title: Expression analysis of DamP mRNAs using expressed molecular barcodes

status: Public on Jan 10 2014

city: Paris

first: Cosmin

last: Saveanu

address: 25-28 rue du docteur Roux

department: Genomes and Genetics

institute: Institut Pasteur

summary:
We have generated 979 yeast strains in which the natural 3' UTR of essential gene mRNAs has been replaced by the same long 1.4 kb artificial 3' UTR (DAmP modification). Nonsense mediated mRNA decay (NMD) of these mRNA reporters was tested by using Agilent barcode microarrays by taking advantage of molecular barcodes introduced just downstream the stop codon during strain construction. We introduced in each DAmP strain either a neutral mutation (deletion of YEL068C) or the deletion of essential factors for NMD: NAM7 and NMD2. The resulting haploid cells were tested for changes in DAmP mRNA levels by comparing an RNA sample with a DNA genomic sample. Differences between the samples indicate the sensibility of the DAmP mRNAs to degradation through NMD. The large scale results were validated by Q-PCR analysis of individual strains.
A strong negative correlation between the level of destabilization elicited by a long 3' UTR and the size of the coding sequence suggests that long ORF mRNAs can escape NMD even in the presence of a long 3' UTR.

overall_design: Three samples were analysed and for each sample a technical replicate was performed, starting from the raw cellular material. YEL068C samples represent the reference population while NMD2 and NAM7 samples are the ones important for the analysis. Only a very limited part of the Agilent barcode microarray signal (barcodes corresponding to the “up” tag in the DamP strain) was used for the interpretation of the data.

first: Laurence

last: Decourty


title: Gene profiling of mouse liver NK and NKT  cell subsets

status: Public on Jan 29 2014

city: Lyon

first: Thierry

last: Walzer

address: 21 avenue tony garnier

country: France

institute: CIRI, centre international de recherche en infectiologie

summary: This study shows that liver Eomes- NK cells are not precursors of classical Eomes+ NK cells but rather constitute a distinct lineage of innate lymphoid cells. Gene profile analyses show that Eomes- NK cells share part of their transcriptional program with NKT cells that includes genes involved in liver homing, NK cell receptors, and several cytokines and cytokine receptors.

overall_design: Eomes- NK cells, Eomes+ Nk cells and NKT cells were sorted by flow cytometry from Eomes-GFP reporter mice. Total RNA was extracted and hybridized to Affymetrix microarrays.


title: INFLORESCENCE DEFICIENT IN ABSCISSION (IDA) and its receptors HAE/HSL2 are  required for cell expansion and cell separation during floral organ abscission in Arabidopsis thaliana (part 2)

status: Public on Dec 30 2013

city: Oslo

first: Reidunn

middle: B.

last: Aalen

address: P.O.Box 1066 Blindern

department: Department of Biosciences

country: Norway

institute: University of Oslo

summary: Plants have the ability to shed organs that are no longer in use. In Arabidopsis thaliana abscission of floral organs involves cell wall remodeling and cell expansion prior to cell wall dissolution.  IDA encodes a secreted peptide that signals through the leucine-rich repeat receptor-like kinases (LRR-RLKs) HAESA (HAE) (At4g28490) and HASEA-LIKE2 (HSL2) (At5g65710).

overall_design: Arabidopsis thaliana (ecotype Colombia-0)  plants were kept in growth chambers with a 16/8 h (light/dark) photoperiod at 22 °C, and 100 mE m-2 s-1 light intensity. 4 biological replicates were prepared from each sample, each containing abscission zone regions of siliques position 4 to 8 (when counting from the flowe at anthesis at the top of the inflorescence) from  plants with at least 20 siliques. Differences in transcriptional responses were measured by comparing genes expression in abscission zones of ida-2  plants  (SALK_133209) against abscission zones from control plants.

first: Bin

last: Liu

first: Melinka

middle: A

last: Butenko

first: Tore

last: Brembu

middle: B

first: Grethe-Elisabeth

last: Stenvik

first: Torfinn

last: Sparstad

first: Ane

middle: K

last: Vie

first: Chun-Lin

last: Shi

first: Per

last: Winge

first: Atle

middle: M

last: Bones


title: INFLORESCENCE DEFICIENT IN ABSCISSION (IDA) and its receptors HAE/HSL2 are  required for cell expansion and cell separation during floral organ abscission in Arabidopsis thaliana

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

overall_design: Refer to individual Series


title: Microarray analysis of beta-catenin regulated target genes in SW480 colon cancer cells

status: Public on Dec 27 2013

city: West Point

first: Michele

last: Cleary

state: PA

address: 770 Sumneytown Pike

department: Genetics and Pharmacogenomics

country: USA

institute: Merck and Co., Inc.

summary: Deregulation of the canonical Wnt/beta-catenin pathway is one of the earliest events in the pathogenesis of colon cancer. Mutations in APC or CTNNB1 are frequent in colon cancer and cause aberrant stabilization of beta-catenin, which activates Wnt target genes by binding to chromatin via TCF/LEF transcription factors. In a comprehensive study, we conducted an integrative analysis of genome-wide chromatin occupancy of beta-catenin by chromatin immunoprecipitation coupled with high-throughput sequencing (ChIP-seq) along with gene expression profiling changes resulting from RNAi-mediated knockdown of beta-catenin in colon cancer cells. This experiment series represents the gene expression changes detected by microarray as a result of CTNNB1 perturbation.

overall_design: SW480 cells were transfected with control and beta-catenin siRNAs.  Twenty-four hours after transfection, RNA was extracted from the cells using the RNeasy kit (Qiagen, Valencia, CA) and genome-wide cDNA microarray expression analysis was performed.   The data reported here are the microarray data as processed by the standard Rosetta Resolver(R) ratio method for Agilent microarrays.

first: Brian

middle: S

last: Roberts

first: William

middle: T

last: Arthur

first: Julja

last: Burchard

first: Xing

last: Dai


title: Expression data of BRCA1 shRNA and Rad51 shRNA knockdown and control shRNA in MCF-10A cells

status: Public on Jan 24 2014

city: Houston

first: Chun-Jen

middle: Curtis

last: Lin

state: Texas

address: 7345 Fannin Street

department: Systems Biology

institute: University of Texas MD Anderson Cancer Center

summary: Homologous recombination-mediated DNA repair deficiency (HRD) predisposes to cancer development, but also provides therapeutic opportunities. Here, we identified an HRD gene signature that robustly predicted HRD status. Unexpectedly, concurrent loss of PTEN in BRCA1-deficient cells might extensively rewire the HR repair network and confer resistance to PARP inhibitor, partially through over-expression of TTK. We used the HRD gene signature as a drug discovery tool and found several PARP-inhibitor-synergizing agents through the connectivity map. Thus gene expression profiling can be used to define the functional status of the HR repair network providing prognostic and therapeutic information.

overall_design:
Various shRNAs that target genes involved in homologous recombination (HR) were transfected in MCF-10A non-transformed breast cells lines. Stable HR gene knockdown MCF-10A cells were seeded 200000 at 10 cm plate. Cells were harvested after 48 hours culturing and used for gene expression profiling.

The shRNAs that target PTEN or BRCA1 genes were transfected in MCF-10A non-transformed breast cell line by lentiviral particles. Stable BRCA1 and PTEN knockdown MCF-10A cells were selected. Scrambled control shRNA-transfected MCF-10A cells were applying as control.  All knockdown and control MCF-10A cells were seeded with 2 x 10^5 cells at 10 cm culture plate. Cells were cultured in MCF-10A medium and harvested after 48 hours culturing.  mRNA was extracted from collected cells and performing gene expression profiling. Four biological replicates were applied. Four biological replicates were applied.

first: Guang

last: Peng

first: Curtis

middle: C

first: Wei

last: Mo

first: Hui

first: Yun-Yong

last: Park

first: Soo-Mi

last: Kim

first: Qianxing

first: Yang

first: Stefan

last: Siwko

first: Ruozhen

last: Hu

first: Ju-Seog

last: Lee

first: Bryan

last: Hennessy

first: Samir

last: Hanash

first: Gordon

last: Mills

first: Shiaw-Yih


title: Osteoblastic response in human bone marrow stromal cells

status: Public on Dec 23 2013

city: Seattle

first: Ilsa

last: Coleman

state: WA

address: 1100 Fairview Ave N, E2-112

department: Human Biology

institute: Fred Hutchinson Cancer Center

summary: Our goal was to determine whether osteoblastic LuCaP 23.1 prostate cancer xenograft tumors can elicit an osteoblastic response at the gene expression level in human bone marrow stromal cells.

overall_design: Custom Agilent 44K whole human genome expression oligonucleotide microarrays were used to profile bone marrow stroma cells isolated from three patients and treated with either mineralization media or LuCaP 23.1 conditioned medium.  Total RNA was isolated and amplified prior to hybridization against a common reference pool of prostate tumor cell lines.

first: Sandy

middle: R

last: Larson

first: Jessica

last: Chin

first: Xiaotun

last: Zhang

first: Lisha

middle: G

last: Brown

first: Bryce

last: Lakely

first: Martin

last: Tenniswood

first: Eva

last: Corey

first: Peter

last: Nelson

first: Robert

middle: L

last: Vessella

first: Colm

last: Morrissey


title: Expression data from Sinorhizobium meliloti 1021 wild-type and SMc03169 gene deletion mutant

status: Public on Dec 22 2013

city: Lisboa

first: Leonilde

middle: Morais

last: Moreira

address: A. Rovisco Pais

department: Bioengineering

country: Portugal

institute: Instituto Superior Tecnico

summary: Within this work we identified and characterized SMc03169 (hhrA) as a new Sinorhizobium meliloti gene product with relevance to biological nitrogen fixation symbiosis with leguminous plants. HhrA belongs to the TetR-family of repressors and its deletion from S. meliloti genome affected considerably gene expression as well as several phenotypic traits.

platform_organism:
Sinorhizobium meliloti
Medicago sativa
Medicago truncatula

overall_design: For expression profiling, triplicates of the wild-type Sinorhizobium meliloti 1021 or the SMc03169 (delta hhrA) deletion mutant were grown in GMS liquid medium supplemented with 10 micromolar of luteolin for 4 hours at 30ºC and 180 rpm, followed by total RNA extraction.

first: Mário

last: Santos

first: Jorg

middle: D

last: Becker


title: Genomic content analysis of Clostridium botulinum type F strains

status: Public on Dec 19 2013

city: Atlanta

first: Brian

middle: H

last: Raphael

state: GA

address: 1600 Clifton Road

department: Enteric Diseases Laboratory Branch

institute: Centers for Disease Control and Prevention

type: Genome binding/occupancy profiling by genome tiling array

summary: The purpose of this study was to determine the level of genomic content similarity among selected strains of Clostridium botuinum type F strains.

overall_design: In this study, strains were selected that had already been chacaterized by botulinum neurotoxin gene sequencing.  Strains harboring bont/F1, bont/F4 and bont/F5 were compared.

first: Marite

last: Bradshaw

first: Suzanne

last: Kalb

first: Lavin

last: Joseph

first: Carolina

last: Luquez

first: John

last: Barr

first: Susan

middle: E

last: Maslanka


title: Suppression of MicroRNA-9 by Mutant EGFR Signaling Induces FOXP1 to Enhance Glioblastoma Tumorigenicity

status: Public on Dec 20 2013

city: La Jolla

first: Frank

last: Furnari

state: CA

address: 9500 Gilman Dr.

