title: In vitro responses of PBMC and fibroblasts from patients with TRIF deficiency after TRIF dependent and independent stimuli

status: Public on Oct 20 2011

city: Molndal

last: Israelsson

address: Pepparedsleden 1

department: Translational Biology

country: Sweden

institute: AstraZeneca, IMED RIA

summary: We report here unrelated HSE patients with autosomal recessive (AR) or autosomal dominant (AD) TRIF deficiency. The AR form of the disease is due to a homozygous nonsense mutation, resulting in a complete absence of the TRIF protein. Both the TLR3 and the TRIF-dependent TLR4 signaling pathways are abolished. The AD form of TRIF deficiency is due to a heterozygous missense mutation resulting in a dysfunctional protein. The TLR3 signaling pathway is impaired, whereas the TRIF-dependent TLR4 pathway is unaffected. Both patients however showed reduced capacity to respond to cytosolic double stranded RNA, consistent with recent reports of TRIF’s involvement in the DExD/H-box helicases pathway.

overall_design:
Skin fibroblast cell lines were derived from healthy controls (n=3), patient with deficiencies for TRIF (n=1),  MYD88 (n=1), and TLR3 (n=1) and cultured for 4 hours in the presence of IL1B (20ng/ml) or poly I:C (25ng/ml) or left unstimulated for the same length of time.
PBMCs (previously frozen) collected from a healthy control (n=1) and patients with deficiencies for TRIF (n=1), and MYD88 (n=1) were cultured together with LPS (10ng/ml) or R848 (3ug/ml) for 2hrs or left unstimulated for the same length of time.

first: Vanessa

last: Sancho-Shimizu

first: Rebeca

last: Pérez de Diego

first: Lazaro

last: Lorenzo

first: Rabih

last: Halwani

first: Abdullah

last: Alangari

first: Sylvie

last: Fabrega

first: Annabelle

last: Cardon

first: Jerome

last: Maluenda

first: Megumi

last: Tatematsu

first: Farhad

last: Mahvelati

first: Melina

last: Herman

last: Ciancanelli

first: Yiqi

last: Guo

first: Zobaida

last: AlSum

first: Nouf

last: Alkhamis

first: Abdulkarim

last: Al-Makadma

first: Ata

last: Ghadiri

first: Soraya

last: Boucherit

first: Sabine

last: Plancoulaine

first: Capucine

last: Picard

first: Flore

last: Rosenberg

first: Marc

last: Tardieu

first: Pierre

last: Lebon

first: Emmanuelle

last: Jouanguy

first: Nima

last: Rezaei

first: Tsukasa

last: Seya

first: Misako

last: Matsumoto

first: Damien

last: Chaussabel

first: Anne

last: Puel

first: Shen-Ying

last: Zhang

first: Laurent

last: Abel

first: Saleh

last: Al-Muhsen

first: Jean-Laurent

last: Casanova


title: Midbrain floor plate dopamine neurons from human ESCs efficiently engraft in murine and primate models of PD

status: Public on Nov 07 2011

city: New York

first: Jeffrey

last: Zhao

state: NY

address: 1275 York Avenue

department: Genomics Core

country: USA

institute: Memorial Sloan Kettering Cancer Center

summary: Human pluripotent stem cells (hPSCs) are a promising source of cells for applications in regenerative medicine. Directed differentiation of hPSCs into specialized cells such as spinal motoneurons or midbrain dopamine (DA) neurons has been achieved.  However the effective use of hPSCs for cell therapy has lagged far behind. While mouse PSC-derived DA neurons have shown efficacy in models of Parkinson’s disease, DA neurons derived from human PSCs generally display poor in vivo performance. There are also considerable safety concerns for hPSCs related to their potential for teratoma formation or neural overgrowth. Here we present a novel floor plate-based strategy for the derivation of human DA neurons that efficiently engraft, suggesting that past failures were due to incomplete specification rather than a specific vulnerability of the cells. Midbrain floor plate precursors are derived from hPSCs in days following exposure to small molecule activators of sonic hedgehog (SHH) and canonical WNT signaling. Engraftable midbrain DA neurons are obtained by day 25 and can be maintained in vitro for several months. Extensive in vitro molecular profiling, biochemical and electrophysiological data define developmental progression and confirm identity of hPSC-derived midbrain DA neurons. In vivo survival and function is demonstrated in PD animal models in three host species. Long-term engraftment in 6-OHDA-lesioned mouse and rats demonstrates robust survival of midbrain DA neurons, complete restoration of amphetamine-induced rotation behavior and improvements in tests of forelimb use and akinesia. Finally, scalability is demonstrated by transplantation into Parkinsonian monkeys. Excellent DA neuron survival, function and lack of neural overgrowth in the three animal models tested indicate considerable promise for the development of cell based therapies in PD.

overall_design:
Differentiated hESC with three conditions (LSB, LSB/S/F8, LSB/S/F8/CHIR) were subjected to RNA extraction in specific timepoint (day 0, 1, 3, 5, 7, 11, 13, 25) and hybridization on Illumina microarrays. Each sample has 3 or 4 biological repeats.

