title: Identification of targets specifically regulated by a 'super hybrid p53'

status: Public on Feb 04 2012

city: Sapporo

first: Yasushi

last: Sasaki

address: S-1, W-17, Chuo-ku

department: Cancer Research Institute

institute: Sapporo Medical University

summary: p63, like its homologue, the tumor suppressor p53, is also able to induce apoptosis in several cancer cell types. p53 family proteins are composed of three characteristic domains which are: 1) an N-terminal transactivation domain (TAD); 2) a central DNA-binding domain (DBD); and 3) an oligomerization domain (OD). In this study, we constructed recombinant adenoviruses containing hybrid genes composed of fragments of p53 and TAp63γ genes by connecting coding sequences of their three functional domains. The potency of tumor growth suppression of these hybrid molecules was evaluated using in vitro and in vivo models. One of the p53-p63 hybrid molecules, p63-53O, was observed to be the most potent activator of human cancer cells to apoptosis when compared to the p53, TAp63γ or several alternative p53-p63 hybrid molecules. p63-53O hybrid is composed of TAD and DBD of TAp63γ and OD of p53. In an effort to identify specific targets regulated by pro-apoptotic hybrid p63-53O, we next performed Affymetrix Genechip analysis and compared expression patterns in a human osteosarcoma cell line Saos-2 transfected separately with Ad-p53, Ad-TAp63γ and Ad-p63-53O.

overall_design: Saos-2 osteosarcoma cells were either transduced with adenoviral vectors expressing p53, TAp63gamma, p53-p63 hybrid (p63-53O), or GFP. After 24 hours, mRNA was isolated and analyzed by hybridization to Affymetrix HG-U133 plus 2 arrays.

first: Takashi

last: Tokino


title: Transient telomere dysfunction induces chromosomal instability and promotes carcinogenesis in telomerase-proficient mice

status: Public on Mar 31 2012

city: Ulm

first: Hans

middle: A

last: Kestler

address: Albert-Einstein-Allee 11

department: Research Group Bioinformatics and Systems Biology

country: Germany

institute: University of Ulm

type:
Expression profiling by array
Genome variation profiling by array

summary: Background and Aims: Telomere dysfunction can increase tumor initiation by induction of chromosomal instability, but initiated tumor cells need to reactivate telomerase for genome stabilization and tumor progression. However, this concept has not been proven in vivo since appropriate mouse models were lacking. Here, we analyzed hepatocarcinogenesis (i) in a novel mouse model of inducible telomere dysfunction on a telomerase-proficient background, (ii) in telomerase knockout mice with chronic telomere dysfunction (G3 mTerc-/-), and (iii) in wild-type mice with functional telomeres and telomerase. Transient or chronic telomere dysfunction enhanced the rates of chromosomal aberrations during hepatocarcinogenesis, but only telomerase-proficient mice exhibited significantly increased rates of macroscopic tumor formation and cancer cell proliferation in response to telomere dysfunction. In contrast, telomere dysfunction resulted in pronounced accumulation of DNA damage, cell cycle arrest and apoptosis in telomerase-deficient liver tumors. Together, these data provide the first in vivo evidence that transient telomere dysfunction during early and late stages of tumorigenesis can promote chromosomal instability and carcinogenesis in telomerase-proficient mice in the absence of additional genetic checkpoint defects at germline level.

overall_design: RNA from liver tumors derived from from DEN treated TTD+ mice TTD- mice and RNA from normal liver 48h-72h after doxycycline induced transient telomere dysfunction in TTD+ and TTD- liver were isolated and RNA was extracted. Agilent Mouse 4x44K v2 arrays were used. DNA from liver tumors and corrresponding kidney as control derived from from DEN treated TTD+ mice, TTD- mice and mTERC-/- G3 mice was isolated and extracted using Phenol/Chloroform. Agilent Mouse 4x44K and Mouse 1x244K arrays were used.

first: Yvonne

last: Begus-Nahrmann

first: André

last: Lechel

first: K

middle: L

last: Rudolph


title: Expression data from mouse tissues and MEFs: insights into the physiological activation of p53-p66Shc pathway

status: Public on Apr 02 2012

city: Milano

first: Simone

middle: Paolo

last: Minardi

state: Italy

address: Via Adamello

department: Microarray and NGS Unit

country: Italy

institute: Cogentech

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

overall_design: Refer to individual Series


title: Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation

status: Public on Jan 20 2012

city: Singapore

first: Guoliang

last: Li

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

department: Computational and Systems Biology

country: Singapore

institute: Genome Institute of Singapore

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Higher-order chromosomal organization for transcription regulation is poorly understood in eukaryotes. Using genome-wide Chromatin Interaction Analysis with Paired-End-Tag sequencing (ChIA-PET), we mapped long-range chromatin interactions associated with RNA polymerase II in human cells and uncovered widespread promoter-centered intragenic, extragenic, and intergenic interactions. These interactions further aggregated into higher-order clusters, wherein proximal and distal genes were engaged through promoter-promoter interactions. Most genes with promoter-promoter interactions were active and transcribed cooperatively, and some interacting promoters could influence each other implying combinatorial complexity of transcriptional controls. Comparative analyses of different cell lines showed that cell-specific chromatin interactions could provide structural frameworks for cell-specific transcription, and suggested significant enrichment of enhancer-promoter interactions for cell-specific functions. Furthermore, genetically-identified disease-associated noncoding elements were found to be spatially engaged with corresponding genes through long-range interactions. Overall, our study provides insights into transcription regulation by three-dimensional chromatin interactions for both housekeeping and cell-specific genes in human cells.

overall_design: RNA polymerase II (RNAPII) bound chromatin interactions were extracted with Chromatin Interaction Analysis with Paired-End Tag (ChIA-PET) sequencing, in order to study the transcription regulations with RNAPII-associated long-range chromatin interactions. Five cell lines, namely MCF7 (ATCC# HTB-22), K562 (ATCC# CCL-243), HCT116 (ATCC# CCL-247), HeLa (ATCC# CCL-2.2), and NB4 (Roussel and Lanotte, 2001) (provided by Dr. Sherman Weissman, Yale University), were grown under standard culture conditions and harvested at log phase. Harvested cells were cross-linked using 1% formaldehyde followed by neutralization with 0.2M glycine. Chromatin was isolated and subjected to ChIA-PET protocol as described in Fullwood et al (Fullwood et al: An oestrogen-receptor-alpha-bound human chromatin interactome. Nature 2009, 462(7269):58-64). The ChIA-PET sequence reads were processed and analyzed using ChIA-PET Tool (Li et al: ChIA-PET tool for comprehensive chromatin interaction analysis with paired-end tag sequencing. Genome Biol 2010, 11(2):R22).

first: Xiaoan

last: Ruan


title: Microarray gene expression profiles from mature gonad tissues of Atlantic Bluefin Tuna, Thunnus Thynnus in the Gulf of Mexico

status: Public on Feb 20 2012

city: Pacific Grove

first: Luke

last: Gardner

state: California

address: 120 Ocean View Blvd, Hopkins Marine Station

country: USA

institute: Stanford University

summary: The aim of this investigation was to compare transcription profiles from the ovaries and testes of mature T. thynnus to establish sex specific variations underlying their reproductive physiology.

overall_design: Two condition experiment, testis vs ovarian tissue. Biological replicates 4 male testes and 4 female ovaries.

first: Nishad

last: Jayasundara

first: Pedro

last: Castillo

first: Barbara

last: Block


title: Roles for ATF6-regulated miRNAs in the ER stress response

status: Public on Jan 02 2012

city: San Diego

first: Peter

middle: J

last: Belmont

state: CA

address: 10724 Science Center Drive

institute: Pfizer

summary: We wished to determine the effects of activating the transcription factor, ATF6, on global miRNA expression. We utilized transgenic mice with a conditionally tamoxien-responsive form of ATF6 and assessed cardiac lysates from NTG and TG mice, both treated with tamoxifen and untreated, in order to identify differentially expressed miRNAs. We then focused on miRNAs of interest as well as the genes they are predicted to regulate.

overall_design: Four sample groups were assessed for miRNA expression: non-transgenic (NTG) mice treated with vehicle, NTG mice treated with tamoxifen, ATF6 transgenic (TG) mice treated with vehicle, and TG mice treated with tamoxifen

first: Chris

last: Glembotski


title: Effect of hBD3 on transcription in TLR4-stimulated macrophages

status: Public on Jan 01 2012

city: Edinburgh

first: Graeme

middle: Richard

last: Grimes

address: Western General Hospital, Crewe Road

department: Human Genetics Unit

country: United Kingdom

institute: University of Edinburgh, The Institute of Genetics and Cancer


title: p53-dependent transcription program in HepG2 cells

city: Rehovot

first: Ido

last: Goldstein

address: POB 26

country: Israel

institute: The Weizmann Institute of Science

summary:
In order to obtain a global picture regarding regulation of p53 in liver cells we used HepG2 hepatoma cells.We created two isogenic sub-cultures of HepG2 cells with altered expression of p53.
HepG2 cells were infected with a retroviral vector harboring either small-hairpin RNA targeting p53 (termed HepG2sh-p53) or a non relevant small-hairpin RNA (termed HepG2sh-con).

overall_design: Cells were treated with two different p53 stimulators - Nutlin and AICAR

first: I

first: V

last: Rotter


title: T. Brucei, Nup-1 Depletion

status: Public on Dec 15 2011

city: Seattle

first: Bruz

last: Marzolf

state: WA

institute: Institute for Systems Biology

summary: Organization of the genome into compacted chromatin is a eukaryotic innovation facilitating increased sophistication in transcriptional regulation. In metazoa coiled-coil lamin proteins are major components of the chromatin organizer at the nuclear periphery and maintain nuclear integrity. While identifiable lamin homologues are restricted to metazoans, morphologically analogous structures maintaining nuclear organization in other eukaryotic lineages are known, but the molecular constituents remain undefined. Trypanosoma brucei NUP-1 is a large coiled-coil protein associated with fibrils at the inner face of the nuclear envelope. Using transcriptome analysis in combination with RNA interference and various imaging techniques, we demonstrate that NUP-1 forms a stable immobile cage around the nucleus, is required for viability and nuclear structural integrity, directs the positional organization of nuclear pore complexes, and serves to organize chromatin and specifically repress genes located at the nuclear periphery involved in immune evasion. Based on architectural similarity and functionality, we propose that NUP-1 is a novel, highly divergent lamin

overall_design: The effect of Nup-1  depletion on the transcriptome was examined in three independent experiments (A, B, & C).  T. brucei cultures were either treated with RNAi (plus) or left untreated (minus) and RNA was extracted from each sample at the indicated time point (0h, 6h, 12h, 24h, or 48h).  Two color microarrays were performed comparing treated and untreated samples at each time point.   Dye swaps were performed and are indicated.  Replicates of t=12h and t=24h for sample B were also included.