institute: Ludwig Institute for Cancer Research

summary: The EGF-receptor (EGFR) is amplified and mutated in glioblastoma (GBM) where its common mutation, (∆EGFR, also called EGFRvIII) has a variety of activities that promote growth and inhibit death, thereby conferring a strong tumor-enhancing effect. This range of activities suggested to us that ∆EGFR might exert its influence through pleiotropic effectors and we hypothesized that microRNAs (miRs) might serve such a function. To test this, we determined the miR profiles of GBM cells with activated wild type EGFR (wtEGFR) and mutant EGFR (∆EGFR) to cells with non-activated EGFR or kinase dead ∆EGFR.

overall_design: To identify miRs regulated by EGFR, RNA from 2 different glioma cell lines (U87 and U373) were hybridized to miR expression arrays and analyzed. Each cell type was engineered to express wild type EGFR (wtEGFR), dead kinase ∆EGFR (DK) or ∆EGFR at elevated levels similar to those observed in primary glioblastomas displaying EGFR overexpression. Parental cells expressing endogenous EGFR and wtEGFR cells stimulated with EGF for 1hr were also included in the analyses.


title: Dynamic Chromatin Modification Sustains Epithelial-Mesenchymal Transition following Inducible Expression of Snail-1 (gene expression)

status: Public on Dec 18 2013

city: Boston

first: Ben

middle: S.

last: Wittner

state: MA

address: 149 13th Street

department: Center for Cancer Research

institute: Massachusetts General Hospital

summary: Epithelial-Mesenchymal Transition (EMT) is thought to contribute to cancer metastasis, but its underlying mechanisms are not well understood. To define early steps in this cellular transformation, we analyzed human mammary epithelial cells with tightly regulated expression of Snail-1, a master regulator of EMT. Following Snail-1 induction, epithelial markers were repressed within 6 hours and mesenchymal genes induced at 24 hours. Snail-1 binding to its target promoters was transient (6-48 hours) despite continued protein expression and it was followed by both transient and long-lasting chromatin changes.

overall_design: To generate a potent reversible EMT-inducing stimulus, we created a Snail-1 retroviral expression construct, using a fused estrogen receptor (ER) response element to mediate regulation by exogenous 4-hydroxy-tamoxifen (4-OHT). Since Snail-1 protein stability and nuclear localization are suppressed by GSK3-beta-mediated phosphorylation, we substituted the six targeted amino acids (ER-Snail-1(6SA)), thus conferring constitutive activity to the induced protein (Zhou et al., 2004, Pubmed ID 15448698). Infection of non-transformed, immortalized human mammary epithelial MCF10A cells with ER-Snail-1(6SA), followed by treatment with 4-OHT, triggered morphological and biomarker characteristics of EMT. At 3, 6, 12, 24, 72 and 120 hours after beginning exposure to 4-OHT in ethanol (or, for controls, ethanol only) we extracted RNA and did gene expression analysis using microarrays. We perfomed three replicates of each.

first: Sarah

last: Javaid

first: Jianmin

last: Zhang

first: Endre

last: Anderssen

first: Josh

last: Black

first: Ken

last: Tajima

first: David

last: Ting

first: Gromoslaw

last: Smolen

first: Matthew

last: Zubrowski

first: Rushil

last: Desai

first: Shyamala

last: Maheswaran

first: Sridhar

last: Ramaswamy

first: Johnathan

last: Whetstine

first: Daniel

last: Haber


title: Genes induced by VEGF on the chick CAM after 24h

city: Talence

first: Martin

last: Hagedorn

address: Av des Facultes

department: Biology

institute: University Bordeaux 1

summary: We determined gene expression profiles which were induced in the chick chorio-allantoic membrane 24 h after application of recombinant human VEGF.

overall_design: Three individual CAMs with clearly visible induction of new capillaries were compared to a pool of three normal CAMs of the same developmental day.

first: Sophie

last: Javerzat

first: Joerg

last: Wilting

first: Natalia

last: Platonova


title: Molecular and metabolic profiles suggest that increased lipid catabolism in adipose tissue contributes to leanness in domestic chickens

city: Knoxville

first: Bo

last: Ji

state: TN

address: 2640 Morgan Circle Drive

department: Animal Science

institute: University of Tennessee

summary: Domestic chicken has been intensively studied because of its role as an efficient source of lean meat. However, commercial broilers resulting from genetic selection for rapid growth demonstrate detrimental traits, such as excess deposition of abdominal adipose tissue, metabolic disorders, and reduced reproduction. Therefore fast-growing broilers represent “obese” chickens compared to slow-growing egg layers (e.g, Leghorn) or wild strain of meat-type chickens (e.g., Fayoumi). Fayoumi chickens, originating from Egypt, represent a harder stain of chickens, which are more resistant to diseases. Leghorn chickens are the original breed of commercial U.S layers. Both lines were maintained highly inbred by Iowa State University poultry geneticists with an inbreeding coefficient higher than 0.95. Both Fayoumi and Leghorn demonstrated lean phenotype compared to broilers, and these three lines of chickens are genetically distant from each other.

overall_design: In this study, we used affymetrix microarray to profile global gene expression of three distinct genetic lines of chickens to identify functional pathways associated with leanness of domestic chickens.

first: Jessie

last: Middleton

first: Ben

last: Ernest

first: Arnold

last: Saxton

first: Susan

middle: J

last: Lamont

first: Shawn

last: Campagna

first: Brynn

last: Voy


title: Microarray analysis of fruit flesh of European pear ‘La France’ during fruit development

city: Tsukuba

first: Kenji

last: Nashima

state: Ibaraki

address: Fujimoto 2-1

country: Japan

institute: NARO institute for fruit tree science

summary: Comprehensive investigation of gene expression during fruit development and ripening in European pear (Pyrus communis).

overall_design: Gene expression of fruit flesh development of European pear was measured from -7 to 182 days after full bloom (DAFB). 150 DAFB is harvested stage and 182 DAFB is after ripening by chilling treatment (2°C 12 days, then 15°C 20 days).

first: Hirokazu

last: Takahashi

first: Mikio

last: Nakazono

first: Tokurou

last: Shimizu

first: Chikako

last: Nishitani

first: Toshiya

last: Yamamoto

first: Akihiro

last: Itai

first: Kanji

last: Isuzugawa

first: Toshio

last: Hanada

first: Tadashi

last: Takashina

first: Katsuhiro

last: Shiratake


title: Lead exposure disrupts global DNA methylation in human embryonic stem cells and alters their neuronal differentiation

status: Public on Feb 01 2014

city: Detroit

first: Douglas

last: Ruden

state: Michigan

address: 275 E. Hancock Ave., Room  291.1

department: Department of Obstetrics and Gynecology

institute: Wayne State University

type: Methylation profiling by genome tiling array

summary: Exposure to lead (Pb) during childhood can result in learning disabilities and behavioral problems.  Although described in animal models, whether Pb exposure also alters neuronal differentiation in the developing brains of exposed children is unknown.  Here, we investigated the effects of physiologically relevant concentrations of Pb (from 0.4 to 1.9 µM or 0 to 40µg/dl) on the capacity of human embryonic stem cells (hESCs) to progress to a neuronal fate.  We found that neither acute nor chronic exposure to Pb prevented hESCs from generating neural precursor cells (NPCs).  NPCs derived from hESCs chronically exposed to 1.9 µM or 40µg/dl Pb throughout the neural differentiation process generated 2.5 times more TUJ1-positive neurons than those derived from control hESCs.  Pb exposure of hESCs during the stage of neural rosette formation resulted in a significant decrease in the expression levels of the neural marker genes PAX6 and MSI1. Furthermore, the resulting NPCs differentiated into neurons with shorter neurites and less branching than control neurons, as assessed by Sholl analysis.  DNA methylation studies of control, acutely treated hESCs and NPCs derived from chronically exposed hESCs using the Illumina HumanMethylation450 BeadChip® demonstrated that Pb exposure induced changes in the methylation status of genes involved in neurogenetic signaling pathways.  In summary, our study shows that exposure to  Pb subtly alters the neuronal differentiation of exposed hESCs and that these changes could be partly mediated by modifications in the DNA methylation status of genes crucial to brain development.

overall_design: We analyzed the methylation profile of undifferentiated (n=2 independent experiments) and differentiating (n=2 independent experiments) human embryonic stem cells (hESCs) acutely exposed to losed to lead (Pb) and neural precursor cells derived from hESCs chronically exposed to Pb throughout the neural differentiation process (n=3 independent experiments).

first: Marie

last: Claude Senut

first: Arko

last: Sen

first: Pablo

last: Cingolani

first: Asra

last: Shaik

last: Land


title: Expression profile of Medicago truncatula roots inoculated with human enteric pathogens.

city: Madison

first: Jean-Michel

last: Ane

state: Wisconsin

address: 1575 Linden Drive

department: Agronomy

institute: University of Wisconsin Madison

summary:
Disease outbreaks due to the consumption of legume seedlings contaminated with human enteric bacterial pathogens like Escherichia coli O157:H7 and  Salmonella enterica are reported every year. We found surface and internal colonization of Medicago truncatula by Salmonella enterica and Escherichia coli O157:H7 even with inoculum levels as low as two bacteria per plant.
Expression analyses using microarray revealed that some Medicago truncatula genes were regulated in a similar manner in response to both of these enteric pathogens.

overall_design: Medicago truncatula roots were inoculated with low inoculum levels of two enteric bacteria per plant (E. coli O157:H7 and Salmonella). 10 days post inoculated plants were used for RNA extraction and hybridization on Affymetrix microarrays.

first: Dhileepkumar

last: Jayaraman

last: Ané


title: Neuroblastoma: MYCN normal vs. MYCN amplified

status: Public on Dec 17 2013

city: Taipei

first: Pei-Yi

last: Wu

address: 1 Roosevelt Rd., Sec. 4

country: Taiwan

institute: National Taiwan University

summary: To evaluate the expression of genes associated with MYCN in NB, 10 tumors with MYCN amplification and 10 with normal MYCN copy number were subjected to oligonucleotide microarray using Agilent oligo microarray chips.

overall_design: Two-condition experiment, MYCN normal vs. MYCN amplified 10 NB patient tissues for each group.

first: Wen-Ming

last: Hsu


title: Dynamic Chromatin Modification Sustains Epithelial-Mesenchymal Transition following Inducible Expression of Snail-1

first: Ben

last: Wittner


title: De novo copy number variations in cloned dogs

city: seoul

first: SeungHyun

last: Jung

state: seoul

address: catholic university, medical college, banpo-dong

department: Department of Biochemistry

country: South Korea

institute: Catholic University of Korea

type: Genome variation profiling by genome tiling array


title: De novo copy number variations in cloned dogs (Nimblegen)

summary:
De novo copy number variations in cloned dogs from the same nuclear donor
In this study, we aimed to identify de novo post-cloning CNV events and estimated the rate of CNV mosaicism in cloned dogs with the identical genetic  background.

