title: Identification of PHLPP1 as a tumor suppressor reveals the role of feedback compensation in PTEN-mutant prostate cancer progression

status: Public on Aug 17 2011

city: Cold Spring Harbor

first: Muhan

last: Chen

address: 1 Bungtown Rd

institute: Cold Spring Harbor Laboratory

summary: Hyper-activation of the PI 3-Kinase/ AKT pathway is a driving force of many cancers. Here we identify the AKT-inactivating phosphatase PHLPP1 as a prostate tumor suppressor. We show that Phlpp1-loss causes neoplasia and, upon partial Pten-loss, carcinoma in mouse prostate. This genetic setting initially triggers a growth suppressive response via p53 and the Phlpp2 ortholog, and reveals spontaneous Trp53 inactivation as a condition for full-blown disease. Surprisingly, the co-deletion of PTEN and PHLPP1 in patient samples is highly restricted to metastatic disease and tightly correlated to deletion of TP53 and PHLPP2. These data establish a conceptual framework for progression of PTEN-mutant prostate cancer to life-threatening disease.

overall_design: To better assess the role of Phlpp in prostate we performed micorarray analysis of gene expression in the WT and Pten+/-; Phlpp1-/- mice.

first: Christopher

middle: P

last: Pratt

first: Martha

last: Zeeman

first: Nikolaus

last: Schultz

first: Barry

middle: S

last: Taylor

first: Audrey

last: O'Neill

first: Mireia

last: Castillo-Martin

first: Dawid

middle: G

last: Nowak

first: Adam

last: Naguib

first: Danielle

last: Grace

first: Jernej

last: Murn

first: Nick

last: Navin

first: Gurinder

last: Atwal

first: Chris

last: Sander

first: William

middle: L

last: Gerald

first: Carlos

last: Cordon-Cardo

first: Alexandra

last: Newton

first: Brett

last: Carver

first: Lloyd

last: Trotman


title: Gene expression signature of DMBA induced hamster buccal pouch carcinomas: Modulation by chlorophyllin, and ellagic acid

status: Public on Jun 02 2011

city: Tamil Nadu

first: Nagini

last: Siddavaram

address: Annamalainagar

department: Department of Biochemistry & Biotechnology

country: India

institute: Annamalai Universuty

summary: To examine the mechanism underlying chemoprevention and changes in gene expression pattern induced by chlorophyllin and ellagic acid during 7,12-dimethylbenz[a]anthracene (DMBA)-induced hamster buccal pouch (HBP) carcinogenesis

overall_design: Two-condition experiment, Control vs. DMBA, Control vs. DMBA+chloophyllin, Control vs. DMBA+ellagic acid. Biological replicates: 2 control replicates, 2 DMBA replicates, 2 DMBA+chlorophyllin replicates, 2 DMBA+ellagic acid replicates.

first: Ramamurthi

last: Vidya

first: Siddavaram

last: Nagini


title: Gene expression analysis of Yersinia Pestis temperature shift.

status: Public on Jul 14 2011

city: Rockville

first: John

last: Braisted

state: MD

address: 9704 Medical Center Dr

department: PFGRC

country: USA

institute: J Craig Venter Institute

summary: The study aims to to determine temperature sensitive genes across the strains COW5,PBIB15 and pestoidesF.

overall_design: Samples were hybridized on aminosilane coated slides with 70-mer oligos.

first: Marcus

middle: B

last: Jones

first: Vladamir

last: Motin

first: Rosslyn

last: Maybank

first: Bryan

last: Frank

first: Scott

middle: N

last: Peterson

first: Lakshmi

last: Appalla


title: Transcriptional analysis of Schistosoma mansoni treated with sub-lethal doses of the anthelmintic drug praziquantel

status: Public on May 27 2011

city: Albuquerque

first: Jarrett

last: Hines-Kay

state: NM

address: 1 University of New Mexico

department: Biology

institute: University of New Mexico

summary: Schistosoma mansoni is one of the most common etiological agents responsible for the disease schistosomiasis. More than 200 million people suffer from this disease making it the most severe tropical disease after malaria in terms of morbidity. Praziquantel (PZQ) is the treatment of choice for schistosomiasis and has been used almost exclusively to treat the disease since the 1970s. However, while the drug is lethal for sexually mature schistosomes, it is ineffective against juveniles. Thus, while morbidity can be eased, a cure is difficult to achieve. As a result there is an urgent need to develop a new generation of anti-schistosomal drugs, a task that will be made easier by understanding the mechanism of action of PZQ. As yet, neither the molecule to which PZQ binds nor the means by which it kills mature schistosomes is known. The overarching aim of this study was to understand the molecular basis of PZQ sensitivity in S. mansoni. We believe that juvenile worms survive PZQ treatment in vivo due to the induction of, as yet, unidentified protective molecular pathways. To address this hypothesis juvenile and adult PR1 S. mansoni were treated in vitro with sub-lethal concentrations of PZQ. mRNA was extracted from replicate samples, cRNA prepagreen and labeled with cyanine dyes for analysis using a 44K S. mansoni microarray. The data was then analyzed using Genespring. Our findings suggest that a number of genes associated with drug transport, iron homeostasis and apoptosis are induced in juvenile but not adult schistosomes and that this allows the juvenile worms to protect themselves against the lethal effects of PZQ long enough for the drug to be metabolized by the human host.

overall_design:
42 days post exposure (DPE) male schistosomes were exposed to 0 and 1 µg/mL praziquantel (PZQ) for 1 or 20 h and 10 µg/mL PZQ for 1 h.  42 DPE female schistosomes were exposed to 0, 1 and 10 µg/mL PZQ for 20 h.  28 DPE mixed-sex schistosomes were exposed to 0, 1 and 10 µg/mL PZQ for 1 and 20 h.  All experiments were performed in biological triplicates.  The 0 µg/mL PZQ exposures were used as controls to the appropriate groups and a universal reference was used in all experiments that was comprised of RNA derived from 100 mixed sex, unexposed 42 DPE schistosomes spiked with 0.5 % (v/v) RNA isolated from 42 DPE mixed sex worms exposed to 10 µg/mL PZQ, 0.5 % (v/v) RNA isolated from 28 DPE worms exposed to 10 µg/mL PZQ and 0.5 % (v/v) RNA isolated from 28 DPE worms unexposed to PZQ.
Transcriptional response to praziquantel exposure by time and concentration


title: Transcriptional targets of Xenopus EBF3 in the presence of Noggin : Untreated animal caps vs. Dexamethasone (DEX) treated animal caps

status: Public on May 25 2011

city: Salt Lake City

first: Monica

last: Vetter

state: UT

address: 50 N. Medical Dr. 517 Wintrobe

department: Neurobiology and Anatomy

institute: University of Utah

summary: Transcriptional profiling comparing the genes upregulated or downregulated by active hGR-Xebf3 by treating hormone DEX to those by non-active hGR-Xebf3 in Xenopus animal caps.

overall_design: Three experimental conditions, Noggin and hGR-Xebf3 without DEX treatment (1), Noggin and hGR-Xebf3 with DEX treatment (2), and Noggin and hGR with DEX treatment (3). Comparison, 1 vs.2 and 1 vs. 3.  Biological replicates, 4 times

first: Yangsook

last: Green


title: Expression data from adult rat subventricular zone cells

status: Public on May 10 2011

city: München-Neuherberg

first: Dietrich

last: Trümbach

address: Ingolstädter Landstraße 1

department: Institute for Developmental Genetics

country: Germany

institute: German Research Center for Environmental Health

summary:
Transforming growth factor (TGF)-ß1 is a multifunctional cytokine regulating a number of physiological and patho-physiological processes in the adult brain. Its expression is elevated during neurodegeneration, which is associated with reduced levels of neurogenesis. We have postulated that TGF-ß1 might be one of the crucial factors involved in limiting neurogenesis in the diseased brain.
We used microarrays to detail the gene expression profile after TGFbeta-1 treatment and identified distinct classes of up- and downregulated genes.

Keywords: control versus TGFbeta1 treated group

overall_design: Adult rat subventricular zone cells were cultured for 7 days under proliferation conditions. Control cells were exposed to HCl/BSA whereas TGFbeta-1 treated cells received 10 ng/ml TGFbeta-1 dissolved in HCl/BSA 3 times per week. RNA was extracted followed by hybridization on Affymetrix microarrays.

first: Bernadette

last: Lehner

first: Ludwig

last: Aigner


title: Expression data from cell lines originating from patients with multiple myeloma, plasmacytoma and diffuse large B-cell lymphoma

status: Public on Apr 30 2011

city: Aalborg

first: Martin

last: Boegsted

address: Sdr. Skovvej 15

department: Department of Haematology

country: Denmark

institute: Aalborg Hospital, Aarhus University Hospital

summary: A predictive gene list for response to high dose melphalan therapy in patients diagnosed with multiple myeloma is generated by combining results from dose response experiments and microarray data using a B-cell line panel and the introduction of multivariate regression techniques.

overall_design: 18 malignant B-cell lines were analyzed by gene expression microarrays and screened for melphalan median dose dependent growth inhibition. Results are used to build a predictive gene list for response to high dose melphalan therapy in multiple myeloma.

first: Johanne

middle: M

last: Holst

first: Kirsten

last: Fogd

first: Steffen

last: Falgreen

first: Suzette

last: Sørensen

first: Alexander

last: Schmitz

first: Anne

last: Bukh

first: Hans

middle: E

last: Johnsen

first: Mette

last: Nyegaard

first: Karen

last: Dybkaer


title: Differential gene expression in immortal DF-1 chicken embryo fibroblast cell line

status: Public on May 12 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: Transcriptional profiling of chicken embryo fibroblast (CEF) cells comparing CEF derived immortal chicken embryo fibroblast cell line (DF-1). Goal was to determine differentially expressed genes of CEF which were changed responding DF-1.

overall_design: Two-condition experiment, CEF vs. DF-1. Biological replicates: 1 control CEF sample, 1 DF-1 experimental sample.

first: Lee

last: Jeong Yoon

first: Kong

last: Byung-Whi


summary:
Transforming growth factor (TGF)-ß1 is a multifunctional cytokine regulating a number of physiological and patho-physiological processes in the adult brain. Its expression is elevated during neurodegeneration, which is associated with reduced levels of neurogenesis. We have postulated that TGF-ß1 might be one of the crucial factors involved in limiting neurogenesis in the diseased brain.

We used microarrays to detail the gene expression profile after TGFbeta-1 treatment  and identified distinct classes of up- and downregulated genes.

