaired t-test. The p-values were corrected by applying the false discovery rate (FDR) correction (Benjamini and Hochberg, 2000).

first: M

first: G

last: Dhandapani

first: K

middle: V

last: Padmalatha

last: Savitha

first: N

last: Prabhakaran

first: V

last: Mishra

last: Vamadevaiah

first: IS

last: Katageri

last: Reddy

first: A

middle: U

last: Solanke

first: P

last: Kumar


title: Analysis of sigma factor-dependent gene expression in Pseudomonas aeruginosa by RNA sequencing

first: Denitsa

last: Eckweiler

summary: Sigma factors are master regulators of bacterial transcription which direct gene expression of specific subsets of genes. In particular, alternative sigma factors are well-known to be key players of bacterial adaptation to changing environments. To elucidate the regulatory network of sigma factors in P. aeruginosa, an integrative approach including sigma factor-dependent mRNA profiling was performed to define the primary regulon of each sigma factor.

overall_design: Sigma factor hyper-expressing strains harboring the sigma factor gene in trans under control of the araBAD promoter and sigma factor deletion mutants were constructed. Under optimal conditions regarding sigma factor activity and optional induction of sigma factor expression, bacteria were harvested and total RNA was extracted. Upon mRNA enrichment, RNA was fragmented and ligated to specific RNA-adapters containing a hexameric barcode sequence for multiplexing. These RNA-libraries were reverse transcribed and amplified resulting in cDNA libraries which were sequenced on Illumina platforms. Sequence reads were separated according to their barcodes and barcode sequences were removed. The short reads were mapped to the genome sequence of the reference strain P. aeruginosa PA14 wild-type using stampy with default settings. The R package DESeq was used for differential gene expression analysis.

first: Sebastian

last: Schulz

first: Susanne

last: Häussler


title: Genome-wide analysis of kainic acid-induced gene expression in dentate gyrus from CTR and SRF knockout mice.

status: Public on Feb 02 2015

city: Krakow

first: Marcin

last: Piechota

address: Smetna 12

department: Molecular Neuropharmacology

country: Poland

institute: Institute of Pharmacology PAS

summary: To identify genes regulated by SRF in response to increased neuronal activity whole-genome expression profiling (Illumina Mouse WG-6 microarrays) of kainic acid-induced genes were performed. We found that loss of SRF in DG leads to specific deficits in activity-induced gene expression. Identified genes functions are associated with synapse plasticity, epilepsy, outgrowth of neurites, behavior and MAPK signaling pathway.

overall_design: The microarray experiment was performed to identify SRF-dependent activity-induced genes, using brain-specific, inducible SRF gene knockout mice. Conditional mutants of Srf were obtained by crossing mice in which Srf gene was flanked by loxP sites (Srf f/f) with an CaMKCreERT2 line to ablate its expression exclusively in excitatory forebrain neurons.  Knockouts (KO = Srf f/f;CaMKCreERT2) and control littermates (CTR = Srf f/f) were used in the experiments. To enable time-specific induction of SRF deletion, adult mice, were injected with tamoxifen. Global gene expression induced by kainic acid (KA, 35-50 mg/kg) was analyzed. At 6 hours after seizures induction (seizures severity 5; according to modified Racine scale) or saline injection, CTR and KO animals were sacrificed and dentate gyrus was microdissected and used for RNA isolation. In order to identify SRF-regulated genes, we used Illumina MouseWG-6 v2.0 Expression BeadChips.

first: Bozena

last: Kuzniewska

first: Leszek

last: Kaczmarek

first: Katarzyna

last: Kalita


title: ChIP-seq study of sigma factors in Pseudomonas aeruginosa

summary: Sigma factors are master regulators of bacterial transcription which direct gene expression of specific subsets of genes. In particular, alternative sigma factors are well-known to be key players of bacterial adaptation to changing environments. To elucidate the regulatory network of sigma factors in P. aeruginosa, an integrative approach including ChIP-seq of 11 polyhistidine-tag sigma factors was performed to define the primary regulon of each sigma factor.

overall_design: Sigma factor genes were fused to a polyhistidine-tag and provided in trans. Under optimal conditions regarding sigma factor activity and induction of sigma factor expression, DNA-sigma factor interactions were conserved by formaldehyde treatment. Upon DNA fragmentation by sonication, the complexes were specifically immunoprecipitated by polyclonal anti-6X His-tag antibodies and the purified DNA was analyzed by Illumina sequencing. DNA enrichment to a control strain was calculated and used for peak calling within promoter region (-500,+100) to identify directly regulated genes/operons.


title: Genome wide binding and expression profiling defines a Bapx1-Sox9 axis in vertebral column, Gut, Spleen and limbs in developing mouse embryo.