overall_design: We analyzed CNVs in seven cloned dogs using the nuclear donor genome as reference by array-CGH

first: Seung-Hyun

first: Yeun-Jun

last: Chung


title: Comparision of time-course gene expression in wild-type Drosophila and an Alzheimers disease model

status: Public on Dec 16 2013

city: Cambridge

first: Giorgio

last: Favrin

address: 80 Tennis Court Road

country: United Kingdom

institute: University of Cambridge

summary: The strongest risk factor for developing Alzheimer's Disease (AD) is age. Here, we study the relationship between ageing and AD using a systems biology approach that employs a Drosophila (fruitfly) model of AD in which the flies overexpress the human Aβ42 peptide. We identified 712 genes that are differentially expressed between control and Aβ-expressing flies. We further divided these genes according to how they change over the animal's lifetime and discovered that the AD-related gene expression signature is age- independent. We have identified a number of differentially expressed pathways that are likely to play an important role in the disease, including oxidative stress and innate immunity. In particular, we uncovered two new modifiers of the Aβ phenotype, namely Sod3 and PGRP-SC1b.

overall_design: Transcript level measured using microarrays in biological quadruplicate (except day 20 which is in biological triplicate), each array is Aβ vs control at the same timepoint (defined by % survival), one replicate per array with dye-swaps.

first: Daniel

last: Bean

first: Elizabeth

last: Bilsland

first: Helene

last: Boyer

first: Bettina

last: Fischer

first: Steven

last: Russel

first: Damian

last: Crowther

first: Howard

middle: A

last: Baylis

first: Stephen

last: Oliver

first: Maria

last: Giannakou


title: The sulfated laminarin triggers a stress transcriptome before priming the SA- and ROSdependent defenses during grapevine's induced resistance against Plasmopara viticola

city: Verona

first: Alberto

last: Ferrarini

state: Veneto

address: Strada le Grazie, 15

department: Scientific and Technological Department

country: Italy

institute: University of Verona

summary:
Cultivated grapevine (Vitis vinifera) is susceptible to many pathogens which cause significant losses to viticulture worldwide. Chemical control is available, but agro-ecological concerns have raised interest in alternative methods, especially in elicitation of plant immunity by bio-molecules such as Pathogen Associated Molecular Patterns (PAMPs). We have demonstrated that the beta-glucan laminarin (Lam) and its sulfated derivative (PS3) induce a PAMP-triggered immunity in grapevine against downy mildew (Plasmopara viticola). However, if Lam elicits classical grapevine defenses, PS3 triggered grapevine resistance via a poorly understood priming phenomenon. The aim of this study was to discover the mechanism of the PS3-induced resistance. On uninfected grapevine, we first investigated defense signaling and performed microarray experiments to identify early events and genes directly triggered by PS3.   Our results showed that PS3 i) was unable to elicit ROS and NO production, cytosolic Ca2+ variations, MAPK activation but triggered a long lasting plasma membrane depolarization in grapevine cells ii) up-regulated a stress-responsive transcriptome close to the one induced by Lam but only partly overlapping the ones triggered by salicylate (SA) or jasmonate (JA).  Finally, in response to P. viticola infection, PS3 specifically primed the SA- and ROS-dependent defense pathways leading to grapevine triggered immunity against this biotroph.
Keywords:  cell death, induced resistance, oomycete, priming, reactive oxygen species, salicylate, sulfated laminarin, transcriptomics, Vitis vinifera.

overall_design: 6 samples (Adj, PS3, Lam, ctrl, SA, JA) were analized with 3 biological replicates each, Adj and ctrl samples are reference samples

first: Adrien

last: GAUTHIER

first: Sophie

last: TROUVELOT

first: Jani

last: KELLONIEMI

first: Patrick

last: FRETTINGER

first: David

last: WENDEHENNE

first: Xavier

last: DAIRE

first: Jean-Marie

last: JOUBERT

last: FERRARINI

first: Massimo

last: DELLEDONNE

first: Victor

last: FLORS

first: Benoît

last: POINSSOT


title: De novo copy number variations in cloned dogs (Illumina SNP)

first: SeungHyun

last: Jung

first: Seung-Hyun

first: Yeun-Jun

last: Chung


title: Porcine gene response following incision with energized devices

status: Public on Dec 15 2013

city: Mississippi state

first: Bindu

last: Nanduri

state: MS

address: Box 6100 Spring Street

department: Basic Sciences

institute: Mississippi State University

summary:
This study compares the gene expression changes in Sus scrofa in response to two different methods for abdominal surgical incisions ; electrosurgery and harmonic blade.
As the use of laparoscopic surgery has become more widespread in recent years, the need has increased for minimally-invasive surgical devices that effectively cut and coagulate tissue with reduced tissue trauma. Although electrosurgery (ES) has been used for many generations, newly-developed ultrasonic devices (HARMONIC® Blade, HB) have been shown at a macroscopic level to offer better coagulation with less thermally-induced tissue damage. We sought to understand the differences between ES and HB at a microscopic level by comparing mRNA transcript and protein responses at the 3-day timepoint to incisions made by the devices in subcutaneous fat tissue in a porcine model

overall_design: This study used four 4-cm midline caudal abdominal incisions created with the test devices in two female pigs.  The test devices were monopolar electrosurgery and Harmonic blade. Each animal had two Harmonic Blade incisions and two Electrosurgery incisions for a total of 8 incisions

first: Shane

last: Burgess

first: Donna

last: Korvick


title: Gene expression of non-typeable Haemophilus influenzae strain R2866 and R2866Δ0112 mutant grown in supplemented brain-heart infusion medium for 7 hours

status: Public on Dec 13 2013

city: Nijmegen

first: Jeroen

middle: Daniel

last: Langereis

address: PO Box 9101

department: Department of Pediatrics

country: Netherlands

institute: Radboud University Medical Centre

summary:
Gene expresison profiles of the R2866 WT and  R2866Δ0112 mutant gorwn 7 hours in supplemented brain-heart infusion medium. This experiment was conducted  to determine the effects of R2866_0112 gene deletion on overall gene expression profile.
The results from this study are further discussed in: Modified lipooligosaccharide structure protects nontypeable Haemophilus influenzae from IgM-mediated complement killing in experimental otitis media.  Langereis JD, Stol K, Schweda EK, Twelkmeyer B, Bootsma HJ, de Vries SP, Burghout P, Diavatopoulos DA, Hermans PW. MBio. 2012 Jul 3;3(7):e00079-12. doi: 10.1128/mBio.00079-12. Print 2012.

overall_design:
R2866 wild-type (n=4) and R2866Δ0112 mutant (n=4) were grown for 7 hours in supplemented brain-heart infusrion medium
The 4hr and 7hr analyses were performed separately and, therefore, the background corrections are different between the two experiments.

first: Kim

last: Stol

first: Elke

last: Schweda

first: Brigitte

last: Twelkmeyer

first: Hester

last: Bootsma

first: Stefan

middle: P

last: de Vries

first: Peter

last: Burghout

first: Dimitri

last: Diavatopoulos

middle: W

last: Hermans


title: An improved, low-cost, hydroponic system for growing Arabidopsis and other model plant species under sterility conditions (Arabidopsis transcriptional profile in early response to Pi starvation)

status: Public on Dec 12 2013

city: Irapuato

first: Enrique

middle: Ibarra

last: Laclette

state: Guanajuato

address: Km 9.6 Libramiento Norte Carretera Irapuato-León, A.P. 629

country: Mexico

institute: Laboratorio Nacional de Genomíca (LANGEBIO), Centro de Investigación y Estudios Avanzados del IPN (CINVESTAV)

summary: Transcriptional profiling of roots from 12 days-old Arabidopsis thaliana seedlings transfered to Pi-deficient medium in hydroponic solution in a 10 min, 30 min, and 2 hrs time course period.

overall_design: A dye balanced modified loop design was implemented. This experiment involved a total of twelve sets of microarray hybridizations, including direct and dye swap comparisons between treatments as well as across time points for the same treatment. This design allowed us to determine differences in gene expression between Pi-deprived and control seedlings, and whether the differences were time dependent. Four biological replicates representing each sampling point were obtained.

first: Alatorre-Cobos

last: Fulgencio

first: Calderón-Vázquez

last: Carlos

first: Ibarra-Laclette

last: Enrique

first: Yong-Villalobos

last: Lenin

first: Pérez-Torres

last: Claudia-Anahí

first: Oropeza-Aburto

last: Araceli

first: Méndez-Bravo

last: Alfonso

first: González-Morales

last: Sandra-Isabel

first: Alanís-Gutiérrez

last: Dolores

first: Chacón-López

last: Alejandra

first: Peña-Ocaña

last: Betsy-Anaid

first: Herrera-Estrella

last: Luis


title: The DNA Double-Strand Break Response Is Abnormal in Myeloblasts From Patients With Therapy-Related Acute Myeloid Leukemia [NimbleGen]

first: Matt

last: Walter

address: 4940 parkview

department: oncology

institute: washington university in st.louis school of medicine

summary: In order to examine if acquired copy number alterations in DNA repair genes is commonly observed in therapy-related AML, we used this custom built NimbleGen array with dense tiling of probes in 170 DNA repair genes to interrogate paired normal (skin) and tumor (bone marrow) samples.

overall_design: DNA was extracted from bone marrow cells or skin biopsy samples  taken directly from patients after written informed consent. DNA was labeled and hybridized to custom built NimbleGen array CGH chips containing dense tiling in 170 DNA repair genes to detect copy number amplification.

first: Meagan

last: Jacoby

first: Rigoberto

last: de Jesus Pizarro

first: Jin

last: Shao

first: Daniel

last: Koboldt

first: Robert

middle: S

last: Fulton

first: Gongfu

last: Zhao

first: Richard

middle: K

last: Wilson

first: Matthew


title: MiRNA Expression data from human radioresistant and radiosensitive Nasopharyngeal Carcinoma Cells

status: Public on Dec 10 2013

city: Changsha

first: Jia-Quan

last: QU

state: Hunan

address: Xiangya street No.87

department: Xiangya Hospital

country: China

institute: Central South University

summary: Most of the NPC patients suffer from local recurrences and distant metastases within 1.5 years after radiotherapy due to radioresistance. Distinct patterns of miRNa expression and signatures were found in NPC, and have been used to associate them with cell proliferation, apoptosis, invasion and metastasis, but few miRNA expression profiling studies have been focused on the tumor radioresistance.We used miRNA expression microarray analyses to identify the difference of miRNA in radioresistant NPC CNE2-IR cells and radiosensitive CNE2 cells.

overall_design: Radioresistant subclone of nasopharyngeal carcinoma CNE2-IR cell line was cultured and produced according to the experienment schedule to undergo five rounds of sublethal dose of irradiation (11 Gy),and the parent cell line CNE2 sensitive to radiotherapy as the control

first: Zhiqiang

last: Xiao

first: Xinhui

last: Li

first: Jiaquan

last: Qu


title: Transcriptomic analysis of chic embryos forebrain lacking Notch signalling

city: Rennes

first: Valérie

last: Dupé

address: 2 av leon Bernard

summary: The generation of diverse neuronal types and subtypes from multipotent progenitors during development is crucial for assembling functional neural circuits in the adult central nervous system. It is well known that Notch signalling pathway through the inhibition of proneural genes is a key regulator of neurogenesis in the vertebrate central nervous system. However, its role during hypothalamus formation along with its downstream effectors remains poorly defined. Here, we have transiently blocked Notch activity in chick embryos and used global gene expression analysis to provide evidence that Notch signalling modulates the generation of neurons in the early developing hypothalamus by lateral inhibition. Most importantly, we have taken advantage of this model to identify novel targets of Notch signalling, such as Tagln3 and Chga, which were expressed in hypothalamic neuronal nuclei. This data gives essential advances into the early generation of neurons in the hypothalamus. We demonstrate that inhibition of Notch signalling during early development of the hypothalamus enhances expression of several new markers. These genes must be considered as important new targets of the Notch/proneural network.