first: Alexander

middle: V

last: Ratushny

first: John

middle: D

last: Aitchison


title: Expression Data from International C.elegans Experiment 1st

city: Tsukuba

first: Akira

last: Higashibata

state: Ibaraki

department: Department of Space Biology and Microgravity Sciences

country: Japan

institute: Japan Aerospace Exploration Agency

summary: The effect of microgravity on gene expression in C.elegans was comprehensively analysed by DNA microarray. This is the first DNA microarray analysis for C.elegans grown under microgravity. Hyper gravity and clinorotation experiments were performed as reference against the flight experiment.

overall_design: Total RNA was extracted from 100,000 worms of each experimental group

first: Mari

last: Imamizo


title: Late-stage embryonic gene expression in three cartilaginous fishes

city: Orono

first: Benjamin

last: King

state: ME

address: 5735 Hitchner Hall

department: Molecular and Biomedical Sciences

institute: University of Maine

type: Expression profiling by high throughput sequencing

summary: Gene expression profiling of pooled late stage embryos from Leucoraja erinacea, Scyliorhinus canicula and Callorhinchus milii show that HOXC cluster genes are not expressed in the two elasmobranch fishes, L. erinacea and S. canicula.  This finding supports the observations that these genes are not found in whole genome shotgun sequencing of L. erinacea or genomic clones from S. canicula.

sample_organism:
Leucoraja erinaceus
Scyliorhinus canicula
Callorhinchus milii

overall_design: Profile gene expression in pooled late stage embryos from three species (L. erinacea, S. canicula and C. milii)

first: J

last: Gillis

first: Heather

middle: R

last: Carlisle

first: Randall

last: Dahn


title: Choroid Plexus Expression Data from Add1 Null Mice on the C57BL/6J Background Strain

status: Public on Apr 09 2012

city: Bar Harbor

first: Raymond

middle: F

last: Robledo

address: 600 Main Street

department: Research

institute: The Jackson Laboratory

summary:
Add1 Null mice on the C57BL/6J background develop hydrocephalus that may be due to gene expression changes in the choroid plexus.
We used microarrays to detail choroid plexi gene expression prior to the manifestation of hydrocephalus.

overall_design: Choroid plexi from the four ventricle were dissected out, for RNA extraction and hybridization to Affymetrix microarrays, from  male Add1 wildtype, heterozygous and null mice at three weeks of age.  Five mice were selected for each genotype to assess gene expression prior to the development of hydrocephalus.

first: Luanne

last: Peters


title: Genetic and epigenetic determinants of neurogenesis and myogenesis [ChIP-seq]

status: Public on Mar 26 2012

first: Stephen

last: Tapscott

state: WASHINGTON

address: 1100 Fairview N. Ave

department: Human Biology

institute: Fred Hutch Cancer Research Center

summary: The regulatory networks of differentiation programs have been partly characterized; however, the molecular mechanisms of lineage-specific gene regulation by highly similar transcription factors remain largely unknown. Here we compare the genome-wide binding and transcription profiles of NEUROD2-mediated neurogenesis with MYOD-mediated myogenesis. We demonstrate that NEUROD2 and MYOD bind a shared CAGCTG E-box motif and E-box motifs specific for each factor: CAGGTG for MYOD and CAGATG for NEUROD2. Binding at factor-specific motifs is associated with gene transcription, whereas binding at shared sites is associated with regional epigenetic modifications but not as strongly associated with gene transcription. Binding is largely constrained to E-boxes pre-set in an accessible chromatin context that determines the set of target genes activated in each cell type. These findings demonstrate that the differentiation program is genetically determined by E-box sequence whereas cell lineage epigenetically determines the availability of E-boxes for each differentiation program.

overall_design: Comparing NeuroD2 induced neurogenesis and MyoD induced myogenesis by examining NeuroD2/MyoD binding sites in fibroblasts and P19 cells and corresponding changes in AcH4 using Chip-Seq. Assess chromatin accessibility using PvuII assay followed by high throughput sequencing.

first: Abraham

middle: P

last: Fong

first: Zizhen

last: Yao

first: Jun

middle: W

last: Zhong

first: Yi

last: Cao

first: Walter

last: Ruzzo

first: Robert

middle: C

last: Gentleman


title: Gene expression profiles in synovial biopsies from patients with arthritis

status: Public on Mar 27 2012

city: Brussels

first: Bernard

middle: Robert

last: Lauwerys

address: Avenue Hippocrate 10

department: Institut de Recherches Expérimentales et Cliniques

country: Belgium

institute: Université catholique de Louvain

summary:
Rheumatoid arthritis (RA) is an inflammatory joint disorder that results in progressive joint damage when insufficiently treated. In order to prevent joint destruction and functional disability in RA, early diagnosis and initiation of appropriate treatment with Disease-Modifying Antirheumatic Drugs (DMARDs) is needed. However, in daily clinical practice, patients may initially display symptoms of arthritis that do not fulfil the classification criteria for a definite diagnosis of RA, or any other joint disease, a situation called “Undifferentiated Arthritis” (UA). Out of the patients with UA, 30 to 50% usually develop RA, and early identification of these remains a challenge.

At the present time, although several risk factors associated with the development of RA have been identified (6-9), a model that reliably predicts the probability of evolution of UA into RA in individual patients is lacking. In order to better identify early RA patients, an American College of Rheumatology (ACR)/European League Against Rheumatism (EULAR) collaboration recently developed new classification criteria. Although these criteria are more sensitive, the risk of over-diagnosis is an important issue to consider, especially in very early disease. In this context, the present study explores the feasibility of a molecular diagnosis of arthritis, based on the identification of disease-specific transcriptomic profiles in synovial biopsies from patients with arthritis according to the underlying condition.

In a previous study, we performed global analyses of gene expression in synovial biopsies from patients with RA, Systemic Lupus Erythematosus (SLE) and Osteoarthritis (OA), using high-density oligonucleotide spotted microarrays. We found that the gene expression profiles are strikingly different according to the underlying condition. Thus, the majority of the genes up-regulated in SLE are type I Interferon-inducible genes, as compared with the up-regulation genes involved in T cell and B cell activation in RA, and in extracellular matrix homeostasis in OA. Based on these results, similar analyses were performed in synovial biopsies from patients with seronegative arthritis (SA) and microcrystalline arthritis (MIC), in order to identify disease-specific molecular signatures.

overall_design: GeneChip® Human Genome U133 Plus 2.0 Arrays (Affymetrix UK Ltd., High Wycombe, UK) were hybridized in monoplicates with 10 μg biotinylated cRNA, using synovial biopsy samples obtained in 4 patients with SA (based on the presence of psoriasis or x-ray evidence of sacro-iliacal joint involvement), 5 patients with MIC, based on the identification of urate or calcium pyrophosphate crystals in the synovial fluid, 7 patients with RA (ACR 1987 criteria), 4 patients with SLE (ACR criteria) and 5 patients with OA (based on x-ray evidence of osteoarthritis)


title: Human Beta-Defensin 3 attenuates the pro-inflammatory effects of KDO2-Lipid A (KLA) at 6 hour

first: Graeme

last: Grimes

summary:
We examine the global effect of hBD3 on transcription in TLR4-stimulated macrophages and for the first time show that hBD3 inhibits the transcription of critical pro-inflammatory genes.
Among the repressed genes we detect significant enrichment of groups involved in the positive regulation of NFkappaB including components of Toll-like receptor signaling pathways.

overall_design: Total RNA obtained from bone marrow derived macrophages (BMDM) that have been subjected to 6 hour treatment with KLA, KLA&hBD3, hBD3 or untreated. There are 3 biological replicates per group.

first: Fiona

last: Semple

first: Julia

last: Dorin

first: Sheila

last: Webb

first: Colin


title: Escherichia coli K-12 grown in the presence of glycerol exhibits upregulation in genes for acid stress chaperones and concomitant downregulation in genes involved in generation of acidic metabolites

status: Public on Dec 09 2011

city: Hyderabad

first: kotakonda

last: Arunasri

state: Andhra Pradesh

address: Habsiguda

country: India

institute: Centre for Cellular and Molecular biology

summary:
This study explores the effects of glycerol, on whole genome expression of Escherichia coli.
DNA microarray analysis imply that E. coli in the presence of glycerol generates acidic metabolites to which it adapts by upregulation of genes involved in acid stress and by simultaneously downregulating genes involved in high pH stress.

overall_design: E.coli was grown in the presence and absence of glycerol. RNA was extracted from these samples, cDNA was prepared, fragmented cDNA was labled with labeling reagent and hybridized with Affymetrix E.coli2.0 genome array chips.Data was analysed to get the effect of glycerol on E.coli gene expression

first: S

last: Shivaji

first: K

first: M

last: Adil


title: Human Beta-Defensin 3 attenuates the pro-inflammatory effects of LPS at 1 hour

overall_design: Bone marrow derived macrophages from 3 separate mice were used for each treatment condition. ie macrophages from 3 mice were left untreated, macrophages from 3 mice were treated with LPS, macrophages from 3 mice were treated with LPS and hBD3, macrophages from 3 mice were treated with hBD3. We examined the differences in gene expression between each treatment group.


title: Expression data from mouse embryo fibroblast (MEFS)

first: Simone

last: Minardi

summary:
The role of p53 in assuring longevity through prevention of cancer is well established, but how it specifically regulates aging is still controversial. Our assumption is that distinct p53-pathways regulate tumor suppression and aging and that p66Shc is one of the master regulators of the p53 aging function. p66Shc longevity determinant protein acts as a downstream target of p53 and it is indispensable for the ability of activated p53 to induce elevation of intracellular oxidants and apoptosis.
We used microarray to gain insight into the mechanism through which p66Shc could regulate p53 oxidative stress dependent activity.

overall_design: Total RNA was extracted from Primary murine embryonic fibroblasts (MEFs) were isolated from 13.5-day-old embryos according to standard procedures from WT, p53KO and p66ShcKO mice. Treatment: Early passage (p.2) MEFs were washed twice with PBS1X solution, and then incubated in DMEM media containing 400 μM of H2O2 or 0.25μg/ml of Doxorubicin (SIGMA) at 37°C for four hours.

first: Enrica

last: Migliaccio


title: Three-Dimensional Tumor Profiling Reveals Minimal mRNA  Heterogeneity in Esophageal Squamous Cell Carcinoma

status: Public on Nov 04 2011

city: Gaithersburg

first: Wusheng

last: Yan

address: 8717 Grovemont Circle

institute: NCI

summary: We microdissected discrete sub-regions of esophageal squamous cell carcinoma (ESCC) and analyzed the transcriptomes throughout three-dimensional (3D) tumor space.

overall_design: Nine cases were used for TP/TC comparison, five cases were used for 3D analysis, one normal case was set as a control.