Keywords: control versus TGFbeta1 treated group


title: Genetic identification, replication, and functional fine-mapping of expression quantitative trait loci in primary human liver tissue [Agilent]

status: Public on Jun 27 2011

city: Chicago

first: Christopher

middle: David

last: Brown

state: IL

department: Human Genetics

institute: University of Chicago

summary: Most loci identified in genome wide association studies (GWAS) of complex traits reside in non-coding DNA and may contribute to phenotype via changes in gene regulation. The discovery of expression quantitative trait loci (‘eQTLs’) can thus be used to more precisely identify modest but real disease associations and provide insights into their underlying molecular mechanisms. This is particularly true for analyses of expression in non-transformed cells from tissues relevant to the complex traits of interest. We have conducted two independent studies to identify genetic, including both SNPs and copy-number variants, and environmental determinants of human liver gene expression variation. We analyzed two sets of primary livers (primary dataset: n=220; replication dataset: n=60) using Agilent and Illumina expression arrays and Illumina SNP genotyping (550K). At least 30% of genetic and non-genetic factors that meet genome-wide significance (p <1 x10-9) in one study fail to replicate in the second study, suggesting that artifacts, like unknown SNPs that affect RNA-probe hybridization or hidden confounding variables, often result in statistically significant but biologically irrelevant correlations. These data confirm the value of independent replications to enrich for truly predictive eQTLs, and given our study design we are able to identify hundreds of reproducible correlations. We show that such information can be used to provide insights into disease-relevant phenotypes, with specific examples including eQTLs related to lipid levels (e.g. LDL cholesterol), immune system function (e.g. HLA), and drug response (e.g. warfarin). Furthermore, in the interest of both fine-mapping and mechanistic annotation, we hypothesized that promoters and 3’UTRs are enriched for causal eQTL variants. Therefore, we re-sequenced the promoter and 3’UTR regions of 25 genes with eQTLs, cloned each discovered haplotype, and quantified their impact on transcription using a luciferase-based assay. These data reveal multiple examples of robust, haplotype-specific in vitro functional differences that correlate directly with in vivo expression levels. This suggests that many eQTLs can be rapidly fine-mapped to one or a few single-nucleotide variants and mechanistically characterized using such assays. Integration of functional assays with eQTL discovery, and eQTLs with complex trait associations, is a powerful means to exploit GWAS data and improve their biological interpretability.

overall_design:
RNA expression levels were quantified on Agilent gene expression microarrays for 206 normal human livers (464 unique arrays corresponding to those samples). Genotypes were also derived from 224 of these samples using Illumina SNP chips.  Expression quantitative trait loci were identified by genome wide association mapping.

This submission represents the primary transcriptome component of study.

middle: D

first: Federico

last: Innocenti


title: Transcriptional targets of Xenopus EBF3 in the absence of Noggin : Untreated animal caps vs. Dexamethasone (DEX) treated animal caps

first: Monica

last: Vetter

overall_design: Three experimental conditions, hGR-Xebf3 without DEX treatment (1), hGR-Xebf3 with DEX treatment (2), and hGR with DEX treatment (3). Comparison, 1 vs.2 and 1 vs. 3.  Biological replicate, one time

first: Yangsook

last: Green


title: Expression profiling of human DCIS and invasive ductal breast carcinoma

status: Public on Apr 11 2011

city: Berlin

first: Celine

last: Schäfer

address: Augustenburger Platz 1

department: Med. Kl. m.S. Hepatologie und Gastroenterologie

institute: Charité

summary:
Human healthy tissue samples, DCIS and invasive mammary tumors were analyzed in order to identify marker genes which show enhanced expresssion in DCIS and invasive ductal carcinomas.
Using this approach, we were able to identify a set of genes which might allow a better detection of DCIS and invasive carcinomas in the future.

overall_design: 5 healthy tissue samples, 9 DCIS and 5 invasive ductal carcinomas were analysed.

first: Céline

last: Schaefer

first: Wolfgang

last: Kemmner


title: Expression profiling of murine DCIS and invasive ductal breast carcinoma

summary:
Murine healthy tissue samples, DCIS and invasive mammary tumors were analyzed in order to identify marker genes which show enhanced expresssion in DCIS and invasive ductal carcinomas.
Using this approach, we were able to identify a set of genes which might allow a better detection of DCIS and invasive carcinomas in the future.

overall_design:
Samples consists of:
5 wild type breast tissue samples
5 healthy breast tissue sapmles of WAP-TNP8 mice
5 samples of mice one month, 5 samples of mice two month, 5 samples of mice three month, 5 samples of mice four month, and 5 samples of mice five month after activation of the SV40 oncogene
5 invasive tumors


title: Expression data from parthenogenetic and WT iPS samples and their parental fibroblasts

status: Public on May 31 2011

city: Jerusalem

first: Yonatan

last: Stelzer

address: Givat-Ram

department: Genetics

country: Israel

institute: The Hebrew University of Jerusalem

summary:
Three parthenogenetic induced pluripotent stem cell (PgHiPSCs) lines were generated from each of the ovarian teratoma cell lines (two distinct individuals).  Two normal iPS cell lines were generated from normal fibroblasts. Three biological replicates of normal embryonic stem cells (H9, HESCs) were perfomed.
We used microarrays to study the gene expression profiles of the PgHiPSCs, and compared the expression of genes to both embryonic and induced pluripotent stem cell, to identify paternally expressed genes that are down-regulated in the PgHiPSC lines.

overall_design: All parthenogenetic and normal iPS cell lines, were tested for pluripotency assays (inclusing, morphology, immuno stanings and qRT-PCR for known pluripotency markers, differentiation capacity in vivo and  in vitro)

first: Nissim

last: Benvenisty


title: Gene expression signature-based screening identifies new broadly effective influenza antivirals

status: Public on Mar 22 2011

city: Lyon

first: Julien

last: Textoris

address: Hôpital Edouard herriot - Pavillon P; 5 place d'Arsonval

department: Medical Diagnostic Discovery Department (MD3)

country: France

institute: bioMérieux

summary:
Classical antiviral therapy inhibit viral proteins and are subject to resistance. To counteract this emergence, alternative strategy has been developed that target cellular factors. We hypothesized that such approach could also be useful to identify broad antivirals. Influenza A virus was used as a model for viral diversity and need for therapy against unpredictable viruses as recently underlined by the H1N1 pandemic.
We proposed to identify a gene-expression signature associated with infection with different influenza A virus subtypes which could help to identify potential antiviral drugs with broad spectrum. Cellular gene expression response to infection with five different human and avian influenza viruses strains was analyzed and 300 genes were determined as differentially expressed between infected and non-infected samples. Strikingly, only a few genes were induced by infection and related to immune response. A more concise list was used to screen connectivity map, a database of drug-associated gene expression profiles, for molecules with inverse profiles than the signature of infection. We hypothesized that such compounds would induce an unfavorable cellular environment for influenza virus replication. Eight potential antivirals including ribavirin were identified, and six inhibited influenza viral growth in vitro. The new pandemic H1N1 virus, which was not used to define the gene expression signature of infection, was inhibited by five of the eight identified molecules, demonstrating that this strategy could help to identify broad spectrum antivirals. This is the first study showing that a gene expression based-screening can be used to identify antivirals. Such approaches could accelerate the drug discovery progress and could be extended to other pathogens.

overall_design: A549 (human lung epithelial cells) were infected with 5 different influenza A strains (A/New Caledonia/20/99 (H1N1), A/Moscow/10/99 (H3N2), A/Lyon/969/09 (H1N1 SOI-V), A/Turkey/582/2006 (H5N1), A/Finch/England/2051/94 (H5N2), and A/Chicken/Italy/2076/99 (H7N1)) or mock infected. Five independant replicates were done and hybridized on a different microarray. The overall design is thus composed of 5 mock samples, and 5x5 infected samples.

first: Laurence

last: Josset

first: Béatrice

last: Loriod

first: Olivier

last: Ferraris

first: Bruno

last: Lina

first: Catherine

last: N'Guyen

first: Jean-Jacques

last: Diaz

first: Manuel

last: Rosa-Calatrava


title: Gene expression profiling of mouse sclera during post-natal development

city: Singapore

first: Wan'e

last: Lim

address: 11 Third Hospital Ave

country: Singapore

institute: Singapore Eye Research Institute

summary:
Although there have been studies conducted on cornea and retina growth and development, postnatal gene expression studies on sclera growth during postnatal growth has not been well characterised. Given that the mouse genome has 85% homology to the human genome and has been completely sequenced, mouse model for the study of ocular growth has advantages over other animal models. Thus, we aimed to study the biology and genetics behind sclera growth during post-natal development in Balb/cJ mice as a means to understand genetic changes that cause scleral growth and development during post-natal eye development
The purpose of this study was to identify the genes underlying the development of mouse sclera post-natal growth of the posterior chamber of the eye using microarray

overall_design: Total RNA was isolated from single cryogenically ground mouse sclera (n=30, 6 samples each from week 1-, 2-, 3-, 6-and 8-old mice), reverse-transcribed and hybridized onto a Affymetrix mouse gene 1.0 ST array.We sought to use microarray to determine the gene expression profiles of mouse sclera from different age groups and identify the developmental genes that are involved in postnatal ocular growth.

first: Jia

last: Kwan

first: Liang

middle: K

last: Goh

first: Roger

middle: W

last: Beuerman

first: Veluchamy

middle: A

last: Barathi


title: Genomic Analysis of Individual Differences in Ethanol Drinking: Evidence for Non-genetic Factors in C57BL/6 Mice

status: Public on Mar 01 2011

city: Richmond

first: Jonathan

last: Warner

state: Virginia

address: 1220 E. Broad St.

department: Pharmacology and Toxicology

institute: Virginia Commonwealth University

summary:
Here, we identify persistent and substantial variation in ethanol drinking behavior within an inbred mouse strain and utilize this model to identify gene networks influencing such non-genetic variation in ethanol intake. C57BL/6NCrl mice showed persistent inter-individual variation of ethanol intake in a two-bottle choice paradigm over a three week period, ranging from less than 1 g/kg to over 14 g/kg ethanol in an 18h interval.
Whole genome microarray expression analysis in nucleus accumbens, prefrontal cortex and ventral tegmental area of individual animals identified gene expression patterns correlated with ethanol intake.  Results included several gene networks previously implicated in ethanol behaviors, such as glutamate signaling, BDNF and genes involved in synaptic vesicle function.  Additionally, genes functioning in epigenetic chromatin or DNA modifications such as acetylation and/or methylation also had expression patterns correlated with ethanol intake.  Our results thus implicate specific brain regional gene networks, including chromatin modification factors, as potentially important mechanisms underlying individual variation in ethanol intake.

overall_design: Voluntary two-bottle choice drinking was performed as described previously (Khisti et al. 2006).  Briefly, two bottles containing 10%(w/v) ethanol (Aaper Alcohol and Chemical Co. Shelbyville, KY) or tap water were placed into the home cage at the beginning of the dark cycle.  Tube position was varied every two days (L, L, R, R).  Drinking sessions lasted 18 hours/day followed by 6 hours access to water only.  Mice had four consecutive drinking sessions followed by four days of abstinence repeated four times to give 16 total drinking sessions.  Three brain regions were harvested 6 days after the last drinking session: prefrontal cortex (PFC), nucleus accumbens (NAc) and ventral tegmental area (VTA) as previously described (Kerns et al. 2005).  Labeled cRNA from individual animals (n=19) was hybridized to a single microarray for each brain region (n=58 total microarrays).

first: Jennifer

middle: T

last: Wolstenholme

first: Maria

middle: I

last: Capparuccini

first: Kellie

middle: J

last: Archer

first: Michael

middle: F

last: Miles


title: Effect of hpyAVIBM, a C5 cytosine methyltransferase deletion on the Helicobacter pylori transcriptome

status: Public on Mar 16 2011

city: BANGALORE

first: RITESH

last: KUMAR

address: DEPARTMENT OF BIOCHEMISTRY, INDIAN INSTITUTE OF SCIENCE

institute: INDIAN INSTITUTE OF SCIENCE

summary: Helicobacter pylori genome is rich in restriction - modification (R-M) systems. Around 4 % of the genome codes for components of R-M systems. hpyAVIBM, which codes for a putative phase-variable C5 - cytosine methyltransferase (MTase) from H. pylori lacks a cognate restriction enzyme.