Based on previous study* of dual SMAD inhibition neural induction, we developed new midbrain dopamine neuron protocol. It depends on time specific treatment of below factors (LSB/S/F8/CHIR):
L (LDN193189 (BMP inhibitor) , day 0-11), SB (SB431542 (TGF-b signal inhibitor), day 0-5), S (SHH + Purmorphamine (Smo agonist), day 1-7), F8 (FGF8, day 1-7) and CHIR (CHIR99021 (GSK3b inhibitor), day 3-13)
LSB and LSB/S/F8 are limited control conditions of dual SMAD only (LSB) or traditional patterning with Sonic and FGF (LSB/S/F8)
*Chambers,S.M. et al. Highly efficient neural conversion of human ES and iPS cells by dual inhibition of SMAD signaling. Nat. Biotechnol. 27, 275-280 (2009).

first: Jae-won

last: Shim

first: Sonja

last: Kriks

first: Lorenz

last: Studer


title: Transcriptomic datat of senescence WI-38 cell

status: Public on Nov 16 2011

city: paris

first: Moussa

last: BENHAMED

address: Institut pasteur

country: France

institute: Institut Pasteur

summary: Senescence in WI-38 cell context was induce by RASv12 over expression Cellular senescence is a permanent cell cycle arrest that is triggered by cancer-  initiating or promoting events in mammalian cells and is now considered a major tumour suppressor mechanism. Here, we did a transcriptomic analysis and compared WI-38 contol wich is a human fibroblaste cell line and WI-38 that overexpressed RASv12  a G protein that induce senescence. The goal of our project is to compare transciptomic profile of human growing fibroblast (WI-38 control) and senescent human fibroblast (WI-38 OERAS)

overall_design: Comparaison WI-38 vs WI-38 OE RAS

first: Oliver

last: Bischof


title: Gene Expression Profile of 57 human T-ALL samples collected in human clinical trial E2993 (Marks et al., 2009)

status: Public on Nov 05 2011

first: Alberto

last: Ambesi-Impiombato

address: 1130 St. Nicholas Avenue

department: ICG

institute: Columbia University

summary: Analysis of microarray gene expression signatures in adult T-ALL demonstrated a high prevalence of early immature leukemias and revealed a close relationship between these tumors and myeloid leukemias.

overall_design: 57 adult T-ALL samples were analyzed

first: Pieter

last: Van Vlierberghe

first: Arianne

last: Perez-Garcia

first: Erika

middle: J

last: Haydu

first: Isaura

last: Rigo

first: Michael

last: Hadler

first: Valeria

last: Tosello

first: Giusy

last: Della Gatta

first: Elisabeth

last: Paietta

first: Janis

last: Racevskis

first: Peter

middle: H

last: Wiernik

first: Jacob

middle: M

last: Rowe

first: Montserrat

last: Rue

first: Adolfo

middle: A

last: Ferrando


title: Expression data from human skin exposed to solar-simulated radiation with or without sunscreen

status: Public on Oct 19 2011

city: Bethesda

first: Atsushi

last: Terunuma

state: MD

address: 37 Convent Drive, 37/3050

department: Dermatology Branch

institute: National Cancer Institute

summary: Despite widespread use of sunscreens that minimize erythema by blocking ultraviolet B (UVB) radiation, incidence rates of melanoma continue to rise.  In considering this disparity between intervention and disease prevalence, we investigated the in vivo transcriptome of human skin treated with sunscreen and solar-simulated radiation (ssR).  A focal skin area of healthy participants was exposed to ssR at 1 minimal erythema dose (MED), 0.1 MED or 100 J/m2 with or without prior application of sunscreen, or to non-UVB-spectrum of ssR (solar-simulated UVA/visible/infrared radiation: ssA).  Skin biopsies were analyzed using expression microarrays.

overall_design: Ninety-eight microarrays from 14 healthy human volunteers were analyzed.  Focal skin areas of all 14 volunteers were exposed to 0 J/m2, 100 J/m2, 1 minimal erythema dose (MED), and 0.1 MED of solar-simulated radiation (ssR).  Eight of the 14 volunteers (Group 1) were also exposed to ssA (ssR minus UVB) that were generated by removing UVB from 0 J/m2, 100 J/m2, 1 minimal erythema dose (MED), and 0.1 MED of ssR.  Additionally, 6 of the 14 volunteers (Group 2) were treated with sunscreen of sun protection factor (SPF) 15, and exposed to 0 J/m2, 100 J/m2, 1 minimal erythema dose (MED), and 0.1 MED of ssR.  Biopsy was taken 24 hours after exposure from each focal skin area for RNA extraction.

first: Christine

middle: L

last: Tock

first: Lexa

middle: R

last: Turner

first: Jonathan

middle: C

last: Vogel


title: Gene Expression Array of Human Ovarian Cancer.

status: Public on Oct 17 2011

city: Cold Spring Harbor

first: Kazimierz

middle: O.

last: Wrzeszczynski

address: One Bungtown Rd.

institute: Cold Spring Harbor Laboratory

summary:
The identification of genetic and epigenetic alterations from primary tumor cells has become a common method to identify genes critical to the development and progression of cancer. We provide a bioinformatic analysis of copy number variation and DNA methylation covering the genetic landscape of ovarian cancer tumor cells. We individually examined the copy number variation and DNA methylation for 44 primary ovarian cancer samples and 7 ovarian normal samples using our MOMA-ROMA technology and Affymetrix expression data as well as 379 tumor samples analyzed by The Cancer Genome Atlas. We have identified 346 genes with significant deletions or amplifications among the tumor samples. Utilizing associated gene expression data we predict 156 genes with significantly altered copy number and correlated changes in expression. We identify changes in DNA methylation and expression for all amplified and deleted genes. We predicted 615 potential oncogenes and tumor suppressors candidates by integrating these multiple genomic and epigenetic data types.
Expression data accompaniment to CSHL ROMA and MOMA3 human ovarian analysis.

overall_design: Correlation of expression to Methylation and Copy Number Variation in ovarian cancer.

first: Robert

last: Lucito

first: Douglas

last: Levine

middle: O

first: Elena

last: Lum

first: Faina

last: Bogomolniy

first: Jeff

last: Boyd

first: Agnes

last: Viale


title: Effects of E. coli Shiga toxin on the gene expression profile of human microvascular endothelial cells

status: Public on Oct 11 2011

city: Toronto

first: Philip

last: Marsden

state: ON

address: Li Ka Shing Knowledge Institute, St. Michael's Hospital 209 Vicotria St, rm 526

department: Faculty of Medicine

country: Canada

institute: University of Toronto

summary: Changes in endothelial phenotype induced by E. coli-derived Shiga toxins (Stx) are believed to play a critical role in the pathogenesis of hemolytic uremic syndrome. Stx inactivate host ribosomes, but also alter gene expression at concentrations that minimally affect global protein synthesis. The effect of Stx on the gene expression profile of human microvascular endothelial cells was examined using the Affymetrix HG-U133A platform.  Data were processed using 13 different methods and revealed 369 unique differentially expressed genes, 318 of which were up-regulated and 51 of which were down-regulated.  These studies implicated activation of the CXCR4/CXCR7/SDF-1 chemokine pathway in Stx-mediated pathogenesis.

