title: Global transcriptome analysis of Human Bone Marrow Stromal Cells (BMSCs)

status: Public on Sep 21 2011

city: Doha

first: Francesco

middle: Maria

last: Marincola

address: Al Nasr Tower, AL Corniche Street, PO Box 26999

country: Qatar

institute: Sidra Medical and Research Center

summary: Abstract Background: Bone marrow stromal cells (BMSCs) are being used for immune modulatory, anti-inflammatory and tissue engineering applications, but the properties responsible for these effects are not completely understood. Human BMSCs were characterized to identify factors that might be responsible for their clinical effects and biomarkers for assessing their quality. Methods: Early passage BMSCs prepared from marrow aspirates of 4 healthy subjects were compared to 3 human embryonic stem cell (hESC) samples, CD34+ cells from 3 healthy subjects and 3 fibroblast cell lines. The cells were analyzed with oligonucleotide expression microarrays with more than 35,000 probes. Results: BMSC gene expression signatures of BMSCs differed from those of hematopoietic stem cells (HSCs), hESCs and fibroblasts. Genes up-regulated in BMSCs were involved with cell movement, cell-to-cell signaling and interaction and proliferation. The BMSC up-regulated genes were most likely to belong to integrin signaling, integrin linked kinase (ILK) signaling, NFR2-mediated oxidative stress response, regulation of actin-based motility by Rho, actin cytoskeletal signaling, caveolar-mediated endocytosis, clathrin-mediated endocytosis and Wnt/beta catenin signaling pathways. Among the most highly up-regulated genes were structural extracellular (ECM) proteins: alpha1 and beta1 integrin chains, fibronectin, collagen type IIIalpha1, and collagen type Valpha1 and functional EMC proteins: connective tissue growth factor (CTGF) and transforming growth factor beta induced protein (TGFBI) and ADAM12. Conclusions: Global analysis of human BMSCs suggests that they are mobile, metabolically active, proliferative and interactive cells that make use of integrins and integrin signaling. They produce abundant ECM proteins; some of which may contribute to their clinical immune modulatory and anti-inflammatory effects.

overall_design: Seven samples from early passage BMSCs were prepared from marrow aspirates of healthy subjects and compared to 3 human embryonic stem cell (hESC) samples, CD34+ cells from 3 healthy subjects and 3 fibroblast cell lines. Total RNA from a pool of PBMCs from six healthy subjects was extracted and amplified into aRNA to serve as a reference.


title: Corynebacterium glutamicum ATCC13032 Cells: Control (Wild-Type) vs cg0196 Deletion Mutant

status: Public on Oct 04 2011

city: Seoul

first: Jeong Eun

last: Hyeon

address: Anamdong

country: South Korea

institute: Korea University

summary: Transcriptional profiling of Corynebacterium glutamicum cells comparing wild-type cells with cg0196 deletion mutant cells by site-specific gene deletion using the non-replicable integration vector. cg0196 is gene conding transcriptional regulator related carbon metabolism.

overall_design: Two-condition experiment, Wild vs. Δcg0196 cells. Independently grown and harvested. One replicate per array.

first: Jeong

middle: E

first: Sung

middle: O

last: Han


title: Constitutive over-expression of LjMyb14 in Lotus japonicus.

status: Public on Sep 16 2011

city: Fredriksberg

first: Dale

last: Shelton

address: Thorvaldsensvej 40

department: Dept. Plant Biology and Biotechnology

country: Denmark

institute: University of Copenhagen

summary: To identify the regulatory targets of the R2R3-Myb transcription factor, LjMyb14, the gene was constitutively over-expressed in Lotus japonicus under the Lotus ubiquitin promoter.

overall_design: The gene expression levels of three biological replicates of the Lotus japonicus (MG20) were averaged and compared to the the gene expression levels of three independent lines of Lotus japonicus japonicus constituitively over expressing LjMyb14 using the Lotus ubiquitin promoter.


title: Transcriptome analysis of oocyst, tachyzoite, and bradyzoite development in the type II Toxoplasma gondii strain M4.

status: Public on Oct 01 2011

city: Stanford

first: Kerry

middle: R

last: Buchholz

state: California

address: Fairchild Bld, 299 Campus Drive D305

department: Microbiology and Immunology

country: USA

institute: Stanford University

summary:
There were three primary objectives to the overall experiment.
I.  Describe the transcriptome of the oocyst through its development beginning with the freshly excreted, unsporulated oocyst at “Day 0” to a fully sporulated and mature oocyst at “Day 10” and including a mid-sporulation timepoint at “Day 4”.
II. Compare the transcriptomes of in vitro vs. in vivo derived bradyzoites.
III. Compare expression data from three life stages (oocyst, bradyzoite and tachyzoite) from the same parasite isolate, M4, which has been been characterized as a Type II strain.

overall_design:
Each array represents seperately isolated and processed RNA samples. (Two samples per time point/developmental stage)
RNA samples were obtained from:
1.      Oocysts harvested from kitten feces and purified for RNA extraction at Day 0, (not sporulated), Day 4 post-induction of sporulation (mid-sporulation) and Day 10 post-induction of sporulation (fully sporulated).  Oocysts were collected and combined from two kittens that were infected with the same starting material (mouse brains containing bradyzoite cysts of the same parasite strain).  Duplicate samples were obtained from feces collected and purified on separate days.
2.      Bradyzoite cysts harvested from the brains of mice that were infected with oocysts from the same strain (obtained from the oocysts harvested from kittens as described for the oocyst RNA). Mice were treated with 0.44 µg/ml sulfadiazine in their water days 11-21 pi. Mice were sacrificed on day 21 for cyst purification.
3.      In vitro 4 and 8 dpi bradyzoite and 2 dpi tachyzoite samples are from separately infected cultures of human foreskin fibroblasts (HFFs) (replicates were infected on the same day). The parasites used for the initial infections were derived from the same culture. Samples were harvested independently and kept separate for all the subsequent processing and labeling steps.

first: Heather

middle: M

last: Fritz

first: Patricia

middle: A

last: Conrad

first: John

middle: C

last: Boothroyd

first: Xiucui

last: Chen

first: Blythe

last: Durbin-Johnson

first: David

last: Rocke


title: Transcriptome analysis of the zebrafish embryonic host response to Edwardsiella tarda infection using a static immersion systems [experiment A]

city: Amsterdam

first: Oliver

last: Stockhammer

state: NH

address: Meibergdreef 15

department: Medical Microbiology

country: Netherlands

institute: AMC

summary: In this study we analyzed the zebrafish embryonic host response induced by E. tarda (FL6-60) immersion. The E. tarda induced transcriptome profile was compared to those induced by either E. coli or Pseudomonas aeruginosa immersion using the same experimental setup.

overall_design: All infection experiments were performed using mixed egg clutches of Albino strain zebrafish. At 24 hpf embryos were dechorionated using 2mg/ml pronase and left to recover for one hour in egg water. Subsequently embryos were immersed in a bacterial suspension (E. tarda (1E8 CFU/ml), E. coli (1E8 CFU/ml), Pseudomonas aeruginosa PAO1 (1E9 CFU/ml) or P. aeruginosa PA14 (1E9 CFU/ml)) and incubated for 5 hours at 28 ˚C. After the incubation period the embryos were snap-frozen in liquid nitrogen. All treatment groups were analyzed using a common reference approach.

first: J

middle: J

last: van Soest

first: O

middle: W

first: G

middle: V

last: Bloemberg

first: H

middle: P

last: Spaink

first: A

middle: H

last: Meijer


title: Gene expression in leucocytes of patients with autosomal dominat neronal ceroid lipofuscinosis (Kufs disease)

city: Prague

first: Viktor

last: Stranecky

address: Ke Karlovu 2

department: 1st Faculty of Medicine

country: Czech Republic

institute: Charles University

summary: Identification of differentially expressed genes in lecocytes of patients with autosomal dominat neronal ceroid lipofuscinosis (Kufs disease)

overall_design: Leucocyte RNA expression of consanguineous Kufs disease cases (n=4) and unrelated healthy controls (n=4)

first: Lenka

last: Noskova

first: Stanislav

last: Kmoch


title: Delayed phosphate starvation response in cells with abundant high-affinity transporters

status: Public on Sep 15 2011

city: Rehovot

first: sagi

last: levy

address: Hertzel

department: Molecular Genetics and Physics of Complex Systems

country: Israel

institute: Weizmann Institute of Science

summary: Wild-type cells and cells with abundant high-affinity transporters (PHO84C) were transferred from rich medium (SD) to medium containing 0.5mM phosphate

overall_design: Cells were grown to logarithmic phase in SC medium (OD=0.5), washed and then incubated in SC medium with intermediate phosphate level (0.5mM, initial OD=0.05). During the experiment (0, 1, 5, 8 and 23 hours) cells were harvested, pelleted and frozen for further analysis. Total RNA was extracted using MasterPure™fication Kit (Epicentre). The samples were amplified, labeled, hybridized to yeast dual color expression microarrays and scanned, all using standard Agilent protocols, reagents, and instruments. The scanned images were analyzed using SpotReader software (Niles Scientific).

first: Sagi

last: Levy

first: Miri

last: Carmi

first: Naama

last: Barkai


title: The expression profiling of mouse kidneys during early developmental stages

city: Boston

first: Vishal

middle: S

last: Vaidya

state: MA

address: 77 Avenue Louis Pasteur

department: Medicine

institute: Brigham and Women's Hospital. Harvard Medical School

summary: Comparative analysis of gene expression patterns between prenatal (embryonic e16d) and postnatal (p1d and p7d) mouse kidney

overall_design: Total RNA was isolated of e16 kidney embryos, and kidneys from mice at posnatal day 1 and day 7

first: Tae-Min

last: Kim

first: Victoria

last: Ramírez

first: Jonatan

last: Barrera

first: Norma

last: Bobadilla

first: Peter

last: Park


title: LPS inflammation model and thalidomide effect using PBMC cells

status: Public on Sep 30 2011

city: rio de janeiro

first: renata

middle: torres de

last: paiva

state: rio de janerio

address: cidade universitária, centro de tecno

department: Biomedical Engeneering

country: Brazil

institute: Federal University of Rio de Janeiro

summary: In this research, we use DNA microarray analysis to clarify the gene expression responses from thalidomide in PBMC cells after lipopolysaccharide (LPS) treatment.

overall_design: Analysis used PBMC as control samples for comparison to the experimental samples: PBMC stimulated with LPS and PBMC stimulated with LPS treated with LPS. Indirect comparisons were made across multiple arrays with raw data pulled from different channels for data analysis and comparison to the control data.

first: Ulisses

middle: G

last: Lopes

first: Alessandra

last: Saliba

first: Tatiana

last: Fulco

first: Elizabeth

last: Sampaio

first: Euzenir

middle: N

last: Sarno

first: Renata

middle: T

last: Paiva

first: Flavio

middle: F

last: Nobre


title: Gene expression alteration after RBSDV infection

city: Beijing

first: Zaifeng

last: Fan

address: Yuanmingyuan west road No.2

country: China

institute: China Agricultural University

summary: We investigated the alterations of genes expression in maize infected by RBSDV, and detected about 4000 genes alterations which were significant according to the identification standards influenced by RBSDV infection, including resistance related genes, cellulosesynthesis and development related genes. Expression alterations was varified in the same RNA samples by RT- PCR.

overall_design: Two sets samples, RBSDV-infected vs mock;  Biological replicates: 4 RBSDV-infected, 4 mock; independently inoculated and harvested.