sample_organism:
Helicobacter pylori
Helicobacter pylori 26695
Helicobacter pylori SS1

overall_design: To analysis the effect of deleting hpyAVIBM on the Helicobacter pylori transcriptome, microarray analysis was done with the wild type strains and corresponding hpyAVIBM deletion strains.

first: Ritesh

last: Kumar

first: D

last: Rao

first: Asish

last: Mukhopadhyay


title: Hepatic gene expression during liver regeneration in response to partial hepatectomy: early time points (0.5h,1h,2h,4h)

status: Public on Feb 16 2011

city: Houston

first: Scott

middle: Andrew

last: Ochsner

state: TX

address: One Baylor Plaza

department: Molecular and Cellular Biology

institute: Baylor College of Medicine

summary: The process of liver regeneration can be divided into a series of stages that include initial inductive or priming events through cellular mitosis.  Following two-thirds liver resection, the liver undergoes the “priming” phase, in which cytokines TNF-a and IL-6 activate their respective receptors in hepatocytes. This leads to the activation of several key transcription factors: NF-kB, AP-1, Stat 3, Stat 1, and C/EBP-b and -d . These transcription factors induce the expression of immediate early genes. HGF is also expressed at this time and involved in the transition of quiescent hepatocytes into the G1 phase of the cell cycle. During the G1 phase, delayed early genes are expressed followed by induction of cell cycle–related genes, both of which require new protein synthesis for their production. Increased expression of FoxM1B and TGF-a occurs at the G1/S transition and is correlated with increased expression of cyclinD1 and decreased expression of cdk inhibitors. During the G2/M phase of the cell cycle, FoxM1B directly elevates cyclinB1, cyclinB2, and cdc25B expression. Additionally, FoxM1B is associated with increased cyclinF and p55cdc, which are involved in completion of the cell cycle following partial hepatectomy.  In mice, two-thirds partial hepatectomy promotes proliferation of liver cells and rapid growth of the remaining liver tissue, resulting in complete restoration of organ mass in approximately 7 days (Mackey S. et al. Hepatology 2003 Dec;38(6):1349-52).

overall_design: Liver tissue was collected 0h, 0.5h, 1h, 2h, and 4h after partial hepatectomy or sham surgery from both young (5-6 months) and old (25-27 months) CB6F1 mice. All control and partial hepatectomy samples were assayed in triplicate. Relative gene expression levels were determined using Affymetrix Murine Genome U74 Version 2 Array.

first: Pallavi

last: Singh

first: Gretchen

last: Darlington


title: Characterization of hepatic gene expression during liver regeneration in response to partial hepatectomy

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

overall_design: Refer to individual Series


title: Expression data for derivation of septic shock subgroups

status: Public on Jan 13 2011

city: Cincinnati

first: Hector

middle: R

last: Wong

state: OH

address: 3333 Burnet Avenue

department: Pediatrics

institute: Cincinnati Children's Hospital Medical Center

summary: Background:  Septic shock is a heterogeneous syndrome within which probably exist several biological subclasses. Discovery and identification of septic shock subclasses could provide the foundation for the design of more specifically targeted therapies. Herein we tested the hypothesis that pediatric septic shock subclasses can be discovered through genome-wide expression profiling. Methods:  Genome-wide expression profiling was conducted using whole blood-derived RNA from 98 children with septic shock, followed by a series of bioinformatic approaches targeted at subclass discovery and characterization. Results:  Three putative subclasses (subclasses A, B, and C) were initially identified based on an empiric, discovery-oriented expression filter and unsupervised hierarchical clustering. Statistical comparison of the 3 putative subclasses (ANOVA, Bonferonni correction, p < 0.05) identified 6,934 differentially regulated genes. K means clustering of these 6,934 genes generated 10 coordinately regulated gene clusters corresponding to multiple signaling and metabolic pathways, all of which were differentially regulated across the 3 subclasses. Leave one out cross validation procedures indentified 100 genes having the strongest predictive values for subclass identification. Forty-four of these 100 genes corresponded to signaling pathways relevant to the adaptive immune system and glucocorticoid receptor signaling, the majority of which were repressed in subclass A patients. Subclass A patients were also characterized by repression of genes corresponding to zinc-related biology. Phenotypic analyses revealed that subclass A patients were younger, had a higher illness severity, and a higher mortality rate than patients in subclasses B and C. Conclusions:  Genome-wide expression profiling can identify pediatric septic shock subclasses having clinically relevant phenotypes.

overall_design: Expression data from 98 children with septic shock and 32 normal controls were generated using whole blood-derived RNA samples representing the first 24 hours of admission to the pediatric intensive care unit. The controls were used for normalization. Subsequently, we used the expression data to derive expression-based subclasses of patients using discovery oriented expression and statistical filters, followed by unsupervised hierarchical clustering.


title: Gene Expression Profiling In Murine Corneal Neovascularization Models

status: Public on Feb 08 2011

city: Suzhou

first: Yiqiang

last: Wang

state: Jiangsu

address: 111 Renai Road

country: China

institute: Xi'an Jiaotong-Liverpool University

summary: In order to find out the vital genes during the corneal neovascularization (CNV), we set up two CNV models, one being induced by suture placement and the other by alkali burn to the corneal center. Young adult Balb/c and C57BL/6 were used. The corneas were checked daily for CNV development and some of the corneas were removed at two pre-determined time points for RNA extraction. Preliminary experiment indicated slightly different dynamics in suture- or chemical burn-induced CNV. Vigorous growth appeared at day 5 and day 6 in S-CNV and CB-CNV, and reached maximum length around day 10 and day 14, respectively, in S-CNV and CB-CNV. To check whether genetic MHC background has any effect on development of CNV, we compared CB-CNV in Balb/c and C57BL/6 mice at day 6.

overall_design: Corneas from Balb/c mice were isolated 5 and 10 days after suture-induced CNV, and 6 and 14 days after chemical burn-induced CNV. Corneas from C57BL/6 mice were isolated 6 days after chemical burn-induced CNV. Each time point had two or three biological replications.

first: Yiqang

first: Chunxia

first: Changkai

last: Jia

first: Shengwei

last: Ren

first: Lingling

last: Yang


title: Hepatic gene expression during liver regeneration in response to partial hepatectomy: late time points (24h, 38h, 48h)

overall_design: Liver tissue was collected 0h, 24h, 38h, and 48h after partial hepatectomy or sham surgery from both young (5-6 months) and old (25-27 months) CB6F1 mice.  All control and partial hepatectomy samples were assayed in triplicate.  Relative gene expression levels were determined using Affymetrix moe430_2 oligo arrays.


title: Expression data from validation cohort of children with septic shock

summary: Background:  Septic shock heterogeneity has important implications for the conduct of clinical trials and individual patient management. We previously addressed this heterogeneity by indentifying 3 putative subclasses of children with septic shock based on a 100-gene expression signature corresponding to adaptive immunity and glucocorticoid receptor signaling. Herein we attempted to prospectively validate the existence of these gene expression-based subclasses in a validation cohort. Methods:  Gene expression mosaics were generated from the 100 class-defining genes for 82 individual patients in the validation cohort. Patients were classified into 1 of 3 subclasses (“A”, “B”, or “C”) based on color and pattern similarity relative to reference mosaics generated from the original derivation cohort. Separate classifications were conducted by 21 individual clinicians and a computer-based algorithm. After subclassification the clinical database was mined for clinical phenotyping. Results:  In the final consensus subclassification generated by clinicians, subclass A patients had a higher illness severity, as measured by illness severity scores and maximal organ failure, relative to subclasses B and C. The k coefficient across all possible inter-evaluator comparisons was 0.633. Similar observations were made based on the computer-generated subclassification. Patients in subclass A were also characterized by repression of a large number of genes having functional annotations related to zinc biology. Conclusions:  We have validated the existence of subclasses of children with septic shock based on a biologically relevant, 100-gene expression signature. The subclasses can be indentified by clinicians without formal bioinformatics training, at a clinically relevant time point, and have clinically relevant phenotypic differences.

overall_design: Expression data from 82 children with septic shock and 21 normal controls were generated using whole blood-derived RNA samples representing the first 24 hours of admission to the pediatric intensive care unit. The controls were used for normalization. Subsequently, we used the expression data from 100 class defining genes to validate the existence of pediatric septic shock subclasses having phenotypic differences.


title: Expression data from in-vitro induced Interfascicular Cambium of Arabidopsis thaliana

status: Public on Dec 31 2010

city: Wien

first: Javier

last: Agusti

address: Dr. Bohr-Gasse 3

country: Austria

institute: Gregor Mendel Institute

summary:
In-vitro induced establishment and activity of the interfascicular cambium in Arabidopsis thaliana stems under auxin treatments.
We used microarrays to detail the global programme of gene expression underlying the establishment and activity of the interfascicular cambium and identified tissue-speciffic up-regulated genes during this process.

overall_design: Different tissue types from in-vitro auxin treated stems were selected at successive stages of cambium establishment using laser capture microdissection for RNA extraction and hybridization on Affymetrix microarrays. We aimed to obtain genes exclussively upregulated in the interfascicular region responsible for cambium establishment and activity.

first: Thomas

last: Greb


title: Transcriptome-wide characterization of gene expression associated with unruptured intracranial aneurysms

status: Public on Feb 01 2011

city: Jinan

first: Fan

last: Jiang

state: Shandong

address: 107 Wen Hua Xi Road

institute: Shandong University

summary: The biological mechanisms by which cerebral aneurysms emerge, enlarge and rupture are not totally understood. In the present study, we analyzed the genome-wide gene expression profile in human intracranial aneurysms using cDNA microarrays.

overall_design: Intracranial arterial aneurysm samples (n = 3) and normal superficial temporal artery samples (control, n = 3) were obtained from individual subjects. All aneurysm samples were unruptured aneurysms confirmed by Magnetic Resonance Image or Digital Subtraction Angiography. Affymetrix HU133 Plus 2.0 microarrays were used to compare gene expression levels between aneurismal and normal blood vessels.