city: Potsdam

first: Thomas

last: Lufkin

address: 8 Clarkson Avenue

institute: Clarkson University


title: Transient Pairing of Homologous Oct4 Alleles Accompanies the Onset of Embryonic Stem Cell Differentiation

status: Public on Feb 03 2015

city: Cold Spring Harbor

first: Cinthya

last: Zepeda-Mendoza

address: 1 Bungtown Road

institute: Cold Spring Harbor Laboratory

summary: The relationship between chromatin organization and transcriptional regulation is an area of intense investigation. We have characterized the spatial relationships between alleles of the Oct4, Sox2, and Nanog genes in single cells during the earliest stages of mouse embryonic stem cell (ESC) differentiation and during embryonic development. We describe homologous pairing of the Oct4 alleles during ESC differentiation and embryogenesis, and present evidence that pairing is correlated with the kinetics of ESC differentiation. Importantly, we identify critical DNA elements within the Oct4 promoter/enhancer region that mediate pairing of Oct4 alleles. Finally, we show that mutation of OCT4/SOX2 binding sites within this region abolishes inter-chromosomal interactions and affects accumulation of the repressive H3K9me2 modification at the Oct4 enhancer. Our findings demonstrate that chromatin organization and transcriptional programs are intimately connected in ESCs, and that the dynamic positioning of the Oct4 alleles is associated with the transition from pluripotency to lineage specification.

overall_design: Examination of chromatin contacts between Oct4 alleles using PE-4Cseq

first: Megan

last: Hogan

last: Zepeda Mendoza

first: David

middle: L

last: Spector


title: human hTERT-RPE1 cell spheroid : Control siRNA transfected vs. YAP1 siRNA transfected

status: Public on Feb 01 2015

city: Kamakura

first: Satoshi

last: Kondo

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

summary: Transcriptional profiling of human hTERT-RPE1 cell spheroids comparing Control siRNA transfected hTERT-RPE1 cell spheroids with those transfected with YAP1 siRNA.

overall_design: Two-condition experiment, Control siRNA vs.YAP1 siRNA hTERT-RPE1 cell spheroids. Biological replicates: 1 Control siRNA, 1YAP1 siRNA transfected, independently  grown and harvested. Bothreplicates per array.

first: Tatsuo

last: Miyamoto

first: Makoto

last: Furutani-Seiki


title: Transcriptional profiling of cutaneous Mrgprd free nerve endings and C-LTMRs

city: Marseille

first: Ana

last: Reynders

address: Parc Scientifique de Luminy, 163 Avenue de Luminy

country: France

institute: IBDM

summary: Cutaneous C-unmyelinated free nerve endings and hair follicles-innervating C-LTMRs convey two opposite aspects of touch sensation: a sensation of pain and a sensation of pleasant touch. The molecular mechanisms underlying these diametrically opposite functions are unknown. Here we used a mouse model that genetically marks C-LTMRs and the free nerve endings MRGPRD+ neurons in combination with fluorescent cell surface labeling, flow cytometry and RNA deep-sequencing technology. Cluster analysis of the RNA-Seq profiles of the purified neuronal subsets revealed 156 and 184 genes differentially expressed in MRGPRD-expressing neurons and C-LTMRs, respectively. 48 MRGPD- and 67 C-LTMRs-enriched genes were validated using a triple staining experiment approach and the Cav3.3 channel, found to be exclusively expressed in C-LTMRs, was validated using electrophysiology. Furthermore, our study greatly expands the molecular characterization of C-LTMRs and suggests that this particular population of neurons shares common transcriptional signatures with A and A low threshold mechanoreceptors.

overall_design: RNA profiles of FACS-sorted subsets of sensory neurons, namely Mrgprd+ neurons (DP, double-positive=IB4+GINIP+), C-LTMRs (IB4-GINIP+) and remaining cells (DN, double-negative=IB4-GINIP-) were generated by deep sequencing in duplicate using Illumina HiSeq 2000.

first: Annabelle

last: Mantilleri

first: Pascale

last: Malapert

first: Stéphanie

last: Rialle

first: Sophie

last: Lafrey

first: Corinne

last: Beurrier

first: Emmanuel

last: Bourinet

first: Aziz

last: Moqrich

first: Sabine

last: Nidelet


title: RNA-seq and Microarray in Transcriptome Profiling of Anterior Cruciate Ligament Tears: Implications for Prognostic Biomarkers Discovery

status: Public on Jan 30 2015

city: St. Louis

first: Muhammad Farooq

last: Rai

address: 660 S. Euclid Ave.