first: Meng-ao

last: Jia

first: Yongqiaog

last: Li


title: Genome-wide Analysis of Class IIa Histone Deacetylase Regulation of Hepatic Gluconeogenesis

status: Public on Sep 09 2011

city: La Jolla

first: Ruth

last: Yu

state: CA

address: 10010 N. Torrey Pines Rd.

institute: Salk Institute

summary: Analysis of Class II Histone Deacetylase (HDAC) regulation of hepatic gluconeogenesis at the gene expression level. We show that in liver, Class IIa HDACs (HDAC4, 5, and 7) are all phosphorylated and excluded from the nucleus by AMPK family kinases. In response to the fasting hormone glucagon, Class IIa HDACs rapidly translocate to the nucleus where they directly bind to the promoters of gluconeogenic enzymes such as G6Pase. In turn, HDAC4/5 mediate the acute transcriptional induction of these genes via deacetylation and activation of Foxo family transcription factors. Loss of Class IIa HDACs in the murine liver results in inhibition of FOXO target genes and lowers blood glucose, resulting in increased glycogen storage.

overall_design: Total RNA obtained from primary hepatocytes infected with shGFP or shHDAC4 & 5 subjected to 2 or 4 hours treatment with DMSO or forskolin.

first: Maria

last: Mihaylova

first: Reuben

last: Shaw


title: Anthrax Lethal Toxin-Inducd Gene Expression Changes in Mouse Lung

status: Public on Sep 07 2011

city: Oklahoma City

first: Bart

last: Frank

state: OK

institute: OMRF

summary:
Enhanced susceptibility of A/J mice to death by systemic anthrax lethal toxin (LeTx) administration compared to the C57BL/6 strain was observed. In this study we investigated whether systemic exposure of mice to LeTx would induce gene expression changes associated with vascular/capillary leakage in lung tissue.
Lungs of the less susceptible C57BL/6 strain showed 80% fewer differentially expressed genes compared to lungs of the more sensitive A/J strain.

overall_design: Total RNA obtained from lung tissue of C57Bl/6 and A/J strain mice exposed for 6 and 12 hrs to wild-type and mutant Bacillus anthracis.

first: Eric

last: Dumas

first: Charles

last: Fullenwider

first: Melissa

last: Nguyen

first: Mark

middle: B

first: Igor

last: Dozmorov

first: Judith

last: James

first: Amy

middle: D

last: Farris


title: Timecourse of total and polysome-associated mRNA levels post glucose deprivation

status: Public on Sep 05 2011

city: Cambridge

first: Joshua

last: Arribere

address: 31 Ames St

department: Biology

institute: MIT

summary: Cell survival in changing environments requires appropriate regulation of gene expression, including post-transcriptional gene regulatory mechanisms. Based on reporter gene studies in glucose-starved yeast, it was proposed that translationally silenced eukaryotic mRNAs accumulate in P-bodies and can return to active translation. We present evidence contradicting the notion that this model is a widespread and general phenomenon. First, genome-wide measurements of mRNA abundance, translation, and ribosome occupancy following glucose withdrawal show that most mRNAs are lost from the cell coincident with their loss from polysomes. Second, only a very limited sub-population of translationally repressed transcripts, comprising fewer than 400 genes, can be reactivated for translation upon glucose re-addition in the absence of new transcription. This highly selective post-transcriptional regulation could be a mechanism for cells to minimize the energetic costs of reversing gene-regulatory decisions in rapidly changing environments by transiently preserving a pool of transcripts whose translation is rate-limiting for growth.

overall_design: Sigma 1278b yeast were grown to OD600=1.0-1.1 in YPD in baffled flasks at 30C with vigorous shaking. Cells were harvested by centrifugation and resuspended in pre-warmed YPA medium lacking glucose. Cells were returned to 30C for shaking for 10,20,30,60, or 120 minutes.

first: Jennifer

last: Doudna

first: Wendy

last: Gilbert


title: C57Bl/6N Mice on High Fat Diet Display Reduced Intestinal and Hepatic Cholesterol Levels despite a Plasma Hypercholesterolemia

status: Public on Sep 01 2011

city: Marseille Cedex 5

last: Desmarchelier

address: 27 Boulevard Jean Moulin

department: Nutriments Lipidiques et Prévention des Maladies Métaboliques

country: France

institute: UMR INRA 1260 / INSERM 476 - Universités Aix-Marseille I & II

summary:
Background
Small intestine and liver greatly contribute to whole body lipid, cholesterol and phospholipid metabolism but to which extent cholesterol and phospholipid handling in these tissues is affected by high fat Western-style obesogenic diets remains to be defined. We therefore quantified cholesterol and phospholipid concentrations in intestine and liver and determined fecal neutral sterol and bile acid excretion in C57Bl/6N mice fed for 12 weeks either a cholesterol-free high carbohydrate control diet or a high fat diet containing 0.03 % (w/w) cholesterol. To identify underlying mechanisms of dietary adaptation in intestine and liver, changes in gene expression were assessed by microarray and qPCR profiling, respectively.
Results
Animals on high fat diet showed increased plasma cholesterol levels, associated with the higher dietary cholesterol supply, yet, significantly reduced cholesterol levels were found in intestine and liver. Transcript profiling revealed evidence that expression of numerous genes involved in cholesterol synthesis and uptake via LDL, but also in phospholipid metabolism, underwent compensatory regulations in both tissues. Alterations in glycerophospholipid metabolism were confirmed at the metabolite level by phospolipid profiling via mass spectrometry.
Conclusions
Our findings suggest that intestine and liver react to a high dietary fat intake by an activation of de novo cholesterol synthesis and other cholesterol-saving mechanisms, as well as with major changes in phospholipid metabolism, to accommodate to the fat load.

overall_design: The proximal or distal part of the intestine of mice fed either a control or a high fat diet were analyzed. 5 replicates each.

first: Christoph

last: Dahlhoff

first: Sylvia

last: Keller

first: Manuela

last: Sailer

first: Gerhard

last: Jahreis

first: Hannelore


title: Directed differentiation of embryonic stem cells allows exploration of novel transcription factor genes for pancreas development

status: Public on Sep 02 2011

city: Perth

first: Munish

last: Mehta

state: WA

address: MRF Building, 50 Murray Street

country: Australia

institute: WAIMR UWA

summary: Our bioinformatics analyses of sequential microarray datasets allowed identification of over 20 novel TF genes potentially important for pancreas development.

overall_design: Microarray analyses were performed on differentiating ESC cells at days 0, 4, 8 and 15 of their sequential differentiation.

first: FX

last: Jiang

first: Q

first: M

first: G

last: Morahan


title: Post-transcription initiation function of the ubiquitous SAGA complex in tissue-specific gene activation (gene expression)

status: Public on Aug 22 2011

city: Kansas City

first: Chris

last: Seidel

state: MO

department: Genomics

institute: Stowers Institute

summary: SAGA is a highly conserved transcriptional co-activator complex involved in multiple steps of transcription with activities that function both pre and post initiation. Loss of individual subunits results in developmental defects, suggesting a role in development. In particular, SAGA contains a ubiquitin protease activity involved in the transition from transcription initiation to elongation. Loss of the Sgf11 SAGA subunit causes loss of deubiquitination activity, and leads to defects in axon targeting and embryonic lethality. To better understand the roles of SAGA functions in developmental gene expression we examined its composition, binding profile, and the effects of subunit loss on gene expression in two distinct cell types in late stage Drosophila embryos: muscle and neurons.

overall_design: To confirm cell types, RNA from GFP labeled neuronal (elav+) or muscle (mef2+) cells isolated by FACS from late stage embryos was compared to RNA isolated from whole embryos in quadruplicate, with dye swaps as indicated. To examine the effect of subunit loss, RNA from embryonic wt and sgf11 mutant muscle cells isolated by FACS was compared in quadruplicate, with dye swaps as indicated.

first: Vikki

last: Weake

first: Jerry

middle: L

last: Workman


title: LEC1::GR induction: Establishing the network of seed gene expression and analysis of its biodiversity

status: Public on Aug 31 2011

city: Beaucouze

first: sandrine

last: balzergue

address: Rue G. Morel

institute: INRA

summary: lec1::gr induction - Identification of LEC1 target genes - Induction of 14 days old LEC1::GR seedlings , different treatments (EtOH, DEX, DEX+ABA, induction) for 8 hours

overall_design: 6 dye-swap - CATMA arrays

first: Sandrine

last: Balzergue

first: Junker

last: Astrid

first: Jean-Pierre

last: Renou


title: Global microRNA expression profiling of microdissected tissues from diseased and non-diseased pancreatic tissues

status: Public on Sep 28 2011

city: Bochum

first: Stephan

last: Hahn

address: Universitaetsstrasse 150

department: MGO

country: Germany

institute: Ruhr-University Bochum

summary: Global microRNA expression profiling of microdissected pancreatic tissues were collected using Agilent miRNA microarrays (G4470B, Sanger 10.1) carrying 723 individual human miRNA probes. Four different sources of RNA were analyzed: microdissected normal pancreatic ductal cells (ND, n=4),microdissected acinar cells (AC, n=4),  macrodissected chronic pancreatitis (CP, n=5) and micordissected xenograft tissues derived from primary pancreatic ductal adenocarcinomas (PDAC, n=5).

overall_design: Four condition (AZ, ND, PDAC, CP), each condition is represented by 4 to 5 biological replicates


title: Tumor bearing mice: One group was caged in 24-hour light cycle (L/L), the other group was caged in 12-hour light/dark cycle (L/D)

status: Public on Sep 12 2011

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

country: Japan

institute: Toray Industries,Inc.

summary: Abnormal circadian rhythms, including exposure to light at night, are associated with a higher cancer risk and a poorer prognosis, which may be one of the reasons that the incidence of cancer is increasing in individuals subjected to these stresses. However, the molecular or systemic mechanisms involved in tumor growth under artificial illumination stress conditions have not been identified. In fact, the question of whether artificial illumination stress promotes tumor growth at all is still controversial. To identify the possible mechanisms underlying tumor progression related to circadian rhythms, we set up nude mouse xenograft models. Eight-week-old male nude mice (BALBc nu/nu) were injected with 100ul (1x106 cells) of Hela cells suspension at two separate dorsal sites. Mice were randomly caged (5/cage) and subdivided into L/L (24-hour light cycle; circadian rhythm disruption model) and L/D (12-hour light/dark cycle; normal circadian rhythm model) groups. 11days after injection, we sacrificed one L/L mouse and one L/D mouse, tumors were immediately preserved using liquid nitrogen. Total RNA from tumors were isolated using QIAshredder and RNeasy-Mini kits (Qiagen).

overall_design: We compared the transcriptional profiling of L/L tumor which was derived from  24-hour light cycle (L/L) caging mice with the transcriptional profiling of L/D tumor which was derived from 12-hour light/dark cycle (L/D) caging mice.