first: Li

last: Li

first: Xinjian

first: Gregory

last: Dusting

first: Zhongxue

last: Wu


title: Comparative transcriptome profiling analyses during the lag phase uncover YAP1, PDR1, PDR3, RPN4 and HSF1 as key regulatory genes in genomic adaptation to the lignocellulose derived inhitibor-stress for saccharomyces cerevisiae

city: Peoria

first: Z Lewis

last: Liu

address: 1815 N University

institute: USDA-ARS

summary: The yeast Saccharomyces cerevisiae is able to adapt and in situ detoxify lignocellulose derived inhibitors such as furfural and HMF. The length of lag phase for cell growth in response to the inhibitor challenge has been used to measure tolerance of strain performance. Mechanisms of yeast tolerance at the genome level remain unknown. Using systems biology approache, this study investigated comparative transcriptome profiling, metabolic profiling, cell growth response and gene regulatory interactions of yeast strains and selective gene deletion mutations in response to HMF challenges during the lag phase of growth. Three hundred and sixty-five candidate genes were identified and found at least three significant components involving some of these genes that enable yeast adaptation and tolerance to HMF in yeast. First, functional enzyme coding genes such as ARI1, ADH6, ADH7 and OYE3, as well as gene interactions involved in the biotransformation and inhibitor detoxification were direct driving force to reduce HMF damages in cells. Expressions of these genes were regulated by YAP1 and its closely related regulons. Second, a large number of PDR genes, mainly regulated by PDR1 and PDR3, were induced during the lag phase and the PDR gene family-centered functions, including specific and multiple functions involving cellular transport such as TPO1, TPO4, RSB1, PDR5, PDR15, YOR1, and SNQ2, promoted cellular adaptation and survival in order to cope with the inhibitor stress. Third, expressed genes involving degradation of damaged proteins and protein modifications such as SHP1 and SSA4, regulated by RPN4, HSF1 and other co-regulators, were necessary for yeast cells to survive and adapt the HMF stress. A deletion mutation strainΔrpn4 was unable to recover the growth in the presence of HMF. Complex gene interactions and regulatory networks as well as co-regulations exist in yeast adaptation and tolerance to the lignocellulose derived inhibitor HMF. Both induced and repressed genes involving diversified functional categories are accountable for adaptation and energy rebalancing in yeast to survive and adapt the HMF stress during the lag phase of growth. Transcription factor genes YAP1, PDR1, PDR3, RPN4 and HSF1 appeared to play key regulatory rules for global adaptation in the yeast S. cerevisiae.

overall_design: Cells were incubated on SC medium with HMF(30 mM) 6 h after pre-culture.Cultures grown under the same conditions without the HMF served as control. cells were harvested from 0, 10, 30, 60, 120 min, immediately frozen on dry ice, and then stored at -80 ℃. Two replicated experiments were carried out for each condition. Total RNA was isolated by hot phenol method and purified using RNeasy Mini Kit. Genome microarray of S. cerevisiae was fabricated with a version of 70-mer oligo set representing 6,388 genes. A mini-array consisting of quality control genes was designed on the top of the target array. Cy5 labeled RNA at 0 time point was designated as a reference and Cy3 was used to label test samples. An equal amount of at least 30 pmol Cy3 and Cy5 labeling reaction was applied for hybridization. Hybridization was performed based on Hegde et al (2000) with modifications using HS 4800 Hybridization station.

first: Menggen

last: Ma

first: Z


title: aCGH data from mouse APL tumors

status: Public on Dec 30 2010

city: StLouis

first: Nobish

last: Varghese

state: MO

address: 4444 Forest Park Ave.

institute: Washington University in St.Louis

type: Genome variation profiling by genome tiling array

summary: Acute Promyelocytic Leukemia (APL) is characterized by the t(15;17)(q22;q11.2) translocation, which creates a PML-RARA fusion gene that can initiate APL in mice. To discover cooperating mutations in this model, we sequenced a mouse APL genome to 15.6x haploid coverage, and discovered three somatic, non-synonymous mutations, of which one (Jak1 V657F) was recurrent. This mutation is identical to the JAK1 V658F mutation previously found in human APL and ALL samples. JAK1 V658F cooperates in vivo with PML-RARA, causing a rapidly fatal leukemia. We also discovered a somatic 150kb deletion involving the Kdm6a/Utx gene in the mouse APL genome; 3/14 additional mouse APL samples had similar deletions involving Kdm6a/Utx. Kdm6A/Utx, a histone H3K27 demethylase, was also deleted in 1/150 human AML samples tested. Whole genome sequencing of mouse cancer genomes provides an unbiased approach for discovering functionally relevant mutations that are also present in human leukemias.

overall_design: DNA from 15 mouse APL tumors on the Bl/6 Taconic background (F10), DNA from one WT 129/SvJ mouse spleen, and pooled DNA derived from the spleens of 6-week-old, wild type, Bl/6 Taconic (parental strain) mice were analyzed using the Nimblegen Mouse CGH 3x720K WGT platform.


title: Expression data from Tamoxifen resistant Breast Cancer Cell lines

city: London

first: Helen

middle: C

last: Hurst

address: Charterhouse Square

department: Centre for Tumour Biology

country: United Kingdom

institute: Institute of Cancer

type:
Expression profiling by array
Third-party reanalysis

summary:
Tamoxifen Resistant (TR) gene profile from Breast cancer cell lines T47D and ZR75-1 with their oestrogen-deprieved conterparts were analysed for gene associated with TR.
We used Microarray Affymetrix HU133plus 2.0 chips for gene expression of TR cell lines, normalised them against GEO data available for normal T47D (GSM70667) and ZR75-1 (GSM70668).

overall_design: We grew parental breast cancer cell lines in tamoxifen containing media (0.1 microM) for 6 months and labelled them tamoxifen resistant (TR). Oestrogen-Deprieved cells were grown in charcoal-stripped media for 6 months then tamoxifen (0.1 microM) was added to the media and cells maintained a further 6 months and termed Oestrogen deprieved-tamoxifen resistant (ODTR) .

first: Cheng

last: Yeoh

first: Claude

last: Chelala


title: Conserved progression mutations revealed by sequencing a mouse acute promyelocytic leukemia genome

status: Public on Dec 29 2010


title: Exon array data from mouse APL tumors

overall_design: Spleens from Bl/6 Taconic mice were harvested and total RNA was extracted. A total of 15 specimens were analyzed using the Affymetrix Mouse Exon 1.0 ST platform.


title: Transcriptome profiling of cells initially attached to different surfaces

status: Public on Dec 07 2010

city: Marburg

first: Julia

last: Gödeke

address: Karl-von-Frisch-Strasse 10

department: Ecophysiology

institute: Max Planck Istitute for terrestrial Microbiology

summary: Initial attachment to a surface marks the onset of a bacterial life style switch from planktonic to biofilm mode of growth. Among dissimilatory iron reducing bacteria, S. oneidensis MR-1 is notable due to its extensive respiratory versatility. It has been hypothesized that direct interaction of Shewanella cells with, or close proximity to, an appropriate surface facilitates the deposition of electrons. In fact, Shewanella species have been demonstrated to adhere to various surfaces and form biofilms. Global transcriptome profiling was performed on cells in the transition to surface-associated growth using different surfaces and conditions to understand molecular mechanisms underlying the initiation of microbe-surface interactions and the switch from planktonic to sessile life style.

overall_design: In the study presented, expression profiles of two independent replicates of Shewanella oneidensis MR-1 wild type cells attached  to glass for 0.25 h and 1 h, respectively, under hydrodynamic conditions  were compared to two independent replicates of planktonic grown Shewanella oneidensis MR-1 wild type cells. Furthermore, expression profiles of two independent replicates of Shewanella oneidensis MR-1 wild type cells attached for 1 h to iron surface under hydrodynamic conditions were compared to two independent replicates of Shewanella oneidensis MR-1 wild type cells attached to glass for 1 h. All samples were obtained from aerobically grown cells in LM.

first: Kai

last: Thormann


title: Effect of LAE1 gene deletion on gene expression in Trichoderma

status: Public on Jan 01 2011

city: Vienna

first: Christian

middle: P.

last: Kubicek

address: Getreidemarkt 9

institute: TU Vienna

summary: The mitosporic fungus Trichoderma reesei is an industrial producer of enzymes for degradation of lignocellulosic polysaccharides to soluble monomers that can be fermented to biofuels. The genes encoding these enzymes in T. reesei have recently been shown to be clustered in the genome.  Here we will show that the expression of these genes is epigenetically controlled at the heterochromatin level by the protein methyltransferase LAE1. Deletion of lae1 led to a loss of expression of the major cellulase and hemicellulase encoding genes, and resulted in an inability to grow on cellulose. The cellulase null phenotype was also seen with known soluble inducers of enzymes active on cellulose. In contrast, introduction of a second copy of lae1 or its enhanced expression under a strong constitutive promoter resulted in increased levels of cellulases. Thus, our  data provides an experiment-based explanation for the advantage for clustering of cellulases in the genome of T. reesei, and imply that the heterochromatin structure is a major determinant of cellulase gene expression and hence an attractive target for strain improvement.

overall_design: We used two biological replicas of four T. reesei strains growing on lactose, the parent strain (QM9414),  a delta-lae1, and two overexpressing strains (tef1:lae1 mutant 1 and mutant 2).

middle: P


title: Gestational taurine supplementation of mice: effect on offspring gene expression in liver and skeletal muscle

status: Public on Dec 01 2010

city: Copenhagen N

first: Ole

middle: Hartvig

last: Mortensen

address: Panum 6.5.28, Blegdamsvej 3

department: Department of Biomedical Sciences

institute: University of Copenhagen

summary:
Taurine is known to be important for fetal well being and to be able to prevent effects of a low birthweight phenotype when supplemented to pregnant dams.
We hypothesized that gestational taurine supplementation would affect gene expression level in 4w offspring liver and skeletal muscle.

overall_design: Pregnant mouse dams were subjected to different diet schemes from day 1 of pregnancy until birth. Pups were killed at 4 weeks of age and liver and quadriceps skeletal muscle taken out and frozen at -80C until analysis. Diet schemes: Normal Protein (20% casein; NP), Normal Protein + taurine (1% taurine supplementation in water ad libitum; NP+tau). The liver and muscle samples were normalized separately.

middle: H

first: Hanne

middle: L

last: Olsen

first: Lis

last: Frandsen

first: Peter

last: Nielsen

first: Finn

first: Niels

last: Grunnet

first: Bjørn

last: Quistorff


title: Human primary subcutaneous preadipocytes: Control vs PBMC co-culture

status: Public on Dec 03 2010

first: Jacob

last: Couturier

address: 6431 Fannin St., MSB 2.112

institute: University of Texas Medical School at Houston

summary: Transcriptional profiling of human preadipocytes comparing preadipocytes cultured in control media vs co-culture with PBMC's after 3 days.  Goal was to elucidate novel expression patterns in preadipocytes during exposure to human immune cells.

overall_design: 2-condition experiment, Preadipocytes+Media vs Preadipocytes+PBMC.  Biological replicates: 4 experimental replicates.

first: Dorothy

last: Lewis


title: Modulation of host gene expression by Hepatitis E virus ORF3 protein

city: New Delhi

first: Shahid

last: Jameel

state: Delhi

address: Aruna Asaf Ali Marg

institute: The International Centre for Genetic Engineering and Biotechnology (ICGEB)

summary: Analysis of human liver cell line (Huh7) infected with HEV ORF3 expressing (Ad-orf3-egfp) and control recombinant adenovirus (Ad-egfp). Hepatitis E virus ORF3 protein (pORF3) is known to modulate the host cell. Results provide insight into the role of this protein for HEV infection and pathogenesis.

overall_design: The gene expression experiment of Huh7 hepatoma cell line infected with ORF3 expressing recombinant adenoviruses (Ad-orf3-egfp) and with control recombinant adenoviruses (Ad-egfp) was performed in replicates of three.

first: Vivek

last: Chandra

first: Dhrubaa

last: Ghosh

first: Debarshi

last: Chakrabarti

first: Muralidhara

last: Padigaru


title: Expression data of QK mutant and wild type of Arabidopsis after heat shock

status: Public on Dec 23 2010

city: Shulin City, Taipei County

first: Hsiang-chin

last: Liu

address: 9F., No.332, Xuefu Rd.