overall_design: Primary human dermal microvascular endothelial cells were treated with vehicle or Shiga toxin (10 fM, 24 h, n = 6) and changes in steady-state mRNA levels were determined by hybridization to Affymetrix HG-U133A arrays

first: Tania

middle: N

last: Petruzziello

first: Charles

last: Matouk


title: Characterization of Human Induced Pluripotent Stem Cell Lines Derived from Neonatal and Adult Human Dermal Fibroblasts

status: Public on Oct 04 2011

city: Frederick

first: Jack

last: Chen

address: SAIC-Frederick Miller Dr

institute: NIH

summary: Somatic cells can be reprogrammed to Induced Pluripotent Stem Cells (iPSCs) by expressing four transcription factors, Oct4, Sox2, Klf4 and c-Myc. Co-expressing Rarg (retinoic acid receptor gamma) and Lrh-1 (liver receptor homolog 1, Nr5a2) with the four factors greatly accelerated reprogramming so that reprogramming of mouse embryonic fibroblast cells (MEFs) to ground state iPSCs requires only four days’ induction of these six factors. The six-factor combination readily reprogrammed primary human neonatal and adult fibroblast cells to exogenous-factor-independent iPSCs, which resembled ground state mouse ES cells in growth properties, gene expression and signalling dependency. Our findings demonstrate that signalling through RARs has critical roles in molecular reprogramming and the synergistic interaction between Rarg and Lrh1 directs reprogramming towards ground state pluripotency.

overall_design:
SH-iPS20-1, -3 and -9 lines were derived from HDFa (439656), SH-iPS24-1, -2 and -11 lines were derived from HDFa (709590), and SH-iPS28-23, -25 and -27 lines were derived from HDFn (617769). Parental HDF lines were used as control.
SH-iPS15-5 and -10 lines were derived from HDFn (617769, Invitrogen). H1 hESC were obtained from Wicell (Madison, USA). SH-iPSCs were cultured in both 2i+LIF and FGFconditions. Expression pattern of SH-iPSCs was compared to H1 hESC cultured in FGF conditions. S1, S2 and S3 are three indpendent subcultures of a cell line.

first: Wei

last: Wang

first: Xiongfeng

first: Pentao

last: Liu


title: Impact of RAP2.12 alterations on gene expression in hypoxic and aerobic conditions

status: Public on Oct 14 2011

city: Pisa

first: Francesco

last: Licausi

address: Via Mariscoglio 34

department: Institute of Life Sciences

country: Italy

institute: Scuola Superiore Sant'Anna

summary:
In this study we analyzed the effect of overexpression of an HA-tagged version of the ERF RAP2.12 on the transcriptome levels in aerobic and hypoxic-treated (O2 21% and 1%, respectively) Arabidopsis thaliana rosettes.
We also analyzed the effect of a RAP2.12 and RAP2.2 simultaneous silencing in aerobic and hypoxic-treated (O2 21% and 1%, respectively) Arabidopsis thaliana rosettes.

overall_design:
We treated Arabidopsis Col-0 (wt) rosettes and transgenic HA::RAP2.12 and amiRAP2.2-12 , 5-week old, grown in 8/16 light/dark photoperiod with:
-Control (22°C, dark, 21% O2, 1.5h).
-Hypoxia (22°C, dark, 1% O2, 1.5h).

first: Federico

last: Giorgi

first: Joost

middle: T

last: van Dongen


title: Comparison of salt stress resistance genes in transgenic Arabidopsis thaliana indicates that extent of transcriptomic change may not predict secondary phenotypic or fitness effects

status: Public on Oct 06 2011

city: Wuhan

first: Zhulong

last: Chan

state: Hubei

address: Wuchang District, Moshan

country: China

institute: Wuhan Botanic Garden, Chinese Academy of Sciences

summary:
Engineered abiotic stress resistance is an important target for increasing agricultural productivity.There are concerns, however, regarding possible ecological impacts of transgenic crops. In contrast to the first wave of transgenic crops, many abiotic stress resistance genes can initiate
complex downstream changes. Transcriptome profiling has been suggested as a comprehensive non-targeted approach to examine secondary effects. We compared phenotypic and transcriptomic effects of constitutive expression of genes intended to confer salt stress tolerance by three different mechanisms: a transcription factor, CBF3/DREB1a; a metabolic gene, M6PR,
for mannitol biosynthesis; and the Na+/H+ antiporter, SOS1. Transgenic CBF3, M6PR, and SOS1 Arabidopsis thaliana were grown together in the growth chamber, greenhouse and field. In the absence of salt, M6PR and SOS1 lines performed comparably to wild type; CBF3 lines exhibited dwarfing as reported previously. All three transgenes conferred fitness advantage when subjected to 100 mM NaCl in the growth chamber. CBF3 and M6PR affected transcription of numerous abiotic stress- related genes as measured by Affymetrix microarray analysis. M6PR additionally modified expression of biotic- and oxidative- stress genes. Transcriptional effects of SOS1 in the absence of salt were smaller and primarily limited to redox-related genes. The extent of transcriptome change, however, did not correlate with effects on growth and reproduction. Thus, magnitude of global transcriptome differences may not predict phenotypic differences upon which environment and selection act to influence fitness. These observations have implications for interpretation of transcriptome analyses in the context of risk assessment and emphasize importance of evaluation within a phenotypic context.