first: Yoshihiro

last: Yasuniwa

first: Kimitoshi

last: Kohno


title: Wild type Lec1 transgene induction by DEX: Establishing the network of seed gene expression and analysis of its biodiversity (wt dex induction)

summary: wt dex induction - Identification of LEC1 target genes - Induction of 14 days old WT seedlings , different treatments ( EtOH, DEX induction) for 8 hours

overall_design: 2 dye-swap - CATMA arrays


title: Gene expression profiles of NSCLC tumors

city: Vancouver

first: Raj

last: Chari

state: BC

address: 675 West 10th Avenue

department: Cancer Genetics and Developmental Biology

country: Canada

institute: BC Cancer Research Centre

summary: A custom microarray was used to measure the gene expression of NSCLC tumors.  This represents a subset of samples which also have matched DNA copy number profiles from array CGH experiments

overall_design: 49 microdissected NSCLC tumor samples

first: William

last: Lockwood

first: Wan

last: Lam


title: Progesterone activates multiple innate immune pathways in Chlamydia trachomatis-infected endocervical cells

status: Public on Aug 03 2011

city: Brisbane

first: Charles

last: Wan

state: Queensland

address: 60 Musk Ave

institute: QUT

summary: In this project we examined the in-vitro effect of female sex hormones (estradiol and progesterone at average physiological concentrations) during a infection mediated by Chlamydia trachomatis serovar D, on the gene expression of human endometrial cell line ECC-1

overall_design: The effects of the female sex hormones progesterone and oestradiol while infected by Chlamydia trachomatis were examined at two timepoints.

first: Joanna

last: Latter

first: Ashkan

last: Amirshahi

first: Ian

last: Symonds

first: Jane

last: Finnie

first: Nikola

last: Bowden

first: Rodney

last: Scott

first: Kelly

last: Cunningham

first: Peter

last: Timms

first: Kenneth

last: Beagley


title: Human ependymoma samples, Subgrouping [aCGH - German Cancer Research Center human 33K BAC array]

status: Public on Aug 15 2011

city: Heidelberg

first: Hendrik

last: Witt

state: BW

address: INF 580

department: Molecular Genetics

institute: German Cancer Research Center

type: Genome variation profiling by genome tiling array

summary:
Whole-genome array comparative genomic hybridization (aCGH) of human ependymoma tumors.
DOP-PCR products were spotted in triplicate onto NexterionTM Slide E epoxysilane-coated slides (PEQLAB, Erlangen, Germany) using a spotting robot (VersArray ChipWriterTM Pro system,BioRad, Munich, Germany) at 20C and 40% humidity. After spotting, slides were cross-linked,baked for 1 hr at 80C, and cross-linked again.

overall_design: Fresh frozen tumor material was collected during tumor resection. Copy number aberrations represent the status at diagnosis.


title: Decoding differentially regulated epithelial and stromal pathways in colorectal cancer

status: Public on Aug 10 2011

first: Mohammed

last: Abba

address: Im Neuenheimer Feld 280

department: Molecular Oncology of Solid Tumors

institute: German Cancer Research Center (DKFZ)

summary:
Analysis of differentially expressed genes from dissected whole tissue and laser capture microdissected colorectal cancer tissue samples
The analysis, in colorectal cancer tissues, of compartmental and whole tissue expression profiles as well as the significantly active pathways that were differentially deregulated between the epithelial and stromal compartments when compared alongside that of whole tissue dissection

overall_design: Comparison of tumor epithelium vs normal epithelium; tumor stroma vs normal stroma and tumor whole tissue vs normal whole tissue

first: Axel

last: Benner


title: lincRNAs act in the circuitry controlling pluripotency and differentiation

status: Public on Aug 30 2011

first: Mitchell

last: Guttman

address: 7 Cambridge Center

institute: Broad Institute

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

summary: While thousands of large intergenic non-coding RNAs (lincRNAs) have been identified in mammals, few have been functionally characterized leading to debate about their biological role. To address this, we performed loss-of-function studies on most lincRNAs expressed in mouse embryonic stem cells (ESC) and characterized the effects on gene expression. Here we show that knockdown of lincRNAs have major consequences on gene expression patterns, comparable to knockdown of well-known ESC regulators. Notably, lincRNAs primarily affect gene expression in trans. We identify dozens of lincRNAs whose knockdown causes an exit from the pluripotent state or upregulation of lineage commitment programs. We integrate lincRNAs into the molecular circuitry of ESCs and show that lincRNA genes are regulated by key transcription factors and that lincRNA transcripts physically bind to multiple chromatin regulatory proteins to affect shared gene expression programs. Together, the results demonstrate that lincRNAs have key roles in the circuitry controlling ESC state.

overall_design: We generated five lentiviral-based shRNAs targeting each of the 237 lincRNAs previously identified in ESCs. These shRNAs successfully targeted 147 lincRNAs and reduced their expression by an average of ~75% compared to endogenous levels in ESCs. As positive controls, we generated shRNAs targeting ~50 genes encoding regulatory proteins, including both transcription factor and chromatin factor genes that have been shown to play critical roles in ESC regulation; we obtained validated hairpins against 40 of these genes. As negative controls, we performed independent infections with lentiviruses containing 27 different shRNAs with no known cellular target RNA.

first: Julie

last: Donaghey

first: Eric

last: Lander


title: siRNA off-target effects can be reduced at concentrations that match their individual potency

status: Public on Aug 01 2011

city: Worcester

first: Daniel

middle: R

last: Caffrey

address: 364 Plantation St

institute: UMASS Medical School

summary: This study demonstrates that siRNA off-targets (e.g. 3'UTR off-targets), can be significantly reduced when cells are treated with a relatively low dose of siRNA (e.g. 1nM) that is sufficient to effectively silence the intended target.

overall_design: Cells were treated with different concentrations of either unmodified siRNA or modified siRNA that targeted either hexokinase2 or STAT3 (HK2-3581, HK2-4031, HK2-3581M, STAT3-1676, STAT3-1676M). As transfection efficiencies can vary according to the ratio of nucleotide to transfection reagent, each dose was supplemented with non-targeting/negative control siRNA (siGenome2 or Allstars negative control), such that the total RNA concentration was equal across experiments. RNA was purified 48 hours post-transfection using the RNeasy mini kit from Qiagen. Biological replicates were normalized using the RMA method and analyzed using various Bioconductor tools.


title: C. elegans : Control vs. Chorpyrifos (0.5mg/l) + Diazinon (1 mg/l) treatment

city: London

first: Ana

last: Viñuela

state: London

address: St.Thomas' Hospital Campus Westminster Bridge Road

department: Twin Research & Genetic Epidemiology

country: United Kingdom

institute: King's College London

summary: Transcriptional profile of C. elegans comparing control vs. nematodes treated with 0.5 mg/l of Chorpyrifos and 1mg/l of Diazinon (DZN) at 24°C. Toxicant was added to agar and nematode culture on petri dishes for 72h before harvesting.

overall_design: One condition experiment with six biological replicates in a dye swap design.

first: Jan

middle: E

last: Kammenga


title: C. elegans : Control vs. Diazinon (0.5mg/l) treatment

summary: Transcriptional profile of C. elegans comparing control vs. nematodes treated with 0.5mg/l of Diazinon (DZN) at 24°C. Toxicant was added to agar and nematode culture on petri dishes for 72h before harvesting.


title: DNA copy number and gene expression profiles of resected non-small cell lung cancer tumors

first: Raj

last: Chari

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

overall_design: Refer to individual Series


title: C. elegans : Control vs. Chlorpyrifos (0.5mg/l) treatment

summary: Transcriptional profile of C. elegans comparing control vs. nematodes treated with 0.5mg/l of Chorpyrifos (CPF) at 24°C. Toxicant was added to agar and nematode culture on petri dishes for 72h before harvesting.


title: Context-Specific Regulation of NF-κB Target Gene Expression by EZH2 in Breast Cancers

city: Singapore

first: Peiyong

last: Guan

address: 60 Biopolis Street, Genome, #02-01

country: Singapore

institute: Genome Institute of Singapore

summary: Both EZH2 and NF-κB contribute to aggressive breast cancer, yet whether the two oncogenic factors have functional cross-talk in breast cancer is largely unknown. Here, we uncover an unexpected role of EZH2 in conferring the constitutive activation of NF-κB target gene expression in ER-negative basal-like breast cancer cells.  This function of EZH2 is independent of its histone methyltransferase activity but requires the physical interaction with RelA/RelB to promote the expression of NF-κB targets. Intriguingly, EZH2 acts oppositely in repressing NF-κB targets in ER-positive luminal-like breast cancer cells by interacting with ER and directing repressive histone methylation. Thus, EZH2 function as a double-facet molecule in breast cancers, functioning either as a transcriptional activator or repressor of NF-κB targets, in a cell context-dependent manner. These findings reveals an additional mechanism by which EZH2 promotes breast cancer progression and also underscore the need for developing context-specific strategy for therapeutic targeting of EZH2 in breast cancers.

overall_design: 12 samples were analyzed including three replicates of siNC CTRL and siEZH2 CTRL.

first: Shuet

last: Lee

first: Zhimei

last: Li

first: Zhenlong

last: Wu

first: Meiyee

last: Aau

first: R

middle: K

last: Karuturi

first: Yih

middle: C

last: Liou

first: Qiang

last: Yu


title: Rapid maize leaf and immature ear responses to UV-B radiation

status: Public on Jul 31 2011

city: Stanford

first: John

last: Fernandes

address: 385 Serra Mall

department: Bio Sci

institute: Stanford University

summary:
This study looked for early response signals produced in UV-B irradiated leaves and induced in shielded leaves and shielded ears that modulate physiological responses in maize.  Transcriptome profiling tracked changes in
exposed and shielded organs.  Metabolic profiling was examined for signaling molecules.   The top 2 leaves were exposed to 10, 30, or 60 minutes of ~3x normal UV-B and then tissue samples were taken from all 3 tissue types.
Over 250 transcripts are differentially expressed at least 2 fold in irradiated leaves by 10 min of UV-B.  At 30 min this decreased to ~150 then increased to over 500 transcripts at 60 min.  Different pathways are affected at the various
time exposures and specific responses are modulated by the time of exposure. Shielded leaves had a smaller number of transcripts affected at each time point but over 60% were in common with the irradiated leaves results at 10 min.
and ~20% overlaps were found at 30 and 60 min. Metabolite samples were analyzed after 5, 10, 15, 30, and 90 min of UV-B. We identified 14 compounds with a statistically significant change from untreated plants in at least one time point.

overall_design: Compared transciptomes of irradiated leaves, shielded leaves, and shielded ears from plants whose top 2 leaves were exposed to ~3x normal UV-B for 10, 30, and 60 minutes.

first: Paula

last: Casati

first: Darren

middle: J

last: Morrow

first: Virginia

last: Walbot


title: miRNA expressions in non-cancerous and cancerous human gastric tissues

city: Basel

first: Chia-Huey

last: Ooi

address: Grenzacherstrasse 124

country: Switzerland

institute: F. Hoffmann-La Roche Ltd.

summary: We investigated the involvement of microRNAs (miRNAs)  in gastric cancers.  MiRNA expression was profiled from  40 cancerous and 40 non-cancerous tissues obtained from the National Cancer Centre, Singapore, and Singhealth Tissue Repository, Singapore.  We identified 80 differentially expressed miRNAs in tumors compared with normal tissues. Among these miRNAs, we identified hsa-mir-486-5p (mir-486) as a significantly downregulated miRNA in GC. Subsequent functional characterization revealed that mir-486 playing a tumor suppressor role. We also observed frequent genomic deletion of mir-486 in 20-30% of GCs. To our knowledge, mir-486 represents one of the first tumor suppressor miRNAs in GC inactivated through genomic deletion.

overall_design: MiRNA expression was profiled on Agilent Human miRNA Microarrays (V2) representing 723 human and 76 human viral miRNAs in 40 normal and 40 cancerous gastric tissues.