department: Orthopaedic Surgery

institute: Washington University School of Medicine

summary: Injury to anterior cruciate ligament (ACL) is common in young individuals and a frequent cause of functional instability and early onset of osteoarthritis. The healing potential of an injured ACL is known to decay over time. The molecular origin of this healing deficiency largely remains elusive but plausibly involves gene transcripts associated with tissue healing. To explore this possibility, we set out to identify transcript expression differences in injured ACL remnants recovered at the time of surgical reconstruction, via microarray (n=24) and RNA-seq (n=8) technologies in transcriptome profiling. We found that time-from-injury was an important determinant of changes in gene expression signatures predominately resulting in repression of several biological processes as identified by gene ontology. The most interesting observation was a time-dependent decline in the gene transcripts as well as the biological processes common to both microarray and RNA-seq analyses. Compared to acute tears, in chronic several important biological processes were namely extracellular matrix organization, angiogenesis, cell adhesion, wound healing, mesenchyme transition, and response to hypoxia. Furthermore, the cross-platform concordance in terms of differentially expressed transcripts or enriched pathways was linearly correlated (r=0.64). Microfluidic digital PCR confirmed the expression of selected differentially expressed transcripts. These intriguing findings suggest an initial attempt of the injured ACL to repair, which drops with time. These findings have implications for efforts to repair the ACL and may be relevant for its reconstruction. These findings also emphasize the utility of differentially expressed transcripts as prognostic biomarkers in patients with ACL injury.

overall_design: Examination of transcript expression differences by time-from-injury in anterior cruciate ligament

first: Muhammad

first: Eric

middle: D

last: Tycksen

first: Robert

last: Brophy

first: Linda

last: Sandell


title: Inhaled Ozone (O3)-Induces Changes in Serum Metabolomic and Liver Transcriptomic Profiles in Rats

status: Public on Jan 31 2015

city: Durham

first: William

last: Ward

state: NC

address: 109 TW Alexander Dr

department: NHEERL

institute: United States EPA

summary: Long-term exposure to particulate air pollutants has been linked to increased incidence of Type 2 Diabetes (T2DM). Recently, we showed that the gaseous pollutant, O3, induced glucose intolerance, and increased serum leptin and epinephrine in Brown Norway rats. In this study, we hypothesized that O3 exposure will cause broad scale changes in metabolic homeostasis involving liver, muscle and adipose tissues, and that serum metabolomic and liver transcriptomic profiling will provide mechanistic insights into pollutant-induced metabolic alterations. In the first experiment, male Wistar Kyoto (WKY) rats were exposed to filtered air (FA) or O3 at 0.25, 0.50, or 1.00 ppm, 6h/day for two consecutive days to establish concentration-related effects on glucose tolerance and lung injury. In a second experiment, rats were exposed to FA or 1.0 ppm O3, 6h/day for either one day or two consecutive days and systemic metabolic responses were determined immediately after each exposure or after an 18h recovery period. In WKY rats, O3 increased serum fasting glucose and leptin on day 1. Glucose intolerance persisted through two days of exposure but reversed 18h post second exposure. O3 exposure increased circulating metabolites of glycolysis, long-chain free  fatty acids, branched chain amino acids (BCAA) and cholesterol while 1,5- anhydroglucitol, bile acids and metabolites of TCA cycle were decreased, indicating impaired glycemic control, muscle proteolysis and adipose lipolysis. Liver gene expression profile after O3 exposure reflected a response to the serum metabolite changes, as evidenced by increased expression of genes for glycolysis, TCA cycle and gluconeogenesis, and decreased expression of genes involved in steroid and fat biosynthesis. In conclusion, short-term O3 exposure induced hormonal changes and  global metabolic disorder reflective of changes in peripheral glucose, lipid, and amino acid metabolism, representative of a stress-response. It remains to be examined if these metabolic alterations contribute to insulin resistance upon chronic exposure.

overall_design: Rats were exposed to filtered air (FA) or Ozone at 1 ppm, 6h/day for two consecutive days to establish ozone-exposure related effects on transcriptomic profiles.  Samples were taken at three time points: 1 day (1day0hrs) - at the end of the 6 hour exposure period, 2 days (2day0hrs) - at the end of the of the second day 6 hour exposure period) and 2 days 18 hours (2day18hrs) - 18 hours after the 6 hour exposure period on the second day.  Total liver RNA was isolated from ~20 mg tissue with a commercially available RNeasy mini kit (Qiagen, Valencia, CA) using silica gel membrane purification.  Liver RNA was resuspended in 30μl of RNAse- free water.  RNAse inhibitor was added and RNA yield was determined spectrophotometrically on a NanoDrop 1000 (Thermo Scientific, Wilmington, DE). RNA integrity was assessed by the RNA 6000 LabChip® kit using a 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA). We examined global gene expression changes using the Affymetrix platform (RG- 230 PM Array strip). Biotin-labeled cRNA was produced from total RNA using an Affymetrix “IVT-express labeling kit “(cat# 901229).

first: Desinia

middle: B

last: Miller

first: Ed

last: Karoly

first: Jan

last: Jones

middle: O

first: Beena

last: Vallanat

first: Debora

last: Andrews

first: Mette

last: Schladweiler

first: Virginia

last: Bass

first: Andrew

last: Ghio

first: Wayne

middle: E

last: Cascio

first: Allen

last: Ledbetter

first: Urmila

last: Kodavanti


title: Dynamics of the human skeletal muscle transcriptome in response to exercise training - part 1

status: Public on Jan 21 2015

city: Solna

first: Joakim

last: Lundeberg

address: Tomtebodavägen 23A

department: Gene Technology

country: Sweden

institute: KTH-Science for Life Laboratory

summary: A total of 23 participants (data available in present submission and in GSE58608) completed three months of supervised aerobic exercise training of one leg. Skeletal muscle biopsies have been collected before and after the training period. We have investigated differences between trained and untrained leg and before and after training by studying the gene and isoform expression. Additional samples present in this study has been previously published (GEO accession number GSE58608).