overall_design: Four sets of samples were used for analysing transcriptome changes in DAPT treated chicl embryos. The rostral part of the head (including the anterior forebrain, optic vesicles and overlying tissue) was collected from control embryos and DAPT-treated embryos at stage HH13.

first: Leslie

last: Ratié

first: Véronique

last: David


title: Microarray analysis to detect whether the genome-wide gene expression profile of fibroblast-induced neurons resembles primary neurons

status: Public on Dec 05 2013

city: Beijing

first: Jianwei

last: Jiao

state: Beijing

address: 1 Beichen West Road

department: State Key Laboratory of Reproductive Biology

institute: Institute of Zoology, Chinese Academy of Sciences

summary: To explore more details in the similarities and differences between ABN+Rarg+Nr5a2 iN cells and primary neurons, we compared the global gene expression pattern of matured iN cells 12 days post infection with mouse primary neurons and MEFs by microarray analysis.

overall_design: In the study presented here, a total of 26423 unique genes were detected in primary mouse embryonic fibroblasts, induced neurons from MEFs by Ascl1+Brn2+Ngn2+Rarg+Nr5a2 at 12 days after infection and primary neurons from postnatal day 0 hippocampus, leading to more details about the similarities and differences among the three groups.

first: Zixiao

last: Shi


title: Impact of intramammary treatment on gene expression profiles of bovine mammary gland tissue after challenge with E. coli

city: Ithaca

first: Anja

last: Sipka

state: NY

address: S3 114 Schurman Hall

department: Population Medicine and Diagnostic Sciences

institute: Cornell University College of Veterinary Medicine

summary:
The benefit of treatment in mild to moderate cases of E. coli mastitis in dairy cows remains a topic of discussion.
We investigated the effect of intramammary treatment with Cefapirin + Prednisolone compared to Cefapirin only on gene expression profiles in experimentally induced E. coli mastitis.

overall_design: Five midlactating Holstein Friesian cows were challenged with 100 CFU in 3 quarters and treated with Cefapirin only in one quarter and the combination of Cefaprirn and Prednisolne in another quarter at 4, 12, 24 and 36h post challenge. After 24h (n=2) or 48h (n=3) post challenge cows were sacrificed and mammary gland tissue was collected from each quarter. From each cow total RNA of one non challenged quarter, one challenged not treated quarter, on Cefapirin treated and one Cefapirin + Prednisolone treated quarter was subjected to microarray analysis. Data were analyzed separately for the two sample time points

first: Suzanne

last: Klaessig

first: Gerald

last: Duhamel

first: Andrew

last: Skidmore

first: Jantijn

last: Swinkels

first: Pascal

last: Rainard

first: Ynte

last: Schukken


title: Gene expression profiling to identify uterine chicken proteins associated with the supply of minerals and potentially actives on the biomineralisation process during eggshell formation

city: Nouzilly

first: Joel

last: Gautron

address: UR83 Recherches avicoles

institute: INRA

summary: We used a transcriptomic approach based on the comparison of the expression in the uterine tissue when an hard-shelled egg was in calcification (normal) versus uterine tissue collected after premature expulsion of the egg before mineralization has begun (expelled) to better appreciate which uterine chicken proteins are associated with the supply of minerals and potentially actives on the biomineralisation process during eggshell formation.

overall_design: A total of 16 microarray slides were used for hybridization of the 8 uterine tissues collected when an hard-shelled egg was in calcification (normal), and mixed to the 8 uterine tissues collected after premature expulsion of the egg before mineralization has begun (expelled) were analysed, with an experimental design in dye swap (all the slides labeled with fluorophore Alexa 555 and with Alexa 647 for each condition).

first: A

last: Brionne

first: J

first: C

last: Hennequet-Antier

first: Y

last: Nys


title: Expression Profiles of PMH treated with 7µM of the genotoxic compound cisplatin

city: Maastricht

first: Linda

last: Rieswijk

address: Universiteitssingel 50

department: Toxicogenomics

institute: Maastricht University

summary: The transcriptomic changes induced in primary mouse hepatocytes (C57BL/6 ) by  7µM of cisplatin after treatment for 24 and 48h

overall_design: The study investigated differential gene expression in PMH mRNA following 24 and 48 hours of exposure to  7µM of cisplatin and its solvent. Three biological replicates per compound/solvent. In total 12 arrays.


title: Characterization of cisplatin-induced transcriptomics responses in primary mouse hepatocytes, HepG2 cells and mouse embryonic stem cells shows a strong conservation of involved transcription factors

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Expression data from OCI Ly3 SP vs. nonSP cells

status: Public on Dec 07 2013

city: Goettingen

first: Raphael

last: Koch

address: Robert Koch Str

department: Hematology

country: Germany

institute: University Medicine of Goettingen

summary: Gene expression profile OCI Ly3 Side Population Cells vs non Side Population

overall_design: OCI Ly3 cells were cultured and stained with Hoechst33342. FACS analysis identified a distinct Side Population. Side Population Cells were sorted separatly from nonSide Population cells. We used microarray analysis to identify differentialy expressed genes.

first: Koch

last: Raphael

first: Wulf

last: Gerald


title: Quality control of spliced mRNAs requires the shuttling SR-proteins Gbp2 and Hrb1

status: Public on Dec 04 2013

city: Göttingen

first: Klaus

last: Jung

address: Humboldtallee 32

department: Medical Statistics

institute: University Medical Center Göttingen

type:
Expression profiling by array
Other

summary: Eukaryotic cells have to prevent the export of unspliced pre-mRNAs until intron removal is completed to avoid the expression of aberrant and potentially harmful proteins. Only mature RNAs associate with the export receptor Mex67 (mammalian TAP) and enter the cytoplasm. The underlying nuclear quality control mechanisms are still unclear. Here we show that two shuttling SR-proteins Gbp2 and Hrb1 are key surveillance factors for the selective export of spliced mRNAs in yeast. Their absence leads to the significant leakage of unspliced pre-mRNAs into the cytoplasm. They bind to pre-mRNAs and the spliceosome during splicing, where they are necessary for the surveillance of splicing and the stable binding of the TRAMP-complex to the spliceosome-bound transcripts. Faulty transcripts are marked for their degradation at the nuclear exosome. On correct mRNAs the SR-proteins recruit Mex67 upon completion of splicing to allow a quality controlled nuclear export. Altogether, these data identify a role for shuttling SR-proteins in mRNA surveillance and nuclear mRNA quality control.

overall_design: 6 samples, i.e. 2 replicates per protein Gbp2, Hrb1 and Npl3

last: Hackmann

first: H

last: Wu

first: U

last: Schneider

first: K

last: Meyer

last: Krebber


title: Gene expression timecourse in ΔrpaA strain

first: Joseph

middle: Scott

last: Markson

address: 52 Oxford St, Room 445

department: Molecular and Cellular Biology

institute: Harvard Univ / Howard Hughes Medical Institut

summary: The goal of the experiment was to determine whether gene expression oscillates in the absence of rpaA.  It was reported previously (e.g., Takai et al, PNAS 2006) that activity of a handful of individual expression reporters was arrythmic, and we conducted this microarray timecourse to determine whether expression is arrhythmic geneome-wide.

sample_organism: Synechococcus elongatus PCC 7942 = FACHB-805

overall_design: Cultures were grown in a turbidostat as described previously (Vijayan et al, PNAS 2009).  Cultures were entrained with two consecutive light/dark cycles and released into continuous light at time T = 0.  Cultures were samples every 4 hours for 48 h between T = 24 h and T = 72 h, inclusive.  Gene expression at each timepoint was compared to the time-averaged gene expression (determined using a pool of equal mass quantities of RNA from all timepoints) using a two-color Agilent microarray.

last: Piechura

first: Anna

middle: M

last: Puszynska

first: Erin

last: O'Shea


title: Microarray analysis of gene response to contaminant accumulation in wild largescale suckers

city: Costa Mesa

first: Alvine

middle: C

last: Mehinto

address: 3535 Harbor Blvd, Suite 110

institute: Southern California Coastal Water Research Project

summary: Toxic compounds such as organochlorine pesticides (OCs), polychlorinated biphenyls (PCBs), and polybrominated diphenyl ether flame retardants (PBDEs) have been detected in fish, birds, and aquatic mammals that live in the Columbia River or use the river as a food source. We developed a custom microarray for largescale suckers (Catostomus macrocheilus) and used it to investigate the molecular effects of contaminant exposure on wild fish in the Columbia River. Using Significance Analysis of Microarrays (SAM) we identified 72 probes representing 69 unique genes with expression patterns that correlated with hepatic tissue levels of OCs, PCBs, or PBDEs. These genes were involved in many biological processes previously shown to respond to contaminant exposure, including drug and lipid metabolism, apoptosis, cellular transport, oxidative stress, and cellular chaperone function. The relation between gene expression and contaminant burden suggests that these genes may respond to environmental contaminant exposure and are promising candidates for further field and laboratory studies to develop biomarkers for monitoring exposure of wild fish to contaminant mixtures found in the Columbia River Basin

overall_design: Correlation between contaminant exposure and gene expression profiles of wild largescale suckers collected from three different sites in the Columbia River. At each site, liver samples of six to eight different fish were analyzed using microarrays.

first: Helena

last: Christiansen

first: Fahong

last: Yu

first: Russell

last: Perry

first: Nancy

last: Denslow

first: Alec

middle: G

last: Maule

first: Matthew

last: Mesa


title: Transcriptional profiling of Streptococcus mutans UA159 grown in continuous culture using TV media supplemented with 10 mM versus 100 mM glucose.

status: Public on Dec 03 2013

city: Gainesvile

first: Zachary

last: Moye

state: Florida

address: 1395 Center Dr. Box 100424

department: Oral Biology

institute: University of Florida

summary: The genetic and phenotypic responses of Streptococcus mutans, an organism known to be strongly associated with the development of dental caries, to changes in carbohydrate availability were investigated. S. mutans UA159 or a derivative of UA159 lacking ManL, which is the EIIAB component (EIIABMan) of a glucose/mannose permease of the phosphoenolpyruvate:sugar phosphotransferase system (PTS) and a dominant effector of catabolite repression, were grown in continuous culture to steady-state in conditions of excess (100 mM) or limiting (10 mM) glucose. Microarrays using RNA from S. mutans UA159 revealed that 174 genes were differentially expressed in response to changes in carbohydrate availability (P < 0.001). Glucose-limited cells possessed higher PTS activity, could acidify the environment more rapidly and to a greater extent, and produced more ManL protein than cultures grown with excess glucose. Loss of ManL adversely affected carbohydrate transport and acid tolerance. Comp  arison of the HPr protein in S. mutans UA159 and the manL deletion strain indicated that the differences in behaviors of the strains were not due to major differences in HPr pools or HPr phosphorylation status. Therefore, carbohydrate availability alone can dramatically influence the expression of physiologic and biochemical pathways that contribute directly to the virulence of S. mutans, and ManL has a profound influence on this behavior.