first: H-K

last: Oh

first: A

last: Tan

first: C-H

first: N-T

last: Deng

first: I

first: E

last: Beillard

first: J

first: K

last: Ramnarayanan

first: S-Y

last: Rha

first: N

last: Palanisamy

first: M

last: Voorhoeve

first: P


title: Lipopolysaccharide (LPS) response in macrophages from TLR4-deficient mice

city: Malmö

first: Harry

last: Björkbacka

address: CRC 91:12, UMAS entrance 72

department: Dept. of Clinical Sciences, Malmö

country: Sweden

institute: Lund University

summary: Lipid A (a hexaacylated 1,4  bis-phosphate) is a potent immune stimulant for TLR4/MD-2. Upon lipid A ligation, the TLR4/MD-2 complex dimerizes and initiates signal transduction. Historically, studies also suggested the existence of TLR4/MD-2-independent LPS signaling. Here we define the role of TLR4 and MD-2 in LPS signaling by using genome wide expression profiling in TLR4- and MD-2-deficient macrophages after stimulations with peptidoglycan-free LPS and synthetic E.coli lipid A. Of the 1,396 genes found significantly induced or repressed by any one of the treatments in the wildtype macrophages, none was present in the TLR4- or MD-2-deficient macrophages, confirming that the TLR4/MD-2 complex is the only receptor for endotoxin, and are both absolutely required for responses to LPS. Using a molecular genetics approach, we investigated the mechanism of TLR4/MD-2 activation by combining the known crystal structure of TLR4/MD-2 with computer modeling. We used lipid IVa, a defined lipid A mimetic to model the activation of mouse TLR4/MD2. The two phosphates on lipid A were predicted to interact extensively with the two positively charged patches mouse TLR4 according to our dimeric murine TLR4/MD-2/lipid IVa model. These two patches are composed of K263, R337, and K360 (Positive Patch 1), and K367 and R434 (Positive Patch 2). When either Positive Patch was abolished by mutagenesis into Ala, the responses to LPS and lipid A were almost abrogated. Thus, ionic interactions between the two phosphates on lipid A and the two positively charged patches on murine TLR4 appear to be essential for LPS receptor activation.

overall_design: Bone marrow-derived macrophages were pooled from four individual WT or TLR4-deficient mice and stimulated with either 10 ng LPS /mL, 100 ng lipid A/mL or 10 nM Pam2 for 2 hours and compared to PBS-stimulated control cells. We also compared PBS-stimulated WT cells directly to PBS-stimulated TLR4-deficient cells to compare the basal expression of genes in the two genotypes. This experiment was repeated once in its entirety.

first: Jianmin

last: Meng

first: Mei

last: Gong

last: Bjorkbacka

first: Douglas

last: Golenbock


title: Genome wide expression profiling and mutagenesis studies reveal an absolute TLR4 and MD-2 requirement for LPS responsiveness dependent upon intermolecular ionic interactions


title: Effect of zebularine on primary human liver cancer cell lines

city: Copenhagen

first: Jesper

last: Andersen

address: Ole Maaloes Vej 5

department: Biotech Research and Innovation Centre

institute: Copenhagen University

summary:
Transcriptomic changes in human liver cancer cell lines caused by the demethylating drug zebularine.
Epigenomic changes such as aberrant hypermethylation and subsequent atypical gene silencing are characteristic features of human cancer. Here, we report a comprehensive characterization of epigenomic modulation caused by zebularine, an effective DNA methylation inhibitor, in human liver cancer. Using transcriptomic and epigenomic profiling, we identified a zebularine signature that classified liver cancer cell lines into two major subtypes with different drug-responses. In drug-sensitive cell lines, zebularine caused inhibition of proliferation coupled with increased apoptosis, whereas drug-resistant cell lines were associated with upregulation of oncogenic networks (e.g. E2F1, MYC, and TNF) driving liver cancer growth in vitro and in mice. Assessment of zebularine-based therapy in xenograft mouse models demonstrated potent therapeutic effects against tumors established from zebularine-sensitive but not zebularine-resistant liver cancer cells leading to increased survival and decreased pulmonary metastasis. Integration of zebularine gene expression and demethylation response signatures differentiated patients with HCC according to their survival and disease recurrence and identified a subclass of patients within the poor survivors likely to benefit from therapeutic agents that target the cancer epigenome.

overall_design:
Each cell line was mock treated or treated with 100uM and 200uM zebularine for 7 days, respectively

*** This Series represents the gene expression component of the study.

first: Snorri

last: Thorgeirsson


title: Androgen Receptor Gene Expression in Prostate Cancer is Directly Suppressed by the Androgen Receptor Through Recruitment of Lysine Specific Demethylase 1

status: Public on Aug 16 2011

city: Seattle

first: Ilsa

last: Coleman

address: 1100 Fairview Ave N, E2-112

department: Human Biology

institute: Fred Hutchinson Cancer Center

summary: Androgen receptor (AR) is reactivated in castration resistant prostate cancer (CRPC) through mechanisms including marked increases in AR gene expression. We identify an enhancer in the AR second intron contributing to increased AR expression at low androgen levels in CRPC. Moreover, at increased androgen levels the AR binds this site and represses AR gene expression through recruitment of lysine specific demethylase 1 (LSD1) and H3K4me1,2 demethylation. AR similarly represses expression of multiple genes mediating androgen synthesis, DNA synthesis and proliferation, while stimulating genes mediating lipid and protein biosynthesis. Androgen levels in CRPC appear adequate to stimulate AR activity on enhancer elements, but not on suppressor elements, resulting in increased expression of AR and AR repressed genes that contribute to cellular proliferation.

overall_design: Custom Agilent 44K whole human genome expression oligonucleotide microarrays were used to profile pre-castrated androgen dependent, 4d-post-castrated, and relapsed castration resistant VCaP xenograft tumors in 3 mice.  Total RNA was isolated and amplified prior to hybridization against a common reference pool of prostate tumor cell lines.

first: Changmeng

last: Cai

first: Housheng

last: He

first: Sen

last: Chen

first: Hongyun

last: Wang

first: Zi

last: Fang

first: Shaoyong

first: Peter

last: Nelson

first: X

last: Liu

first: Myles

last: Brown

first: Steven

last: Balk


title: C. elegans : Control vs. Chlorpyrifos and Diazinon treatments at 24oC

first: Ana

last: Viñuela


title: Copy number data and Stage I/II Breast Cancer

status: Public on Aug 17 2011

city: Houston

first: Spiridon

last: Tsavachidis

state: TX

address: 1515 Holcombe Blvd.

department: Epidemiology

institute: MD Anderson Cancer Center

summary: Search for copy number imbalances and allelotype in 971 early stage breast cancer using molecular inversion probe arrays

overall_design:
Affymetrix MIP arrays were performed according to the manufacturer's directions on DNA extracted from paraffin embedded formalin fixed Stage I and II Breast Cancers
Copy number analysis of Affymetrix Oncoscan Version 1 MIP arrays was performed for 971 Stage I and II breast cancers.

first: Melissa

last: Bondy

first: Gordon

last: Mills


title: Bj H2O2 prolonged exposure vs. non-treatment

status: Public on Jul 30 2011

city: Arlington

first: Woo-Suk

last: Chang

address: 501 S. Nedderman Dr. , Life Science Building 216

institute: University of Texas at Arlington

summary: Genome-wide transcriptional profiling of cells exposed to 0.3 mM H2O2 from time of inoculation.

overall_design: Three independent biological materials were prepared for cells exposed to 0.3 mM H2O2 during growth and non-treated cells. A total 6 arrays which includes dye swap were analyzed

first: Jeong-Min

last: Jeon

first: Hae-In

last: Lee

first: Andrew

last: Donati

first: Dipen

last: Sangurdekar

first: Jae-Seong

last: So


title: Bj H2O2 shock vs. non-treatment

summary: Genome-wide transcriptional profiling of cells subjected to a H2O2  shock treatment (10 mM for 10 minutes).

overall_design: Three independent biological materials were prepared for cells shock treated with H2O2 and non-treated cells. A total 6 arrays which includes dye swap were analyzed.


title: An mRNA Expression Signature of Gleason Grade Predicts Lethal Prostate Cancer

status: Public on May 01 2012

city: Boston

first: Kathryn

last: Penney

address: 181 Longwood Ave

institute: Brigham and Women's Hospital

type:
Expression profiling by array
Third-party reanalysis

summary: PSA screening has led to enormous overtreatment of prostate cancer, due to the inability to distinguish potentially lethal disease at diagnosis. We reasoned that by identifying an mRNA signature of Gleason grade, the best predictor of prognosis, we could improve prediction of lethal disease among men with moderate Gleason 7 tumors, the most common grade, and most indeterminate in terms of prognosis. Using the complementary DNA (cDNA)–mediated annealing, selection, extension, and ligation assay, we measured the mRNA expression of 6,100 genes in prostate tumor tissue in the Swedish Watchful Waiting cohort (N=358) and Physicians’ Health Study (PHS; N=109). We developed an mRNA signature of Gleason comparing individuals with Gleason ≤6 to those with Gleason ≥8 tumors, and applied the model among Gleason 7 cases to discriminate lethal cases. We built a157-gene signature using the Swedish data that predicted Gleason with low misclassification (AUC=0.91); when this signature was tested in the PHS validation set, the discriminatory ability remained high (AUC=0.94). In men with Gleason 7 tumors, who were excluded from the model building, the signature significantly improved the prediction of lethal disease beyond knowing whether the Gleason score was 4+3 or 3+4 (p=0.006). Our expression signature and the genes identified may improve our understanding of the de-differentiation process of prostate tumors. Additionally, the signature may have clinical applications among men with Gleason 7, by further estimating their risk of lethal prostate cancer and thereby guiding therapy decisions to improve outcomes and reduce overtreatment.

overall_design: 198 cases from the population-based Swedish-Watchful Waiting cohort. The cohort consists of men with localized prostate cancer (clinical stage T1-T2, Mx, N0); expression profiles from tumors with Gleason ≥8 (N=89) were compared to those from tumors with Gleason ≤6 (N=109)

first: K

first: L

last: Mucci


title: Microarray analysis on livers, spleens and hearts of mice given distilled water fed with either a normal diet or an atherogenic diet

status: Public on Jul 26 2011

city: Kajang

first: Soon-Sen

last: Leow

state: Selangor

address: No. 6, Persiaran Institusi, Bandar Baru Bangi

country: Malaysia

institute: Malaysian Palm Oil Board

summary: BALB/c mice were given an atherogenic diet and compared to those given a normal diet to observe for gene expression changes caused by the atherogenic diet. Both groups of mice received distilled water as drinks ad libitum. Livers, spleens and hearts were harvested six weeks after the feeding regimen for gene expression studies. Results from the separate microarray data analysis carried out on the different organs show that the atherogenic diet caused oxidative stress and inflammation in the organs.

overall_design: Total RNA obtained from livers, spleens and hearts of BALB/c mice given an atherogenic diet (six weeks after the feeding regimen) was compared to those from organs of mice given normal diet (liver: four replicates in the treatment group versus four replicates in the control group; spleen and heart: three replicates in the treatment group versus four replicates in the control group for both organs)

first: Shamala

last: Sekaran

first: Ravigadevi

last: Sambanthamurthi


title: The use of non-amplified RNA samples for gene expression analysis by sensitive microarray.

status: Public on Jul 28 2011

first: Hiroko

last: Sudo

address: 6-10-1 Tebiro

department: New Frontiers Research Laboratories

institute: Toray Industries, Inc.

summary: Gene expression profiles were compared based on the rounds of sample RNA amplification procedure.