first: Joanna

last: Shih

first: Jaime

last: Rodriguez-Canales

first: Michael

last: Tangrea

last: Hu

first: Alisa

middle: M

last: Goldstein

first: Philip

last: Taylor

first: Scott

last: Lippman

first: Ignacio

middle: I

last: Wistuba

last: Emmert-Buck

first: Heidi

middle: S

last: Erickson


title: Expression data of bone marrow and peripheral adipocytes from leptin deficient mice and obese mice fed with a high fat diet

status: Public on Nov 29 2011

city: Palo Alto

first: Li Fen

last: Liu

address: 3801 Miranda AVE

department: Medicine

summary:
The aim of this study was to characterize the obesity-related gene expression profiles between bone marrow adipocytes and peripheral white adipocytes from obese mice fed with high fat diet and leptin deficient mice
Alterations of gene expression with high fat diet and in mice lacking leptin were analyzed in bone marrow and peripheral white adipocytes isolated from C57BL/6J male mice using Affymetrix Mouse Gene 1.0 ST arrays.

overall_design: Bone marrow adipocytes and peripheral white adipocytes (n=6-10 animals per group) were isolated from male C57BL/6J mice (6-months, 14-months ) fed with either standard chow or a high fat diet containg 60% calories from fat.  Samples were grouped into diet (standard chow vs. high fat diet) and age (6-month (6M), 14-month (14M) and 18-month (18M)).

first: Li

first: Fredric

middle: B

last: Kraemer


title: Genome-wide gene expression profile of human gastric cancer

status: Public on Nov 15 2011

city: Seoul

first: Dong Yoon

last: Park

address: 134 Shinchon-dong, Seodaemun-gu

department: Biochemistry

country: South Korea

institute: Yonsei University

summary: We performed microarray experiments on gastric tissue samples to identify the differential expression patterns between tumor and normal condition.

overall_design: 40 gastric tumor tissue samples, 12 normal gastric tissue samples

first: Dong-Yoon

first: Ja-Eun

last: Kim


title: Transcriptomic Analysis of Rat Brain Following Exposure to the Organophosphonate Anticholinesterase Sarin

status: Public on Dec 31 2011

city: Aberdeen Proving Ground

first: James

last: Dillman

state: MD

address: 3100 Ricketts Point Rd

department: Cell and Molecular Biology Branch

institute: U.S. Army Medical Research Institute of Chemical Defense

summary: Organophosphorus nerve agents irreversibly inhibit acetylcholinesterase, causing a toxic buildup of acetylcholine at muscarinic and nicotinic receptors.  Current medical countermeasures to nerve agent intoxication increase survival if administered within a short period of time following exposure but may not fully prevent neurological damage.  Therefore, there is a need to discover drug treatments that are effective when administered after the onset of seizures and secondary responses that lead to brain injury.  Methods  To determine potential therapeutic targets for such treatments, we analyzed gene expression changes in the rat piriform cortex following sarin (O-isopropyl methylphosphonofluoridate) exposure.  Male Sprague-Dawley rats were challenged with 1.0 x LD50 sarin and subsequently treated with atropine sulfate, 2-pyridine aldoxime methylchloride (2-PAM), and the anticonvulsant diazepam.  Control animals received an equivalent volume of vehicle and drug treatments.  The piriform cortex, a brain region particularly sensitive to neural damage from sarin-induced seizures, was extracted at 0.25, 1, 3, 6, and 24 h after seizure onset, and total RNA was processed for microarray analysis.  Principal component analysis identified sarin-induced seizure occurrence and time point following seizure onset as major sources of variability within the dataset.  Based on these variables, the dataset was filtered and analysis of variance was used to determine genes significantly changed in seizing animals at each time point.  The calculated p-value and geometric fold change for each probeset identifier were subsequently used for gene ontology analysis to identify canonical pathways, biological functions, and networks of genes significantly affected by sarin-induced seizure over the 24-h time course.  Results  A multitude of biological functions and pathways were identified as being significantly altered following sarin-induced seizure.  Inflammatory response and signaling pathways associated with inflammation were among the most significantly altered across the five time points examined.    Conclusions  This analysis of gene expression changes in the rat brain following sarin-induced seizure and the molecular pathways involved in sarin-induced neurodegeneration will allow a better identification of potential therapeutic targets for the development of effective neuroprotectants to treat nerve agent exposure.

overall_design: Three animals were used for each experimental group (naïve, sarin-exposed non-seizure, non-seizure control [saline], sarin-exposed seizure, and seizure control [saline]) at each time point (0.25, 1, 3, 6, 24 h), with the exception of 1 h seizure control, 3 h sarin-exposed seizure, 24 h sarin-exposed non-seizure, and 24 h sarin-exposed seizure (n=4).

first: Kimberly

last: Spradling

first: Lucille

middle: A

last: Lumley

first: Christopher

last: Robison

last: Meyerhoff


title: Human glioblastoma cells: Tet-on(mutant p53 R175H expression) vs Tet-off(p53-null)

status: Public on Nov 02 2011

city: sendai

first: imai

last: hiroo

state: Miyagi

address: 4-1 seiryo-machi

department: clinical oncology

institute: tohoku university

summary: TP53 R175H mutation is one of the most common mutations in human cancers and cancer cells with this mutation stably express R175H protein in the nucleus. To identify the synthetic lethal gene interacted with the R175H, we conducted the high throughput screening by using tetracyclin inducible R175H expression system in SF126 cells and comprehensive shRNA library carried by lenti virus. We identified 906 candidate gene suppressions that may lead to accelerated cell growth inhibition under the presence of R175H. Inhibitor of differentiation 1 (ID1) was one of the candidate genes and suppression of ID1 by siRNA resulted in acceleration of growth inhibition of cell lines expressing endogenous R175H but not in TP53 null cell lines. The transient expression of R175H in TP53 null cell lines and suppression of ID1 and/or TP53 R175H in cell lines with endogenous R175H revealed that the cell growth inhibition by ID1 suppression was dependent on R175H expression but not other common p53 mutants (R273H). Flow cytometric (FACS) analysis exhibited that ID1 suppression resulted in G1 arrest and the arrest was accelerated by suppression of R175H. In conclusion, ID1 is a synthetic lethal gene interacted with R175H and is considered to be a novel molecular target of cancer therapy for R175H expressing cells.

overall_design: R175H expression(Tet-on) group was labeled by Cy5, and p53-null(Tet-off) group was labeled by Cy3. Three independent experiments were conducted (We have triplicate data).

first: Hiroo

last: Imai

first: Chikashi

last: Ishioka


title: Focused examination of the intestinal lamina propria yields greater molecular insight into mechanisms underlying SIV induced immune dysfunction

status: Public on Dec 10 2011

city: San Antonio

first: Deepak

last: Kaushal

state: TX

address: 8715 W Military Dr

department: HPI

institute: Texas Biomedical Research Institute

summary: In this study three Indian rhesus macaques were infected with Simian Immunodeficiency Virus (SIVmac251). This generates a chronic infection mirroring AIDS in the animals. Prior to infection (day 0) and at two different time-points post-infection (day 21 and day 90), intestinal resection biopsies were performed. The intestinal tissue was then separated into different sub-sections including lamina-propria lymphocytes (LPL), intra-epithelial lymphocytes (IEL), stroma or matrix and epithelium. In this study we report the genome-wide transcriptional response at the two different time-points, specific to LPL, relative to pre-infection samples. For this purpose we have used the Affymetrix Rhesus Macaque GeneChip.

overall_design: 3 Rhesus Macaques prior to infection and 21 and 90 days of infection

first: Mahesh

last: Mohan

first: Andrew

last: Lackner


title: T cell receptor dependent transformation of mature memory phenotype T cells

status: Public on Nov 01 2011

city: Boston

first: Xi

last: Wang

state: Massachusetts

address: 44 Binney Street, M654

department: Pediatric Oncology

institute: Dana Farber Cancer Institute

summary: A fundamental goal in cancer research is identification of the cell types and signaling  pathways capable of initiating and sustaining tumor growth as this has the potential to reveal  features that can be exploited therapeutically. Stem and progenitor cells have been implicated in  the genesis of select lymphoid malignancies but are unlikely to underlie initiation of mature  lymphoid neoplasms, the cellular origin of which remains unclear. Here, we used a conditional  Snf5 model to investigate the origin of peripheral T cell lymphomas. We find that the cell of  origin is a mature CD44hiCD122lo CD8 T cell that resembles a subset of memory cells, a  population with capacities for self-renewal and robust expansion - features shared with stem cells.  We elucidate mechanism by showing that Snf5 loss leads to activation of a Myc network and  stem cell transcriptional program. Finally, we demonstrate that lymphomagenesis depends upon  TCR signaling, establishing a new paradigm for lymphomagenesis. These findings suggest that  the self-renewal and robust proliferative capacities of memory T cells is associated with  vulnerability to oncogenic transformation. Our findings further suggest that agents that impinge  upon TCR signaling may represent an effective therapeutic modality for this class of lethal  human cancers.

overall_design: Stable mouse Snf5-deficient T cell lymphoma cell lines were established. CD44hi and CD44lo subpopulations were purified and used to evaluate gene expression pattern in these two subpopulations. RNA was isolated from each of these samples and used for gene expression profiling on Affymetrix 430A arrays.

first: Charles

last: Roberts


title: Microarray profiling for differential gene expression in PSMG-hCG stimulated pre-ovulatory ovarian follicles of Chinese Erhualian and Large White sows

city: Wuhan

first: Fenge

last: Li

state: Hubei

address: Shizishan Street

country: China

institute: Huazhong Agricultural University

summary:
The Chinese Erhualian is one of the most prolific pig breeds in the world, which farrows at least five more piglets per litter than Western pig breeds partly due to a greater ovulation rate. Differences in the transcriptome of Chinese Erhualian and Large White ovaries directly result in variation of ovulation rate.
To understand the molecular basis related to ovulation rate in Chinese indigenous and Western breeds, samples were collected and used to hybridized. This study reveals many potential avenues of investigation for seeking new insights into ovarian physiology and the genetic control of reproduction.

overall_design: Expression profiling experiments were conducted to identify differentially expressed genes in ovarian follicles at the preovulatory stage of a PMSG-hCG stimulated estrous cycle from 3 Chinese Erhualian and 3 Large White cycling sows by using the Affymetrix Porcine Genechip™.

first: X

last: Sun

first: F


title: SA, elf18 treatment of WT and tbf1 mutant

status: Public on Jan 17 2012

city: Birmingham

first: Karolina

last: Pajerowska-Mukhtar

state: Alabama

address: 1300 University Blvd

department: Department of Biology

institute: University of Alabama at Birmingham

summary: Identification of TBF1-dependent and SA, elf18-responsive genes in Arabidopsis

overall_design: 24 samples total, 2 treatments with corresponding mock, wild type samples served as control, 3 biological replicates

first: Wei

first: Xinnian

last: Dong


title: NMLF response to spinal cord injury in Zebrafish

status: Public on Dec 01 2011

city: Piscataway

first: Ronald

middle: P.

last: Hart

state: NJ

address: 604 Allison Rd Rm B430

department: Cell Biology & Neuroscience

institute: Rutgers University

summary:
The study was designed to identify genes regulated after spinal transection that might contribute to regenerative growth of neurons projecting from the NMLF in Zebrafish.
Zebrafish were injured by surgical transection of the spinal cord at 1 mm caudal to the brainstem-spinal cord junction (Injured).  Animals receiving sham surgery (identical surgical procedures without transection) served as control (Control). The nucleus of the medial longitudinal fascicle (NMLF) was laser capture microdissected from approximately 30 frozen sections.  RNA was prepared, amplified, and run on Affymetrix Zebrafish arrays.