overall_design: Analysis of transcriptome in skeletal muscle biopsy samples in response to exercise training in 22 participants (of the total 23 participants). One biopsy is collected from each leg before and after training period.

first: Beata

middle: W

last: Solnestam

first: Maléne

last: Lindholm

first: Stefania

last: Giacomello

first: Mikael

last: Huss

first: Sanela

last: Kjellkvist

first: Carl

last: Sundberg


title: Common Irf-regulated genomic responses drive pathological inflammation during experimental cerebral malaria as well as protective response against M. tuberculosis

status: Public on Jan 16 2015

city: Bar Harbor

first: Joanne

last: Berghout

state: ME

address: 600 Main St

department: Mouse Genome Informatics

institute: The Jackson Laboratory

summary:
Analysis of transcriptional response to Plasmodium berghei ANKA infection in cerebral malaria susceptible C57BL/6 mouse brains as well as cerebral malaria resistant BXH2 mice which carry a severe hypomorphic Irf8-R294C allele.
Interferon Regulatory Factor 8 (IRF8) is required for development, maturation and expression of anti-microbial defenses of myeloid cells. BXH2 mice harbor a loss-of-function allele at Irf8 (Irf8-R294C) that causes susceptibility to infection with intracellular pathogens, including Mycobacterium tuberculosis. We report that XH2 are completely resistant to the development of cerebral malaria following Plasmodium berghei ANKA infection. Comparative transcriptional profiling of brain RNA as well as chromatin immunoprecipitation and high-throughput sequencing (ChIP-seq) was used to identify IRF8-regulated genes whose expression is associated with pathological acute neuroinflammation. Genes up-regulated by infection were strongly enriched for IRF8 binding sites, suggesting that IRF8 acts as a transcriptional activator in inflammatory programs. These lists were enriched for myeloid-specific pathways, including interferon responses, antigen presentation and Th1 polarizing cytokines. We show that inactivation of several of these downstream target genes confers protection against experimental cerebral malaria. We also report strong overlap between genes bound and regulated by IRF8 during cerebral malaria and genes regulated in the lungs of M. tuberculosis infected mice. This IRF8-dependent network contains several genes recently identified as risk factors in acute and chronic human inflammatory conditions. In summary, this work defines a common core of IRF8-bound genes forming a critical inflammatory host-response network.

overall_design:
Comparison of whole brain transcript profiles for wildype C57BL/6 mice versus severely hypomorphic Irf8-R294C BXH2 mice following experimental infection with Plasmodium berghei ANKA (d7). Baseline (d0) profiles are also compared.

Pleaes note that each sample record represents  2-4 replicates and sample data table contains mean, standard error of the mean (SEM), and quality for the replicates. The non_normalized data matrix contains raw data for each replicate (total 12 samples).

first: David

last: Langlais

first: Irena

last: Radovanovic

first: Mifong

last: Tam

first: John

last: MacMicking

first: Mary

middle: M

last: Stevenson

first: Philippe

last: Gros


title: Tet-mediated imprinting erasure following reprogramming of spermatogonial stem cells to induced pluripotent stem cells

status: Public on Jan 12 2015

city: College Park

first: Bhanu Prakash

last: Telugu

address: 2121 ANSC Lab

department: Animal and Avian Sciences

institute: University of Maryland

summary: We sequenced mRNA from three preparations each of murine Gfra1+ spermatogonial stem cells (SSC), SSC- derived SSEA1+ induced pluripotent stem cells (iPSC), and fibroblast (skin derived mesenchymal cells) derived SSEA1+ iPSC

overall_design: Examination of mRNA levels in SSC and SSC derived iPSC and compared with fibroblast derived iPSC.

first: Bhanu

first: Pablo

last: Bermejo-Alvarez


title: Gene expression analysis of liver and colon cancer primary tumors and metastasis

status: Public on Jan 22 2015

city: Bethesda

first: Xin

middle: Wei

last: Wang

address: 37 Convent Drive

department: Laboratory of Human Carcinogenesis

institute: National Cancer Institute

summary: Enriched tumor epithelium from 61 primary and metastasis tumor specimens was obtained by laser capture microdissection (LCM) as previously described (Boersma et al., 2007).  In brief, frozen 8-μm serial sections from OCT-preserved frozen tissues were prepared and mounted on plain, uncharged microscope slides.  One Hematoxylin/eosin-stained section of each specimen was reviewed by a pathologist to confirm diagnosis and presence of tumor.  The pathologist indicated which representative sections of the tumors should be microdissected.  LCM was performed with the Pixcell II LCM system (Arcturus, Mountain View, CA).  Total RNA was isolated using the PicoPure protocol (Arcturus, Mountain View, CA).  The mRNA was amplified with two linear amplification steps by in vitro transcription using the MEGAscript T7 kit (Ambion, Austin, TX) followed by the labeling step using the BioArray HighYield RNA Transcript Labeling Kit T3 from Enzo Life Sciences (Farmingdale, NY).  Labeled cRNA was hybridized onto Affymetix GeneChip HG-U133 Plus 2.0 Arrays.