overall_design: The intra- and inter-method reproducibility was shown by comparing gene expression profiles from two micoarray data. For the repeatability, CVs calculated from multiple microarray data were compared between different amplification methods. The accuracy of each method was estimated from the correlation with RT-PCR results when the same samples were assayed. The range of differential expression was shown using the brain RNA samples derived from an Alzheimer and non-Alzheimer donors.

first: Atsuko

last: Mizoguchi

first: Junpei

last: Kawauchi

first: Hideo

last: Akiiyama

first: Satoko

last: Takizawa

first: Hitoshi

last: Nobumasa


title: The discovery and validation of ten-gene prognostic classifier in gastric cancer by whole genome expression profiling

status: Public on Jul 13 2011

city: Beijng

first: zheng

middle: yue

last: zhang

address: No.7 Beitucheng West Road, Chaoyang District, Beijing 100029, PR China

institute: Beijing Institute of Genomics

summary: The aim of this study is to identify and verify a prognosis set that is able to distinguish patient overall survival status based on whole genome expression profiling. Using Illumina HumanWG-6 beadarray, we analyzed the expression of 47,296 transcripts in two groups of gastric cancer patients who all underwent surgical resection. Thirty-nine of 46 samples in group one were used as a training set to discover candidates for overall survival prediction by using semi-supervised method, resulting in a panel of 10 genes as prognosis markers. This 10-marker set classified each case into a low or a high risk group with significantly different survival times (P = 0.000047) and maintained independent prognostic value in multivariate analysis. These 10 candidates were then verified in a fully independent validation set comprising 33 samples (P = 0.0009). Furthermore, the prognosis was consistent with the classical TNM staging system, and showed even better prediction. Interestingly, six of ten survival markers are ribosomal proteins, suggesting a possible association between deregulation of ribosome-related expression and poor prognosis. In conclusion, by whole genome expression profiling, 10 markers, including 6 ribosomal proteins, for overall survival prognosis of gastric cancer were found and validated, and which may be parallelly used with the TNM system.

overall_design: We investigated the transcriptome profiles of gastric cancer patients with different prognosis.  Thirty-nine patients from first batch samples were used to discover prognostic markers and another 33 samples from batch two were used for validation.

first: Yuezheng

last: Zhang

first: Lianhai


title: Gene expression changes across multiple regions of the Parkinson’s disease brain

status: Public on Jul 22 2011

city: Bethesda

first: Mark

last: Cookson

state: MD

address: 35 CONVENT DR RM 1A116

department: Lab of Neuorgenetics

institute: NIA, NIH

summary: We have used microarrays to analyze gene expression in Parkinson’s disease (PD). We used four different brain regions, including two that are relatively affected in PD (striatum and cortex) and two that are relatively spared (cerebellum and medulla). We show that while differences between brain regions are strong, expression profile differences between PD and controls are much more modest and that genome-wide significant differences are restricted to the striatum and cerebral cortex.

overall_design: RNA (aRNA) was generated from 500ng of total RNA from the medulla (n=15 control brains, n=14 PD brains), striatum (n=15 control brains, n = 15 PD brains), frontal cortex (n=15 control brains, n = 11 PD brains) and cerebellum (n = 14 control brains, n=15 PD brains).

first: Ravindran

last: Kumaran

first: Marcel

last: van der Brug

first: Jana

last: Vandrovcova

first: Jinhui

last: Ding

first: Simone

last: Sharma

first: Alan

last: Renton

first: Allissa

last: Dillman

first: Andrew

last: Lees

first: Rina

last: Bandopadhyay


title: SNP data from Down syndrome and non-Down syndrome pediatric acute lymphoblastic leukemia cases and controls

status: Public on Jul 12 2011

first: Hon-chiu

middle: Eastwood

last: Leung

address: 1102 Bates Street  Room C1030.09

department: Pediatrics

institute: Baylor College of Medicine

type:
SNP genotyping by SNP array
Genome variation profiling by SNP array

summary:
SNP profiling can reveal copy number abnormalities and loss of heterozygosity associated with distinct biologic subtypes of acute lymphoblastic leukemia (ALL).
We performed SNP profiling of Down syndrome ALL cases and controls to identify unique biologic features of this ALL subgroup.

overall_design: Ficoll-enriched, cryopreserved bone marrow aspirate samples were obtained from patients with B-precursor ALL at diagnosis and in remission; and from control patients without leukemia.

first: Karen

last: Rabin


title: Gene expression profiling of early primary breast cancer to identify prognostic markers and associated pathways

status: Public on Jul 08 2011

city: Oxford

first: Francesca

last: Buffa

address: The Weatherall Institute of Molecular Medicine

institute: University of Oxford

summary: Retrospective series of primary breast cancer patients who received surgery between 1989 and 1992. Patients received adjuvant chemotherapy and/or adjuvant hormone therapy, or no adjuvant treatment. Tamoxifen was used as endocrine therapy for 5 years in ER+ BC patients. Patients who were <50 years of age, with lymph node positive tumors, or ER– and/or >3 cm in diameter, received adjuvant cyclophosphamide, methotrexate, and 5-fluorouracil (CMF) for six cycles, in a thrice weekly intravenous regimen. Patients >50 years of age with ER–, lymph node–positive tumors also received CMF.

overall_design:
Retrospective clinical study to identify breast cancer prognostic markers and associated pathways. 216 early primary breast cancers were considered who had complete 10-years follow-up, clinical and demographics information.
mRNA profiling data.

middle: M

first: Laura

last: Winchester


title: zebrafish liver tumor signatures

status: Public on Jul 07 2011

city: Leiden

first: Herman

middle: Pieter

last: Spaink

address: Einsteinweg 55

department: Institute of Biology

institute: Leiden University

summary: transcriptome profiling of zebrafish liver tumors comparing with healthy liver tissues

overall_design: Zebrafish liver tumors were induced by exposure to 7,12-dimethylbenz(α)anthracene (DMBA). 5 zebrafish liver tumors and 6 healthy zebrafish livers were used to detect gene signatures in zebrafish liver tumors. A mixture of the 11 total RNA samples was used as the common reference.

middle: P

first: Shuning

last: He


title: Microarray analysis on livers, spleens and hearts of mice fed an atherogenic diet and supplemented with either oil palm phenolics (OPP) or distilled water

first: Soon-Sen

last: Leow

summary: OPP (1500 ppm gallic acid equivalent (GAE)) was supplemented to BALB/c mice given an atherogenic diet for six weeks to observe for possible anti-atherogenic effects. The control group received distilled water instead of OPP. Livers, spleens and hearts were harvested six weeks after the feeding regimen for gene expression studies. Results from the separate microarray data analysis carried out on the different organs show that OPP attenuated the effects of the atherogenic diet in the organs.

overall_design: Total RNA obtained from livers, spleens and hearts of BALB/c mice given OPP (six weeks after administration of an atherogenic diet) were compared to controls given distilled water (liver: three replicates in the treatment group versus four replicates in the control group; spleen and heart: three replicates in the treatment group versus three replicates in the control group for both organs)

first: Shamala

last: Sekaran

first: Ravigadevi

last: Sambanthamurthi


title: microRNA expression profiling of early primary breast cancer to identify prognostic markers and associated pathways

overall_design:
Retrospective clinical study to identify breast cancer prognostic markers and associated pathways. 210 early primary breast cancers were considered who had complete 10-years follow-up, clinical and demographics information.
miRNA profiling data.

first: Carme

last: Camps


title: Atherogenic diet supplemented with oil palm phenolics effect on liver, spleen, and heart

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

overall_design: Refer to individual Series


title: Identification of genes expressed during and following exposure to chronic moderate temperature stress in Arctic charr

status: Public on Jul 05 2011

city: Burnaby

first: Nicole

middle: Lisa

last: Quinn

address: 8888 University Drive

department: Molecular Biology and Biochemistry

institute: Simon Fraser University

summary: Arctic charr thrive at high densities and can live in freshwater year round, making this species especially suitable for inland, closed containment aquaculture. However, it is a cold water salmonid, which both limits where the species can be farmed and places wild populations at particular risk to climate change. Previously, we identified genes associated with tolerance and intolerance to acute, lethal temperature stress in Arctic charr. However, there remained a need to examine the genes involved in the stress response to more realistic temperatures that could be experienced during a summer heat wave in grow-out tanks that are not artificially cooled, or under natural conditions. Here, we exposed Arctic charr to moderate heat stress of 15–18ºC for 72 hours, and gill tissues extracted before, during (i.e., at 72 hrs), immediately after cooling and after 72 hours of recovery at ambient temperature (6ºC) were used for gene expression profiling by microarray and qPCR analyses. The results revealed an expected pattern for heat shock protein (Hsp) expression, which was highest during heat exposure, with significantly reduced expression (approaching control levels) quickly thereafter. We also found that the expression of numerous ribosomal proteins was significantly elevated immediately and 72 hrs after cooling, suggesting that the gill tissues were undergoing ribosomal biogenesis while recovering from damage caused by heat stress. We suggest that these are candidate gene targets for the future development of genetic markers for broodstock development or for monitoring temperature stress and recovery in wild or cultured conditions.

sample_organism:
Salmo salar
Salvelinus alpinus

overall_design:
24 microarray slides representing 6 individuals from 4 treatment groups (Control, During, After and Recovery). One test cDNA labeled with Cy5 and the common reference aRNA labeled with Cy3 was hybridized to each slide.
Reference design: 6x control fish, 6x group D fish, 6x group A fish, 6x group R fish.

first: Colin

last: McGowan

first: Glenn

middle: A

last: Cooper

first: Ben

last: Koop

first: William

middle: S

last: Davidson


title: Genome -wide identification of SCL's target genes in Megakaryocyte progenitors

status: Public on Jul 11 2011

first: Hedia

last: Chagraoui

address: john radcliffe hospital headley way headington

department: Molecular Hematology Unit

institute: Weatherall Institute of Molecular Medicine

summary: Megakaryopoiesis is a complex process that involves major cellular changes and relies on controlled coordination of cellular proliferation and differentiation. These mechanisms are orchestrated in part by transcriptional regulators. The key hematopoietic transcription factor SCL/TAL1 is required for specification of the megakaryocytic lineage from hematopoietic progenitors. Here, we report that it also critically controls terminal megakaryocyte maturation. In vivo depletion of SCL specifically in the megakaryocytic lineage affects all key attributes of megakaryocyte progenitors (MkPs), namely proliferation, ploidisation, cytoplasmic maturation, as well as platelet production. Genome-wide expression analysis reveals increased expression of the cell cycle regulator p21 in Scl-deleted MkPs. Importantly, P21 knockdown-mediated rescue assays in Scl-deleted MkPs show full restoration of cell cycle progression and partial rescue of the nuclear and cytoplasmic maturation defects. Therefore, SCL-mediated transcriptional control of p21 is critical for maturation of MkPs. Our study provides a mechanistic link between one of the major hematopoietic transcriptional regulators, cell cycle progression and megakaryocytic differentiation.

overall_design: Total RNA extracted from control TGPF4-CRE;SCL wt/wt sorted MK progenitors  was compared to total RNA extracted from TGPF4-CRE;SCL fl/fl MK progenitors cells where Scl was completely excised

first: Shamit

last: Soneji

first: Catherine

last: Porcher


title: Expression changes during Candida albicans biofilm formation

city: Merced

first: Clarissa

middle: Jane

last: Nobile

address: 5200 North Lake Rd

department: Molecular and Cell Biology

institute: University of California - Merced

summary:
The planktonic versus biofilm gene expression arrays were performed in a/alpha cell types.
Gene expression arrays were performed on planktonic vs biofilm cells grown in Spider medium at 37C. Normalized data is reported in matrix.