overall_design: Both transgenic plants and relative WT plants were grown in the growth chamber in the absence and presence of salt stress. Plants from 20 days after sowing (6 days after salt treatment) were used for RNA extraction and hybridization on Affymetrix microarrays. There were two biological replicates for each genotype and salt treatment combination.

first: Wayne

last: Loescher

first: Rebecca

last: Grumet


title: Expression profiling of RBM38-knocked down and control MCF7 cells with and without doxorubicin treatment

status: Public on Oct 01 2011

city: Tel Aviv

first: Ran

last: Elkon

address: Ramat Aviv

department: Human Genetics

country: Israel

institute: Tel Aviv University

summary: Gene expression analysis of MCF-7 cells transfected with a scramble or RBM38 siRNA and incubated with or without doxorubicin. The hypothesis tested in the present study was to assess the impact of RBM38 depletion on gene expression of normal growing and doxorubicin-stressed MCF-7 cells. Results provide information about doxorubicin and/or RBM38-responsive genes.

overall_design: Total RNA obtained from isolated MCF-7 cells transfected with a scramble or RBM38 siRNA (72h) and incubated with or without doxorubicin (24h).

first: Nicolas

last: Léveillé

first: Reuven

last: Agami


title: Arabidopsis root Fe deficiency transcriptome

city: Lincoln

first: Brian

last: Waters

state: Nebraska

address: 279 Plant Sciences Hall

department: Agronomy and Horticulture

institute: University of Nebraska-Lincoln

summary:
Fe deficiency stimulates a coordinated response involving reduction, transport and redistribution of Fe in the roots. The expression of genes regulated by Fe deficiency in the two contrasting Arabidopsis thaliana ecotypes, Tsu-1 and Kas-1, shows that different ecotypes can respond in diverse ways, with different Fe regulated overrepresented categories.
We use microarrays to analyze the Fe deficiency responses of contrasting Arabidopsis thaliana ecotypes (Tsu-1 and Kas-1).

overall_design: Arabidopsis thaliana roots from the Kas-1 and Tsu-1 ecotypes were exposed to complete or -Fe nutrient solutions and collected after 24 and 48 h for RNA extraction and hybridization on Affymetrix microarrays. Experiments were done using three biological replicates.

first: Ricardo

last: Stein


title: Identification of Tumor Suppressors and Oncogenes from Genomic and Epigenetic Features in Ovarian Cancer

first: Kazimierz

last: Wrzeszczynski

type: Methylation profiling by genome tiling array

type: Genome variation profiling by genome tiling array

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

overall_design: Refer to individual Series


title: Gene expression analysis of interspecific and intraspecific Y chromosome introgessions in Drosophila simulans

status: Public on Sep 30 2011

city: Cambridge

first: Timothy

last: Sackton

state: MA

address: 16 Divinity Ave

department: Organismic and Evolutionary Biology

institute: Harvard University

summary: These arrays measure gene expression across eight Y introgression lines in Drosophila simulans. Four lines (Ya19, Ya23, Ya24, Ya26) carry a D. simulans Y chromosome (from a Cameroon population) and four lines (Sec01, Sec03, Sec08, Sec27) carry a D. sechellia Y chromosome. All lines are otherwise identical with a D. simulans background (UCSD stock center line 14021-0251.092).

overall_design: Four biological replicates of each of eight lines, plus two technical replicates (dye swap), for a total of 32 arrays. Full methods are described in the accompanying publication.

first: T

middle: B


title: Expression data from transfected IB3 cells transfected with CFTR mutants

city: Baltimore

first: Jerry

middle: M.

last: Wright

address: 725 N. Wolfe St

department: Physiology

institute: Johns Hopkins Medical Institutions

summary:
CFTR plasmid constructs were transfected in CF Bronchial IB3 cell cultures using Lipofectamine 2000™.  Global gene mRNA expression profiles at 48 hr after transfection were created with the Affymetrix U133 chip set.
We used microarrays to detail the global changes in gene expression occuring as a result of transfecting cells.

overall_design: CFTR mutants and wild type transfected IB3 cells vs. non-transfected IB3 cells

first: Liudmila

last: Cebotaru

first: Valeriu

first: William

last: Guggino


title: Vreteno, a gonad-specific protein, is essential for germline development and primary piRNA biogenesis in Drosophila

status: Public on Sep 29 2011

city: LYON

first: Jiri

last: ZAVADIL

state: Other

address: 150 COURS ALBERT THOMAS

institute: IARC WHO

summary:
In Drosophila, Piwi proteins associate with Piwi-interacting RNAs (piRNAs) and protect the germline genome by silencing mobile genetic elements. This defense system acts in germline and gonadal somatic tissue to preserve germline development. Genetic control for these silencing pathways varies greatly between tissues of the gonad. Here, we identified Vreteno (Vret), a novel gonad-specific protein essential for germline development. Vret is required for piRNA-based transposon regulation in both germline and somatic gonadal tissues. We show that Vret, which contains Tudor domains, associates physically with Piwi and Aubergine (Aub), stabilizing these proteins via a gonad-specific mechanism, absent in other fly tissues. In the absence of vret, Piwi-bound piRNAs are lost without changes in piRNA precursor transcript production, supporting a role for Vret in primary piRNA biogenesis. In the germline, piRNAs can engage in an Aub/Argonaute 3 (AGO3)-dependent amplification in the absence of Vret, suggesting that Vret function can distinguish between primary piRNAs loaded into Piwi/Aub complexes and piRNAs engaged in the amplification cycle. We propose that Vret acts at an early step in primary piRNA processing where it plays an essential role in transposon regulation.
These studies show that vreteno (vret) has a role in germline development and primary piRNA regulation in Drosophila.

overall_design: Transposable element expression profiles from Drosophila ovaries mutant for vreteno, piwi and aubergine were compared using genome-wide mRNA expression profiling by Affymetrix GeneChip arrays (Drosophila 2.0). Key targets were validated by qPCR experiments.