overall_design: Zebrafish were used because they recover swimming function after spinal transection in about 6 weeks.  The NMLF has been identified as a prominent group of neurons that descend through the site of injury in the spinal cord and that regenerate after injury. Times were selected to distinguish early events from those in the timeframe of regenerative growth.

first: Liping

last: Ma

first: Melitta

last: Schachner


title: Expression data from  hippocampus and cortex of 6- and 12-week curcumin-treated 15-month-old rats

status: Public on Oct 22 2011

city: Shanghai

first: Chunxia

state: Choose a State

address: 3663 Zhongshan Road

department: Key Laboratory of Brain Functional Genomics, Ministry of Education

institute: East China Normal University

summary:
Curcumin has been demonstrated to have many neuroprotective properties, including improvement of cognition in humans and neurogenesis in animals, yet the mechanism of such effects remains unclear. Here, we assessed behavioural performance and hippocampal cell proliferation in aged rats after 6- and 12-week curcumin-fortified diets. Curcumin enhanced non-spatial and spatial memory, as well as dentate gyrate cell proliferation as compared to control diet rats. We also investigated underlying mechanistic pathways that might link curcumin treatment to increased cognition and neurogenesis via microarray analysis of cortical and hippocampal mRNA transcription.
We used microarrays to investigate the effects of short-term (6-week) and long-term (12-week) curcumin-supplemented diet on gene expression of hippocampus and cortex in aged rats.

overall_design: The hippocampus and cortex of every three rats from one group were pooled together, respectively and used for RNA extraction and hybridization on Affymetrix microarrays. To ensure the reliability of the data, we conducted hybridization experiments in duplicate microarrays from each RNA sample. The tissues examined by microarray are as follows: the hippocampus and cortex of 6-week curcumin-treated 15-month-old rats, the hippocampus and cortex of 6-week no curcumin-treated 15-month-old rats (control rats), the hippocampus and cortex of 12-week curcumin-treated 15-month-old rats, the hippocampus and cortex of 12-week no curcumin-treated 15-month-old rats (control rats).

first: Suzhen

first: Qingwen

last: Zeng

first: Yale

last: Duan

first: Zheng

last: Zhao

first: Xiaohua

last: Cao

first: Jyoti

middle: K

last: Tiwari


title: Expression analysis of tumor microenvironment in triple-negative breast carcinoma in xenograft model

status: Public on May 12 2012

city: Philadelphia

first: Renato

middle: V.

last: Iozzo

state: PA

address: 1020 Locust St. Rm 336

department: Pathology, Anatomy, and Cell Biology

institute: Thomas Jefferson University

summary: Decorin, a member of the small leucine-rich proteoglycan gene family, exists and functions wholly within the tumor microenvironment to suppress tumorigenesis by directly targeting and antagonizing multiple receptor tyrosine kinases, such as the EGFR and Met. This leads to potent and sustained signal attenuation, growth arrest, and angiostasis. We thus sought to evaluate the tumoricidal benefits of systemic decorin on a triple-negative orthotopic breast carcinoma xenograft model. To this end, we employed a novel high-density mixed expression array capable of differentiating and simultaneously measuring gene signatures of both Mus musculus (stromal) and Homo sapiens (epithelial) tissue origins. We found decorin modulated the differential expression of 374 genes within the stromal compartment of the tumor xenograft. Further, our top gene ontology classes strongly suggests an unexpected and preferential role for decorin to inhibit genes necessary for immunomodulatory responses, while simultaneously inducing expression of those possessing cellular adhesion and tumor suppressive gene properties. Rigorous verification of the top scoring candidates led to the discovery of three genes heretofore unlinked to malignant breast cancer that were reproducibly found to be induced in several models of tumor stroma. Collectively, our data provide highly novel and unexpected stromal gene signatures as a direct function of systemic decorin administration and reveals a fundamental basis of action for decorin to modulate the tumor stroma as a biological mechanism for the ascribed anti-tumorigenic properties.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: A twelve-array (three arrays per slide) study using total RNA extracted from twelve individual SCID mice with established MDA-MB-231 orthotopic tumor xenografts (n=6 per cohort) treated systemically with decorin for 23 days at 10mg/kg via intraperitneal injections.

first: Simone

last: Buraschi

first: Thomas

last: Neill

first: Rick

middle: T

last: Owens

first: Leonardo

last: Iniguez

first: George

middle: E

last: Purkins

first: Raj

last: Vadigepalli

first: Liliana

last: Schaefer

first: Stephen

last: Peiper

first: Z

middle: X


title: Genetic control of gene expression in whole blood and lymphoblastoid cell lines is largely independent

status: Public on Oct 29 2011

city: Brisbane

first: Joseph

last: Powell

state: Qld

address: St lucia

department: Queensland Brain Institute

country: Australia

institute: University of Queensland

summary: The degree to which the level of genetic variation for gene expression is shared across multiple tissues has important implications for research investigating the role of expression on the aetiology of complex human traits and diseases. In the last few years, a number of studies have been published reporting the extent of overlap in expression quantitative trait loci (eQTL) identified in multiple tissues or cell types. Whilst these studies provide important information on the regulatory control of genes across tissues, their limited power means they can typically only explain a small proportion of genetic variation for gene expression. Here, using expression data from monozygotic twins (MZ), we investigate the genetic control of gene expression in lymphoblastoid cell lines (LCL) and whole blood (WB). We estimate the genetic correlation which represents the combined effects of all causal loci across the whole genome and is a measure of the level of common genetic control of gene expression between the two RNA sources. Our results show that, when averaged across the genome, mean levels of genetic correlation for gene expression in LCL and WB samples are close to zero. We support our results with evidence from gene expression in an independent sample of LCL, T-cells and Fibroblasts. In addition, we provide evidence that housekeeping genes, which maintain basic cellular functions, are more likely to have high genetic correlations between the RNA sources than non-housekeeping gene, implying a relationship between the transcript function and the degree to which a gene has tissue specific genetic regulatory control.

overall_design: In this study, the global genetic control of expression levels for 9555 genes were examined from two samples of RNA sources, collected on pairs of monozygotic (MZ) twins. From each individual, gene expression profiles were generated whole blood (WB), collected using the PAXgeneTM tube system, and lymphoblastoid cell lines (LCL). Using expression data collected from MZ twins is a powerful means of estimating the genetic contribution of expression variation. In particular, the observed phenotypic covariance in gene expression in LCLs and WBs between MZ twins can be partitioned into variation due to within-person environmental effects and between-person genetic effects.

first: Anjali

last: Henders

first: Allan

last: McRae

first: Margaret

middle: J

last: Wright

first: Nicholas

middle: G

last: Martin

first: Emmanouil

last: Dermitzakis

first: Grant

last: Montgomery

first: Peter

last: Visscher


title: COUP-TFII Controls Mouse Postnatal Pancreatic β-Cell Mass through GLP-1 β-Catenin

status: Public on Oct 07 2011

city: Leuven

first: Leentje

last: Van Lommel

address: Herestraat 49 bus 901

department: Molecular cell biology

institute: KULeuven

summary:
ABSTRACT
Background: The control of the functional pancreatic b-cell mass serves the key homeostatic function of releasing the right amount of insulin to keep blood sugar in the normal range. It is not fully understood though how b-cell mass is determined.
Methodology/principal findings: Conditional chicken ovalbumin upstream promoter transcription factor II (COUP-TFII)-deficient mice were generated and crossed with mice expressing Cre under the control of pancreatic duodenal homeobox 1 (pdx1) gene promoter. Ablation of COUP-TFII in pancreas resulted in glucose intolerance. Beta-cell number was reduced at 1 day and 3 weeks postnatal. Together with a reduced number of insulin-containing cells in the ductal epithelium and normal b-cell proliferation and apoptosis, this suggests decreased b-cell differentiation in the neonatal period. By testing islets isolated from these mice and cultured b-cells with loss and gain of COUP-TFII function, we found that COUP-TFII induces the expression of the b-catenin gene and its target genes such as cyclin
D1 and axin 2. Moreover, induction of these genes by glucagon-like peptide 1 (GLP-1) via b-catenin was impaired in absence of COUP-TFII.
The expression of two other target genes of GLP-1 signaling, GLP-1R and PDX-1 was significantly lower in mutant islets compared to control islets, possibly contributing to reduced b-cell mass.
Finally, we demonstrated that COUP-TFII expression was activated by the Wnt signaling-associated transcription factor TCF7L2 (T-cell factor 7-like 2) in human islets and rat b-cells providing a feedback loop.
Conclusions/significance: Our findings show that COUP-TFII is a novel component of the GLP-1 signaling cascade that increases b-cell number during the neonatal period. COUP-TFII is required for GLP-1 activation of the b-catenin-dependent pathwayand its expression is under the control of TCF7L2.

overall_design: We determined the RNA profile of COUP-TFII knockdown β-cells (832/13 INS-1 cells transfected with COUP-TFII specific siRNA) with respect  to control cells (832/13 INS-1 cells transfected with scrambled siRNA) using Affymetrix expression  analysis technical manual 701025Rev.5 (Affymetrix, Santa Clara, California, USA). Briefly, 1 mg  of total cellular mRNA was reverse transcribed into cDNA (SuperScript Choice System Invitrogen,  Carlsbad, CA) using oligo-dT primers and a T7 RNA polymerase promoter site. The cDNA was in  vitro transcribed and biotin-labeled for microarray analysis using the Affymetrix IVT labeling kit.  The concentration of labelled cRNA was measured using a NanoDrop ND-1000  spectrophotometer. Labeled cRNA was fragmented in a fragmentation buffer for 35 min at 94°C.  The quality of labeled and fragmented cRNA was analyzed using the Agilent bioanalyzer 2100  (Van Lommel et al, 2006). Fragmented cRNA was hybridized to the rat 230 2.0 array  (Affymetrix) during 16h at 45°C. Arrays were washed and stained in a fluidics station (Affymetrix) and scanned using the Affymetrix 3000 GeneScanner.

first: Marie

last: Boutant

first: Oscar

middle: H

last: Ramos

first: Cécile

last: Tourrel-Cuzin

first: Jamileh

last: Movassat

first: David

last: Vallois

first: Julien

last: Planchais

first: Jean-Paul

last: Pégorier

first: Frans

last: Schuit

first: Patrice

last: Petit

first: Pascale

last: Bossard

first: Anne

last: Grapin-Botton

first: Mireille

last: Vasseur-Cognet


title: The tudor domain protein Kumo is required to assemble the nuage and to generate germline piRNAs in Drosophila

city: Singapore

first: Toshie

last: Kai

address: 1 Research Link, National University of Singapore

institute: Temasek Life Sciences Laboratory

type: Non-coding RNA profiling by high throughput sequencing

summary: We are submitting two small RNA libraries derived from ovarian tissue of mutant and heterozygous for the Kumo/Qin gene, required for the piRNA production in germline cells. In absence of Kumo/Qin, piRNA production is reduced and transposons are derepressed.