overall_design: Biofilm strains (48 hour biofilms) were compared to planktonic strains (log phase planktonic cells) in Spider medium at 37C.


title: Transcript-level responses of Plasmodium falciparum to thiostrepton

status: Public on Jun 30 2011

city: London

first: Sarah

last: Tarr

address: Gower Street

department: ISMB

institute: UCL

summary: Abstract: The antimalarial activity of the antibiotic thiostrepton has long been attributed to inhibition of apicoplast protein synthesis through binding of apicoplast ribosomal RNA.  However, the kinetics of parasite death upon thiostrepton treatment differ from those seen for other inhibitors of apicoplast housekeeping functions.  We have analysed global changes in gene expression of the malaria parasite, Plasmodium falciparum, in an attempt to shed light on the responses of the parasite to this drug.  Our results indicate a delay in gene expression profiles of thiostrepton-treated parasites.  A small number of genes appear to be regulated outside of this trend; our data suggest a response from genes encoding components of the mitochondrial translational machinery, while little response is seen from genes encoding apicoplast-targeted proteins.  Our findings are consistent with an effect of thiostrepton on mitochondrial protein synthesis, and thus warrant a re-evaluation of the target of thiostrepton in Plasmodium. They also provide some suggestion of mitochondrion – nucleus signalling in the parasite.

platform_organism:
Plasmodium falciparum
Anopheles gambiae

overall_design: 3 biological replicates each for treated and untreated: control (1/2000 DMSO) and LD70 thiostrepton, respectively

first: R

last: Nisbet

first: Christopher

last: Howe


title: Analysis of early primary breast cancer to identify prognostic markers and associated pathways: mRNA and miRNA profiling

first: Francesca

last: Buffa

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

overall_design:
Refer to individual Series.
Supplementary file: Shows correspondence between mRNA and miRNA samples.


title: Subclassification of lung adenocarcinoma

status: Public on Jul 19 2011

city: Kyoto

first: T

last: Fujiwara

address: 46-29 Yoshida Shimoadachi-cho Sakyo-ku

institute: Kyoto University

summary: To elucidate whether or not a subtype of adenocarcinoma with neuroendocrine nature has poor prognosis, we performed gene expression of lung adenocarcinoma profiling by cDNA microarray.

overall_design: adenocarcinoma 154, squamous 10


title: Zebrafish liver tumors

first: Herman

last: Spaink


title: FTO: gene expression and function in skeletal muscle

city: Pierre Bénite

first: emmanuelle

last: meugnier

address: Cens Eli Bat 2 D- Hopital Lyon Sud

summary: We identified the target genes of FTO ("fat mass and obesity associated") in primary cultures of human skeletal muscle cells using adenoviral vectors expressing FTO or GFP and oligonucleotide microarrays.

overall_design: Human myotubes were prepared from 4 different skeletal muscle biopsies. After differentiation, myotubes were infected for 48 hours with recombinant adenovirus expressing either GFP or FTO. Each FTO-infected myotubes culture was compared to GFP-infected myotubes culture. GFP-infected myotubes were regarded as the control. Four biological replicates were processed.

first: Amelie

last: Bravard

first: Sandra

last: Pesenti

first: Emmanuelle

last: Meugnier

first: Jennifer

last: Rieusset


title: Responses of fully proliferating Arabidopsis leaves to short-term osmotic stress

status: Public on Jul 01 2011

city: Gent

first: aleksandra

last: skirycz

address: Technologiepark 927

department: Plant System Biology

country: Belgium

institute: Ghent University

summary: Drought is an important environmental factor affecting plant growth and biomass production. Despite this importance little is known on the molecular mechanisms regulating plant growth under water limiting conditions. The main goal of this work was to investigate, using a combination of growth and molecular profiling techniques, how stress arrests CELl proliferation in Arabidopsis thaliana leaves upon osmotic stress imposition.

overall_design: Plants were grown on nylon meshes overlaying control 0.5MS media. At 9 DAS when third leaf is fully proliferating seedlings were transfered to either mannitol (25mM) or control plates, and proliferating leaves were micro-dissected at 1.5h, 3h, 12h and 24h after stress imposition and using RNAlater solution (25mM). Samples were from three independent biological experiments. Each sample was pooled from multiple plants and multiple plates in one experiment. RNA samples were submitted to ATH1 array hybridization.

first: Aleksandra

last: Skirycz

first: Dirk

last: Inzé


title: Hippocampal gene expression analysis highlights Ly6a/Sca-1 as candidate gene for previously mapped novelty induced behaviors in mice

city: Utrecht

first: Simone

last: de Jong

address: Universiteitsweg 100

department: Medical Genetics

institute: UMC Utrecht

summary: Using gene expression analysis to narrow down a behavioral QTL

overall_design: Hippocampus (left) dissected from frozen tissue of female CSS15F2 population using a punching procedure. N=37

first: Martien

last: Kas

first: Jeffrey

last: Kiernan

first: Annetrude

middle: G

last: de Mooij-van Malsen

first: Hugo

last: Oppelaar

first: Esther

last: Janson

first: Igor

last: Vukobradovic

first: Charles

last: Farber

first: William

last: Stanford

first: Roel

last: Ophoff


title: Murine uterus expression profile during Peri-implantation: Pre-implantation vs. Post-implantation

city: Beijing

first: Jing-Pian

last: Peng

address: , #1 Beichen West Rd., Chaoyang

department: State Key Laboratory of Reproductive Biology

institute: Institute of Zoology, Chinese Academy of Sciences

summary: Anaylsis differentially expressed genes of mouse peri-implanted uteri comparing pre-implantation uteri (Day2, Day3 and Day4) with post-implantation uteri (Day6, Day7 and Day8) by microassay. This study has built a meaningful basis for future investigation in elucidating the molecular nature of maternal-fetal interactions during pregnancy establishment and maintenance.

overall_design: Pre-implantation uteri VS. Post-implantation uteri. Three biological replicates of each experiments: pre-implantation uteri (Day2, Day3 and Day4): 234, 234①, 234②; 3 mixture of post-implantation uteri (Day6, Day7 and Day8): 678, 678①, 678②. Two hybridizations were performed by using a reverse fluorescence strategy (Cy3, Cy5) for each sample.


title: Gene Expression in the Human Mammary Epithelium during Lactation: the Milk Fat Globule Transcriptome through 4 Days

first: Patricia

last: Maningat

address: 1100 Bates St

department: CNRC

country: USA

summary: The 4 day gene expression profile in the lactating mammary gland was demonstrated using the Human Ref-8 BeadChip array (Illumina, Inc). Of the 22,184 gene transcripts on the array, 14,070 genes were consistently expressed and represented the milk fat globule transcriptome. Milk protein genes were among the most highly expressed along with genes involved in the milk syntesis processes.

overall_design: Serial milk samples were collected every 3h for 4 days from 5 normal, lactating women.  RNA was isolated from the milk fat globules and utilized for microarray analyses.

first: Monique

last: Rijnkels

first: Partha

last: Sen

first: Darryl

last: Hadsell

first: Morey

last: Haymond

first: Molly

last: Bray


title: Differential gene expression analysis of Mice liver treated with Amodiaquine and Sulfodoxine-Pyrimethamine

status: Public on Jun 21 2011

city: Lucknow

first: Shrawan

middle: Kumar

last: Mishra

address: MG Marg,Chattar Manzil Palace

department: Toxicology

country: India

institute: CDRI

summary: The study describes the differential gene expression analysis in murine liver following dosing with human therapeutic equivalent doses of Amodiaquine and Sulfodoxine-Pyrimethamine antimalarial drugs.The dosing was decided based on standard antimalarial therapy.

overall_design: Mice (Mus musculus) belonging to control and Amodiaquine and Sulfodoxine -Pyrimethamine administered groups (n=4) were sacrificed. The livers were snap frozen in liquid nitrogen, and subsequently stored at -80ºC till further use. Liver samples were homogenized and total RNA was extracted with TRI reagent. 25 ug of total RNA was converted into labeled cDNA using CyScribe first strand cDNA labeling kit. The Cy5 and Cy3 labeled cDNAs were resuspended in Cyscribe Hyb buffer containing 10ug/ml sheared Salmon sperm DNA and 10ug/ml Yeast tRNA. The labeled samples were hybridized to the arrays and incubated for 16-18hrs at 42ºC. Fluorescent array images were collected for both Cy3 and Cy5 with molecular dynamics III scanner supported with ImageQuant v5.0. Image intensity data were extracted and analyzed with ArrayVision v8.0 analysis software. Background corrected data was LOWESS normalized and log ratios were calculated using Avadis v4. Further, mean log ratios were calculated for duplicate spots. Duplicate experiment were carried out for all the dosages.

first: Prabhat

last: Singh

first: Srikanta

last: Rath


title: Graded Nodal/Activin Signaling Governs ES Cell Fate Decisions via Differential Recruitment of Phospho-Smad2 to Oct4 and Distinct Target Gene Subsets

city: Singapore

first: Kian Leong

last: LEE

state: Singapore

address: #07-21, 8 College Road

department: Duke-NUS Medical School

institute: National University of Singapore (NUS)

summary: Nodal and Activin are morphogens of the TGFbeta superfamily of signaling molecules that direct differential cell fate decisions in a dose- and distance-dependent manner. During early embryonic development the Nodal/Activin pathway is responsible for the specification of mesoderm, endoderm, node and mesendoderm. In contradiction to this drive towards cellular differentiation, the pathway also plays important roles in the maintenance of self-renewal and pluripotency in embryonic and epiblast stem cells. The molecular basis behind stem cell interpretation of Nodal/Activin signaling gradients and the undertaking of disparate cell fate decisions remains poorly understood. Here, we show that any perturbation of endogenous signaling levels in mouse ES cells leads to their exit from self renewal towards divergent differentiation programs. Increasing Nodal signals above basal levels by direct stimulation with Activin promotes differentiation towards the mesendodermal lineages while repression of signaling with the specific Nodal/Activin receptor inhibitor SB431542 induces trophectodermal differentiation. To address how quantitative Nodal/Activin signals are translated qualitatively into distinct cell fates decisions, we performed chromatin immunoprecipitation of phospho-Smad2 the primary downstream transcriptional factor of the Nodal/Activin pathway followed by massively parallel sequencing and show that phospho-Smad2 binds to and regulates distinct subsets of target genes in a dose-dependent manner. Crucially, Nodal/Activin signaling directly controls the Oct4 master regulator of pluripotency by graded phospho-Smad2 binding in the promoter region. Hence stem cells interpret and carry out differential Nodal/Activin signaling instructions via a corresponding gradient of Smad2 phosphorylation that selectively titrates self-renewal against alternative differentiation programs by direct regulation of distinct target gene subsets and Oct4 expression.