first: Andrea

last: Zamparini

first: Marie

middle: Y

last: Davis

first: Colin

middle: D

last: Malone

first: Eric

last: Vieira

last: Zavadil

first: Ravi

last: Sachidanandam

first: Gregory

last: Hannon

first: Ruth

last: Lehmann


title: THE GENE EXPRESSION PROFILE CHANGES OF HUMAN MEIBOMIAN GLAND EPITHELIAL CELLS UNDER DIFFERENTIATION

status: Public on Sep 28 2011

city: Boston

first: David

last: Sullivan

address: 20 Staniford Street

institute: Schepens Eye Research Institute

summary: Analysis of gene expression profile changes of immortalized human meibomian gland epithelial cells under differentiation. Results provide important information of the response of human meibomian gland epithelial cells to different differentiation media, such as serum containing medium, serum-free medium, serum-free medium with 1.2mM Ca2+.

overall_design: Primary cultured human meibomian gland epithelial cells and hTERT immortalized human meibomian gland epithelial cells (3 cells/condition/experiment) were grown in keratinocyte serum-free medium (SFM, Invitrogen-Gibco, Grand Island, NY) on 75cm2 to reach confluence, then change to SFM, SFM with 1.2mM Calcium, or serum containing medium (10% fetal bovine serum in  an equal volume of DMEM and Ham’s F12 with 10ng/ml EGF) for 14 days. Total RNA was extracted from the above cultures. Gene expression was analyzed using Illumina HumanHT-12 v3 Expression Beadchips (San Diego, CA).

first: Shaohui

last: Liu

first: Stephen

last: Richards


title: Gene expression of Ewing tumor cell line SBSR-AKS

city: Halle (Saale)

first: Martin

middle: Sebastian

last: Staege

state: Sachsen-Anhalt

address: Ernst-Grube-Str. 40

department: Universitätsklinik u. Poliklinik für Kinder- u. Jugendmedizin

country: Germany

summary:
Ewing tumor cell line SBSR-AKS grows adherent to the culture vessel. A spontaneously derived sub-line of cell line SBSR-AKS shows growth in suspension.
We used microarrays to analyse gene expression in these Ewing tumor cell lines

overall_design: Established Ewing tumor cell lines were grown under standard conditions

first: Anette

last: Fasan

first: Sabine

last: Rössler

middle: S

first: Stefan

last: Burdach

first: Guenther

last: Richter


title: Genomics of oral cancer cells

status: Public on Oct 05 2011

city: Vienna

first: Boban

last: Erovic

address: Waehringer Guertel 18-20

country: Austria

institute: MUW

summary:
Dynamic changes in RNA and protein levels after exposure to 100µmol/L nimesulide and low-dose 0.5µmol/L cisplatin in oral cancer cells were screened to gain insights into the molecular mechanisms of cell death. After 48 hours of treatment, SCC9 and SCC25 cells were analyzed for apoptosis and necrosis by FACS, immunohistochemistry and analysis of nucleotides by HPLC. Microarray GeneChips and the iTRAQ system were used to measure changes in the whole genome and proteome.
FACS and immunohistochemical analyses showed an increased number of apoptotic and necrotic SCC9 and SCC25 cells after nimesulide and cisplatin exposure. Simultaneously, ATP and the energy charge of the SCC9 cells were significantly decreased. In SCC25 cells, ATP only significantly decreased after combined nimesulide/cisplatin exposure. In the SCC9 cell line, gene and proteome analysis detected and quantified one gene, keratin 6a and 540 proteins, respectively. After combined treatment, significant upregulation of histone H2A, H2B and H4 could be found with a local discovery false rate of 0.003 and 0.0027 for histone H2A and histone H2B, respectively.
Using gene and proteome mapping, we could show that combined treatment of oral cancer cells with nimesulide and low-dose cisplatin induce necrosis and early apoptosis by the intrinsic and extrinsic pathways. Our results suggest potential clinical benefits of a nimesulide/cisplatin combination rather than single cisplatin treatment for oral cancer patients.

overall_design:
Cell culture:
A squamous carcinoma cell line of the tongue, SCC9, was obtained from the American Type Culture Collection (ATCC, Rockville, Maryland, USA). The cell line was cultured in RPMI 1640 medium containing 10% fetal bovine serum and 100U/mL penicillin and 100µg/mL streptomycin (all reagents from Life Technologies Ltd, Paisley, Scotland) and incubated at 37°C in a humidified atmosphere of 5% CO2.
SCC9 cells were maintained in RPMI 1640 medium and seeded at equal densities of 5x10^5 cells in 10cm tissue culture dishes. 24 hours later, cells were harvested using Trypsin/EDTA (Life Technologies Ltd, Paisley Scotland) and treated with 100µmol/L nimesulide, 0.5µmol/L cisplatin or a combination of nimesulide/cisplatin. Control dishes were treated in exactly the same way without the addition of the respective compound. The concentration of 100µmol/L for nimesulide was chosen as this concentration is in a pharmacologically relevant range for humans.

cDNA microarray, hybridization and image analysis:
RNA isolation and preparation of cRNA, hybridization, and scanning of the arrays were performed according to protocols of the manufacturer. Hybridization was done using three sets of human U133A GeneChips (Affymetrix, Ca, USA); only two nimesulide/cisplatin Samples are included in this submission. The arrays were scanned using the GeneArray scanner (Affymetrix). Data normalization was performed using RMA.