overall_design: Analysis of piRNA production in Kumo/Qin mutants

first: Amit

last: Anand


title: Gene expression profile of SYT-SSX2-expressing human bone marrow-derived mesenchymal stem cells

status: Public on Sep 26 2011

city: Nashville

first: Josiane

last: Eid

address: 2220 Pierce Avenue

institute: Vanderbilt University

summary:
Synovial sarcoma is a rare malignancy characterized by the presence of a specific chromosomal translocation t(X;18) that results in the formation of a fusion protein SYT-SSX.
Because it is believed that synovial sarcoma arises from mesenchymal stem or progenitor cells, we used human bone marrow-derived mesenchymal stem cells (MSCs) to determine the changes in gene expression caused by this oncogene in untransformed MSCs.

overall_design: In 2 independent experiments, human bone marrow-derived MSCs were infected with retrovirus carrying either control vector (pOZ) or SYT-SSX2 expression vector.  Total cellular RNA was extracted 4 days post-infection and utilized for microarray analysis on Affymetrix arrays.

first: Christina

last: Garcia


title: Genomewide occupancy of the synovial sarcoma-associated SYT-SSX2 oncoprotein in C2C12 myoblasts

summary: Synovial sarcoma is a rare malignancy that is characterized by the presence of a chromosomal translocation t(X;18).  This genetic abnormality results in the fusion of 2 transcriptional co-regulators, SYT and SSX, which have been shown to mediate transcriptional activation and repression, respectively.  Although the fusion protein does not bind DNA directly, SYT-SSX2 is known to function through interaction with chromatin-modifying complexes.  In this study, we wanted to determine the SYT-SSX2 occupancy across the whole genome in order to further characterize its function by identifying genes that may be deregulated by this protein.

overall_design: C2C12 myoblasts were infected with retrovirus carrying SYT-SSX2-HA-FLAG expression vector.  Chromatin immunoprecipitation (ChIP) was performed on cell lysates with either control IgG antibody (Abcam) or anti-FLAG antibody (Sigma).  Lysates from 2 independent infections were pooled and used to isolate control ChIP DNA (IgG).  DNA from 2 independent FLAG ChIP experiments (each using lysates from 2 independent infections) was pooled for SYT-SSX2 ChIP.


title: Gene expression profile of SYT-SSX2-expressing C2C12 myoblasts

summary: Synovial sarcoma is a rare malignancy characterized by the presence of a specific chromosomal translocation t(X;18) that results in the formation of a fusion protein SYT-SSX.  Because it is believed that synovial sarcoma arises from mesenchymal stem or progenitor cells, we wanted to determine the changes in gene expression caused by SYT-SSX2 in untransformed mesenchymal progenitor cells - murine C2C12 myoblasts in this experiment.

overall_design: In 2 independent experiments, C2C12 myoblasts were infected with retrovirus carrying either control vector (pOZ) or SYT-SSX2 expression vector.  Total cellular RNA was extracted 48 hours post-infection and utilized for microarray analysis on Affymetrix arrays.


title: 183 breast tumors from the Helsinki Univerisity Central Hospital with survival information

status: Public on Oct 01 2011

city: Tampere

first: Dario

last: Greco

address: Arvo ylpön Katu 34

department: Faculty of Medicine and Health Technology

country: Finland

institute: Tampere University

first: Päivi

last: Heikkilä

first: Carl

last: Blomqvist

first: Heli

last: Nevalinna


title: Reprogramming of mesenchymal stem cells by the synovial sarcoma-associated oncogene SYT-SSX2

summary:
Cellular identity is determined by its gene expression programs. The ability of the cell to change its identity and produce cell types outside its lineage is achieved by the activity of transcription controllers capable of reprogramming differentiation gene networks. The synovial sarcoma associated protein, SYT-SSX2, reprograms myogenic progenitors and human bone marrow-derived mesenchymal stem cells (BMMSCs) by dictating their commitment to a pro-neural lineage. It fulfills this function by directly targeting an extensive array of neural-specific genes as well as genes of developmental pathway mediators. Concomitantly, the ability of both myoblasts and BMMSCs to differentiate into their normal myogenic and adipogenic lineages was compromised. Synovial sarcoma is believed to arise in mesenchymal stem cells where formation of the t(X;18) translocation product, SYT-SSX, constitutes the primary event in the cancer. SYT-SSX is therefore believed to initiate tumorigenesis in its target stem cell. The data presented here allow a glimpse at the initial events that likely occur when SYT-SSX2 is first expressed and its dominant function in subverting the nuclear program of the stem cell, leading to its aberrant differentiation, as a first step toward transformation. In addition, we identified the fibroblast growth factor receptor gene, Fgfr2, as one occupied and upregulated by SYT-SSX2. Knockdown of FGFR2 in both BMMSCs and synovial sarcoma cells abrogated their growth and attenuated their neural phenotype. These results support the notion that the SYT-SSX2 nuclear function and differentiation effects are conserved throughout sarcoma development and are required for its maintenance beyond the initial phase. They also provide the stem cell regulator, FGFR2 as a promising candidate target for future synovial sarcoma therapy.

This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Protective Role for the Disulfide Isomerase PDIA3 in Methamphetamine Neurotoxicity

city: Omaha

first: Gurudutt

last: Pendyala

state: NE

address: 985800 Nebraska Medical Center

department: Pharmacology and Experimental Neuroscience

institute: University of Nebraska Medical Center

summary: Methamphetamine abuse continues to be a worldwide problem, damaging the individual user as well as society. Only minimal information exists on molecular changes in the brain that result from methamphetamine administered in patterns typical of human abusers. In order to investigate such changes, we examined the effect of methamphetamine on the transcriptional profile in brains of monkeys. Gene expression profiling of the caudate and hippocampus identified protein disulfide isomerase family member A3 (PDIA3) to be significantly up-regulated in the animals treated with methamphetamine as compared to saline treated control monkeys. Treatment of primary rat neurons with methamphetamine revealed an up-regulation of PDIA3, showing a direct effect of methamphetamine on neurons to increase PDIA3. In vitro studies using a neuroblastoma cell line demonstrated that PDIA3 expression protects against methamphetamine-induced cell toxicity and methamphetamine-induced intracellular reactive oxygen species production, revealing a neuroprotective role for PDIA3. The current study implicates PDIA3 to be an important cellular neuroprotective mechanism against a toxic drug, and as a potential target for therapeutic investigations.

overall_design: To study the effects of chronic METH effects on the brain

first: Howard

last: Fox


title: Colour analysis in Fenneropenaeus merguiensis

status: Public on Sep 15 2011

city: Sippy Downs

first: Nicole

last: Ertl

state: Queensland

address: 90 Sippy Downs Drive

department: FOSHE - GeneCology

institute: University of the Sunshine Coast

summary: Differential gene expression analysis of three F. merguiensis colour groups (dark, light, albino), using custom microarrays.

overall_design: A total of 12 light, 12 dark and 9 albino prawn samples were analysed, using total RNA extracted from cuticle tissue. 3 biological replicates were pooled onto each of the 4 arrays for the light and dark samples; and for the albino samples, groups of 2, 2, 2 and 3 biological replicates were pooled for the 4 arrays. Single colour analysis was carried out, using the Cy3 dye.


title: Transcriptome analysis of rice infected with RGSV

city: Sapporo

first: Kouji

last: Satoh

state: Hokkaido

address: Hitsujigaoka 1

institute: NARO/HARC

summary:
Rice grassy stunt disease is mainly observed in South, Southeast and East Asia, and caused by Rice grassy stunt virus (RGSV). Specific symptom appeared on RGSV infected rice plant is excess tillering. To guess how to induce excess tillering in RGSV infected plant, we analyzed the global gene expression changes in RGSV infected plants.

Keywords: virus infection, disease response

overall_design: Comparison between RGSV and mock infected rice. Biological replicates: 3 control, 3 infected, independently grown and harvested. 1samples derived from 5 plants grown under same conditons

first: Takahide

last: Sasaya

first: Hiroaki

last: Kondoh

first: Hiromi

first: Setsuko

last: Kimura

first: Toshihiro

last: Omura

first: Shoshi

last: Kikuchi


title: Entamoeba invadens encystation transcriptome

city: Shnjuku

first: Ghulam

last: Jeelani

state: Tokyo

department: Parasitology

institute: National Institute of Infectious Diseases

summary: In this study, we used microarray analysis to determine genes involved in encystation.

overall_design: The expression profile more than 9,700 genes during encystation was compared.

first: Aleyla

last: Escueta-de Cadiz

first: Afzal

last: Husain

first: Dan

last: Sato

first: Kumiko

last: Nakada-Tsukui

first: Tomoyoshi

last: Nozaki


title: Expression data from HT-1080 cells incubated or not in the presence of laminin111 coiled-coiled recombinant fragment (rLCC111)

status: Public on Oct 12 2011

city: Majadahonda

first: Patricia

last: Santos Valle

state: Madrid

address: Joaquín Rodrigo 2

department: Molecular Immunology Unit

country: Spain

institute: Hospital Universitario Puerta de Hierro Majadahonda

summary: Laminins are large heterotrimeric cross-shaped extracellular matrix (ECM) glycoproteins with terminal globular domains and a coiled-coil region. We have produced for the first time a recombinant laminin coiled-coil domain and studied the transcriptional profile of cells incubated in coiled-coil-coated wells.

overall_design: Cells were incubated in 24w plates, onto coiled-coil-coated wells or control BSA-coated wells (one each), 24h


title: Expression data from different samples of a single ccRCC patient: 7 primary intra-tumor samples and 2 metastatic tumor samples

status: Public on Aug 25 2011

city: Lyon cedex 08

first: Pierre

last: Martinez

address: 28 rue Laennec

country: France

institute: Cancer Research Centre of Lyon

summary: We have sampled several tumour regions from a single ccRCC patient after 6 weeks everolimus treatment, including both primary and metastatic site samples to investigate intra-tumour heterogeneity.

overall_design: We selected 7 samples from the primary tumour and 2 samples from a chestwall metastatic site sample for expression analysis using microarray data. All samples were fresh frozen upon extraction.