overall_design: A two-condition experiment was performed. Cells of UA159 were grown in continuous culture using TV media supplemented with 10 mM or 100 mM glucose. Three biological replicates were generated per condition, and replicates were independently grown and harvested. One replicate was used per array.

first: Lin

last: Zeng

first: Robert

last: Burne


title: Plasmodium berghei Gametocytogenesis

city: Glasgow

first: Katie

middle: Ruth

last: Hughes

address: 120 University Place

department: GBRC, III, Wellcome Centre for Molecular Parasitology

institute: University of Glasgow

summary:
Transcriptional profiling of gametocyte non-producer lines in Plasmodium berghei
Transcriptome of gametocyte non producer lines (natural and genetic KO) and parental (820) lines.  The aim of the study was to identify key genes involved in the decision to commit to gametocytogenesis in Plasmodium berghei. These microarrays compare naturally selected lines that do not produce gametocytes, and the parental line and additionally a genetic knock out of AP2-G PBANKA_143750.  Data published Sinha, Hughes, et, al Nature tbc.

overall_design: 2- colour microarray comparing to common background pool (containing all life cycle stages). Replicates of different life cycle stages of gametocyte non-producer lines and wild tye (WT) parental control lines

middle: R

first: Abhinav

last: Sinha

first: Andy

last: Waters


title: Identification of Smaug target mRNAs in the early Drosophila embryo using RIP-Chip

city: Toronto

first: Howard

middle: D

last: Lipshitz

state: ON

address: 1 King's College Circle

department: Molecular Genetics

country: Canada

institute: University of Toronto

summary: To identify Smaug’s target mRNAs on a genome-wide scale we used ribonucleoprotein (RNP) co-immunoprecipitation followed by microarray analysis of the co-purifying mRNAs (RIP-Chip). Extracts, prepared from wild-type embryos collected 0-3 hours post-egglaying, were immunoprecipitated with an anti-Smaug antibody (Smaug RIPs) while control immunoprecipitations using non-immune serum served as a negative control (control RIPs). Genome-wide transcript expression in wild-type embryos were also assessed and used as reference.

overall_design: There are 11 array experiments presented here: 1. gene expression profiling of total mRNA sample extracted from wild-type 0-3 hour embryos (3 technical replicates performed using a pooled input reference sample); 2. RNA co-immunoprecipitations of endogenous Smaug (Smaug RIPs) from wild-type 0-3 hour embryos (3 biological replicates and 1 technical replicates); 3. control RNA co-immunoprecipitations (control RIPs) from wild-type 0-3 hour embryos (3 biological replicates and 1 technical replicates).

first: Linan

last: Chen

first: Jason

last: Dumelie

first: Xiao

last: Li

middle: H

last: Cheng

first: Zhiyong

last: Yang

first: John

last: Laver

first: Najeeb

middle: U

last: Siddiqui

first: J

middle: T

last: Westwood

first: Quaid

last: Morris

first: Craig

last: Smibert


title: Identiﬁcation of genes responsible for biosynthesis of kojic acid in Aspergillus oryzae

city: Tsukuba

first: Myco

last: Umemura

address: Higashi 1-1-1

department: Bioproduction Research Institute

institute: National Institute of Advanced Industrial Science and Technology (AIST)

summary: Kojic acid is produced in large amounts by Aspergillus oryzae as a secondary metabolite and is widely used in the cosmetic industry. Glucose can be converted to kojic acid, perhaps by only a few steps, but no genes for the conversion have thus far been revealed. Using a DNA microarray, gene expression proﬁles under three pairs of conditions signiﬁcantly affecting kojic acid production were compared. All genes were ranked using an index parameter reﬂecting both high amounts of transcription and a high induction ratio under producing conditions. After disruption of nine candidate genes selected from the top of the list, two genes of unknown function were found to be responsible for kojic acid biosynthesis, one having an oxidoreductase motif and the other a transporter motif. These two genes are closely associated in the genome, showing typical characteristics of genes involved in secondary metabolism.

overall_design: Analysis in two-color microarray experiments used total RNA isolated from A. oryzae mycelia in three pairs of kojic acid producing to non(less)-producing conditions.  The pairs of culture conditions were: 4 d to 2d; 7d to 4d; nitrate(-) to nitrate(+) in kojic acid producing medium.

first: Y

last: Terabayashi

first: M

last: Sano

first: N

last: Yamane

first: E

last: Ohshima

first: K

last: Tachibana

last: Higa

first: S

last: Ohashi

first: H

last: Koike

last: Machida


title: Comparison of gene expression in ΔrpaA strain and wild-type strain

city: Cambridge

first: Joseph

last: Markson

summary: The goal of the experiment was to determine the difference in gene expression between the wild-type strain and a strain lacking rpaA (ΔrpaA).  Because gene expression is not at steady-state in the wild-type -- it oscillates with a circadian period -- and we did not know a priori whether it is at steady-state in the ΔrpaA strain, we compared the time-averaged gene expression in the wild-type to the time-averaged gene expression in the ΔrpaA strain.

platform_organism: Synechococcus elongatus PCC 7942 = FACHB-805

overall_design: Cultures were grown in a turbidostat as described previously (Vijayan et al, PNAS 2009).  Cultures were entrained with two consecutive light/dark cycles and released into continuous light at time T = 0.  Cultures were samples every 4 hours for 20 h between T = 24 h and T = 44 h, inclusive (no 4 h sample was acquired because, in a circadianly-oscillating culture, it would be duplicative with the 24 h timepoint).  A pool of RNA representing time-averaged wild-type RNA was constructed by pooling equal mass quantities of RNA from each wild-type timepoint.  A pool of RNA representing time-averaged RNA for the ΔrpaA strain was constructed by pooling equal mass quantities of RNA from each ΔrpaA timepoint.  These two pooled RNA samples were compared by two-color Agilent microarray.  To correct for dye biases, two microarrays were performed -- one in which the ΔrpaA pool was labeled with Cy3 and the wild-type pool was labeled with Cy5, and another in which the dyes were swapped.  In the manuscript, the average log2 ratio value from these two microarrays was employed (average of log2(ΔrpaA/wild-type) = 0.5 * (log2(ΔrpaA Cy3 / wild-type Cy5) - log2(wild-type Cy3 / ΔrpaA Cy5)), with the minus sign correcting for the sign changed caused by the dye swap).  See supplementary file linked at foot of Series record.

last: Piechura

first: Anna

last: Puszynska

first: Erin

last: O'Shea


title: Differential gene expression in ap2-g and ap2-g2 mutants of Plasmodium berghei

first: Katarzyna

middle: Kinga

last: Modrzynska

address: Genome Campus

department: Malaria program

institute: Wellcome Trust Sanger Institute

summary: Commitment to and completion of sexual development are essential for malaria parasites to be transmitted through mosquitoes. The molecular mechanism(s) responsible for these processes however, remain largely unknown. We have identified two transcription factors (both belonging to the AP2 family) essential for gametocytogenesis. AP2-G mutants are characterised by a complete inability to produce gametocytes. In AP2-G2 mutants the gametocytaemia is very significantly reduced but not completely abolished. We have performed the microarray experiments in order to cokmpare the transcriptomes of these mutantnts to the WT parasites and between each other. As P.berghei parasites are characterised by asynchronous development in the rodent host, the different stage composition of the sample would impact the analysis. Therefore parasites were harvested and matured in in vitro to the schizont stage

overall_design: Pairwaise comparison between the mutants and parental line was performed. 3 biological replicates of each condition were used.

first: O

last: Billker


title: Gene expression of non-typeable Haemophilus influenzae strain R2866 and R2866Δ0112 mutant grown in supplemented brain-heart infusion medium for 4 hours

first: Jeroen

middle: Daniel

last: Langereis

address: PO Box 9101

institute: Radboud University Medical Centre

summary:
Gene expresison profiles of the R2866 WT and  R2866Δ0112 mutant gorwn 4 hours in supplemented brain-heart infusion medium. This experiment was conducted  to determine the effects of R2866_0112 gene deletion on overall gene expression profile.
The results from this study are further discussed in: Modified lipooligosaccharide structure protects nontypeable Haemophilus influenzae from IgM-mediated complement killing in experimental otitis media.  Langereis JD, Stol K, Schweda EK, Twelkmeyer B, Bootsma HJ, de Vries SP, Burghout P, Diavatopoulos DA, Hermans PW. MBio. 2012 Jul 3;3(4):e00079-12. doi: 10.1128/mBio.00079-12. Print 2012.

overall_design:
R2866 wild-type (n=4) and R2866Δ0112 mutant (n=4) were grown for 4 hours in supplemented brain-heart infusrion medium
The 4hr and 7hr analyses were performed separately and, therefore, the background corrections are different between the two experiments.

first: Kim

last: Stol

first: Elke

last: Schweda

first: Brigitte

last: Twelkmeyer

first: Hester

middle: J

last: Bootsma

first: Stefan

last: de Vries

first: Peter

last: Burghout

first: Dimitri

middle: A

last: Diavatopoulos

last: Hermans


title: miRNA expression signatures in heart tissues of mice simulating posttraumatic stress disorder (PTSD) [Study1]

city: Seattle

first: Ji-Hoon

last: Cho

state: WA

address: 401 Terry Avenue North

institute: Institute for Systems Biology

summary: Using a PTSD mouse model, we investigated the longitudinal transcriptomic changes in heart tissues after the exposure to stress through intimidation

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

overall_design: We designed our initial study (Study I) with four experimental conditions where we varied the length of time that subservient mice were exposed to aggressor mice and the length of rest time after the exposure.  The conditions included were short exposure-short rest (T5R1-T indicates the number of days of trauma exposure; R indicates the number of days of rest after exposure), short exposure-long rest (T5R10), long exposure-short rest (T10R1) and long exposure-long rest (T10R42)

first: Kai

last: Wang

first: Inyoul

last: Lee

first: Rasha

last: Hammamieh

first: David

last: Baxter

first: Kelsey

last: Scherler

first: Alton

last: Etheridge

first: Yue

last: Yuan

first: Sara

last: McClarty

first: Alena

last: Kulchenko

first: Aarti

last: Gautam

first: Seid

last: Muhie

first: Nabarun

last: Chakraborty

first: Marti

last: Jett

last: Galas

first: Leroy

last: Hood


title: DamID of Dam::LMN-1 and Dam::EMR-1 in Caenorhabditis elegans adult worms

status: Public on Dec 02 2013

city: Seville

first: Peter

last: Askjaer

address: UPO Carretera de Utrera km 1

country: Spain

institute: Centro Andaluz de Biología del Desarrollo

summary:
Laminopathies are caused by mutations in components of the nuclear envelope (NE). While most NE components are widely expressed, laminopathies affect only a subset of tissues. However, the understanding of the molecular mechanisms that explain this phenomenon is still elusive.
Here we have performed a genome wide DamID analysis in adult C. elegans nematodes comparing the DNA association profile of two components of the NE, Lamin/LMN-1 and Emerin/EMR-1. Although both proteins were associated to silent DNA, EMR-1 showed a predominant role in the anchoring of muscle and neuronal promoters to the nuclear periphery. Deletion of either EMR-1 or LEM-2, another integral NE protein, caused local changes in nuclear architecture with both increased and decreased LMN-1 association.