first: Stephanie

last: Roessler


title: Comparative genomics of Staphylococcus aureus and the application of a “pan-genome” for assigning RNA-Seq transcript reads from divergent strains and in vivo human nasal samples

status: Public on Jan 05 2015

first: Diego

last: Chaves-Moreno

address: inhoffenstrasse 7

department: Department of Medical Microbiology (MMIK)

institute: Helmholtz Centrum for Infection Research

summary: in vitro comparison between two MRSA grown in rich (BHI) and poor media (SNM), compared with the nasal metatranscriptome reads of S. aureus.

overall_design: Global expression profile of two MRSA strains of S.aureus harvested in two different growth phases and compared with a metatranscriptome nose sample of a S. aureus carrier.

first: Melissa

last: Wos-Oxley

first: Ruy

last: Jáuregui

first: Eva

last: Medina

first: Dietmar

middle: H

last: Pieper

first: Andrew

middle: P

last: Oxley


title: Runx+ HSPC, kdrl+ endothelial, and negative cells sorted from DMSO- or Lycorine-treated 3 dpf zebrafish embryos

status: Public on Jan 15 2015

city: Madison

first: Owen

middle: James

last: Tamplin

state: WI

address: 1111 Highland Ave

department: Cell and Regenerative Biology

institute: University of Wisconsin-Madison

summary:
The zebrafish is a powerful model for the study of hematopoietic stem and progenitor cells (HSPC). We have developed a novel HSPC-specific transgenic line (Runx1+23:GFP). We have used this line in time-lapse live imaging studies to track the migration of HSPC during development. We have also performed a chemical genetic screen to find small molecules that modulate HSPC numbers during development. Treating embryos from 2-3 days post fertilization (2-3 dpf) then fixing for in situ staining with HSPC probes cmyb and runx1, we found the compound lycorine increased HSPC numbers. Applying this compound during time-lapse live imaging showed increased accumulation of Runx+ HSPC in the caudal hematopoietic tissue (CHT). Treatment from 2-3 dpf, then washing off the compound, had a sustained effect on the size of the HSPC with Runx+ numbers higher at 5 and 7 dpf.
We have performed microarray analysis to  elucidate the molecular changes within HSPC and endothelial cells after Lycorine treatment. We treated Runx1+23:GFP;kdrl:DsRed2 embryos from 2-3 dpf with 75 uM lycorine in 1% DMSO. We then dissociated the embryos and sorted the Runx+ GFP cells, the kdrl+ DsRed2 cells, and the non-fluorescent negative cells from the total embryo as a comparator population. Total RNA was amplified and biotin labled for hybridization on Affymetrix microarrays.

overall_design: 18 samples were collected and analyzed. There are 3 biological replicates. There are 3 cell type populations: 1) Runx+ HSPC; 2) kdrl+ endothelial cells; 3) non-fluorescent negative cells. There are cell populations from dissociated Lycorine-treated embryo pools, and control DMSO-treated embryo pools.

first: Leonard

middle: I

last: Zon


title: Dynamic response of P. putida S12 and S12ΔtrgI to sudden addition of toluene

status: Public on Jan 09 2015

city: Leiden

first: Johannes

middle: H.

last: de Winde

address: Rapenburg 70

country: Netherlands

institute: Universiteit Leiden

summary:
Pseudomonas putida S12 is exceptionally tolerant to various organic solvents. To obtain further insight in this bacterium’s primary defence mechanisms towards these potentially harmful substances, we studied its genome wide transcriptional response to sudden addition of toluene. Global gene expression profiles were monitored for 30 minutes after toluene addition. During toluene exposure, high oxygen-affinity cytochrome c oxidase is specifically expressed to provide for an adequate proton gradient supporting solvent efflux mechanisms. Concomitantly, the glyoxylate bypass route was up-regulated, to repair an apparent toluene stress-induced  redox imbalance.
A knock-out mutant of trgI, a recently identified toluene-repressed gene, was investigated in order to identify TrgI function. Remarkably, upon addition of toluene the number of differentially expressed genes initially was much lower in the trgI-mutant than in the wild-type strain. This suggested that after deletion of trgI cells were better prepared for sudden organic solvent stress.   Before, as well as after, addition of toluene many genes of highly diverse functions were differentially expressed in trgI-mutant cells as compared to wild-type cells. This led to the hypothesis that TrgI may not only be involved in the modulation of solvent-elicited responses but in addition may affect basal expression levels of large groups of genes.