first: Andrew

last: Rowan

first: Charles

last: Swanton


title: Angus PRKG2 R678X homozygous (dwarf) cattle vs unaffected growth plate cartilage

city: Ames

first: James

last: Reecy

state: IA

address: 2255 Kildee Hall, Iowa State University

department: Animal Science

institute: Iowa State University

summary: Kinase activity of cGMP-dependant, type II, protein kinase (PRKG2) is required for the proliferative to hypertrophic growth transition of growth plate chondrocytes during endochondral ossification. Loss of PRKG2 function in rodent and bovine models results in dwarfism. We compared growth plate cartilage gene expression profiles of PRKG2R678X/R678X, dwarf and PRKG2R678X/+, unaffected Angus cattle using microarray technology to discover pathways regulated by PRKG2.  Calves used in this analysis were produced by the mating between a dwarf carrier sire and two dams- a mother (carrier) and daughter (dwarf) pair.  Each dam produced three calves by embryo transfer, which were born in two calving groups.  Growth plate cartilage was harvested from the tibia of each animal at approximately 215 days of age.  Total RNA was extracted by a modified Trizol protocol.  The bovine cDNA microarray (GEO Accession: GPL8813) was used for this analysis. Samples were labeled with Cy3 or Cy5 and hybridized by dye swapping the dwarf (4 dwarf animals- 2 per dam/calving group) and unaffected individuals (2 unaffected animals- 1 per dam/ calving group) such that each dwarf was compared to the unaffected full-sib produced in the same calving group.  Each cDNA array was analyzed at three different PMT levels (PMT70,80 and 90), resulting in 12 total image files for statistical analysis.

overall_design: Dwarf PRKG2 R678X homozygous cattle were compared to unaffected, age matched samples.  Samples were labeled with Cy3 or Cy5 and hybridized by dye swapping the dwarf (4 dwarf animals- 2 per dam/calving group) and unaffected individuals (2 unaffected animals- 1 per dam/ calving group) such that each dwarf was compared to the unaffected full-sib produced in the same calving group (i.e. unaffected samples had 2 technical replicates).  Each cDNA array was analyzed at three different PMT levels (PMT70,80 and 90), resulting in 12 total image files for statistical analysis.

last: Koltes


title: Comparison of gene expression profiles in rat sarcomas and masenchymal stem cells (MSCs)

status: Public on Oct 25 2011

city: Kashihara

first: Kanya

last: Honoki

state: Nara

address: 840 Shijo-cho

department: Department of Orthopedic Surgery

institute: Nara Medical University

summary:
To investigate the altered patways among sarcomas and MSCs, gene expression profiles were comared among rat osteosarcoma and malignant histiocytoma (MFH) to mesenchymal stem cells (MSCs) from syngeneic origin.
Several altered pathways have identified including down-regulation of Wnt, Cell adhesion, ECM interaction and up-regulation of Hedgehog, cell cycling pathways in rat sarcomas compared to MSCs.

overall_design: Gene expression array analysis was perfromed for the samples of rat osteosarcoma COS1NR and malignant fibrous histiocytoma MFH1NR cell lines, bothe established from chemically induced tumors in F344 rats by 4-HAQO, and rat mesenchymal stem cells freshly isolated from femur bone marrow of F344 rats.


title: miRNA expression profiles from E18th rat embryonic striatal stem cells under conditioned environments

city: KOTA BHARU

first: SOUMYA

last: PATI

address: KUBANG KERIAN

country: Malaysia

institute: UNIVERSITI SAINS MALAYSIA

summary:
Background:
Striatum is the crucial unit in brain involved in higher-level organizational learning, motor control and cognitive finctions. It also produces dopaminergic neurons, which play an important role in the control of multiple brain functions including voluntary movement and a span of neurobehavioral processes such as, mood, reward, addiction, and stress. Traumatic brain injury (TBI) lead to striatum related persistent cognitive dysfunctions. A number of cell based therapies such as;  induced pluripotent stem cells (ips), neural stem cells (NSCs) and mesenchymal stem cells (MSCs), have been investigated so far for their potential application in TBI. But the journey from bench-to-bedside has not yet been covered sucessfully. As their survival and long-term maintenance in vivo has been huddle so far. So to understand the fate of embryonic striatal stem cells (ESSCs) in long-term neurogenesis in vitro, we have studied the neurogenic potential of rat embryonic striatal stem cells from E18th day embryos under conditioned microenvironments.
Objectives:
To evaluate the neuro-regenerative potential striatum-derived stem cells, we have employed synergestic effects of certain neurotrophins, such as ; EGF, IGF, FGF and LIF as in four combinations (Control/untreated-A, EGF+FGF-B, EGF+FGF+LIF-C, EGF+FGF+IGF-D and EGF+FGF+ IGF +LIF –E) in the microenvironment .
To decipher the regulatory miRNAs involved in ESSC-derived neurogenesis, we have performed detailed miRNA  profiling for ESSCs at passage 3 for groupD and group E derived ESSCs (based on their performance in vitro). Out data has explored cruicial mIRNAs involved in strital neurogenesis .

overall_design:
Striatum has been shown to control the major part in higher-level organizational aspects of learning in human.
To understand the role of striatum-derived neural progenitors in neural repair, miRNA regulation was trapped for ESSCs under conditioned stimuli.
Among different combinatorial stimuli, group D;(EGF+FGF-2+IGF) and group E; EGF+FGF-2+IGF+LIF) tretaed ESSCs were selected at passage 3 for miRNA analysis experiment.

first: Soumya

last: Pati

first: Sangu

last: Muthuraju

first: Jafri

last: Abdullah

first: Hasnan

last: Jaafar


title: Eliminating SF-1 (Nr5a1) Sumoylation In Vivo Results in Ectopic Hedgehog Signaling and Disruption of Endocrine Development.

status: Public on Aug 15 2011

city: San Francisco

first: Holly

last: Ingraham

state: CA

address: 1550 4th street, Rock Hall Rm 281

institute: UCSF

summary: Sumoylation is generally considered a repressive mark for many transcription factors. However, the in vivo importance of sumoylation for any given substrate remains unclear and is questionable because the extent of sumoylation appears exceedingly low for most substrates. Here, we permanently eliminated SF-1/NR5A1 sumoylation in mice (Sf-1K119R,K194R or 2KR) and found that Sf-12KR/2KR mice failed to phenocopy a simple gain of SF-1 function or show elevated levels of well-established SF-1 target genes. Instead, mutant mice exhibited marked endocrine abnormalities and changes in cell fate that reflected an inappropriate activation of hedgehog signaling. In an immortalized embryonic cell line, the highly SUMO-sensitive target gene Shh is ectopically activated by direct recruitment of unsumoylatable SF-1 to non-canonical DNA binding sites. We propose that sumoylation greatly expands the functional capacity of transcription factors such as SF-1, and is leveraged during development to achieve cell type-specific gene expression in multi-cellular organisms.

overall_design: Adult and embryonic gene expression in adrenals and testes from SF-1 wild type and 2KR homozygous mice are compared using MEEBO microarrays.

first: Florence

last: Lee

first: Emily

last: Faivre

first: Miyuki

last: Suzawa

first: Erik

last: Lontok

first: Daniel

last: Ebert

first: Fang

last: Cai

first: Denise

last: Belsham


title: RNA-Seq based transcriptional map of bovine respiratory disease pathogen 'Histophilus somni 2336'

city: starkville

first: Ranjit

last: Kumar

state: MS

address: 240 Wise Center Drive,PO Box 6100

department: Dept of Basic Science

institute: MSU

summary: We used RNA-Seq to experimentally annotate H. somni strain 2336 and construct a single nucleotide resolution transcriptome map. Novel expressed elements were identified, and where appropriate, computational predictions of previously described gene boundaries were corrected.

overall_design: Transcript profiling of a single sample by RNA-Seq

first: Mark

middle: L

last: Lawrence

last: Watt

first: Amanda

last: Cooksey

first: Shane

last: Burgess

first: Bindu

last: Nanduri


title: Mesenchymal Nuclear factor I B regulates cell proliferation and epithelial differentiation during lung maturation

status: Public on Sep 29 2011

city: buffalo

first: Dan

last: Wang

state: NY

address: Elm & Carlton Streets

institute: RPCI

summary: We generated Nfibf/f mice and then cross with Dermo1-Cre mice to obtain Nfibf/f, Dermo1-Cre mice. In these Nfibf/f, Dermo1-Cre mice, there are defects in sacculation and epithelial cell differentiation. We performed micoarray analysis to find the genes which are possibley regulated by NFI-B and related to lung maturation during lung development.

overall_design: We used microarrays to performing transcriptional profiling of Nfibf/f, Dermo1-Cre and Nfibf/f lungs at E18.5

first: Yu-Chiu

last: Hsu

first: Jason

last: Osinski

first: Christine

last: Campbell

first: E

middle: D

last: Litwack

first: Song

last: Liu

first: Richard

last: Gronostajski


title: Expression data from shoot bases of rice seedling after gravistimulation

status: Public on Sep 02 2011

city: shanghai

first: Mei

last: Zhiling

address: 300 Fenglin Road

institute: Institute of Plant Physiology and Ecology

summary: Upper and lower parts (flanks) of rice (Oryza sativa sp. japonica) shoot bases at 0.5 h and 6 h after gravistimulation was used for expression analysis in control and gravistimulated samples.Targets from biological replicates of both control and gravistimulated samples were generated and expression profiles were determined Affymetrix Rice Genome arrays.

overall_design: Control and gravistimulated biological replicates were analyzed

first: Liwei

last: Hu

first: Haiying

last: Chen

first: Zhiling

last: Mei


title: Expression data from epigenetic memory and preferential lineage-specific differentiation in induced pluripotent stem cells derived from human pancreatic islet beta cells

status: Public on Aug 01 2011

city: Boston

first: Ori

last: Bar-Nur

state: MA

address: 185 Cambridge st.

department: Center of Regenerative medicine

institute: Harvard University

summary: Three induced pluripotent stem (iPS) cell lines were generated from pancreatic BCD (beta-cell-derived cells).  One iPS cell clone was derived from pancreatic non-beta cells. We used microarrays to study the gene expression profiles of beta-iPSCs, and compared the expression of genes in their somatic parental cells and other ES and iPS cells.

overall_design: All BiPSC lines were tested in pluripotency assays (including morphology, immunostainings and qRT-PCR) for known pluripotency markers, as well as differentiation capacity in vivo and  in vitro.

first: Nissim

last: Benvenisty


title: Expression of marker genes in the lymph nodes predicts the recurrence of  squamous cell vulvar carcinoma.

city: Warszawa

first: Krzysztof

last: Goryca

address: Banacha 2c

department: CeNT

country: Poland

institute: Uniwersytet Warszawski

summary: BACKGROUND: Regional lymph node (LN) status is a well-known prognostic  factor for vulvar carcinoma (VC) patients. Although the reliable LN  assessment in VC is crucial, it presents significant diagnostic problems.  PURPOSE: We aimed to identify specific mRNA markers of VC dissemination in  the LN and to address the feasibility of predicting the risk of nodal  recurrence by the patterns of gene expression.  EXPERIMENTAL DESIGN: Sentinel and inguinal LN samples from 20 patients who  had undergone surgery for stage T1-3, N0-2, M0 primary vulvar squamous  cell carcinoma were analyzed. Gene expression profiles were assessed in  four metastatic [LN(+)] and four histologically negative [LN(-)] lymph  node samples obtained from four VC patients, by the Affymetrix U133 Plus  2.0 gene expression microarrays. Of the set of genes of the highest  expression in the metastatic LNs compared to LN(-), seven candidate marker  genes were selected PERP, S100A8, FABP5, SFN, CA12, JUP and CSTA, and the  expression levels of these genes were further analyzed by the real-time  reverse transcription polymerase chain reaction (qRT-PCR) in 71 LN  samples.  RESULTS: Five of the genes, PERP, S100A8, FABP5, SFN and CA12, were  significantly increased in LN(+) compared to LN(-) samples. In the initial  validation of the seven putative markers of metastatic LN, the Cox  proportional hazard model pointed to SFN and CA12 expression to  significantly relate to the time to groin recurrence in VC patients.  CONCLUSIONS: PERP, S100A8, FABP5, SFN and CA12 have a potential of marker  genes for the molecular testing of LN involvement in VC patients.

overall_design: Gene expression profiles of 8 tissue samples representing 4 metastatic [N(+)] and 4 histologically negative [N(-)] LN samples

first: Magdalena

last: Kowalewska

first: Jakub

last: Radziszewski

first: Mateusz

last: Bujko

first: Małgorzata

last: Oczko-Wojciechowska

first: Michał

last: Jarzab

first: Janusz

last: Siedlecki

first: Mariusz

last: Bidzinski


title: PVRL Is A Receptor For Measles Virus

status: Public on Jul 29 2011

city: Halifax

first: Christopher

middle: Donald

last: Richardson

state: Nova Scotia

address: 5850 College St. Tupper 7th Floor 7C

department: Microbiology & Immunology

country: Canada

institute: Dalhousie University

summary:
Measles virus infects serum activated airway epithelial cells and many adenocarcinoma cell lines.  A microarray analysis was performed on virus permissive versus non-permissive cells.  Membrane protein genes that were upregulated in permissive cells were tested as receptor/entry factors.