country: Taiwan

institute: Academia sinica

summary: In order to study the importance of HSFA1 in thermotolerance in Arabidopsis, we generated the HSFA1a, b, d and e quadruple mutant (QK). QK is very sensitive to heat. Therefore, we used microarray to study how many genes regulated by HSFA1 after heat shock.

overall_design: Seven-day-old seedlings of Col-0, Ws and QK grown at 22oC on 0.5x MS plates containing 1% sucrose were incubated for 1 h at 37 °C. Subsequently, samples were collected for RNA extraction. The experiment was repeated, and two biological replicates were processed for analysis.

first: Yee-yung

last: Charng


title: Comparison of gene expression of L. reuteri ATCC PTA 6475 and L. reuteri 6475 PocR insertant

status: Public on Dec 10 2010

first: Delphine

last: Saulnier

address: Feigin Center, Suite 830, 1102 Bates Avenue

department: Pathology

summary: Comparison of gene expression between L. reuteri ATCC PTA 6475 and PocR mutant grown in semi-defined medium after 24h of growth at 37C in anaerobic condition

overall_design: Include 3 biological replicate and dye-swap


title: Identification and developmental expression of the full complement of cytochrome P450 genes in zebrafish

status: Public on Oct 21 2010

city: Woods Hole

first: Jared

last: Goldstone

state: MA

address: Redfield 3-52 MS#32

institute: Woods Hole Oceanographic Institution

summary: To determine the expression of cytochrome P450 genes during normal development

overall_design: Zebrafish embryos were collected at 3, 6, 12, 24, 36, and 48 hours post fertilization. Quadruplicate biological replicates of 100 embryos were hybridized.

middle: V

first: John

last: Stegeman

first: Andrew

middle: G

last: Mcarthur


title: Global epigenomic analysis of primary human pancreatic islets provides insights into type 2 diabetes susceptibility loci

status: Public on Nov 02 2010

city: Bethesda

first: Francis

middle: S

last: Collins

address: 1 Center Drive, Rm 126

department: Genome Technology Branch

institute: NHGRI

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Identifying cis-regulatory elements is important to understand how human pancreatic islets modulate gene expression in physiologic or pathophysiologic (e.g., diabetic) conditions. We conducted genome-wide analysis of DNase I hypersensitive sites, histone H3 lysine methylation marks (K4me1, K4me3, K79me2), and CCCTC factor (CTCF) binding in human islets. This identified ~18,000 putative promoters (several hundred novel and islet-active). Surprisingly, active promoter marks were absent at genes encoding islet-specific hormones, suggesting a distinct regulatory mechanism. Of 34,039 distal (non-promoter) regulatory elements, 47% are islet-unique and 22% are CTCF-bound. These findings present a global snapshot of the human islet epigenome and should provide functional context for non-coding variants emerging from genetic studies of T2D and other pancreatic islet disorders.

overall_design: Three different islet samples were tested for DNase I hypersensitivity by DNase-Seq. Five different primary pancreatic islet samples were evaluated for several chromatin modifications (H3K4me3, H3K4me1, H3K79me2) by ChIP-seq. One islet sample was evaluated for CTCF binding via ChIP-seq, All ChIP-seq samples have both non-specific IP (GFP) and input DNA controls.

first: Michael

last: Stitzel

first: Praveen

last: Sethupathy

first: Daniel

last: Pearson

first: Peter

last: Chines

first: Lingyun

last: Song

last: Erdos

first: Ryan

last: Welch

first: Stephen

last: Parker

first: Alan

last: Boyle

first: Laura

last: Scott

first: Elliott

last: Margulies

last: Boehnke

first: Terrence

last: Furey

first: Gregory

middle: E

last: Crawford


title: Signaling to Transcription Networks in the Neuronal Retrograde Injury Response

city: Los Angeles

first: Giovanni

last: Coppola

state: CA

address: 1524 Gonda, 695 Charles Young Drive South

department: Psychiatry and Neurology

institute: UCLA

summary: Retrograde signaling from axon to soma activates intrinsic regeneration mechanisms in lesioned peripheral sensory neurons; however, the links between axonal injury signaling and the cell body response are not well understood. Here, we used phosphoproteomics and microarrays to implicate ~900 phosphoproteins in retrograde injury signaling in rat sciatic nerve axons in vivo and ~4500 transcripts in the in vivo response to injury in the dorsal root ganglia. Computational analyses of these data sets identified ~400 redundant axonal signaling networks connected to 39 transcription factors implicated in the sensory neuron response to axonal injury. Experimental perturbation of individual overrepresented signaling hub proteins, including Abl, AKT, p38, and protein kinase C, affected neurite outgrowth in sensory neurons. Paradoxically, however, combined perturbation of Abl together with other hub proteins had a reduced effect relative to perturbation of individual proteins. Our data indicate that nerve injury responses are controlled by multiple regulatory components, and suggest that network redundancies provide robustness to the injury response

overall_design: Microarrays were run on mRNA extracted from adult rat L4 and L5 DRGs cells after 1,3,8,12,16,18,24, and 28 hours after a sciatic nerve (proximal and distal) lesion.

first: Izhak

last: Michaelevski

first: Yael

last: Segal-Ruder

first: Meir

last: Rozenbaum

first: Katalin

last: Medzihradszky

first: Ophir

last: Shalem

first: Shirley

last: Horn-Saban

first: Keren

last: Ben-Yaakov

first: Shachar

middle: Y

last: Dagan

first: Ida

last: Rishal

last: Geschwind

first: Yitzhak

last: Pilpel

first: Alma

last: Burlingame

first: Mike

last: Fainzilber


title: A systematic spatial bias in microarray hybridizations caused by probe spot position-dependent variability in lateral diffusion

status: Public on Dec 22 2010

first: Doris

last: Steger

state: Vienna

address: Althanstrasse 14

department: Department of Microbial Ecology

institute: University of Vienna

summary: The hybridization of nucleic acid targets with surface-immobilized probes is a widely used assay format for high-throughput detection of many parallel targetsin medical and biological research. Though commonly applied, microarray technology still suffers limitations arising from problems of data robustness and reproducibility across platforms, stemming in part from an incomplete understanding of the complex processes governing surface hybridization behavior. It has been observed that there are non-random spatial variations within individual microarray hybridizations, but the causative mechanisms of positional bias remain largely unexplained. This study identifies a symptomatic spatial bias in surface hybridization signal intensitywith systematically increased signal intensities of spots located at the boundaries of the spotted areas of the microarray slide and characterizes the underlying mechanistic principle of this bias using a simplified block array format. Experimentally-derived hybridization dynamics are compared with a mathematical modeling analysis, which together showthat the driver of the spatial bias is a position-dependent variation in lateral diffusion. Numerical simulations employing a diffusion-based model are used to demonstrate the strong influence of microarray well geometry on this spatial bias and to determine optimal conditions for which this bias can be minimized or eliminated, resulting in increased uniformity of microarray hybridization.

sample_organism: Candidatus Protochlamydia amoebophila UWE25

overall_design:
A simplified square array of 900 identical spotted probes was hybridized using different target concentrations and different time periods to analyze systematically spatial biases in microarray hybridizations.

Whole genome oligonucleotide microarray for Protochlamydia amoebophila.

A simplified square array of 5040 identical spotted probes was hybridized using 300 ng of Cy3 labeled RNA to analyze systematically spatial biases in microarray hybridizations.

first: David

last: Berry

first: Alexander

last: Loy


title: EpCAM expressing Hs578T cells

status: Public on Dec 02 2010

city: Innsbruck

first: Gilbert

last: Spizzo

address: Innrain 66

department: Experimental Oncology

institute: TCRI

summary:
EpCAM is frequently overexpressed in human invasive breast cancer. We reported EpCAM overexpression to be an independent prognostic marker for poor overall survival in node-positive breast cancer.
We used microarrays in order to investigate changes of the transcriptome on EpCAM gene overexpression in human breast cancer cells

overall_design: Hs578T cells were found to express only very little EpCAM mRNA and protein in comparison to established and well characterized breast cancer cell lines such as MCF-7 or SK-BR-3. Hs578T cells were stably transfected with the EpCAM cDNA containing construct pIRESpuro3_EpCAM and the respective empty vector control.


title: Elevated levels of H3K27me3 in Snf5-deficient cells

status: Public on Oct 19 2010

city: Boston

first: Boris

middle: G.

last: Wilson

address: 44 Binney Street

department: Pediatric Oncology

institute: Dana-Farber Cancer Institute

type: Genome binding/occupancy profiling by genome tiling array

summary: Epigenetic alterations have been increasingly implicated in oncogenesis. Analysis of Drosophila mutants suggests that Polycomb and SWI/SNF complexes can serve antagonistic developmental roles. However, the relevance of this relationship to human disease is unclear. Here we have investigated functional relationships between these epigenetic regulators in oncogenic transformation. Mechanistically, we show that loss of the SNF5 tumor suppressor leads to elevated expression of the Polycomb gene EZH2 and that Polycomb targets are broadly H3K27-trimethylated and repressed in SNF5-deficient fibroblasts and cancers. Further, we show antagonism between SNF5 and EZH2 in the regulation of stem cell-associated programs and that Snf5 loss activates those programs. Finally, using conditional mouse models, we show that inactivation of Ezh2 blocks tumor formation driven by Snf5 loss.

overall_design: H327me3 ChIP-chip in wild type, Snf5-deficient MEFs, and murine cerebellum. Ezh2 ChIP-chip in wild type and Snf5-deficient MEFs

first: Charles

last: Roberts


title: Epigenetic antagonism between Snf5 and Ezh2 during oncogenic transformation

overall_design: Mouse Embryonic Fibroblasts (MEFs) conditionally inactivated for Ezh2, Snf5 and Ezh2, or from control WT MEFs were used to evaluated epigenetic antagonism between Snf5 and Ezh2 in the control of gene expression programs. Snf5-deficient lymphoma samples and control CD8+ WT T-cells were used to evaluate genetic programs misregulated by Snf5 inactivation during tumorigenesis. RNA was isolated from each of these samples and used for gene expression profiling on Affymetrix arrays.


title: Epigenetic antagonism between Snf5 and Ezh2 during oncogenic transformation and elevated levels of H3K27me3 in Snf5-deficient cells

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

overall_design: Refer to individual Series


title: Antioxidant response gene expression in the bronchial airway epithelial cells of smokers at risk for lung cancer

status: Public on Oct 01 2010

first: Avrum

last: Spira

address: 715 Albany Street, R304

department: Pulmonary and Critical Care Medicine

institute: Boston University Medical Center

summary:
Prior microarray studies of smokers at high risk for lung cancer have demonstrated that heterogeneity in bronchial airway epithelial cell gene expression response to smoking can serve as an early diagnostic biomarker for lung cancer.  This study examines the relationship between gene expression variation and genetic variation in a central molecular pathway (NRF2-mediated antioxidant response) associated with smoking exposure and lung cancer.  We assessed global gene expression in histologically normal airway epithelial cells obtained at bronchoscopy from smokers who developed lung cancer (SC, n=20), smokers without lung cancer (SNC, n=24), and never smokers (NS, n=8).  Functional enrichment showed that the NRF2-mediated antioxidant response pathway differed significantly among these groups.