overall_design: Four biological replicates consisting of 4 different passages of E14TG2a ES cells at P20, P21, P23 and P24

first: Kian

middle: L

last: Lee

first: Sandy

last: Lim

first: Le

middle: Y

last: Yit

first: Henry

middle: H

last: Yang

first: Lay

middle: T

last: Ang


title: Rabbit heart gene expression in Left ventricle (LV) following banding of the descending thoracic aorta (AOB-LV) vs Sham-control LV and  in Right ventricle (RV) following banding the pulmonary artery (PAB-RV) vs. Sham-control RV

status: Public on Jun 24 2011

first: James

middle: D

last: McCully

address: 77 Avenue Louis Pasteur

department: Cardiothoracic Surgery

institute: BIDMC/Harvard Medical School

summary:
Background: Right ventricular (RV) and left ventricular (LV) myocardium differ in their response to pressure-overload hypertrophy (POH). In this report we use microarray and proteomic analyses to identify pathways modulated by LV-, and RV-POH in the immature heart.
Methods: Newborn New Zealand White rabbits underwent banding of the descending thoracic aorta (LV-POH; n=6). RV-POH was achieved by banding the pulmonary artery (n=6). Sham–control animals (SC; n=6 each) were sham-manipulated. Following 4 (LV-POH) and 6 weeks (RV-POH) recovery, the hearts were removed and matched sample RNA and proteins were isolated for microarray and proteomic analysis.
Results: There was no difference in body weight in RV-, LV-POH vs. SC but there was a significant increase vs. SC in RV (3.2±0.8g vs. 1.2±0.3g; P<0.01) and LV weight (7.08±0.6g vs. 4.02±0.2g; P<0.01). Fractional area change (RV-POH) and shortening fraction (LV-POH) decreased significantly (23±6 vs. 47±6 and 21±4 vs.44±2, respectively, P<0.01).   Microarray analysis demonstrated that LV-POH enriched pathways for oxidative phosphorylation, mitochondria energy pathways, actin, ILK, hypoxia, calcium and protein kinase-A signalling. RV-POH enriched pathways for cardiac oxidative phosphorylation.  Proteomic analysis revealed 19 proteins were uniquely expressed in LV-POH vs. SC. Functional annotation clustering analysis indicated significant enrichment for the mitochondrion, cellular macromolecular complex assembly and oxidative phosphorylation.  RV-POH had 15 uniquely expressed proteins vs. SC. Functional annotation clustering analysis indicated significant enrichment in structural constituents of muscle, cardiac muscle tissue development and calcium handling.
Conclusion: Our results identify unique transcript and protein expression profiles in LV, RV-POH and provide new insight into the biological basis of ventricular specific hypertrophy.

overall_design: 3 different conditions: PAB-RV vs. Sham-control RV, PAB-RV [test] vs. PAB-LV [control], AOB-LV vs. Sham-control LV.


title: An integrated transcriptome analysis to the characterization of host responses against infectious laryngostracheitis virus vaccine infection in chicken embryo lung cells

status: Public on Jun 29 2011

city: Fayetteville

first: Byung-whi

last: Kong

state: AR

address: 1260 W. Maple, POSC, L-426

department: Poultry Science

institute: University of Arkansas

summary: Host gene expression of chicken embryo lung cells infected an infectious laryngotracheitis virus (ILTV) vaccine strain comparing control uninfected lung cells. Goal was to identify the changes of host gene expression by ILTV vaccine infection.

overall_design: Two-condition experiment, uninfected chicken embryo lung cells vs. vaccine infected chicken embryo lung cells. Biological replicates: 1 control uninfected sample, 1 vaccinal ILTV infected experimental sample at each 1, 2, 3 and 4 dpi.

first: Jeong-Yoon

first: Byung-Whi


title: Gene expression analysis of 2 different prostate tumor cell lines isolated from 30 wks old TRAMP mice compared to normal prostate

status: Public on Jun 15 2011

city: Milan

first: Paola

last: Pittoni

state: Italy

address: Via Amadeo, 42

department: Dept. Experimental Oncology

country: Italy

institute: IRCCS Istituto Nazionale dei Tumori

summary: Analysis of gene expression of 2 novel prostate tumor cell lines isolated from TRAMP mice and compared to normal prostate. T1525 cell line is a well differentiated adenocarcinoma with epithelial features, whereas T23 cell line displays the molecular signature of epithelial-to-mesenchymal transition.

overall_design: Total RNA obtained from prostate tumor cell lines isolated from 30 wks old TRAMP mice, compared to normal prostate

first: Giorgio

last: Mauri


title: Genome-wide profiling of diel and circadian gene expression of the malaria vector Anopheles gambiae

city: Notre Dame

first: Samuel

last: Rund

state: IN

address: Galvin Life Science

department: Biological Science

institute: University of Notre Dame

summary: Anopheles gambiae, the primary African malarial mosquito, exhibits numerous behaviors that are under diel and circadian control, including locomotor activity, swarming, mating, host seeking, eclosion, egg laying and sugar feeding. However, little has been performed to elucidate the molecular basis for these daily rhythms. To study how gene expression is globally regulated by diel and circadian mechanisms, we have undertaken a DNA microarray analysis of A. gambiae head and bodies under 12:12 light:dark cycle (LD) and constant dark (DD, free-running) conditions.  Zeitgeber Time (ZT) with ZT12 defined as time of lights OFF under the light:dark cycle, and ZT0 defined as end of the dawn transition. Circadian Time (CT) with CT0 defined as subjective dawn, inferred from ZT0 of the previous light:dark cycle.

overall_design: Adult mated but non-blood fed female mosquito heads and bodies under 12:12 light:dark cycle (LD) and constant dark (DD) conditions were collected every 4 hr to generate 48 hr gene expression profiles, and samples were processed with Affymetrix full genome microarrays.  Downstream analysis identified genes with ~24hr rhythmic expression profiles.

first: Tim

last: Hou

first: Sarah

last: Ward

first: Frank

last: Collins

first: Giles

middle: E

last: Duffield


title: Microarray analysis of Lin- CD66+ and Lin- CD66- cells isolated from primary human cervical cancer

status: Public on Jun 09 2011

city: Bangalore

first: Sudhir

last: Krishna

state: Karnataka

address: UAS-GKVK Campus, Bellary Road

institute: National Centre for Biological Sciences, TIFR

summary: Microarry based whole genome expression analysis was done for the more tumorigenic CaSki spheroids cultures and the less tumorigenic CaSki adherent cultures to identify signaling mechanisms that vary between the two populations. Subsequent to this, an independent array was done to characterize the differences in gene expression between the cancer stem cell-like Lin-CD66+ and the bulk Lin- CD66- cells isolated from primary human cervical carcinomas. The second array was custom-designed and had genes implicated in stemness, epithelial differentiation, signaling pathways implicated in stemness (Notch and Wnt) and cell cylce-regulation.

first: Jeevisha

last: Bajaj

first: Eric

last: Vivien


title: Raf/MEK signatures in zebrafish liver cells

first: Herman

last: Spaink

address: Einsteinweg 55

country: Netherlands

summary: An inducible oncogenic cell line ZFL-ΔRaf1-ER was established, in which oncogenic human Raf-1(ΔRaf1) can be activated in zebrafish liver cells by administration of 4-hydroxytamoxifen (4HT). Transcriptional profilling of the ZFL-ΔRaf1-ER cells with and without administration of 4HT and/or the MEK inhibitor U0126 defined the gene signatures transcriptionally regulated by hyperactive Raf/MEK/MAPK signaling in zebrafish liver cells.

overall_design: The ZFL-ΔRaf1-ER cells were cultured in 12-well plates till confluence. Cell were starved for 4h in plain medium and susequently treated with or without 1µM 4HT and/or 30µM U0126 for 12h. Biological triplications were taken for each condition.

first: Shuning

last: He


title: Gene expression in clonogenic versus non-clonogenic in pooled early passage OCI/AML-4 single cells

status: Public on Jun 01 2011

city: Toronto

first: Christine

last: Ichim

state: ON

address: 2075 Bayview Avenue

institute: Sunnybrook Research Institute

summary: Identification of genes that regulate clonogenicity of AML cells is hindered by the difficulty of isolating pure populations of cells with defined proliferative abilities.  Using early passages of the OCI/AML-4 cell line we sought to determine genes differentially expressed between clonogenic and non-clonogenic cells. We previously shown that OCI/AML-4 clonal siblings display coordinated growth patterns, so that the behaviour of a single cell that is destroyed in the generation of global single cell cDNA may be predicted by the growth patterns of its clonal siblings.  Cells were plated in 96 well plates at limiting dilutions. Localized clusters of four cells were identified and micromanipulated such that three of the constituent cells were placed separately into individual microtitre wells containing growth medium and a feeder layer of OP9 cells, while the fourth cell was lysed and processed for global RT-PCR.  The cells in each culture well were counted at 2 -3 day intervals until growth stopped. In this manner cDNA was generated from individual clonogenic OCI/AML-4 cells (sibling cells able to generate between 9-100 cells) or from individual non-clonogenic OCI/AML-4 cells (sibling cells were not able to generate more than 8 cells). Respective single cell cDNA was then pooled and compared by hybridization to cDNA microarrays.

overall_design: Using early passages of the OCI/AML-4 cell line cDNA was obtained from 17 clonogenic single cells (sibling cells able to generate between 9-100 cells) and 20 non-clonogenic single cells (sibling cells were not able to generate more than 8 cells). These cDNAs were pooled and hybridized to the cDNA microarray was conducted as three replicates, including one replicate which was a dye-swap.

middle: V

first: Harold

last: Atkins

first: Norman

middle: N

last: Iscove

first: Richard

last: Wells


title: CC chemokine ligand 2 and LIF cooperatively promote pluripotency in mouse induced pluripotent cells

city: Suehiro-cho, Tsurumi-ku

first: Yuki

last: Hasegawa

state: Yokohama-city

department: OSC

institute: RIKEN

summary: The pluripotency of mouse embryonic stem cells (ESC) and induced-pluripotent stem cells (iPSC) can be maintained by feeder cells, which secrete Leukemia Inhibitory Factor (LIF). We found that feeder cells provide a relatively low concentration (25 unit/ml) of LIF, which is insufficient to maintain the ESC/iPSC pluripotency in feeder free conditions. In order to identify additional factors involved in the maintenance of pluripotency, we carried out a global transcript expression profiling of mouse iPSC cultured on feeder cells and in feeder-free (LIF-treated) conditions. This identified 17 significantly differentially expressed genes (adjusted p-value<0.05) including 7 chemokines over-expressed in iPSC grown on feeder cells. Ectopic expression of these chemokines in iPSC revealed that CC chemokine ligand 2 (Ccl2) induced the key transcription factor genes for pluripotency, Klf4, Nanog, Sox2 and Tbx3. Further, addition of recombinant Ccl2 protein drastically increased the number of Nanog-GFP-positive iPSC grown in low LIF feeder free conditions. Interestingly, this effect was not observed in the absence of LIF. We further revealed that pluripotency promotion by Ccl2 is mediated by activating the Stat3-pathway followed by Klf4 up-regulation. We demonstrated that Ccl2 mediated increased pluripotency is independent of PI3K and MAPK pathways and that Tbx3 may be directly up-regulated by Klf4. Overall, Ccl2 cooperatively activates the Stat3-pathway with LIF in feeder free condition to maintain pluripotency for ESC/iPSC.

overall_design: Total RNAs were purified from feeder cells (as a reference sample), iPSC grown on feeder cells and iPSC grown in feeder-free condition in triplicates and applied to the arrays. iPSC grown on feeder cells were separated mechanically from the feeder layer to minimize feeder cell contamination.


title: L3MBTL2 protein acts in concert with PcG protein mediated monoubiquitination of H2A to establish a repressive chromatin structure [ChIP-chip data].