The supplementary file 'GSE15308_sample_protocols.txt' contains detailed Sample protocols.


title: The pioneer factor PBX1 guides a distinct ERa signaling in breast cancer [mRNA profiling]

city: Lebanon

first: luca

last: magnani

state: NH

address: NCCC one medical drive

department: Genetics

institute: Dartmouth College

summary: Effect of PBX1 silencing on global gene expression of MCF7 cells stimulated with estradiol. The hypothesis tested was that PBX1 is essential for estrogen signaling in ERa positive breast cancer cells.

overall_design: Total RNA was obtained from MCF7 cells treated with siRNA directed at PBX1 or an siControl for 72h. Cells were then stimulated with estradiol (E2) for 3h prior to RNA extraction.

first: Luca

last: Magnani

first: Mathieu

last: Lupien


title: The MOF-containing NSL complex associates globally with housekeeping genes, but activates only a defined subset

status: Public on Oct 29 2011

city: Munich

first: Christian

last: Feller

address: Schillerstraße 44

department: Molecular Biology

institute: Adolf-Butenandt Institute at the LMU University Munich

type: Genome binding/occupancy profiling by genome tiling array

first: Peter

last: Becker


title: Post-fasting olfactory, transcriptional, and feeding responses in Drosophila

status: Public on Sep 24 2011

city: New York

first: Mayte

last: Suarez-Farinas

address: 1425 Madison Ave, L2-70C, Box 1077,

institute: Mount SinaiSchool of Medicine

summary: The sensation of hunger after a period of fasting and the sensation of satiety after eating is crucial to behavioral regulation of food intake, but the biological mechanisms regulating these sensations are incompletely understood. We studied the behavioral and physiological adaptation to fasting in the vinegar fly (Drosophila melanogaster). Here we show that flies demonstrated increased behavioral attraction to food odor when food-deprived with no corresponding increase in sensitivity in the peripheral olfactory system. Flies increased their food intake transiently in the post-fasted state, but returned to a stable baseline feeding level within 24 hr after return to food. This modulation in feeding was accompanied by a significant increase in the size of the crop organ of the digestive system, suggesting that fasted flies responded both by increasing their food intake and storing reserve food in their crop. The post-fasting feeding response was observed in both male and female flies of diverse genetic backgrounds. Expression profiling of head, body, and chemosensory tissues by microarray analysis revealed several hundred genes that are regulated by feeding state, including 247 genes in the fly head. We performed RNA interference-mediated knockdown of, takeout, one of the genes strongly downregulated by fasting in multiple tissues. When takeout was knocked down in all neurons the post-fasting feeding response was abolished. These observations suggest that a coordinated transcriptional response to internal physiological state may regulate both ingestive behaviors and chemosensory perception of food

overall_design: 6 Pool of flies were used for this experiment. For each pool, samples were taken at 0,24 and 48h and separated in each body part. 56 samples were used for the analysis.

first: Shelli

last: Farhadian

first: Leslie

last: Voshall


title: Induction of epididymis specific G-protein coupled receptor-64 (GPR64) in Ewing Tumors supports invasiveness and metastatic spread

summary: Metastatic spread in Ewing Tumors (ET) is hematogenous and malignant features have been shown to correlate with hypoxia and angiogenesis. We identified several Ewing tumor specific genes (Staege MS et al. Cancer Res. 2004;64:8213-21). Microarray analysis confirmed an endothelial signature of this tumor and revealed the G-protein coupled receptor-64 (GPR64), an orphan receptor with normal expression restricted to human epididymis, to be highly induced in ET. Down-regulation of GPR64 in ET lines by RNA interference did not reduce their proliferative capacity in vitro as measured by plastic adherence dependent proliferation or contact independent growth in colony forming assays. Of interest inhibition of GPR64 expression in ET cell lines resulted in impaired endothelial differentiation in tube formation assays. Furthermore, GPR64 suppression substantially inhibited tumor growth and metastatic spread in immunodeficient Rag2-/-gammaC-/- mice. Microarray analysis of ET after GPR64 knock down revealed a GPR64-mediated induction of VEGF receptor 1 ligand placental growth factor (PGF) in ET. PGF itself was induced by EWS-FLI1 in mesenchymal stem cells. Repression of PGF expression in ET cell lines resulted in a similar phenotype as observed after GPR64 knockdown. GPR64 as well as PGF knock down correlated with a reduced proteolytic activity of Matrix Metalloproteinase MMP1 and invasiveness in vitro. MMP1 specific knock down resulted in the abrogation of metastasis of ET in Rag2-/-gammaC-/- mice. We conclude, that GPR64 and subsequent PGF up-regulation in ET orchestrate and promote endothelial invasiveness and metastatic spread and play a pivotal role in the pathogenesis and aggressiveness of this tumor.

overall_design: Established Ewing tumor cell lines were transfected with siRNA with specificity for CHM1 (control) or GPR64. RNA was extracted and hybridized with Affymetrix HG_U133A microarrays.


title: Expression data from paired matched breast cancer Fine needle aspiration (FNA) or Core needle biopsies (CBX)

status: Public on Oct 31 2011

city: Houston

first: TAKAYUKI

last: IWAMOTO

state: TX

address: 1515 Holcombe Blvd

department: Breast medical Oncology

institute: UT MD Anderson

summary:
Paired FNA and CBX specimens were prospectively collected from 37 breast cancers before any systemic therapy during a biomarker discovery study at The University of Texas M. D. Anderson Cancer Center.
We identified 293 probe sets overexpressed in core biopsies; these included five highly  coexpressed gene clusters (metagenes) corresponding to immune functions and extracellular  matrix components.
We compared gene expression profiles of pairs of fine-needle (stroma-poor) and core-needle (stroma-rich) biopsies from 37 cancers to identify stroma-associated genes

overall_design: Pre-treatment paird matched FNA and CBX from primary tumors were obtained and RNA extracted and hybridized to afymetrix microarrays according to manufacturer protocol.

first: Lajos

last: Pusztai

first: Giampaolo

last: Bianchini

first: Yuan

last: Qi

first: Takayuki

last: Iwamoto


title: Dual Role of FoxA1 in Androgen Receptor Binding to Chromatin, Androgen Signaling and Prostate Cancer [Expression Array]

status: Public on Sep 14 2011

city: Helsinki

first: Olli

middle: A.