overall_design: Comparison of Dam::LMN-1 and Dam::EMR-1 DNA assotiation in wild type strains and Dam::LMN-1 DNA association in wild type, lem-2(tm1582) and emr-1(gk119) mutant backgrounds.

first: Cristina

last: González-Aguilera


title: Gene expression timecourse in clock rescue strains

first: Joseph

last: Markson

summary: The goal of this experiment was to determine whether global circadian gene expression oscillation depends strictly on the presence of rpaA, even when the KaiABC post-translational oscillator is oscillating with a circadian period.  Strains deleted for rpaA lack functional KaiABC post-translational oscillators because their reduced kaiBC expression level leads to a non-permissive Kai protein stoichiometry.  We restored KaiABC post-translational oscillator function in a ΔrpaA ΔkaiBC strain by ectopic expression of kaiBC from the Ptrc promoter and used microarrays to measure the timecourse of gene expression globally.  As a control, we used microarrays to measure the gene expression timecourse in a ΔkaiBC Ptrc::kaiBC strain, in which gene expression was expected to be rhythmic (Y Murayama et al, J. Bac. 198, 2008), as it is in the pure wild-type strain.

overall_design: Cultures were grown in a flasks bubbled with 1% CO2 in air, initially in the absence of IPTG.  Cultures were treated with two consecutive light/dark cycles and released into continuous light at time T = 0, at which time IPTG was added to a final concentration of 6 µM.  Cultures were samples every 4 hours for 44 h between T = 24 h and T = 68 h, inclusive.  Gene expression at each timepoint was compared to the time-averaged gene expression (determined using a pool of equal mass quantities of RNA from all timepoints) using a two-color Agilent microarray.

last: Piechura

first: Anna

last: Puszynska

first: Erin

last: O'Shea


title: Microarray analysis of alternative splicing in PTBP2 knockout mouse brain

status: Public on Dec 01 2013

city: Los Angeles

first: Areum

last: Han

address: 6577 MacDonald Research Lab. 675 Charles E. Young Dr. South

institute: UCLA

summary: The splicing regulator PTBP2 controls a program of embryonic splicing required for neuronal maturation. The splicing regulatory proteins PTBP1 and PTBP2 show distinct temporal expression profiles in the developing brain. Neuronal progenitor cells predominantly express PTBP1, whereas developing neurons express high levels of PTBP2, which are subsequently reduced late in neuronal maturation. We show here that PTBP2 and the program of splicing it controls are essential to proper neuronal maturation and survival. To investigate its in vivo function, we generated conditional PTBP2 null alleles in mice. Loss of PTBP2 in neuronal progenitor cells leads to neonatal death without gross defects in brain architecture. Mice with specific depletion of PTBP2 in the cortex and forebrain are viable. However over the first three postnatal weeks, when the normal cortex expands and develops mature circuits, the PTBP2 null cortices degenerate. We find that PTBP2-/- neurons cultured from embryonic brain show the same initial viability as wild type cells with proper early marker expression and neurite outgrowth. Strikingly, between 10 and 20 days in culture PTBP2 null neurons undergo a catastrophic failure to mature and die. To assess the target transcripts leading to these phenotypes, we examined the genomewide splicing changes in the PTBP2 null brains. This identified a large number of mis-regulated exons that share a temporal pattern of regulation; in the absence of PTBP2 many isoforms normally found in adults are precociously expressed in the developing brain. Transcripts following this pattern encode essential neuronal proteins affecting neurite growth, pre- and post-synaptic assembly, and synaptic transmission. Our results define a new genetic regulatory program essential for neuronal survival and maturation, where PTBP2 acts to temporarily repress expression of protein isoforms until the final maturation of the neuron.

overall_design: Mice carrying a conditional floxed PTBP2 allele of PTBP2 were crossed to mice carrying Cre recombinase driven by the nestin promoter. The resulting knockout mutant mouse brains were analyzed for changes in gene expression and alternative splicing. Knockout mice were compared to wildtype littermates. Whole mouse brain polyA plus RNA was isolated from three Nestin-cre knockout embryos at embryonic day 18 and compared to three wildtype littermates. RNA was converted to cDNA and used to probe Affymetrix MJAY splicing sensitive microarrays and analysed by Omniviewer to identify changes in splicing.

first: Qin

last: Li

first: Sika

last: Zheng


title: Efficient identification of microRNAs for classification of tumor origin (II)

city: Lund

first: Rolf

last: Søkilde

address: Scheelevägen 2

department: Department of Oncology

country: Sweden

institute: Lund University, Sweden

summary: Carcinomas of unknown primary origin constitute 3-5% of all newly diagnosed metastatic cancers, of which the primary source is difficult to classify with current histological methods. Effective cancer treatment depends on early and accurate identification

overall_design: 220 samples

first: Thomas

last: Litman


title: Efficient identification of microRNAs for classification of tumor origin (I)

summary: Carcinomas of unknown primary origin constitute 3-5% of all newly diagnosed metastatic cancers, of which the primary source is difficult to classify with current histological methods. Effective cancer treatment depends on early and accurate identification of the tumor, which is why patients with metastases of unknown origin have poor prognosis and short survival. Because microRNA expression is highly tissue specific, the microRNA profile of a metastasis may be used to identify its origin. As a first step to realize this goal, we evaluated the potential of microRNA profiling for identification of the primary tumor of known metastases.   208 formalin-fixed paraffin-embedded samples representing 15 different histologies were profiled on an LNA-enhanced microarray platform, which allows for highly sensitive and specific detection of microRNA. Based on these data, we developed and cross-validated a novel classification algorithm, LASSO (Least Absolute Shrinkage and Selection Operator), which had an overall accuracy of 85%. When the classifier was applied on an independent test set of 48 metastases, the primary site was correctly identified in 42 cases (88% accuracy).  Our findings suggest that microRNA expression profiling on paraffin tissue can efficiently predict the primary origin of a tumor, and may provide pathologists with a molecular diagnostic tool that can improve their capability to correctly identify the origin of hitherto unidentifiable metastatic tumors, and eventually, enable tailored therapy.

overall_design: 94 samples


title: MALDI imaging MS reveals candidate lipid markers of polycystic kidney disease

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

summary:
Autosomal recessive polycystic kidney disease is a severe, monogenetically inherited kidney and liver disease and PCK rats carrying the orthologous mutant gene serve as a model of human disease. We combined selective MALDI imaging of sulfated kidney lipids and Fisher discriminant analysis of imaging data sets for identification of candidate lipid markers of progressive disease in PCK rats. Our study highlights strong increases in lower mass lipids as main classifiers of cystic disease. Structure determination by high resolution mass spectrometry identifies these altered lipids as taurine-conjugated bile acids. Beside increased levels of serum-cholesterol these sulfated lipids are selectively elevated in the PCK rat model but not in models of related hepatorenal fibrocystic diseases suggesting that they be molecular markers of the disease.
Genome-scale gene expression profiling of PCK and SD livers as control was performed to attempt elucidation of some of the underlying mechanisms leading to increases of cholesterol and taurine-conjugated bile acids in the PCK rat. Several pathways were found to be changed in cystic livers with up regulation or down regulation of important gene sets. Enhanced expression of steroid biosynthesis genes might result in the observed increased levels of cholesterol. In contrast, primary bile acid biosynthesis was found to be down regulated in diseased livers. These findings might be explained by compensatory mechanisms of liver metabolism to reduce toxic levels of accumulated bile acids.

overall_design: Snap-frozen liver tissue of 10 week old rats were subjected for RNA extraction and hybridization on Affymetrix microarrays to perform genome-scale gene expression profiling of n = 6 diseased PCK and n = 6 Sprague Dawley rat livers as control.

first: Hermelindis

last: Ruh

first: Theresia

last: Salonikios

first: Jens

last: Fuchser

first: Matthias

last: Schwartz

first: Bernhard

last: Wirnitzer

first: Norbert

last: Gretz

last: Hopf


title: AMPD2 Regulates GTP Synthesis and is Mutated in a Potentially-Treatable Neurodegenerative Brainstem Disorder

city: San Diego

first: Eric

last: Scott

state: California

address: 9500 Gilman Dr.

department: School of Medicine

institute: UC San Diego

summary: Purine biosynthesis and metabolism, conserved in all living organisms, is essential for cellular energy homeostasis and nucleic acids synthesis. The de novo synthesis of purine precursors is under tight negative feedback regulation mediated by adenine and guanine nucleotides. We describe a new early-onset distinct neurodegenerative condition resulting from mutations in the adenosine monophosphate deaminase 2 gene (AMPD2). Patients have characteristic brain imaging features of pontocerebellar hypoplasia (PCH), due to loss of brainstem and cerebellar parenchyma. We found that AMPD2 plays an evolutionary conserved role in the maintenance of cellular guanine nucleotide pools by regulating the feedback inhibition of adenosine derivatives on de novo purine synthesis. AMPD2 deficiency results in defective GTP-dependent initiation of protein translation, which can be rescued by administration of purine precursors. These data suggest AMPD2-related PCH as a new potentially treatable early-onset neurodegenerative disease.

overall_design: An 18 chip study, that compares iPSC derived neural progenitor cells from two individuals: a patient with pontocerebellar hypoplasia and an unaffected parent. Samples are run as either non-treated, treated with Adenosine, or treated with Adenosine and AICAr. Three replicates are included for every individuals in every treatment condition.

first: Naiara

last: Akizu

first: Vincent

last: Cantagrel

first: Joe

last: Gleeson


title: Efficient identification of microRNAs for classification of tumor origin

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

overall_design: Refer to individual Series


title: Natural blood feeding and temperature shift modulate the global transcriptional profile of Rickettsia rickettsii.

city: São Paulo

first: Maria

middle: Fernanda

last: Galletti

state: São Paulo

address: Av. Prof. Lineu Prestes, 1374 sala 39

department: Department of Parasitology

country: Brazil

institute: Universidade de São Paulo - Instituto de Ciências Biomédicas - Departamento de Parasitologia

middle: F

first: Andre

last: Fujita

first: Camila

last: Malossi

first: Marcelo

middle: B

last: Labruna

first: Adriano

last: Pinter

first: Joao

last: Soares

first: Milton

middle: Y

last: Nishiyama-Jr

first: Sirlei

last: Daffre

first: Andrea

last: Fogaça


title: Rickettsia rickettsii transcriptome - Elevation of temperature response

summary: One of the most important vectors of the Brazilian Spotted Fever, the tick Amblyomma aureolatum in Brazil was used in this study. We laboratorial controlled the infection of adult females of A. aureolatum with the virulent brazilian strain Taiacu of Rickettsia rickettsii. The group of ticks was divided into 2 testing groups, group 1 (G1) composed of adult females incubated at 25°C for 3 days and group 2 (G2) composed of adult females incubated at 35°C for 3 days. Right after incubation of both groups, ticks were individually dissected and all internal organs were transferred to RNAlater® Solution (Life Technologies) until gDNA and total RNA simultaneously isolation. A total of 14 ticks of each group were analyzed in two biological replicates (7 ticks each). Dye-swap was also applied to construct the technical replicate of each biological sample

overall_design: total RNA from both experimental samples (G1 and G2) was used for hybridization to dual channel arrays. Two biological replicates were used for each experimental group.