Keywords: Global mRNA expression profiling

overall_design:
21 total arrays (20 unique patients) run on total RNA obtained from Bronchial Epithelium of Smokers with Lung Cancer
30 total arrays (24 unique patients) run on total RNA obtained from Bronchial Epithelium of Smokers without Lung Cancer
9 total arrays (8 unique patients) run on total RNA obtained from Bronchial Epithelium of Never Smokers

first: Xuting

last: Want

first: Brian

middle: N

last: Chorley

first: Gary

last: Pittman

first: Steven

last: Kleeberger

first: John

last: Brothers

first: Gang

last: Liu

first: Douglas

middle: A

last: Bell


title: Evidence of Distinct Tumor Initiating Cells with Different Properties in Primary Human Hepatocellular Carcinoma.

status: Public on Oct 02 2010

city: milan

first: Federico

last: Colombo

address: via F. Sforza 35

country: Italy

institute: fondazione IRCCS Ca' Granda

summary: Increasing evidences have been recently reported on tumor cells heterogeneity within several malignancies, but data on liver tumours are still lacking. The aim of this study was to investigate and characterize tumor initiating cell (TIC) compartments within human hepatocellular carcinoma (HCC). After long term culture, we were able to identify 3 morphologically different tumor cell populations from an individual HCC specimen. These cell populations were extensively characterized by flow cytometry, fluorescence microscopy, single cell cloning, xenotransplantation in NOD/SCID IL2Rgamma -/- mice, karyotyping and microarray analyses. The 3 primary cell populations, hcc-1, -2 and -3, and the 2 clones (clone-1/7 and -1/8) generated by limiting dilution from hcc-1 showed different expression profiles for several tumor associated stem cell markers, including EpCAM, CD49f, CD44, CD133, CD56, Thy-1, ALDH and CK19. Moreover, they showed different doubling time and drug resistance. The tumorigenic potential was higher for hcc-1 and clone-1/7. Karyotyping analyses revealed a clonal evolution of cell populations and clones within the primary tumor. Importantly, we noticed that the primary tumor cell population with a higher tumorigenic potential and drug resistance was that showing more chromosomal alterations and containing different clones with both epithelial and mesenchymal features. Individual HCC can harbor different self-renewing tumorigenic cell types expressing a variety of morphology and phenotypic markers, karyotypic evolution and different gene expression profiles. This finding suggests that the therapeutic approach for HCC eradication should take into account the possible TIC heterogeneity due to intratumor clonal evolution.

overall_design: The aim was to analyse the whole genome expression profile of 3 HCC cell lines (Hcc-1, Hcc-2 and Hcc-3) and two clones (Clone-1/7 and Clone-1/8) cells obtained from one patient. Tumor sample was dissociated and cells cultured on collagen coated Petri dishes. When cell colonies appeared in culture, they were detached and cultured separately; clones were obtained fron HCC-1 cell lines by means of limiting dilution. Total Five independent total RNA extractions were performed for each cell line and clone and after checked the quality, concentration and integrity of the purified RNA, only samples showing the better results were chosen to be further processed. After the acquisition of the raw intensity data matrix with the corresponding annotations, probes corresponding to "predicted" genes or not associated to a Entrez ID were discarded from the analysis; moreover, different probe signals corresponding to the same Entrez ID were converted into unique intensity signal, corresponding to the median of the values for each array, in order to obtain a single signal for each Entrez ID. After this process, we generated a boxplot of 16964 intensity signals whose values were log2-transformed and quantile normalized using the aroma.light package for Bioconductor. Genes with a differential expression value of at least 2 fold (on log2 transformed scale) were considered differentially expressed.

first: Francesca

last: Baldan

first: Silvia

last: Mazzucchelli

first: Ines

last: Martin-Padura

first: Paola

last: Marighetti

first: Alessandra

last: Cattaneo

first: Barbara

last: Foglieni

first: Marta

last: Spreafico

first: Silvana

last: Guerneri

first: Marco

last: Baccarin

first: Francesco

last: Bertolini

first: Giorgio

last: Rossi

first: Vincenzo

last: Mazzaferro

first: Massimiliano

last: Cadamuro

last: Maggioni

first: Paolo

last: Rebulla

first: Daniele

last: Prati

first: Laura

last: Porretti

first: Luca

last: Agnelli


title: Stress response regulators identified through genome-wide transcriptome analysis of the (p)ppGpp-dependent response in Rhizobium etli

status: Public on Sep 15 2010

city: Leuven

first: Kristof

last: Engelen

address: Kasteelpark Arenberg 20

country: Belgium

institute: KULeuven

type: Expression profiling by genome tiling array

summary: The impact on gene expression by the alarmone (p)ppGpp during growth and non-growth was determined by comparing the transcriptome of R. etli CFN42 wild type and rel mutant. This allowed us to better understand the pleiotropic stress phenotype of the rel mutant as well as identifying specific (p)ppGpp-dependent stress regulators.

overall_design: In order to study expression, R. etli CFN42 wild type and rel mutant was grown at 30˚C in acid minimal salts medium supplied with 10 mM NH4Cl and 10 mM succinate while monitoring the optical density (OD) of the culture. Samples were taken at OD600 = 0.3, 0.7 and 6 hours after reaching the maximum OD, representing early/late exponential and stationary phase, respectively.

first: Maarten

last: Vercruysse

last: Fauvart

first: Jan

last: Michiels

first: Lore

last: Cloots


title: MicroRNA expression profiling of the porcine developing cortex and cerebellum

status: Public on Sep 14 2010

city: Frederiksberg C

first: Agnieszka

last: Podolska

address: Grønnegårdsvej 3 2nd floor

department: Department of Basic Animal and Veterinary Sciences

institute: Faculty of Life Sciences, University of Copenhagen,

summary: MicroRNA expression profiling using microRNA microarrays was performed on the porcine developing brain. Two tissues, cortex and cerebellum, were sampled at each of three different developmental stages: gestation day 50 (F50), gestation day 100 (F100) and three months old (named adult), respectively. The aim was to find developmental stage-, as well as tissue-specific, microRNA candidates and validate them with qPCR.

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

overall_design: RNA samples containing the small RNA fraction were subjected to microarray analysis. Three replicates per developmental stage/tissue.

first: Bogumil

last: Kaczkowski

first: Peter

middle: K

last: Busk

first: Rolf

last: Søkilde

first: Thomas

last: Litman

first: Merete

last: Fredholm

first: Susanna

last: Cirera


title: HeLa cells: overexpression of importin alpha2

status: Public on Nov 24 2010

city: Clayton

first: Yoichi

last: Miyamoto

state: VIC

address: Building 77 Level 1, Wellington Road

department: Biochemistry and Molecular Biology

country: Australia

institute: Monash University

summary: To test whether nuclear importin alpha2 can regulate transcription, we sought to examine gene expression changes in cells with nuclear accumulation of importin alpha2 by performing microarray analysis. We designed an experiment in which EGFP-fused full-length importin alpha2 was transfected into HeLa cells. To exclude the possibility that exogenous, full-length importin alpha2 protein enhances nuclear transport of karyophilic proteins such as transcription factors and thereby directly influences gene expression, a mutant of importin alpha2 which is mutated in the C-terminal CAS-binding domain was also transfected, so that it is never recycled to the cytoplasm and shows complete nuclear localization. We undertook to investigate whether there were changes in gene expression common to cells expressing the full-length importin alpha2 and the C-terminal mutant (C-mutant) isoform.

overall_design: EGFP vs. EGFP-importin alpha2 full length, or EGFP vs EGFP-importin alpha2 CAS-binding mutant. One replicate each. EGFP-expressing cells are used as a control.

first: Yoshihiro

last: Yoneda


title: Genetic regulation of gene expression of barley in response to stem rust (Pgt isolate TTKS)

status: Public on Nov 15 2010

city: Ames

first: PLEXdb Curator

middle: Sudhansu

state: IA

address: 1023  Crop Genomes Informatics Lab (Iowa State University)

department: Virtual Reality Application Center

institute: Iowa State University

summary: The QxSM doubled-haploid mapping population was generated from a single Q21861 x SM89010 F1 plant (Borovkova et al. 1995; Steffenson et al. 1995). Four flats (each flat contained 75 DH lines + 4 replicates of each parent = 81 cones/flat) were grown in a completely randomized design at the ARS Cereal Disease Lab, University of Minnesota, St. Paul.  The four flats were divided into two replicates of two flats each.  Nine days after sowing, one flat of each replicate was inoculated (INOC) with TTKS urediniospores were suspended in Soltrol oil with an inoculum weight of 0.25 mg per flat and the other was mock-inoculated (MOCK).  Each (MOCK and INOC) replicate was incubated in its own dew chamber overnight.  After inoculation, replicates were placed in separate mist chambers for 16 hours in the dark, followed by lights for 5 hours, and then moved to the greenhouse for 2 hours.  The growth stage of barley was first leaf unfolded (PO:0007094) and five seedlings were harvested and placed in liquid nitrogen for each line in the population within a 1.5 hour period at 24 hours after inoculation (hai).   ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor,  Roger P. Wise.  The equivalent experiment is BB64 at PLEXdb.]

overall_design: 166 hybridizations

first: Roger

last: Wise


title: The Transcriptional Landscape of Bovine Skeletal Muscle

city: St Lucia

first: Sean

last: McWilliam

state: Queensland

address: 306 Carmody Road

department: Agriculture and Food

institute: CSIRO

summary: Transcriptional profiling of Bovine skeletal muscle was conducted comparing age of cattle and dietary regimes

overall_design: 4 prenatal time points, 4 postnatal time points, 2 dietary regimes at 3 time points

first: A

last: Reverter

first: N

last: Hudson


title: Functional blockade of α5β1 integrin induces scattering and genomic landscape remodeling of hepatic progenitor cells

status: Public on Aug 27 2010

city: Porto

first: Rune

last: Matthiesen

address: Rua Dr. Roberto Frias s/n

country: Portugal

institute: IPATIMUP

summary: Cells treated with a specific antibody against α5β1 integrin exhibited cell spreading and scattering, over-expression of liver stem/progenitor cell markers and activation of the ERK1/2 and p38 MAPKs signaling cascades, in a similar manner to the process triggered by HGF/SF1 stimulation. Gene expression profiling revealed marked transcriptional changes of genes involved in cell adhesion and migration, as well as genes encoding chromatin remodeling factors. These responses were accompanied by conspicuous spatial reorganization of centromeres, while integrin genes conserved their spatial positioning in the interphase nucleus.

overall_design: Untreated cells versus HGF/SF1 treated or α5β1 integrin-mediated cell migration

first: Luciano

last: Vellón

first: Luis

last: Parada


status: Public on Sep 01 2010

city: St. Louis

first: Olga

last: Agapova

address: 660 S Euclid Ave

department: Ophthalmology and Visial Sciences

institute: Washington University School of Medicine

summary: Gene expression profiling of ABCB1 positive and ABCB1 negative OCM1A cells.  ABCB1 is an ATP-dependent transporter efflux pump.  OCM1A cell line is derived from uveal melanomas.