last: Jänne

department: Inst. of Biomedicine/Physiology

country: Finland

institute: University of Helsinki

summary: We report the dual role of FoxA1 in androgen receptor recruitment to the chromatin of androgen responsive prostate cancer cell line LNCaP-1F5 using ChIP-sequencing. Depletion of FoxA1 reprograms both androgen and glucocorticoid receptor recruitment and subsequent gene expression. The ChIP-seq has been performed using AR, FoxA1, GR, H3K4me2 antibodies. We have also mapped the DNaseI-hypersensitive sites (DHS) using deep sequencing.

overall_design: LNCaP-1F5 cells were depleted of FoxA1 using siRNAs. Parental cells and FoxA1 depleted cells (siFoxA1) were treated with vehicle or 100 nM DHT or (100 nM DEX) for 24 hours followed by RNA isolation and hybridization to Illumina arrays. All the experiments have been performed in biological duplicates. Parental cells treated with DHT (or DEX) were analyzed for differentially expressed genes compared to vehicle treated parental cells. Similarly siFoxA1 cells treated with DHT (or DEX) were analyzed for differentially expressed genes compared to vehicle treated siFoxA1 cells.

first: Biswajyoti

last: Sahu

first: Marko

last: Laakso

first: Kristian

last: Ovaska

first: Tuomas

last: Mirtti

first: Johan

last: Lundin

first: Antti

last: Rannikko

first: Anna

last: Sankila

first: Juha-Pekka

last: Turunen

first: Mikael

first: Juho

last: Konsti

first: Tiina

last: Vesterinen

first: Stig

last: Nordling

last: Kallioniemi

first: Sampsa

last: Hautaniemi


title: Expression data for primary localized prostate cancer versus castration-resistant bone metastatic prostate cancer

status: Public on Sep 22 2011

first: Changmeng

last: Cai

address: 330 Brookline Avenue

department: hematology-oncology

institute: Beth Israel Deaconess Medical Center

summary:
We compared 22 primary Pca (hormone-dependent) versus 29 metastatic Pca (CRPC). The expression of genes related to cell cycle, proliferation, DNA synthesis, and androgen metablism are significantly increased in CRPC group. The expression of AR-stimulated genes were partially reactivated.
TMPRSS2-ERG fusion status was determined for the samples by PCR. The expression of ERG was highly increased in fusion positive versus negative.

overall_design: 120 snap-frozen CT-guided bone marrow biopsies from patients with castration-resistant prostate cancer were collected as a source of material. 29 independent biopsies containing mostly tumor were identified as CRPC group through carefully microscopical examination. 4 samples containing no tumor were identified as normal bone marrow group. Primary tumor was isolated by LCM from frozen biopsies of hormone-naive patients. 22 samples were selected as primary PCa group.

first: Michael

last: Stanbrough

first: Phillip

middle: G

last: Febbo

first: Steven

middle: P

last: Balk


title: Prognostic DNA Methylation Patterns in Cytogenetically Normal Acute Myeloid Leukemia are predefined by Stem Cell Chromatin Marks [gene expression]

status: Public on Sep 07 2011

city: Stockholm

first: Stefan

last: Deneberg

department: Internal medicine/Huddinge

institute: Karolinska Institutet

summary: GEP of 10 diagnostic bone marrow samples of CN-AML used to correlate promoter DNA methylation to mRNA levels.

overall_design: Ficoll separated MNC

first: Sören

last: Lehmann


title: Molecular Organization of Drosophila Neuroendocrine Cells by DIMMED: Global Profiling of Pan-Neuronal DIMMED Expression Effects

status: Public on Sep 06 2011

city: Saint Louis

first: Tarik

last: Hadzic

state: MO

address: 660 S. Euclid Ave

department: Psychiatry

institute: Washington University in St Louis School of Medicine

summary: To amass candidate DIMM targets in addition to Phm (Park et al., 2008a), we used genome-wide microarray profiling by over-expressing DIMM throughout the embryonic nervous system. We compared profiles from experimental (elav>dimm) and control (elav-GAL4) embryos at 22-26 hr and 28-32 hr after egg laying (AEL). The design was intended to identify transcripts consistently up-regulated shortly after the induction of DIMM; in so doing, we could circumvent the lethality that ensues in late embryonic, and/ or by early larval stages, due to pan-neuronal DIMM expression.

overall_design:
Eight microarrays were used to hybridize cDNAs from experimental dimm::myc-expressing and control flies, sampled at two different embryonic stages. Four microarrays were hybridized with cDNA from the dimm::myc-expressing embryos of genotype w;UAS-dimm2A3/+;elav-GAL4/+; (prefix 'ED'). Another four microarrays were hybridized with cDNAs from the control (maternal) strain: w;;elav-GAL4 (prefix 'E'). Samples ED3 and ED4, E3 and E4 were hybridized with cDNA from stage 14 embryos (24-26hr development at 18C). Samples ED1 and ED2, E1 and E2 were hybridized with cDNA from stage 16 embryos (28-32 hr old embryos at 18C). A pair of GeneChip Drosophila Genome 2.0 arrays (Affymetrix Co., Santa Clara, CA) were tested with each RNA sample (two experimental and two control, for each of two time points).
Affymetrix GeneChip Drosophila Genome 2.0 Array

first: Dongkook

last: Park

first: Paul

last: Taghert


title: Formalin Fixation at Low Temperature Better Preserves Nucleic Acid Integrity

status: Public on Sep 05 2011

city: Candiolo

first: Enzo

last: Medico

state: TO

address: Strada Prov. 142, km 3,95

department: Oncology

institute: Candiolo Cancer Institute, University of Torino

summary:
INTRODUCTION. Fixation with formalin, a widely adopted procedure to preserve tissue samples, leads to extensive degradation of nucleic acids and thereby compromises procedures like microarray-based gene expression profiling. We hypothesized that RNA fragmentation is caused by activation of RNAses during the interval between formalin penetration and tissue fixation. To prevent RNAse activation, a series of tissue samples were kept under-vacuum at 4°C until fixation and then fixed at 4°C, for 24 hours, in formalin followed by 4 hours in ethanol 95%.
RESULTS. The cold-fixation (CF) procedure preserved DNA and RNA, so that RNA segments up to 660 bp were efficiently amplified. Histological and immunohistochemical features were fully comparable with those of standard fixation. Microarray-based gene expression profiles were comparable with those obtained on matched frozen samples for probes hybridizing within 700 bases from the reverse transcription start site. In conclusion, CF preserves tissues and nucleic acids, enabling reliable gene expression profiling of fixed tissues.