Membrane protein genes that were upregulated in smooth airway epithelial cells (SAEC) following growth in 10% fetal calf serum that made the cell line permissive to measles virus were identified.

Membrane protein genes that were upregulated in adenocarcinoma cells that were permissive to wild type measles virus infection were identified.

overall_design:
[SAEC]: Airway cells (SAEC) grown in serum free media (SAGM) were purchaced from Lonza.  Half the cells were cultured in SAGM, the other half were transferred into Dulbecco's 10% fetal calf serum for 24 hrs.  RNA was harvested from the cells by the Qiagen RNAeasy

[Adenocarcinoma cells]: MCF7, MDA-MB-468, T47D, NCI-H358, NCI-H125, MGH24 cells were permissive and A549 and MDA-MB-231 cells were non-permissive.


title: Genome-wide transcriptional response of primary alveolar macrophages (PAMs) following infection with porcine circovirus type 2

status: Public on Jul 27 2011

city: Wuhan

first: Tao

middle: Wen

last: Li

state: Hubei

address: No.1, Shizi_shan street, Hongshan district

department: Division of Animal Infectious Disease

institute: Huazhong agricultural university, State Key Laboratory of Agricultural Microbiology

summary:
Porcine alveolar macrophages (PAMs) play impoartant role in innate immunity. Porcine circovirus type 2 (PCV2) has been identified as the causal agent of postweaning multisystemic wasting syndrome, an economically important multifactorial disease of the swine industry worldwide.
We used microarrays to study the transcriptome of PAMs infection with PCV2.

overall_design: PAMs were collected by bronchoalveolar lavage from health piglets (free of PCV2, PRRSV, PRV, CSFV, PPV), and PAMs were cultured for 48 hours and inoculated with 5 moi of PCV2.

first: Wentao

first: Shuqing

last: Liu


title: Microarrays reveal oocyte lipid storage droplet gene as key factor in reproductive dysfunction of captive-reared  P. monodon

first: Abigail

last: Elizur

address: Sippy Downs Drive

department: Science and Education

summary:
Background: Aquaculture of the black tiger prawn Penaeus monodon remains severely constrained by an almost total dependence on wild-caught broodstock. Reliance on wild-caught broodstock stems, for the most part, from reduced reproductive potential of captive-reared females. Reproductive performance of captive-reared females is usually characterised by longer latency period, lower egg production, egg hatch rates and post-larval survivorship compared with their wild-caught counterparts. Improved understanding of the cellular and associated molecular events occurring during peneaid ovarian maturation could therefore be fundamental to improving reproductive success of captive-reared animals.
Methodology/Principle Findings: In support of other studies, our histological analyses of developing oocytes revealed differences between wild-caught and captive-reared P. monodon, including reduced lipid accumulation in oocytes of captive-reared animals. We have employed oligonucleotide microarray analysis to compare expression profiles of genes involved in ovarian maturation among wild-caught and captive-reared animals. Custom oligonucleotide microarrays were constructed and screened with transcripts derived from the ovary, cephalothorax and eyestalk from animals of all ovarian maturation stages. Ovarian maturation-related differential expression patterns were observed for 111 transcripts, with 53 transcripts displaying differential expression between wild-caught and captive-reared animals. Notably transcripts encoding vitellogenin - the major egg yolk protein precursor, and a lipid storage droplet protein (which we named pmLSD) which is involved in lipid accumulation, were found to be more highly expressed in wild-caught animals. pmLSD transcripts localise to pre-vitellogenic oocytes of wild-caught animals and the pmLSD protein is exclusively localised to the surface of lipid droplets of oocytes at vitellogenic and cortical rod stages.

overall_design: We have employed oligonucleotide microarray analysis to compare expression profiles of genes involved in ovarian maturation among wild-caught and captive-reared animals.  Target preparation and microarray hybridisation. Ovarian RNA samples from nine wild-caught  animals representing six ovarian maturation stages (P, 2, 24, V, R, E) were used in microarray  hybridisations. Similarly, RNA samples from three captive-reared animals representing four maturation  stages (P, 24, V, E) were used in microarray hybridisations. For wild-caught animals, samples from  each ovarian maturation stage were pooled into groups of four and five, enabling two hybridisations.  For captive-reared animals, samples from each ovarian maturation stage from all three animals were  pooled enabling one hybridisation for each stage. Importantly, as the four stages for captive-reared  animals were (1) pre-ablation pre-vitellogenic, (2) post-ablation pre-vitellogenic, (3) post-ablation  vitellogenic, (4) post-ablation vitellogenic with cortical rods, this arrangement allowed for 2 samples of  captive-reared pre-vitellogenic and 2 samples of captive-reared vitellogenic, thereby enabling t-tests  between samples, while also allowing analysis across the whole 4 stages via cluster analysis. All  hybridisations were single channel hybridisations conducted using equal amounts of RNA pooled from  each individual.

first: Philip

last: Brady

first: Scott

middle: F

last: Cummins

first: Richard

last: Williams

first: Wayne

middle: R

last: Knibb


title: Nutrient-dependent growth of NIH3T3 and NIH3T3 K-ras cell lines.

status: Public on Jul 14 2011

city: Milan

first: Ferdinando

last: Chiaradonna

address: Piazza della scienza, 2

department: Biotechnology and Biosciences

country: Italy

institute: University of Milano-Bicocca

summary: Expression profiling of normal NIH3T3 and transformed NIH3T3 K-ras cell lines grown for 72 hours in optimal glucose availability (25 mM glucose) or low glucose availability (1 mM). Low glucose induces apoptosis in transformed cells as compared to normal ones.

overall_design: We performed genome-wide analysis by using Affymetrix GeneChip oligonucleotide microarrays to identify those genes whose expression levels are modulated by glucose availability in NIH3T3 and NIH3T3 K-ras cell lines. The cells, to be used for the transcription analysis, were collected at 18h from the initial seeding, time corresponding to the change of medium (25 or 1 mM glucose, indicated as T0) and then at 24, 48 and 72h upon medium change.

first: Chiara

last: Balestrieri


title: Expression profile of FAC-sorted murine retinal cells

status: Public on Jul 12 2011

city: Dresden

first: Kai

last: Postel

address: Fiedlerstraße 42

country: Germany

institute: DFG-Center for Regenerative Therapies Dresden

summary: Microarray experiments were performed using FAC-sorted young photoreceptors to analyze their transcriptome in comparison to remaining retinal cells at same developmental stage and retinal progenitors.

overall_design: For each replicate, retinae of 6 to 8 postnatal day 0 pNestin-GFP or postnatal day 4 rhoEGFP mice were dissected and FAC-sorted based on GFP expression. RNA of fractions was isolated and subsequently analyzed with microarray experiment.

first: Marius

last: Ader


title: Differential gene expression in a Cryptococcus neoformans ccr4Delta mutant during host-temperature adaptation

status: Public on Jul 11 2011

city: Buffalo

first: John

middle: C.

last: Panepinto

address: 955 Main St., Suite 5229

department: Microbiology and Immunology

country: USA

institute: University at Buffalo SUNY

summary:
Analysis of ccr4 Delta vs. wild type shifted from 30oC to 37oC for 10 minutes
To determine the effect of ccr4 deletion on temperature stress-responsive changes in gene expression in C. neoformans

overall_design: Replicate cultures of the wild type (Control) and ccr4Delta mutant were grown to mid log phase at 30oC, harvested and resuspended in 37oC pre-warmed medium for 10 minutes. Pooled biological replicate cultures were hybridized in duplicate (2 slides, 2 arrays/slide)

middle: C


title: Global transcriptome analysis of two ameiotic1 alleles in maize anthers: defining steps in meiotic entry and progression through prophase

status: Public on Jul 15 2011

city: Stanford

last: Fernandes

address: 385 Serra Mall

department: Bio Sci

institute: Stanford University

summary:
This study compared the transcriptomes of maize anthers at both 1mm and 1.5mm lengths from male sterile mutants with either the am1-489 or am1-pra alleles as well as from fertile siblings of the mutant plants.
Comparisons were done varying just the stage (1mm vs 1.5 mm), just the allele (am1-pra vs am1-489 at the same stage), and wild-type vs mutant (same stage and allele).  Genes were categorized as On (expressed) or Off (not detected) and if both channels produced an intensity, the differential expression was determined.  AM1 seems to be involved in establishing or stabilizing meiotic chromosomes and it had a profound impact on gene expression in the pollen mother cells during the maturation phase from 1.0 to 1.5 mm anther length.  The two alleles shared some transcript changes but am1-489 showed a more dramatic loss (>3400) at 1.5mm than am1-pra.  Most differentially expressed transcripts were allele-specific.
KEYWORDS: male sterility, maize, microarray, meiosis

overall_design: Compared wild-type and male-sterile anthers from 2 ameiotic1 alleles at 2 stages of anther growth (1mm and 1.5mm)

first: Guo-Ling

first: Arnaud

last: Ronceret

first: Rachel

last: Wang

first: W

middle: Z

last: Cande

first: Virginia

last: Walbot


title: Expression data from C3(1)Tag mammary tumors, tumor derived cell line (M6) and normal mammary tissue (FVB)

status: Public on Sep 01 2011

city: Bethesda

first: Jeffrey

last: Green

state: MD

address: Rm 4054, 37 Convent Drive

institute: NCI

summary:
M6 cells expression a similar genetic signature as the parent tumor, C3(1)Tag tumor. The mammary tumors, and tumor cell line, are distinct from normal mammary epithelial tissue (FVB)
BRCA/p53, cmyc, h2n, p53ERneg, p53ERpos, pymt and ras samples were not reported in this paper.