title: Rickettsia rickettsii transcriptome - Blood feeding response

summary: One of the most important vectors of the Brazilian Spotted Fever, the tick Amblyomma aureolatum in Brazil was used in this study. We laboratorial controlled the infection of adult females of A. aureolatum with the virulent brazilian strain Taiacu of Rickettsia rickettsii. The group of ticks was divided into 2 testing groups, group 2 (G2) composed of adult females incubated at 35°C for 3 days that were not fed after molting to adults and group 3 (G3) composed of adult females fed on its favorite natural host, the dog (Canis familiaris) also for 3 days. Right after incubation or feeding, ticks were individually dissected and all internal organs were transferred to RNAlater® Solution (Life Technologies) until gDNA and total RNA simultaneously isolation. A total of 14 ticks of each group were analyzed in two biological replicates (7 ticks each). Dye-swap was also applied to construct the technical replicate of each biological sample

overall_design: total RNA from both experimental samples (G2 and G3) was used for hybridization to dual channel arrays. Two biological replicates were used for each experimental group.


title: Circadian transcriptional profile of Synechococcus without KaiC phosphorylation cycling

status: Public on Nov 28 2013

city: Tokyo

first: Hideo

last: Iwasaki

address: TWIns 1F 2-2 Wakamatsu-cho, Shinjuku

department: Electrical Engineering & Bioscience

institute: Waseda University

summary:
In the unicellular cyanobacterium, Synechococcus elongatus PCC 7942, essentially all promoter activities are under the control of the circadian clock in continuous light (LL) conditions. Here, we employed high-density oligonucleotide arrays to investigate comprehensive profiles of genome-wide Synechococcus gene expression in the kaiCEE mutant strains in which the KaiC phosphorylation cycling is abolished under LL..
In the kaiCEE mutant strain more than 23% of transcripts significantly oscillated with a period of about 48 h. 409 cyclic genes were shared with the wild type strains.

overall_design:
kaiCEE mutant strain was analyzed under continuous light (LL) using Affymetrix high-density oligonucleotide microarrays (GeneChip CustomExpress Arrays) representing predicted 2,515 protein-coding genes on the genome of Synechococcus elongatus PCC 6301, which can be used also to the almost homologous strain, S. elongatus PCC 7942: a single experiment in kaiCEE mutant under LL from hour 8 to 96 in LL
timecourse data (8~96 hours under continuous light) from Synechococcus elongatus PCC 7942 (kaiCEE mutant) strains

first: Miki

last: Umetani


title: Revealing the genetic basis of natural bacterial phenotypic divergence

status: Public on Nov 30 2013

city: Ann Arbor

first: Lydia

last: Freddolino

state: MI

address: 1150 W. Medical Center Dr., MSRB 3 room 3315

department: Biological Chemistry

institute: University of Michigan

summary: Application of a genome-wide linkage method to identify genotype-phenotype relationships between distantly related strains of E. coli. Each hybridization compares transposon footprinting results from a linkage library under a selective condition with those under a nonselective condition.

overall_design: For each of three conditions, we compare transposon footprinting for a library selected under that condition with those under a reference condition (glucose minimal media). Each experiment was performed in duplicate.

first: Peter

middle: L

first: Hani

last: Goodarzi

first: Saeed

last: Tavazoie


title: Spider mite responses to feeding on Col-0, myb28 myb29 cyp79b2 cyp79b3, and atr1D Arabidopsis plants

status: Public on Nov 25 2013

city: Gent

first: Nicky

last: Wybouw

address: Coupure Links 653

department: Department of Crop Protection

country: Belgium

institute: University of Ghent

summary: Our goal was to investigate the transcriptional response of T. urticae to different Arabidopsis plants with varying levels of indole glucosinolates.

overall_design:
Bean is the ancestral host plant for the T. urticae strain used in this study. Adult female spider mites were transferred to the three Arabidopsis lines (Col-0, qKo, atr1D) or bean, and after 24 hours, the gene expression levels were analyzed.
12 samples were investigated; 4 biological replicates for three comparisons: QKO (qKo vs. Col-0), ATR1D (atr1D vs. Col-0), and COL-0 (Col-0 vs. bean).

first: Vladimir

last: Zhurov

first: Thomas

last: Van Leeuwen

first: Vojislava

last: Grbic


title: Real-time quantitative PCR analysis of mice lung tissue (1)

status: Public on Nov 26 2013

city: UNSW, SYDNEY

first: Kenneth

middle: K

last: Hsu

state: NSW

address: Rm422, 4E, Wallace Wurth Bld,

department: School of Medical Sciences

country: Australia

institute: University of New South Wales

summary: Recombinant-murine S100A8 and the corresponding Cys42 to Ala42 mutant were used at 10 mg/50 ml HBSS administered onto the nares of BALB/C mice. To assess direct effects, mice were sacrificed 1, 4, 6, 12 or 20 h post-inhalation of S100A8 or 12 and 20 h post-inhalation of Ala42S100A8. For comparison with Dex inhalation (used at 10 mg/50 ml HBSS), lungs were harvested 6 and 12 h post administration. Because S100A8 is reported to initiate proinflammatory responses by ligating TLR4 and/or RAGE, a quantitative PCR array was developed to analyse 63 genes, selected to reflect potential acute inflammatory changes induced by ligation of these receptors.

overall_design: Expression of inflammatory genes was evaluated with the RT-qPCR array. Relative quantities of mRNA in duplicate samples were obtained using the LightCycler® 480 Software 1.5 and the Efficiency-Method.

first: Yuka

last: Hiroshima


title: Real-time quantitative PCR analysis of mice lung tissue


title: Population level analysis of evolved mutations underlying improvements in plant cellulose and hemicellulose fermentation by Clostridium phytofermentans

status: Public on Nov 20 2013

city: Amherst

first: Jeffrey

last: Blanchard

state: MA

address: 203 Morrill Science Center IVN

department: Biology

country: USA

institute: University of Massachusetts Amherst

summary: The complexity of the plant cell walls creates many challenges for microbial decomposition.  Clostridium phytofermentans, an anaerobic bacterium isolated from forest soil, directly breaks down and utilizes many plant cell wall carbohydrates.  The objective of this research is to understand constraints on rates of plant decomposition by C. phytofermentans and identify molecular mechanisms that may overcome these limitations.  Experimental evolution via repeated serial transfers during exponential growth was used to select for C. phytofermentans genotypes that grow more rapidly on cellobiose, cellulose and xylan.  To identify the underlying mutations an average of 13,600,000 paired-end 100bp paired end reads were generated per population resulting in ~300 fold coverage of each site in the genome.  A mixture of alleles fixed in the population down to frequencies of 5% could be identified with statistical confidence.  Many mutations are in carbohydrate-related genes including the promoter regions of glycoside hydrolases and amino acid substitutions in ABC transport proteins involved in carbohydrate uptake, signal transduction sensors that detect specific carbohydrates, proteins that affect the export of extracellular enzymes, and regulators of unknown specificity.   Protein structural modeling of the ABC transporter complex proteins suggests that mutations in these genes may alter the recognition of carbohydrates by substrate-binding proteins and communication between the intercellular face of the transmembrane proteins and the ATPase binding protein.  Experimental evolution was effective in identifying molecular constraints on the rate of cellulose and hemicellulose fermentation and selected for putative gain of function mutations that do not typically appear in traditional molecular genetic screens.  The results reveal new strategies for evolving and engineering microorganisms for faster growth on plant carbohydrates.

overall_design: Experimental evolution via repeated serial transfers during exponential growth was used to select for C. phytofermentans genotypes that grow more rapidly on cellobiose.  Microarray analysis was performed on 1 time point from the evolved lines and the initial founder

first: Supratim

last: Mukherjee

first: Lynmarie

last: Thompson

first: Stephen

last: Godin

first: Wendy

last: Schackwitz

first: Joel

last: Martin

first: Anna

last: Lipzen


title: Roles of Snail-regulated miRNAs in colon cancer progression

city: Taipei

first: Wei-Lun

last: Hwang

address: No.155, Sec.2, Linong Street

department: Department of Biotechnology and Laboratory Science in Medicine

institute: National Yang Ming Chiao Tung University

summary: The transcription factor Snail is known as an EMT regulator to promote cancer metastasis. Identification Snail-regulated miRNAs helps to uncover mechanisms governing CRC metastasis

platform_organism:
Primates
Homo sapiens

overall_design: The stable SW480-vector and Snail-expressing cells were established for miRNA microarray analysis.

first: Hsei-Wei

last: Wang


title: Expression analysis of wild-type and transcription factor mutants in response to rapamycin

status: Public on Nov 15 2013

city: Austin

first: Vishy

last: Iyer

state: TX

address: 2500 Speedway Dr. MBB 3.212

department: Molecular Biosciences

institute: University of Texas at Austin

summary: Transcript level changes in transcription factor mutants after rapamycin treatment, compared to the wild-type strain. This data set accompanies the study "Widespread Misinterpretable ChIP-seq Bias in Yeast" (GSE51251)

overall_design: Four separate wild-type cultures of yeast were grown, and each culture was split into two. Then, one was treated with DMSO and the other one was treated with rapamycin. For transcription factor mutants, two separate cultures were grown, and rapamycin was treated in the same way as treated to the wild type. Total RNA was recovered from each culture, then labeled oligo was prepared following NimbleGene standard protocol. Each chip measures the expression levels of 5,777 genes from yeast.

first: Vishwanath


title: Expression data from longissimus dorsi of backcross Iberian x Landrace individuals

status: Public on Nov 22 2013

city: Madrid

first: Ana

middle: Isabel

last: Fernandez

state: Madrid

address: Ctra. Coruña Km7.5

department: Animal Breeding and Genetics

institute: INIA

summary:
The integration of the results of QTL fine-mapping with microarray expression data offers a promising tool for understanding the genetic mechanisms influencing complex traits as fatty acid composition in pigs. The expression level of each probe may be treated as a quantitative trait and the marker genotypes used to map loci with regulatory effect on the gene expression level (eQTL)
According to our previous linkage results, we carry out an eQTL scan focused on chromosomal regions showing tissue-consistent effects on fatty acids with Longissimus dorsi gene expression data in order to detect potentional candidate genes underlying the QTL previously detected.

overall_design: 102 IberianxLandrace backcross pigs were selected for RNA extraction and  hybridization on Affymetrix microarrays. An eQTL scan was carried out with the data of 470 probes of the microarray taking into account they were related with fatty acid metabolism

first: María

last: Muñoz

first: M

middle: C

last: Rodríguez

first: Estefania

last: Alves

first: Josep

middle: M

last: Folch

first: Noelia

last: Ibañez-Escriche

first: Luis

last: Silió

middle: I

last: Fernández


title: CpG island-specific demethylation pathway in ES cells

status: Public on Nov 17 2013

city: Jerusalem

first: Ofra

last: sabag

address: Ein kerem

country: Israel

institute: The Hebrew university

summary: Following erasure in the early animal embryo, a new bimodal DNA methylation pattern is regenerated at the time of implantation in each individual through a wave of generalized de novo modification with CpG islands specifically left unmethylated. In this paper, we ask whether CpG islands are “protected” from de novo methylation or, alternatively, acquire their unmodified state through “demethylation.” Using a genetic approach, we demonstrate that ES cells indeed have the ability to specifically demethylate CpG islands through pathways involving hydroxymethylation (Tet1), deamination (Aid), glycosylation (Mbd4) and excision repair (Gadd45a) genes. Surprisingly, this demethylation system is not actually necessary for generating the overall bimodal methylation pattern in ES cells. This general activity does, however, appear to be involved both in somatic cell reprogramming, as well as the normal methylation reprogramming that takes place in the early embryo.