overall_design: 6 samples (3 ABCB1 positive and 3 ABCB1 negative) from 3 independent ABCB1 shift assays were analysed

first: Solange

last: Landreville


title: Elevated AKR1C3 expression promotes prostate cancer cell survival and prostate cell-mediated endothelial cell tube formation: Implications for prostate cancer progression

status: Public on Aug 10 2010

city: Oklahoma City

first: Hsueh-Kung

last: Lin

state: OK

address: Room 462, 800 Research Parkway

department: Urology

institute: University of Oklahoma Health Sciences Center

summary: Background:  Aldo-keto reductase (AKR) 1C family member 3 (AKR1C3), one of four identified human AKR enzymes, catalyzes steroid, prostaglandin, and xenobiotic metabolism.  In the prostate, AKR1C3 is up-regulated in localized and advanced prostate adenocarcinoma, and is associated with prostate cancer (PCa) aggressiveness.  Here we provide initial evidence for potential roles of AKR1C3 in PCa progression.    Methods:  Spatial distribution of AKR1C3 was analyzed using immunohistochemical staining in prostate adenocarcinoma tissue array.  Human PCa PC-3 cells were stably transfected with AKR1C3 cDNA to establish PC3-AKR1C3 transfectants.  Microarray and bioinformatics analyses were performed to identify pathways that are activated by elevated AKR1C3 expression in PCa cells.  Functional confirmation of microarray and bioinformatics results was performed by immunoblot analysis and an in vitro Matrigel angiogenesis assay.   Results:  Elevated AKR1C3 expression was specifically limited to human prostate adenocarcinoma.  Microarray and bioinformatics analysis suggested that elevated AKR1C3 expression in PC-3 cells modulates estradiol and androgen metabolism and activates insulin growth factor (IGF)-1 and Akt signaling pathways.  Immunoblots confirmed that phosphorylated levels of IGF-1 receptor (IGF-1R) and Akt are significantly up-regulated in PC3-AKR1C3 as compared to mock transfectants.  PC3-AKR1C3 transfectants promoted endothelial cell tube formation in Matrigel as compared to parental PC-3 cells and mock transfectants.    Conclusion:  Microarray and bioinformatics data followed by biological analyses suggest that elevated AKR1C3 expression in PC-3 cells promotes PCa angiogenesis and aggressiveness.  These results suggest AKR1C3 can promote the aggressiveness of PCa through modulating estrogen and androgen metabolism with subsequent activation of growth factor IGF-1 and cytoplasmic Akt signaling pathways.

overall_design: Total RNA from mock- and ACR1C3 transfected PC-3 cells was isolated, with 2 or 3 biological replicates each. Gene expression data from AKR1C3 transfected PC-3 cells were compared with mock-transfected data.

first: Mikhail

last: Dozmorov

first: Joseph

middle: T

last: Azzarello

first: Jonathan

middle: D

last: Wren

first: Kar-Ming

last: Fung

first: Randal

last: May

first: Qing

last: Yang

first: Robert

last: Hurst

first: Trevor

middle: M

last: Penning


title: Alpha-synuclein deficiency affects brain Foxp1 expression and ultrasonic vocalization

status: Public on Jul 22 2010

city: Tuebingen

first: Michael

middle: H.

last: Walter

address: Calwer Str. 7

department: Department of Medical Genetics

institute: University of Tuebingen

summary: Alpha-synuclein is an abundant protein implicated in synaptic function and plasticity, but the molecular mechanism of its action is not understood. Missense mutations and gene duplication/triplication events result in Parkinson's disease, a neurodegenerative disorder of old age with impaired movement and emotion control. Here, we systematically investigated the striatal as well as the cerebellar transcriptome profile of alpha-synuclein-deficient mice via a genome-wide microarray survey in order to gain hypothesis-free molecular insights into the physiological function of alpha-synuclein. A genotype-dependent, specific and strong downregulation of forkhead box P1 (Foxp1) transcript levels was observed in all brain regions from postnatal age until old age and could be validated by qPCR. In view of the co-localization and heterodimer formation of FOXP1 with FOXP2, a transcription factor with a well established role for vocalization, and the reported regulation of both alpha-synuclein and FOXP2 expression during avian song learning, we performed a detailed assessment of mouse movements and vocalizations in the postnatal period. While there was no difference in isolation-induced behavioral activity in these animals, the alpha-synuclein-deficient mice exhibited an increased production of isolation-induced ultrasonic vocalizations (USVs). This phenotype might also reflect the reduced expression of the anxiety-related GABA-A receptor subunit gamma 2 (Gabrg2) we observed. Taken together, we identified an early behavioral consequence of alpha-synuclein deficiency and accompanying molecular changes, which supports the notion that the neural connectivity of sound or emotion control systems is affected.

overall_design: Factorial design comparing SNCA knock-out mice with wild type littermates in two different tissues (striatum, cerebellum) at two different timepoints (6 and 21 month)

first: Alexander

last: Kurz

first: Markus

last: Wöhr

last: Bonin

first: Georg

last: Auburger

first: Suzana

last: Gispert

first: Rainer

last: Schwarting


title: Impact of RNA degradation on gene expression profiling

status: Public on Aug 19 2010

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

institute: Universitaetsmedizin Goettingen

summary: 1.) Background: Gene expression profiling is a highly sensitive technique which is used for profiling of tumor samples for medical prognosis. RNA quality and degradation influences the analysis results of gene expression profiles. The impact of this influence on the profiles and its medical impact is not fully understood. As patient samples are very valuable for clinical studies, it is necessary to establish criteria for the RNA quality to use these samples in later analysis. 2.) Methods: To investigate the effects of RNA integrity on gene expression profiling whole genome expression arrays were used. We therefore used tumor biopsies from patients diagnosed with locally advanced rectal cancer. To simulate degradation, the isolated total RNA of all patients was subjected to heat-induced degradation in a time-dependent manner. Expression profiling was then performed and data were analyzed bioinformatically to assess  the differences. 3.) Results: The biological differences between the patients largely over-weighed the differences introduced by RNA degradation. Only a relatively small number of probes (275 out of 41000) show a significant effect due to degradation. The genes that show the strongest effect due to RNA degradation were especially those with short mRNAs and probe positions near the 5' end. 4.) Conclusions: RNA from tumor samples with differing realistic qualities (> 5) can still be used to perform gene expression analysis. A much higher biological variance between patients is observed compared to the effect that is imposed by degradation of RNA. Nevertheless there are genes that are prone to degradation, especially very short ones and those with the probe binding side close to the 5´-end. Therefore, these genes should be excluded from gene expression analysis when working with degradated RNA.

overall_design: Biopsies were taken from 3 different patients with 4 time-points of degradation per patient. The resulting 12 samples were separately hybridised (OneColor Array Design).

first: Lennart

last: Opitz

last: Salinas-Riester

first: Marian

last: Grade

first: Klaus

last: Jung

last: Ghadimi

first: Tim

last: Beissbarth

first: Jochen

last: Gaedcke


title: High-throughput gene expression profiling of Salmonella enterica serovar Paratyphi A in the blood of bacteremic patients in Bangladesh

status: Public on Sep 06 2010

first: Richelle

middle: C.

last: Charles

address: 55 Fruit Street, Gray 504

department: Infectious Diseases

institute: Massachussetts General Hospital

summary: In this work, we applied an RNA analysis method, Selective Capture of Transcribed Sequences (SCOTS), and cDNA hybridization-microarray technology to identify S. Paratyphi A transcripts expressed by bacteria in the blood of three patients in Bangladesh.  In total, we detected 1798 S. Paratyphi A mRNAs expressed in the blood of infected humans (43.9% of the ORFeome).  Of these, we identified 868 in at least two patients, and 315 in all three patients.  S. Paratyphi A transcripts identified in at least two patients encode proteins involved in energy metabolism, nutrient and iron acquisition, vitamin biosynthesis, stress responses, oxidative stress resistance, and pathogenesis.  A number of detected transcripts are expressed from PhoP and SlyA-regulated genes associated with intra-macrophage survival, genes contained within Salmonella Pathogenicity Islands (SPIs) 1-4, 6, 10, 13, and 16, as well as RpoS-regulated genes.  The largest category of identified transcripts are those encoding proteins with unknown function.  When comparing level of bacterial mRNA detection using in vivo samples collected from infected patients to samples from in vitro grown organisms, we found significant differences for 347, 391, and 456 S. Paratyphi A transcripts in each of three individual patients (approximately 9.7% of the ORFeome).  Of these, expression of 194 transcripts (4.7% of ORFs) was concordant in two or more patients, and 41 in all patients.  Genes encoding these transcripts are contained within SPI-1, 3, 6 and 10, are PhoP-regulated genes, are involved in energy metabolism, nutrient acquisition, drug resistance, or are uncharacterized genes.  Using quantitative RT-PCR, we confirmed increased gene expression in vivo for a subset of genes identified in our analyses.

sample_organism: Salmonella enterica subsp. enterica serovar Paratyphi A

overall_design: We compared transcriptional profiles of S. Paratyphi A from the blood of infected humans to S. Paratyphi A grown in vitro. Replicates and dye-swaps were performed.

first: Alaullah

last: Sheikh

first: Sean

last: Rollins

first: Jason

middle: B

last: Harris

first: Md

last: Bhuiyan

first: Farhana

last: Khanam

first: Archana

last: Bukka

first: Anuj

last: Kalsy

first: Steffen

last: Porwollik

first: W

last: Brooks

first: Regina

middle: C

last: LaRocque

last: McClelland

first: Tanya

last: Logvinenko

first: Alejandro

last: Cravioto

first: Stephen

last: Calderwood

first: James

last: Graham

first: Firdausi

last: Qadri

first: Edward

last: Ryan


title: Expression data from pediatric AML patients

status: Public on Oct 21 2010

city: Rotterdam

first: Brian

last: Balgobind

address: Dr. Molewaterplein 60

department: Pediatric Oncology/Hematology

country: Netherlands

institute: Erasmus MC - Sophia Children's Hospital

summary:
Pediatric acute myeloid leukemia (AML) is a heterogeneous disease characterized by non-random genetic aberrations related to outcome. Detecting these aberrations however still lead to failures or false negative results. Therefore, we focused on the potential of gene expression profiles (GEP) to classify pediatric AML.
Gene expression microarray data of 237 children with AML were generated and cases were split into a discovery cohort (n=157) and an independent validation cohort (n=80). Next, a double-loop cross validation approach was used to generate a subtype-predictive GEP in the discovery cohort which was then tested for its true predictive value in the independent validation cohort.

overall_design: 237 bone marrow and peripheral blood samples were collected at diagnosis and frozen. They were later thawed and hybridized to Affymetrix U133 Plus 2.0 arrays.

first: Monique

last: den Boer


title: Chromatin Structure and Gene Expression Programs of Human Embryonic and Induced Pluripotent Stem Cells (ChIP-seq)

status: Public on Aug 09 2010

city: Cambridge

first: Garrett

last: Frampton

address: 9 Cambridge Center

department: Biology

institute: Whitehead Instute - MIT

summary: Knowledge of both the global chromatin structure and the gene expression programs of human embryonic stem (ES) cells and induced pluripotent stem (iPS) cells should provide a robust means to assess whether the genomes of these cells have similar pluripotent states.  Recent studies have suggested that ES and iPS cells represent different pluripotent states with substantially different gene expression profiles.  We describe here a comparison of global chromatin structure and gene expression data for a panel of human ES and iPS cells.  Genome-wide maps of nucleosomes with histone H3K4me3 and H3K27me3 modifications indicate that there is little difference between ES and iPS cells with respect to these marks.  Gene expression profiles confirm that the transcriptional programs of ES and iPS cells show very few consistent differences.  Although some variation in chromatin structure and gene expression was observed in these cell lines, these variations did not serve to distinguish ES from iPS cells.