status: Public on Jun 07 2011

city: Columbus

first: Victor

middle: X

last: Jin

state: OH

address: 333 West 10th Ave

department: Biomedical Informatics

institute: OSU Medical Center

type: Genome binding/occupancy profiling by genome tiling array

summary: Human  MBT  domain‐containing  protein  L3MBTL2  was  found  to  be  an  integral  component  of   a  protein  complex  that  we  termed  Polycomb  Repressive  Complex  1‐like  3  (PRC1L3)  given  the  presence   of  the  PcG  proteins  RING1,  RING2  and  PCGF6.  L3MBTL2  binds  chromatin  in  a  histone  modification‐ independent  manner  and  is  required  for  the  repressive  function  of  PRC1L3.  PRC1L3  also  contains  E2F6   and  CBX3,  two  factors  with  well‐established  functions  in  transcriptional  repression.  Genome‐wide   profiling  identified  several  hundred  genes  that  are  simultaneously  bound  by  L3MBTL2  and  E2F6,   preferentially  around  transcriptional  start  sites.  Importantly,  these  genes  are  largely  distinct  from   those  targeted  by  other  E2Fs  or  L3MBTL,  another  MBT‐domain  containing  protein  that  interacts  with   RB1.  H3K27  or  H3K9  methylation,  two  chromatin  modifications  implicated  in  gene  silencing,  are  not   present  on  all  L3MBTL2  target  genes.  L3MBTL2‐specific  RNAi  results  in  altered  target  gene  expression   patterns  and  affects  the  differentiation  program  of  hematopoietic  cells.  Our  data  suggest  that   repression  of  transcription  via  chromatin  modulation,  reflective  of  PRC1  function,  can  be  achieved  by   multiple  players  and  does  not  necessarily  require  the  presence  of  histone  lysine  methylation  marks.

overall_design: 12 total ChIP-seq datasets; one E2F6 dataset and one Input dataset done from MCF7 cells on Nimblegen ENCODE arrays; one L3MBTL1 dataset and one Input dataset done from MCF7 cells on Nimblegen ENCODE arrays; one L3MBTL2 dataset and one Input dataset done from MCF7 cells on Nimblegen ENCODE arrays; one E2F6 dataset and one Input dataset done from MCF7 cells on Nimblegen 1.5kb promoter arrays; one L3MBTL1 dataset and one Input dataset done from MCF7 cells on Nimblegen 1.5kb promoter arrays; one L3MBTL2 dataset and one Input dataset done from MCF7 cells on Nimblegen 1.5kb promoter arrays.

first: Alina

middle: R

last: Cao

first: Peggy

middle: J

last: Farnham


title: Transcriptomic analysis of the zebrafish inner ear points to growth hormone mediated regeneration following acoustic trauma

status: Public on Jun 02 2011

city: Bowling Green

first: Michael

middle: E.

last: Smith

state: KY

address: 1906 College Heights Blvd.

department: Department of Biology

institute: Western Kentucky University

summary: Transcripts for GH, MHC Class I and II genes, and heavy- and light-chain myosins, as well as many others genes, were differentially regulated in the zebrafish inner ear following overexposure to sound.

overall_design: Following acoustic trauma in the zebrafish inner ear, we used microarray analysis to identify genes involved in inner ear repair following acoustic exposure by comparing the gene expression levels of 2 days and 4 days post-sound exposure (NE-ZF-2d and NE-ZF-4d, respectively) to controls without sound exposure (C-ZF).

first: Julie

middle: B

last: Schuck

first: Huifang

last: Sun

first: William

last: Penberthy

first: Nigel

last: Cooper

first: Xiaohong

last: Li


title: miR-371-3 expression predicts neural differentiation potential in human pluripotent stem cells

city: New York

first: Jeffrey

last: Zhao

state: NY

address: 1275 York Avenue

department: Genomics Core

institute: Memorial Sloan Kettering Cancer Center

summary: The use of pluripotent stem cells in regenerative medicine and disease modeling is complicated by the variation in differentiation properties between lines. In this study, we characterized 13 human embryonic stem cell.  (hESC) and 26 human induced pluripotent stem cell (hiPSC) lines to identify markers that predict neural differentiation behavior. At a general level, markers previously known to distinguish mouse ESCs from epiblast stem cells (EpiSCs) correlated with neural differentiation behavior. More specifically, quantitative analysis of miR-371-3 expression prospectively identified hESC and hiPSC lines with differential neurogenic differentiation propensity and in vivo dopamine neuron engraftment potential. Transient KLF4 transduction increased miR-371-3 expression and altered neurogenic behavior and pluripotency marker expression. Conversely, suppression of miR- 371-3 expression in KLF4-transduced cells rescued neural differentiation propensity. miR-371-3 expression level therefore appears to have both a predictive and a functional role in determining human pluripotent stem cell neurogenic differentiation behavior.

overall_design:
[mRNA profiling (Illumina)]: Four human ESC lines (H9, I4, I6, HUES6) at undifferentiation stages were purified with stem cell surface marker SSEA4 and subjected to RNA extraction and hybridization on Illumina microarrays. Each sample has 3 biological repeats, one of which has two technical repeats.

[miRNA profiling (Agilent)]: Four human ESC lines (H9, I4, I6, HUES6) at undifferentiation stages were purified with stem cell surface marker SSEA4 and subjected to RNA extraction and hybridization on Agilent microarrays. Each sample has 3 biological repeats, one of which has two technical repeats.

first: Hyesoo

last: Kim

first: Lorenz

last: Studer


title: Arctic charr exposed to acute thermal stress

city: Burnaby

first: Nicole

middle: Lisa

last: Quinn

state: BC

address: 8888 University Drive

department: Molecular Biology and Biochemistry

institute: Simon Fraser University

summary: Arctic charr is an especially attractive aquaculture species given that it features the desirable tissue traits of other salmonids, but can be bred and grown at inland freshwater tank farms year round. It is therefore of interest to develop upper temperature tolerant (UTT) strains of Arctic charr to increase the robustness of the species in the face of climate change, as well as to enable production in more southern regions. We conducted an acute temperature trial to identify temperature tolerant and intolerant Arctic charr individuals. Specifically, approximately 200 fish were transferred to an experimental tank (diameter: 1.86 m, depth 50 cm) and left to acclimate for 48 h at ambient temperature. After acclimation, 10 fish were removed to act as a control group, then water that had been diverted through a heat exchanger was added to the flow-through system to increase the water temperature in the tank by 6°C/h until it reached 22°C, then 0.5°C every 30 min until the water reached 25°C, the observed lethal temperature for these fish. When the water temperature reached 25°C, the temperature was held constant and the fish were closely monitored for signs of stress. The first and last 10 individuals to show loss of balance were quickly removed from the tank for sampling, thus representing the 5% least and most temperature tolerant fish, respectively. A reference design microarray study was then performed with the cGRASP 32K microarray using six samples from each group (Intolerant, Tolerant, Control) to identify genes differentially expressed between groups. The results of this study will feed into an ongoing Arctic charr marker-assisted selection based broodstock development program, and may contribute to population-based conservation initiatives for salmonids in general.

overall_design:
18 microarray slides representing 6 individuals from 3 treatment groups (Intolerant, Tolerant and Control). One test cDNA labeled with cy5 and the common reference aRNA labeled with Cy3 was hybridized to each slide
Reference design: 18 slides (6 x Tolerant fish, 6x Intolerant fish, 6x Control fish) were used.

first: Colin

last: McGowan

first: Glenn

middle: A

first: Ben

middle: F

last: Koop

middle: S

last: Davidson


title: Gene expression and biological pathways in tissue of men with prostate cancer in a randomized clinical trial of lycopene and fish oil

city: San Francisco

first: Mark

last: Magbanua

state: CA

address: 1450 3rd Street, PO Box 589001

department: HemOnc

institute: UCSF/Helen Diller Familiy Comprehensive Cancer Center

summary: Animal and epidemiological studies suggest that lycopene and fish oil may modify the risk or delay progression of prostate cancer, however, the molecular mechanisms involved are poorly understood. We examined the effects of these micronutrients on prostate gene expression in a double-blind placebo-controlled randomized clinical trial (Molecular Effects of Nutritional Supplements, MENS).

overall_design: Eighty-four men with low risk prostate cancer were stratified based on self-reported dietary consumption of fish and tomatoes and then randomly assigned to a 3-month intervention of lycopene (intervention B; n = 29) or fish oil (intervention C; n = 27) supplementation or placebo (intervention A; n = 28). Gene expression in morphologically normal prostate tissue was studied at baseline and at 3 months via cDNA microarray analysis. Differential gene expression and pathway analyses were performed to identify genes and pathways modulated by dietary intake of fish or tomato or by lycopene or fish oil supplementation.

first: Ritu

last: Roy

first: Eduardo

last: Sosa

first: Vivian

last: Weinberg

first: Scott

last: Federman

last: Mattie

first: Millie

last: Hughes-Fulford

first: Jeff

last: Simko

first: Katsuto

last: Shinohara

first: Christopher

middle: M

last: Haqq

first: Peter

last: Carroll

first: June

last: Chan


title: Gene Expression Profiles of PBMC Characterize Inflammation Stages in the Acute Lung Injury in Mice

city: Marseille

first: Isabelle

last: Lesur Kupin

address: 163 av. de Luminy - case 928

department: Bioinformatics

institute: INSERM U928

summary: Acute respiratory distress syndrome (ARDS) carries about a 50 percent mortality and is frequently associated with an infection (sepsis). Life-support treatment with mechanical ventilation rescues many patients, although superimposed infection or multiple organ failure can result in death. The outcome of a patient developing sepsis highly depends on the degree of pre-existing inflammation prior to the infection. In this study, we describe each stage of the inflammation process using a transcriptional approach and an animal model. Femelle C57BL6/J mice received an intraveinous oleic acid injection to induce an acute lung injury. PBMC expression patterns have been analyzed using a 9900 cDNA mouse microarray (MUSV29K). Our gene-expression analysis revealed marked changes in the immune and inflammatory response metabolic pathways, notably lipid metabolism and transcription. The early pro-inflammatory stage (1H-1H30) is characterized by the release of immune response and activation of inflammatory mechanisms. Later (3H-4H), the immune cells migrate into inflamed tissues through interaction with vascular endothelial cells. Finally, at late stages of lung inflammation (18H-24H), metabolism is deeply disturbed. Highly expressed pro-inflammatory cytokines activate transcription of many genes as well as lipid metabolism. This global overview of critical events occuring during lung inflammation is essential to understand infectious pathologies such as sepsis where inflammation and infection are interwined. From now on, it becomes possible to isolate the impact of a pathogen at the transcriptional level from the global gene expression modifications resulting from the infection associated with the inflammation. Also, our work allowed to identify genes involved in the response to inflammation. Among those, several may be potential target for gene therapy.

overall_design:
Wild-type femelle C57Bl/6J mice, 7 weeks old, were obtained from Charles River and housed in a specific pathogen-free animal facility. We studied 39 mice divided into 6 groups. Each group was identified according to the incubation time: 1H, 1H30, 3H, 4H, 18H and 24H. The 1H group was made up of 6 mice (2 physiological serum and 4 OA); the 1H30 group was made up of 8 mice (2 physiological serum and 6 OA); the 3H group was made up of 7 mice (2 physiological serum and 5 OA); the 4H group was made up of 6 mice (2 physiological serum and 4 OA); the 18H group was made up of 6 mice (2 physiological serum and 4 OA); the 24H group was made up of 6 mice (2 physiological serum and 4 OA). Several RNA samples have been hybridized on 2 filters consisting in technical replicates.

Data normalized by quantile without adjustment on physiological serum linked on Series record.

first: Catherine

last: Nguyen