overall_design: CpG-methylated genomic DNA was enriched using a methyl-DNA immunoprecipitation (mDIP) assay. DNA from the input and bound (enriched) DNA for each sample were labeled and hybridized on the array to define the methylation state of each region.

first: Howard

last: Cedar


title: Genes induced by IFN-beta, IFN-gamma or unphosphoraylted STAT1 in human fibroblasts

status: Public on Sep 18 2013

city: Cleveland

first: HyeonJoo

last: Cheon

state: OH

address: 9500 Euclid Ave

institute: Cleveland Clinic

summary:
A single high dose of IFNβ activates powerful cellular responses in which many antiviral, pro-apoptotic, and anti-proliferative proteins are highly expressed.  Since some of these proteins are deleterious, cells down-regulate this initial response rapidly.  However, the expression of many antiviral proteins that do no harm is sustained, prolonging a substantial part of the initial antiviral response for days and also providing resistance to DNA damage. While the transcription factor ISGF3 (IRF9 and tyrosine-phosphorylated STATs 1 and 2) drives the first rapid response phase, the related factor un-phosphorylated ISGF3 (U-ISGF3), formed by IFNβ-induced high levels of IRF9 and STATs 1 and 2 without tyrosine phosphorylation, drives the second prolonged response. The U-ISGF3-induced antiviral genes that show prolonged expression are driven by distinct interferon stimulated response elements (ISREs). Continuous exposure of cells to a low level of IFNβ, often seen in cancers, leads to steady-state increased expression of only the U-ISGF3-dependent proteins, with no sustained increase of other IFNβ-induced proteins, and to constitutive resistance to DNA damage.
We classified genes into U-ISGF3-induced genes and classical ISGF3-induced genes using microarray data. We identified 150 genes that are up-regulated by IFNβ after 6 h. Among these IFNβ-induced genes, only 29 (20%) were induced by the up-regulation of Y701F-STAT1, indicating that these are induced by U-ISGF3. Among the remaining 121 IFNβ-induced genes (150 minus 29), 73 are induced by IFNγ as well as IFNβ, and 48 are induced only by IFNβ.

overall_design: Total 5 RNA samples were analyzed in duplicate on microarray chips. Untreated cells and empty vector-transfected cells were the control of IFN treated cells and Y701F-STAT1-transfected cells, respectively.

first: George

middle: R

last: Stark


title: Metabolite stress response to butyric acid in Clostridium acetobutylicum ATCC 824

status: Public on Aug 20 2013

city: Newark

first: Eleftherios

middle: Terry

last: Papoutsakis

state: DE

address: 15 Innovation Way

department: Chemical Engineering

institute: University of Delaware

summary: Clostridium acetobutylicum is a Gram positive, endospore forming firmicute that has been known as the model organims for ABE (acetone-butanol-ethanol) fermentation. With its ability to consume a wide variety of substrates, C. acetobutylicum carries out a biphasic ABE fermentation, which consists of the acidogenic growth phase with the formation of butyric acid and acetic acid, followed by the solventogenic stationary phase with the formation of acetone, butanol and ethanol, characterised by the reassimilation of acids.  The production butanol is of renewed ineterest both as a potential biofuel and bulk chemical production. Both butanol and butyric acid posses toxic characteristic and here, we focus on understanding and modeling the stress response of C. acetobutylicum to one of the two important toxic metabolites: butyric acid.

overall_design: C. acetobutylicum cultures were grown, three biological replicates, to mid-exponential phase and then stressed with four levels of butyric acid (0 mM - No stress; 30 mM - Low stress; 40 mM - Medium stress; & 50 mM - High stress). Butyric acid was pH adjusted with 10M KOH to match the pH of the cultures, prior to addition. Samples were collected following the stress at 0, 15, 30, 45, 60 and 75 min, post stress. These sampling times, which are of the order of the doubling time of these cells, were meant to capture largely the direct and immediate impact of these stresses on gene expression.  The RNA extracted from two biological replicates were used for microarray hybridization foloowing cDNA generation and labelling using Agilent 44K arrays, while the third was used for q-RT-PCR validation. For each stress level, 6 time points with 2 biological replicates and dye swaps (Cy3/Cy5) were prepared for comparison. The hybridization was perfomed against an equal amount of oppositely labeled cDNA from common reference pool prepared using equal amounts of  labeled cDNA from all four stress levels.

first: Keerthi

middle: P

last: Venkataramanan

first: Shawn

middle: W

last: Jones


title: Host response to Bifidobacterium bifidum PRL2010 treatment as determined through global transcription profiling

status: Public on Nov 19 2013

city: Parma

first: Marco

last: Ventura

address: Viale delle Scienze 11/A

department: Dept. Life Sciences

institute: University of Parma


title: Real-time quantitative PCR analysis of mice lung tissue (2)

first: Kenneth

last: Hsu

first: Yuka

last: Hiroshima


title: Metabolite stress response to butanol in Clostridium acetobutylicum ATCC 824

summary: Clostridium acetobutylicum is a Gram positive, endospore forming firmicute that has been known as the model organims for ABE (acetone-butanol-ethanol) fermentation. With its ability to consume a wide variety of substrates, C. acetobutylicum carries out a biphasic ABE fermentation, which consists of the acidogenic growth phase with the formation of butyric acid and acetic acid, followed by the solventogenic stationary phase with the formation of acetone, butanol and ethanol, characterised by the reassimilation of acids.  The production butanol is of renewed ineterest both as a potential biofuel and bulk chemical production. Both butanol and butyrate posses toxic characteristic and here, we focus on understanding and modeling the stress response of C. acetobutylicum to one of the two important toxic metabolites: butanol.

overall_design: C. acetobutylicum cultures were grown, three biological replicates, to mid-exponential phase and then stressed with four levels of butanol (0 mM - No stress; 30 mM - Low stress; 60 mM - Medium stress; & 90 mM - High stress). Samples were collected following the stress at 0, 15, 30, 45, 60 and 75 min, post stress. These sampling times, which are of the order of the doubling time of these cells, were meant to capture largely the direct and immediate impact of these stresses on gene expression.  The RNA extracted from two biological replicates were used for microarray hybridization foloowing cDNA generationa nd labelling using Agilent 44K arrays, while the third was used for q-RT-PCR validation. For each stress level, 6 time points with 2 biological replicates and dye swaps (Cy3/Cy5) were prepared for comparison. The hybridization was perfomed against an equal amount of oppositely labeled cDNA from common reference pool prepared using equal amounts of  labeled cDNA from all four stress levels.

middle: T


title: Chronic kidney disease and splicing events

status: Public on Aug 16 2013

city: MARSEILLE

first: Stephane

last: BURTEY

address: 27, boulevard jean moulin

country: France

summary: Renal failure is associated with accumulation of various solutes called Uremic toxins. Post transcriptional regulation related to Chronic kidney disease (CKD) have already been described as RNA based silencing with micro RNA or modifications of mRNA degradation. Until now, alternative splice modification was not mentioned in the course of CKD. However, CKD is associated with modification of gene expression. The aim of the study was to explore modification of the alternative splice pattern in the course in CKD.

overall_design: The expression level of individual exons expression in human fibroblast were compared after culture to 96 hours of uremic condition or control condition. Three independant experiments were performed

first: Burtey

last: stephane

first: Sallee

last: Marion


title: ssa_1972-null mutant of Streptococcus sanguinis SK36

status: Public on Jul 17 2013

city: Tianjin

first: Lei

last: Chen

address: Weijin 92

department: School of Chemical Engineering

institute: Tianjin University

summary: Transcriptional profiling of ssa_1972-null mutant of Streptococcus sanguinis compared with wild type. The ssa_1972 gene was inactivated in Streptococcus sanguinis SK36 and transcriptional profile was compared with wild type SK36. More information can be found at http://www.people.vcu.edu/~pingxu

overall_design: One-condition experiment, Δssa_1972 vs S. sanguinis SK36 cells. Biological replicates: 3 wild type, 3  Δssa_1972, independently grown and harvested. One replicate (one wild type and one Δssa_1972 mixture) per array.

first: Xiuchun

last: Ge

first: Ping

last: Xu


title: Dose and temporal effects of Phenobarbital on the  liver miRNAome of male Fischer rats

status: Public on Jul 03 2013

city: London

first: Nigel

middle: J

last: Gooderham

address: South Kensington Campus

department: Biomolecular Medicine

institute: Imperial College London

summary: Male Fischer rats were fed a control diet or a diet supplemented with 50, 500 or 1000 ppm Phenobarbital. The 500 and 1000 ppm PB doses induced a transient hyperplasia and a sustained hepatomegaly in treated animals. The animals were sacrificed and liver miRNAome was profiled in three animals per group after 1, 3, 7, and 14 days of treatment. The aim was to investigate the time and dose dependent effects of phenobarbital treatment on the liver miRNAome

overall_design: Three animals were profiled from control or each treatment group after 1, 3, 7, and 14 days

first: Costas

last: Koufaris

first: Jayne

last: Wright

first: Richard

last: Currie


title: Alterations of DNA methylome during chemical carcinogenesis

status: Public on Jun 30 2013

city: Duarte

first: Xiwei

last: Wu

state: CA

address: 1500 E. Duarte Rd.

department: Computational and Quantitative Medicine

institute: City of Hope National Medical Center

summary: Similar to other genotoxic polycyclic aromatic hydrocarbons (PAHs),  benzo[a]pyrene (BaP) is known to produce stable DNA adducts and other DNA damage. BaP is a powerful carcinogen and can induce tumors in the accessory sex organs (including  prostate) of rodents. In the present study, we have investigated the potential role of  BaP as an  epimutagen in vivo during chemical carcinogenesis. We have analyzed the DNA methylation profile, genome-wide, of  seminal vesicles of Big Blue® mice exposed to chronic doses of BaP over a period of 6 weeks, both immediately after the termination of exposure and several weeks after-treatment in mice that have developed tumors on the accessory sex organs. Mice treated with chronic doses of DMSO (sham) were used as control.

overall_design: We have used a genome-wide microarray-based approach to catalogue the DNA methylation profile in the seminal vesicles of mice injected intraperitoneally with chronic doses of  BaP (experimental) or DMSO (control).

first: Stella

last: Tommasi

first: Jae-In

last: Yoon

first: Albert

last: Zheng

first: Arthur

middle: X

last: Li

first: Ahmad

last: Besaratinia


title: human epidermoid carcinoma cell: Control (A431-P cells) vs. highly invasive subline (A431-III cells)

status: Public on Jun 18 2013

first: Ming-Ting

last: Lee

address: 128, Academia Road Sec. 2, Nankang,

department: The Institute of Biological Chemistry

country: Taiwan

institute: Academia Sinica

summary: Transcriptional profiling of human epidermoid carcinoma cell comparing control A431-P cells with highly invasive subline A431-III cells

overall_design: No treatmentt, A431-P cells vs. A431-III cells. A431-P cells are used as a reference to invstigate A431-III cells.