overall_design: Differential gene expression after a sudden addition of 5 mM toluene was analysed in early exponential phase cultures (optical density at 600 nm of 0.5-0.6) of P. putida strains S12 (wild-type) and S12ΔtrgI. Samples were drawn immediately before (t=0) and at set intervals (1, 2, 5, 10 and 30 minutes) after toluene exposure. Duplicat samples were drawn. This resulted in 12 samples per strain, 24 in total.

first: Rita

middle: J

last: Volkers

first: L

last: Snoek

first: Harald

last: Ruijssenaars


title: Genome-wide expression profiling reveals putative target genes of the mating type loci (MAT1-1 and MAT1-2)  in Fusarium graminearum during sexual devleopment

status: Public on Jan 01 2015

city: Yongin

first: Yeon-Ki

last: Kim

state: Kyonggido

address: 38-2 Namdong

department: GreenGene Biotech Inc.

country: South Korea

institute: GreenGene Biotech Inc.

summary:
Using a 3′-tiling microarray covering the whole F. graminearum genome, we carried out genome-wide expression analyses of F. graminearum strains deleted for MAT1-1 or MAT1-2 locus, or overexpression the MAT1-2-1 gene during the sexual devleopment
Our study is the first report which elucidated the putative target genes of the mating type genes in Fusarium graminearum during sexual development

overall_design: A total of 12 chips were used for microarray. At 48 h after the removal of aerial mycelia grown on carrot agar for 7 days, total RNAs were extracted from the F. graminearum wild-type strain Z3643 and the F. graminearum strains deleted for MAT loci or overexpressin MAT1-2-1 with two or three biological replicates.

first: Hee-Kyoung

first: Sung-Hwan

last: Yun


title: The placental gene PEG10 promotes progression of neuroendocrine prostate cancer [aCGH]

city: Vancouver

first: Shawn

last: Anderson

state: BC

address: 2660 Oak Street

institute: Vancouver Prostate Centre

type: Genome variation profiling by genome tiling array

summary: Neuroendocrine prostate cancer (NEPC) is proliferative, invasive, and untreatable. Its molecular pathogenesis remains poorly understood but appears to require TP53 and RB1 aberration. In this study we modeled the development of NEPC from conventional prostatic adenocarcinoma using a unique patient-derived xenograft and identified up-regulation of the placental gene PEG10. We found that the androgen receptor and the E2F/RB pathway dynamically regulate distinct post-transcriptional and post-translational isoforms of PEG10 at different stages of NEPC development. In vitro, PEG10 promoted cell cycle progression from G0/G1 in the context of TP53 loss, and regulated Snail expression via TGF-β signaling to promote invasion. Finally we show in vivo proof of principal using antisense oligonucleotide that PEG10 is a novel therapeutic target for NEPC.

overall_design: Six patient-derived xenograft tumors from the LTL331 xenograft lineage (PMID: 24356420; http://www.livingtumorcentre.com/) after differing lengths of time post-host castration. No replicates.

first: Alexander

last: Wyatt

first: Colin

middle: C

last: Collins


title: Suppression of NCALD protects against spinal muscular atrophy by restoring impaired endocytosis

city: Tuebingen

first: Michael

last: Walter

address: Calwer Str. 7

department: Department of Medical Genetics

institute: University of Tuebingen

summary: Spinal muscular atrophy (SMA) is a common genetic motor neuron (MN) disease caused by low levels of the ubiquitously expressed housekeeping survival motor neuron (SMN) protein, whereas concomitant overexpression of plastin 3 (PLS3) protects from SMA. Here we identify neurocalcin delta (NCALD), a neuronal calcium sensor, as a second fully protective SMA modifier, which counteracts SMA pathology when downregulated. We show reduced Ca2+ influx and impaired endocytosis in SMA, which are crucial processes in synaptic vesicle recycling and neurotransmission. Remarkably, both reduced NCALD or increased PLS3 restore endocytosis in cell culture and MN function across species in zebrafish, worm and mouse SMA models, whereas Ca2+ influx remains disturbed. Furthermore, NCALD physically binds clathrin in a Ca2+-dependent manner. We propose that NCALD acts as a Ca2+-regulated inhibitor of endocytosis, and that endocytosis is critically affected in SMA. This finding opens new therapeutic avenues for SMA.

overall_design: Multifactorial design comparing affected patients and unaffected disease carriers against severly affected control group to identify disease modifying transcripts

first: Markus

last: Riessland

first: Kathryn

last: Swoboda

first: Heiko

last: Löhr

first: Cathleen

last: Bradler

first: Maria

last: Dimitriadi

first: Anna

last: Kaczmarek

first: Svenja

last: Schneider

first: Seyed

last: Mohsen

first: Hosseini

last: Barkooie

first: Miriam

last: Peters

first: Nasim

last: Bigliari

first: Vanessa

last: Grysko

first: Sandra

last: Kröber

first: Irmgard

last: Hölker

first: Lutz

last: Garbes

first: Christian

last: Gilissen

last: Hoischen

first: Gudrun

last: Nürnberg

first: Peter

first: Min

last: Kye

first: Anne

last: Hart

first: Matthias

last: Hammerschmidt

last: Kloppenburg

first: Brunhilde

last: Wirth


title: The placental gene PEG10 promotes progression of neuroendocrine prostate cancer [Expression]

first: Shawn

last: Anderson

overall_design: 14 patient-derived xenograft tumors from the LTL331 xenograft lineage (PMID: 24356420; http://www.livingtumorcentre.com/) after differing lengths of time post-host castration. Three replicates present for days 1-3 post-host castration.