overall_design: Examination of two histone modifications (H3K4me3 and H3K27me3) in 6 human ES cell lines, 8 human iPS cell lines, and 1 fibroblast cell line.

first: Matthew

last: Guenther

first: Frank

last: Soldner

first: Dirk

last: Hockemeyer

first: Maya

last: Militipova

first: Rudolf

last: Jaenisch

first: Richard

last: Young


title: Expression profiling of HeLa Tet-off cells expressing Flag-tagged version of WT NIPP1 or PP1 binding mutant of NIPP1.

status: Public on Jul 19 2010

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

institute: VIB

summary: NIPP1, an established interactor of protein phosphatase 1 (PP1), is implicated in PRC2-mediated regulation of gene expression. Here, we explore whether PP1 associated with NIPP1 is involved in NIPP1-mediated regulation of genes. Therefore, we generated Hela Tet-off (HTO) cell lines that stably and inducibly express a Flag-tagged version of wild-type NIPP1 (HTO-NIPP1wt) or mutant NIPP1 (HTO_NIPP1m). The latter mutant lacks the major PP1 binding site by two point mutations in the RVXF-motif, an established PP1 - binding motif. All cell lines were derived from the same parental HeLa Tet-Off (HTO-PT) cell line which expresses only tTA transactivator and is used as a control. The Flag fusions were only expressed in the absence of doxycyline and at levels that were up to twofold higher than that of endogenous NIPP1. We performed a gene expression profiling of the HTO cell lines, using Whole Human Genome Oligo microarrays from Agilent. A Paired SAM analysis identified 1365 genes with an altered expression (P < 0.01) between the Flag-NIPP1 and parental cell lines. Importantly, only 185 genes were differentially expressed (P<0.01) between the Flag-NIPP1m and parental cell lines. Even more strikingly, only 5% of the genes that were affected by the expression of Flag-NIPP1 also showed a significantly different expression in the Flag-NIPP1m cells. A similar small overlap was noted when the analysis was restricted to the 50 genes that were most upregulated or downregulated by the expression of Flag-NIPP1. Finally, scatter plot analysis revealed no significant correlation between the genes that were affected by the expression of Flag-NIPP1 or Flag-NIPP1m. Collectively, these data demonstrate that a moderate increase in the concentration of NIPP1 affects the expression of numerous genes by a mechanism that depends on associated PP1.

overall_design: In total 12 samples were processed. Three different cell lines were analysed: HTO_parental, HTO_NIPP1wt and HTO_NIPP1m. For each cell line 4 replicates were obtained. The HTO_parental cell line is the control cell line. For the HTO_NIPP1wt the 4 replicates were obtained from two replicates of two different transgenic cell lines expressing FlagNIPP1wt (cell line wt n°1 and 2). Each cell line derived from the same parental control cell line.

first: Lijs

last: Beke

first: Nele

last: VanDessel

first: Nikki

last: Minnebo

first: Aleyde

last: VanEynde

first: Janina

last: Görnemann

last: Beullens

first: Nobuhiro

last: Tanuma

first: Hiroshi

last: Shima

first: Mathieu

last: Bollen


title: RNA expression analysis of cells producing the synthetic protein DX over a 4hr time course

status: Public on Jul 21 2010

city: Tempe

first: Joshua

last: Stomel

state: AZ

department: BON

institute: Biodesign Inst. at ASU

summary: We expressed the man-made protein DX in E. coli cells over the course of 4 hours and examined effects on global gene expression.

overall_design: We analyzed the change in RNA expression profiles of E. coli cells expressing the synthetic protein DX every half-hour over a four hour experiment.  These samples were compared to un-induced control cells.   Each sample represents a different time point with the 647nm channel being the DX-expressing samples and the 555nm chanel being the un-induced controls.  Controls contained the DX cassette in the pBAD18 vector and were treated identically to the experimental cells, except the arabinose inducer was omitted from the growth media.  The 2.5 hour time point is omitted because the control cDNA failed to label properly.  No dye swaps or repeats were performed because:  a) we were examining trends over time and any anomalous or faulty spot would be excluded during analysis if it were not part of a general trend, and b) Microarray data is not being used to draw conclusions, but rather to draw a picture of what was changing in the cell and open up avenues of exploration.

first: James

middle: W

last: Wilson

first: Megan

last: Leon

first: Phillip

last: Stafford

first: John

last: Chaput


title: Chromatin Structure and Gene Expression Programs of Human Embryonic and Induced Pluripotent Stem Cells

first: Garrett

last: Frampton

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

overall_design: Refer to individual Series

first: Matthew

middle: G

last: Guenther

first: Frank

last: Soldner

first: Dirk

last: Hockemeyer

first: Maya

last: Militipova

last: Jaenisch


title: Small RNA-based silencing strategies for transposons in the process of invading Drosophila species

city: Cold Spring Harbor

first: Nikolay

middle: V

last: Rozhkov

email: nik.rozhkov@gmail.com, rozhkov@cshl.edu

state: NY

address: 1 Bungtown Rd.

institute: CSHL

type: Non-coding RNA profiling by high throughput sequencing

summary: We investigated a pool of small RNAs derived from transposon Penelope to probe the evolution of small RNA pathways in response to the transposon challenge in natural (D. virilis) and experimentally induced (D. melanogaster) colonization processes. In both species, Penelope was predominantly targeted by endo-siRNAs rather than by piRNAs.  Although we observed correlations between Penelope transcription and dysgenesis, we could not correlate differences in maternally deposited Penelope piRNAs with the sterility of progeny.  Instead, we found that strains, which produced dysgenic progeny, differed in their production of piRNAs from clusters in sub-telomeric regions, possibly indicating that changes in the overall piRNA repertoire underlie dysgenesis.  Considered together, our data reveal unexpected plasticity in small RNA pathways in germ cells, both in the character of their responses to invading transposons and in the piRNA clusters that define their ability to respond to mobile elements.

sample_organism:
Drosophila melanogaster
Drosophila virilis

overall_design: Examination of total small RNA in 0-2h embryos, testes, ovaries and carcasses of several D. virilis strains and their hybrids; total small RNA and Ago2, Piwi, Aub and Ago3-associated small RNA in testes and ovaries of D. melanogaster.

first: Alexei

last: Aravin

first: Elena

middle: S

last: Zelentsova

first: Natalia

last: Schostak

first: Ravi

last: Sachidanandam

first: W

middle: R

last: McCombie

first: Gregory

middle: J

last: Hannon

first: Michael

last: Evgen’ev


title: Sleep Deprivation and Recovery Sleep for 7 Regions of Mouse Brain.

status: Public on Aug 17 2010

city: Seattle

first: Changkyu

last: Lee

state: WA

address: 551 N 34th St

institute: Allen Institute for Brain Science

summary: Analysis of the effects of sleep deprivation, recovery sleep, and three time-of-day controls on seven brain regions laser microdissected from mouse brain. The regions include the locus coeruleus, suprachiasmatic nucleus, hypocretin area, tuberomammillary nucleus, orbital cortex, posteromedial cortical amygdala, and entorhinal cortex.

overall_design: In this study, 7 brain regions were collected by laser microdissection from brain tissue of mice from 5 different treatment groups and used for microarray experiments. Four biological replicates were generated for each regionxcondition. Conditions are: SD, sleep deprivation for 6 hours from ZT0 - 6; SDC, time-of-day control for SD at ZT6; RS, recovery sleep for 4 hours following SD; RSC, time-of-day control for RS at ZT10; W, spontaneous waking at ZT18.

first: Carol

middle: L

last: Thompson

first: Ed

last: Lein


title: RIMD 2210633 wild type versus vtrA or vtrB mutants

status: Public on Jul 16 2010

city: Suita

first: Toshio

last: Kodama

state: Osaka

address: 3-1 Yamadaoka

country: Japan

institute: OSAKA university

summary: Vibrio parahaemolyticus is a Gram-negative marine bacterium. A limited population of the organisms causes acute gastroenteritis in humans. Vibrio parahaemolyticus wild type strain RIMD 2210633 compared with the mutants of VtrA and VtrB have a winged helix-turn-helix DNA binding motif that genes encoded on pathogenicity island loci, at OD600=1.0 in Luria-Bertani containing medium 0.5 % NaCl at 37˚C. Our goal is to determine the VtrA or VtrB regulon.

overall_design: Cohybridized wild type versus vtrA or vtrB mutants on a single array. Biological replicates: three of wild type, three of vtrA mutants and three of vtrB mutants were independently grown and harvested.

first: Kazuyoshi

last: Gotoh

first: Tetsuya

last: Iida


title: Genome-wide analysis of early transcriptional events induced by cytokine IL-4 in human cord blood CD4+ T cells

status: Public on Jun 25 2010

city: Turku

first: Henna

last: Kallionpää

address: P.O. Box 123

department: Turku Centre for Biotechnology

country: Finland

institute: University of Turku

summary: The aim of this dataset was to study in detail the transcription kinetics initiated by cytokine IL-4 in early differentiation of Th2 cells.

overall_design: Total RNA obtained from activated and IL-4 & anti-IL-12 treated cord blood CD4+ T cells, 0.5, 1, 2, 4, 6, 12, 24, 48, and 72 hours after initiation of the cultures, compared to cells which were only activated. 57 samples were analyzed from three biological replicates of the culture. Two of the samples were discarded from the further data analysis due to compromised quality (samples 8=Th0.4h.1 and 11=Th2.6h.1).

first: Laura

last: Elo

last: Järvenpää

first: Soile

last: Tuomela

first: Sunil

last: Raghav

first: Helena

last: Ahlfors

first: Bhawna

last: Gupta

first: Johanna

last: Tahvanainen

first: Riikka

last: Lund

first: Kirtsi

last: Laurila

first: Harri

last: Lähdesmäki

first: Omid

last: Rasool

first: Matej

last: Oresic

first: Kanury

last: Rao

first: Tero

last: Aittokallio

first: Riitta

last: Lahesmaa


title: Genome-wide analysis of STAT6 target genes in IL-4 treated human cord blood CD4+ cells

summary: STAT6 is a major transcription factor driving the polarization of Th2 cells in response to cytokine IL-4. Here we have analyzed on a genome wide level the STAT6 mediated gene expression after IL-4 induction in naive human CD4+ T cells. RNAi mediated STAT6 knockdown was used to reveal the genes specifically regulated by STAT6.

overall_design: Total RNA from STAT6 siRNA treated cord blood CD4+ T cells 12, 24, 48 or 72 hours after culturing the cells in activating (antiCD3+antiCD28) plus or minus IL-4 conditions was compared to total RNA from nonspecific control siRNA treated cells. All together 18 samples were analyzed and 3 biological replicates of the culture were performed for a total of 54 samples.

first: Kirsti

first: David

last: Hawkins


title: Stat6 mediated regulation of transcription to initiate Th2 program in human T cells

first: Henna

last: Kallionpää