overall_design: We used microarrays to determine whether the M6 cell line retains the SV40Tag signature (91 gene signature) that is expressed in C3(1)Tag tumors but not FVB normal mammary tissue.

first: Aleksandra

middle: M

last: Michalowski

first: Christina

middle: N

last: Bennett

first: Christine

last: Tomlinson


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

status: Public on Jun 27 2011

city: Huntsville

first: Greg

last: Cooper

state: AL

address: 601 Genome Way

institute: HudsonAlpha Institute for Biotechnology

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 Illumina gene expression microarrays for 60 normal human livers. Expression quantitative trait loci were identified by genome wide association mapping.

first: Gregory

first: Ian

middle: B

last: Stanaway

first: Mark

last: Rieder

first: Josh

last: Smith

first: Yvonne

last: Lin

first: Allen

last: Rettie

first: Ken

last: Thummel


title: Mouse kidney after systemic endotoxin challenge

first: Samir

last: Parikh

address: 330 Brookline Avenue, RN280C

institute: Beth Israel Deaconess Medical Center

summary:
8 week-old male C57BL6J mice were given Gram-negative endotoxin (LPS O111:B4, 10 mg/kg) intraperitoneally at time 0.  18 hrs thereafter, they were administered 10 ml/kg 0.9% saline.  Mice were sacrificed at 0, 18, or 42 hrs after LPS challenge. Kidneys were immediately collected into TRIzol for RNA preparation. Renal function was measured on blood collected at the time of tissue harvest
At t=0hr, mice had normal baseline renal function. At t=18hr, mice exhibited early renal injury, At t=42hr, mice had either recovered normal renal function or had persistent renal injury. We collected  kidneys from 3 mice per time point.  For the 42 hr time point, we collected kidneys from 3 mice with recovered renal function and kidneys from 3 mice with persistent renal injury.

overall_design: Mouse kidneys selected at successive stages of renal injury and recovery following systemic LPS challenge and volume resuscitation following LPS challenge.

first: Denise

last: Tam

first: Manoj

last: Bhasin

first: Mei

last: Tran

first: Amit

last: Bardia


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

city: Chicago

first: Christopher

middle: David

last: Brown

state: IL

department: Human Genetics

institute: University of Chicago

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

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

overall_design: Refer to individual Series


title: Microarray Expression Analysis of 3 Canonical Toxoplasma infections of human neuroepithelial cells

status: Public on Jun 24 2011

city: Baltimore

first: JC

last: xiao

address: 600 N. Wolfe Street, Blalock 1109

institute: Johns Hopkins University

summary: The outcome of infections with Toxoplasma gondii in humans is dependent in part on the genetic makeup of the infecting organism.  Recent studies have indicated that most infecting Toxoplasma organisms fall into 1 of 3 canonical lineages.  Previous studies have investigated the effects of Toxoplasma on its host cell transcriptome.  Little is known, however, about the effects of three canonical lineages on brain cells, the principal site of parasite lifelong persistence.  In this study, we examined the transcriptional profile of human neuroepithelioma cells in response to T. gondii infection using microarray analysis to characterize the strain-specific host cell response to 3 canonical T. gondii strains.  We found that the extent of the expression changes varied considerably among the three strains.  Neuroepithelial cells infected with type I exhibited the most differential gene expression, whereas type II infected cells had a substantially smaller number of genes which were differentially expressed. Cells infected with type III exhibited intermediate effects on gene expression.  The three strains also differed in the individual genes and gene pathways which were altered following cellular infection.  For example, gene ontology (GO) analysis indicated that type I infection largely affects genes related to central nervous system while type III infection largely alters genes which affect nucleotide metabolism; type II infection does not alter expression of a clearly defined set of genes.  Moreover, Ingenuity pathway analysis (IPA) revealed the sophistication of different strain in its interactions with the host.  These differences may explain some of the variation in the neurobiological effects of different strains of Toxoplasma on infected individuals.

overall_design: We infected SK-N-MC cells with 3 canonical Toxoplasma strains and assessed their gene expression in RNA at 20 hours post-infection using Affymetrix GeneChip. Infections and controls (no tachyzoites) were performed in duplicate and experiments for each strain were carried out on three separate occasions in order to include both technical replicates and biological replicates.

first: J

last: Xiao

first: L

last: Jones-Brando

first: R

last: Yolken

first: S

last: Sabunciyan


title: Expression of SV40 TAg signature in MDAMB231 cells, tumors, and normal human mammary epithelial cells (M98040 and M99005)

first: Jeffrey

middle: E

last: Green

summary:
MDAMB231 cells express the SV40TAg signature.  The normal mammary epithelial tissue does not express the signature.
CK0082, Empty1 and Gata3 samples are not reported in this manuscript

overall_design: We used microarrays to determine whether the MDAMB231 cell lines and tumors express the SV40Tag signature (91 gene signature).

first: Aleksandra

last: Michalowski

first: Christina

last: Bennett

first: Christine

last: Tomlinson


title: Mesenchymal stem cells in local fat depots stimulate breast cancer growth, invasion and desmoplasia

city: Richmond

first: Lynne

last: Elmore

state: VA

address: 1101 E. Marshall St

department: Pathology

institute: VCU

summary: Studies investigating the role of mesenchymal stem cells (MSCs) in mammary carcinogenesis have almost exclusively relied on isolates from bone marrow aspirates or non-breast fat sources often making the general assumption that all MSCs are alike.

overall_design: Here we conduct the first extensive analysis of human breast adipose MSCs to define similarities and differences to MSCs isolated from non-breast sources (subcutaneous abdominal tissue) and bone marrow.

first: Catherine

middle: I

last: Dumur


title: B cell signature during inactive systemic lupus

status: Public on Jun 23 2011

city: STRASBOURG

first: Jean-Nicolas

last: SCHICKEL

address: 15, rue rené descartes

institute: CNRS UPR9021

summary: Systemic lupus erythematosous (SLE) is an autoimmune disease with an important clinical and biological heterogeneity. B lymphocytes appear central to the development of SLE which is characterized by the production of a large variety of autoantibodies and hypergammaglobulinemia. In mice, immature B cells from spontaneous lupus prone animals are able to produce autoantibodies when transferred into immunodeficient mice, strongly suggesting the existence of intrinsic B cell defects during lupus. In order to approach these defects in humans, we compared the peripheral B cell transcriptomes of quiescent lupus patients to normal B cell transcriptomes.

overall_design: 17 patients with quiescent lupus (patient1-17) versus 9 controls (Control1-6,Control8-10).

first: Jean-Claude

last: Garaud

last: Schickel

first: Gilles

last: Blaison

first: Anne-Marie

last: Knapp

first: Doulaye

last: Dembele

first: Julie

last: Ruer-Laventie

first: Anne-Sophie

last: Korganow

first: Thierry

last: Martin

first: Pauline

last: Soulas-Sprauel

first: Jean-Louis

last: Pasquali


title: Temporal Analysis of the Honey Bee Microbiome Reveals Four Novel Viruses and Seasonal Prevalence of Known Viruses, Nosema, and Crithidia

status: Public on Jun 06 2011

city: San Francisco

first: Charles

last: Runckel

department: Biochemistry

institute: UCSF

summary:
Pathogen detection microarrays analyzing honeybee samples taken from the same hives over the course of a year, oligos correspond to specific pathogens or pathogen families of viruses, bacteria, fungi, protists, and other parasites
Samples were analyzed with the E-Predict analysis package

platform_organism:
Fungi
unidentified entomopoxvirus
unidentified baculovirus
Iridovirus
Cypovirus
Birnaviridae
Luteovirus
Black beetle virus
unclassified viruses
Densovirinae
Ascovirus
Betabaculovirus
Gammabaculovirus

overall_design: Twenty hives samples biweekly, Timepoint refers to sample collection week after start, where T01 refers to April 15, 2009.  Hive refers to the specific hive sampled.

first: Michelle

last: Flenniken


title: Alteration of the expression and 17, 20 lyase activity of cytochrome P450 17-hydroxylase/17, 20 lyase and of the expression of other Leydig cells genes in the rat fetal testis directly exposed to Mono-ethyl hexyl phthalate in culture.

status: Public on Jun 01 2011

city: Dunee

first: simon

middle: matthew

last: plummer

state: Angus

address: 2 James Lindsay Place

department: CXR

country: United Kingdom

institute: CXR Biosciences ltd

summary: This study aimed to investigate the direct mechanism(s) of action ofMono-(Ethyl-Hexyl) phthalate (MEHP) on the rat fetal testis with particular emphasis to Leydig cell steroidogenesis, by means of an in vitro system based on culture for 3 days of fetal testes from 14.5 days post-coïtum old rats. We first confirmed that an exposure to MEHP led to a dose-dependent decrease of testosterone and demonstrated that dihydrotestosterone (DHT) production was also inhibited. We then demonstrated that in 10µM MEHP-exposed testis basal 17alpha-hydroxy-progesterone (17OHP) production was increased (+40%) while androstenedione levels decreased (-55%). Furthermore, the addition of the latter steroid but none of the other precursors rescued testosterone thus establishing further that MEHP specifically blocked steroidogenesis at the level of the 17,20 lyase activity of the P450c17 enzyme (CYP17), which converts 17OHP to androstenedione. Furthermore and accordingly, both levels of testicular CYP17 protein (western blot) and cyp17a1 gene (qPCR, microarrays) were found to decrease under MEHP exposure. The microarray analysis also showed that among the few other testicular genes cyp17a1 whose expression was inhibited by MEHP were the genes encoding for the Leydig cell insulin-like peptid 3 (INSL3), involved in the control of testicular descent, and for inhibin A (INHA), that regulates follicular-stimulating hormone secretion.Under in vitro conditions where MEHP is not metabolized and remains at low intratesticular concentration, our findings show in particular that this phthalate directly inhibits several important Leydig cell factors involved in testis development and function.

overall_design:
Transcription profiling of rat fetal testes explants, vehicle or monoethylhexylphthalate (MEHP)-treated (1uM, 10uM)
3 condition experiment, 1-3 biological replicates per treatment. 2 technical replicates per sample.

first: Simon

last: Plummer


title: Transgenic expression of human PON1 in Drosophila melanogaster under the Tub driver

status: Public on May 26 2011

city: Iowa City

first: Alejandro

middle: A

last: Pezzulo

address: 169 Newton Rd 6334 PBDB

department: Internal Medicine

institute: University of Iowa

summary: Human paraoxonase-1 (PON1) is an enzyme with lactonase, esterase and phosphotriesterase activity that has been associated with multiple phenotypes. We expressed hPON1 ubiquitously in Drosophila melanogaster using the Gal4 system Tub driver.

overall_design: RNA from 30 flies from each of 3 genotypes was used to hybridize 4 arrays in a 12-plex array (4 technical replicates, 3 genotypes).

first: Joseph

last: Zabner