first: Alexander

last: Wyatt

first: Colin

last: Collins


title: Insulin-like growth factor-binding protein 2 Induces Epithelial-mesenchymal Transition via Activation of NF-κB Pathway in Pancreatic Ductal Adenocarcinoma

city: Houston

first: Song

last: Gao

state: TX

address: 1515 Holcombe Blvd

department: Pathology

country: USA

institute: UT MD Anderson Cancer Center

summary: IGFBP2 has been shown to act as an oncogene augmenting tumor progression in a number of malignancies. We sought to investigate role of IGFBP2 and its related pathways in PDAC. Gene expression profiling  were used to reveal the key signaling pathways.  Microarray experiments in IGFBP2-overexpressing AsPc-1 cells were carried out.Transcriptional profiling of human pancreatic cancer cells AsPc-1 comparing empty vector transfected control  AsPc-1 cells with AsPc-1 cells transfected with pcDNA3.1-IGFBP2.

overall_design: We performed cDNA microarray analysis to compare IGFBP2 stably expressing cell line originating from AsPc-1 with empty vector control cells. AsPC-1 clones transfected with empty vector were placed in the reference channel in hybridization.

first: Limei

last: Hu

first: Yan

last: Sun

first: Xuebin

last: Zhang

first: Yuexin

last: Liu

first: Corrine

middle: Y

last: Chua

first: Lynette

last: Moore

first: He

last: Ren

first: Huamin

last: Wang

first: Paul

last: Chiao

first: Jihui

last: Hao

first: Wei


title: Time- and phase-dependent expression profile of miRNA and mRNA in human microglial cells (CHME3) infected with Japanese encephalitis virus (JEV) P20778 strain

city: FARIDABAD

first: ARUP

last: BANERJEE

state: Haryana

address: THSTI, 3RD MILE STONE, FARIDABAD GURGAON EXPRESSWAY, NCR BIOTECH CLUSTER

department: VIDRC

institute: TRANSLATIONAL HEALTH SCIENCE & TECHNOLOGY INSTITUTE

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

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

platform_organism:
Homo sapiens
synthetic construct

overall_design: Refer to individual Series


title: Cervical neoplasia genomes

status: Public on Dec 31 2014

city: seoul

first: SeungHyun

last: Jung

state: seoul

address: catholic university, medical college, banpo-dong

department: Department of Biochemistry

institute: Catholic University of Korea

summary:
Cervical intraepithelial neoplasia (CIN), also known as cervical dysplasia, is premalignant lesions of the cervical squamous cell carcinoma (CSCC) that shows abnormal growth of squamous cells in the cervix epithelium. Given the evidence suggesting that differences may exist between CIN and CSCC, we hypothesize that progression may be mediated by subpopulation selection or by acquisition of additional alterations, including gene mutations or chromosomal alterations.
In this study, we analyzed cervical CIN, microinvasive carcinoma (MIC) and CSCC by whole-exome sequencing and array-comparative genomic hybridization (array-CGH) and found that CIN genomes harbored fewer mutations (especially fewer driver mutations) and copy number alterations (CNAs), suggesting that additional genomic alterations might burst onto the CIN genome at the final stage of CIN progression to CSCC or an early stage of CSCC.

overall_design: To find genomic differences between CIN and CSCC, a total of eight cervical neoplasia genomes (three CINs, one MIC, and four CSCC genomes) were analyzed in this study. The hospital pathology department confirmed pathologic features of the cervical neoplasias. All of the picked areas from tumor and normal areas were frozen, cut, and stained with hematoxylin & eosin (H&E). Two pathologists selected cases with rich tumor cell population (at least 70%), which were subsequently used in the study. Copy number profiling was performed using Agilent 180K platform according to the manufacturer's protocol.

first: Seung-Hyun

first: Yeun-Jun

last: Chung


title: Methylation disorder in CLL

city: New York

first: Dan

last: Landau

state: NY

address: 413 East 69th Street

institute: Weill Cornell Medicine

summary:
We performed RRBS and WGBS on primary human chronic lymphocytic leukemia and normal healthy donor B cell samples
Due to patient privacy concerns, the raw data is being made available via controlled access in dbGaP (http://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000435.v1.p1).

overall_design: cross-sectional/longitudinal

first: Kendell

last: Klement

first: Patrick

last: Boyle

first: Catherine

last: Wu

first: Alex

last: Meissner


title: Gene expression profile in the lung of mice during pneumococcal pneumonia: WT vs NLRP3 inflammasome component-deficient mice

city: Kyoto

first: Kohsuke

last: Tsuchiya

address: Yoshida Konoe-cho, Sakyo-ku

department: Microbiology

institute: Kyoto University

summary:
Inflammasomes are multiprotein platforms of caspase-1 activation. The NLRP3 inflammasome is composed of NLRP3, ASC, and procaspase-1. This inflammasome is activated by various endogenous and exogenous stimuli, including pneumococci, and protects from a variety of microbial pathogens.
In the present study, we examined the role of NLRP3 inflammasome components in gene expression in the lung during pneumococcal pneumina.

overall_design: Gene expression was measured in the lung of WT, Casp1-/-, Asc-/-, and Nlrp3-/- mice 24 h after intranasal infection with Streptococcus pneuminiae.

first: Rendong

last: Fang

first: Shunsuke

last: Sakai


title: MicroRNA expression profile in CHME3 cells infected with Japanese encephalitis virus

summary:
CHME3 cells grown on six-wells were infected with Japanese encephalitis virus (JEV) (P20778 strain), and total RNA was isolated from cells at 6, 24 and 48 h of post infection.
MicroRNA expression was significantly altered in JEV-infected human microglial cells. A time-dependent change in microRNA profile was noted. Bioinformatics analysis identified anti-correlation between differentially expressed miRNAs and the gene expression at different time point which ultimately affected several signalling pathways in microglia cells. Brain-enriched microRNAs and a set of microRNA previously designated as NeurimmiRs were also differentially expressed in response to JEV infection.

overall_design: CHME3 cells grown on 6-well plate. Three replicates of uninfected and JEV-infected samples at each time point (6, 24 and 48 h of post infection) were used for microRNA array.

first: Bharti

last: Kumari

first: Arup

last: Banerjee

first: Sudhanshu

last: Vrati

first: Ashish

last: Trivedi


title: Expression data from mammary tumors from a generation 7 Diversity Outcross x PyMT cross

status: Public on Dec 25 2014

first: Kent

last: Hunter

address: 37/4048 37 Convent Drive

department: Center for Cancer Research

summary: Mouse genetic crosses were established between the PyMT model of metastatic breast cancer and the G7 generation of the Diversity Outcross (DO). Tumors were harvested from the animals for gene expression analysis to identify genes association with progression to distant metastatic disease.

overall_design: Gene expression of 159 samples from the PyMT x Diversity Outcross were assayed on Affymetrix chips.


title: The placental gene PEG10 promotes progression of neuroendocrine prostate cancer

first: Shawn

last: Anderson


title: Expression data from intestinal-type and diffuse-type gastric cancers

city: Chuo-ku

first: Hiroki

last: Sasaki

state: Tokyo

institute: National Cancer Center Reseach Institute

summary: To identify the specific genes for intestinal-type and diffuse-type gastric cancers.

overall_design: We selected 18 intestinal-type gastric cancers and 12 diffuse-type gastric cancers showing typical characteristics on the form of cell growth (clustered or scattered) and the degree of differentiation (well/moderate or poor), and performed microarray analysis for obtaining genome-wide mRNA expression profiles.

first: Inaho

last: Danjoh


title: mRNA expression profile in CHME3 cells infected with Japanese encephalitis virus

first: ARUP

last: BANERJEE

summary:
CHME3 cells grown on six-wells were infected with Japanese encephalitis virus (JEV) (P20778 strain ) and total RNA was isolated from cells at 6, 24 and 48 h of post infection
mRNA expression was significantly altered in JEV infected human microglial cells. A time dependant change in microRNA profile was noted. Bioinformatics analysis identified anti correlation between differentially expressed miRNAs and the gene expression at different time point which ultimately affected several signalling pathways in microglia cells. Brain enriched microRNAs and a set of microRNA previously designated as NeurimmiRs were also differentially expressed in response to JEV infection

overall_design: Cells grown on 6-well well plate. Three replicates of uninfected and infected samples at each time point was used for mRNA experiment.

first: B

first: A

first: S


title: A global transcriptome analysis of keratinocytes upon overexpression of microRNA-132

status: Public on Dec 30 2014

city: Stockholm

first: Ning

last: Xu

address: CMM L8:02

institute: Karolinska Institutet

summary:
MiR-132 is one of the most upregulated miRNAs in keratinocytes of human skin wounds during the inflammatory phase of healing; however its biological role during skin wound healing has not been studied.
To study the genes regulated by miR-132, we transfected miR-132 mimics (pre-miR-132) into primary human keratinocytes to overexpress miR-132.
We performed a global transcriptome analysis of keratinocytes upon overexpression of miR-132 using Affymetrix arrays.

overall_design: Expression profiling of primary human keratinocytes transfected with 10nM miR-132 mimics (pre-miR-132) or control oligos (pre-miR-Ctrl) for 48 hours (biological triplicates in each group) was performed using Affymetrix GeneTitan system.

middle: X

last: Landén