overall_design: Thirty samples from human cancers processed in different ways before RNA extraction: (i) Fresh-Freezing (FF), (ii) Standard Fixation with formalin (SF), (iii) Cold-Fixation (CF), a new formalin fixation procedure preserving nucleic acids. The first six samples compare CF with SF and FF in one colorectal cancer (CRC) specimen and one breast cancer (BRCa) specimen. The subsequent 24 samples compare only CF with FF in various cancer specimens. Expression data are neither normalized nor backound subtracted to preserve the original signal distribution for each sample, which is essential to compare expression profiles obtained after different tissue preservation methods.

last: Sapino


title: Investigation of Isogenic Human Embryonic Stem Cells and Derived Induced Pluripotent Stem Cells and Differentiated Line

status: Public on Sep 03 2011

city: London

first: Jonathan

middle: H

last: Teichroeb

state: Ontario

address: 1151 Richmond St.

department: Physiology and Pharmacology

institute: University of Western Ontario

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

summary: Briefly, the well characterized female hES cell line H9 was allowed to differentiate into a clonally purified mortal splanchnopleuric mesodermal somatic cell line EN13. The EN13 line was subsequently virally reprogrammed back to an induced pluripotent state (we term re-H9) using OCT4, SOX2, KLF4 retroviral vectors creating isogenic lines of hESC, hiPSC and mortal cells. Our results reveal several important differences between embryo-derived H9 and the induced re-H9 stem cells.  We find a dysregulation of genes involved in imprinting and altered expression of X-chromosome localized genes in re-H9 cells.

overall_design:
[Expression profiling] 10 Samples: 1 hESC line, 6 isogenic hiPSC lines, 1 non-isogenic hiPSC line, 1 isogenic mortal line, 1 non-isogenic mortal line
Supplementary file contains raw data.

[Genome variation profiling] 6 Samples: 1 hESC line, 4 isogenic hiPSC lines, 1 isogenic mortal line.
Supplementary file contains both raw and processed data (SNP genotype calls were made using the default parameters in Genome Studio and CNV calls were made using the default parameters of the CNV partition plugin in Genome Studio)the following columns for each SNP: Index, Name, Address, Chr, Position, GenTrain Score, Frac A, Frac C, Frac G, Frac T,  and the following columns for each sample: GType, Score, Theta, R, X Raw, Y Raw, X, Y, B Allele Freq, Log R Ratio, Top Alleles

first: Homayoun

last: Vaziri


title: Ovarian Cancer Dataset

status: Public on Oct 03 2011

city: Tampa

last: Eschrich

state: FL

address: 12902 Magnolia Drive

department: Biostatistics & Bioinformatics

institute: Moffitt Cancer Center

summary:
Background. Genome-wide expression changes are associated with development of chemoresistance in patients with ovarian cancer (OVCA); the BCL2 antagonist of cell death (BAD) apoptosis pathway may play a role in clinical outcome.
Methods.  We analyzed specimens and/or genomic data from 1,406 patients and 116 cancer cell lines.  Genome-wide expression changes and cisplatin-resistance were evaluated in OVCA cell lines subjected to a total of 144 (cisplatin)-treatment/recovery cycles. Pathway analysis was performed on genes associated with increasing cisplatin-resistance.  BAD protein phosphorylation was studied in patient samples and cell lines, and small interfering RNAs (siRNA) used to explore the pathway as a therapeutic target. We evaluated the influence of BAD-pathway expression on chemosensitivity and/or clinical outcome using genomic data from 60 human cancer cell lines and ovarian, breast, colon, and brain cancers from 1,258 patients.
Results.  The BAD pathway was associated with evolution of OVCA cell line cisplatin-resistance (P<0.001) and resistance of 7 human cancer cell types to 8 cytotoxic agents (P<0.05).  OVCA chemoresistance was associated with BAD protein phosphorylation, and targeted siRNA modulation produced corresponding changes in chemosensitivity. Expression of a 47-gene BAD-pathway signature was associated with survival of 1,258 patients with ovarian, breast, colon, and brain cancer.  The OVCA BAD-pathway signature survival advantage was independent of surgical cytoreductive status.
Conclusions.  The BAD apoptosis pathway influences the sensitivity of human cancers to a variety of chemotherapies, likely via modulation of BAD-phosphorylation.  The pathway has clinical relevance as a potential biomarker of therapeutic response, patient survival, and as a promising therapeutic target.

overall_design: Twenty-eight (28) advanced-stage serous epithelial ovarian cancers were resected at the time of primary surgery from patients who would receive platinum-based therapy. The tumors were arrayed on Affymetrix HG-U133A GeneChips. The samples were analyzed with respect to the BAD pathway for correlation to overall survival and cisplatin response.

first: Douglas

last: Marchion

first: Johnathan

last: Lancaster


title: MSKCC-A Primary Lung Cancer Specimens

city: Dallas

first: Luc

last: Girard

address: 5323 Harry Hines Blvd

department: Hamon Center for Therapeutic Oncology Research

institute: UT Southwestern Medical Center

summary: Develop an EGFR mutation gene expression signature to aid in predicting response and clinical outcome and to identify genes associated with the EGFR-dependent phenotype

overall_design: 30 primary lung adenocarcinomas and 20 adjacent normal lung controls were analyzed with Affymetrix U133A

first: John

last: Minna

first: William

middle: L

last: Gerald

first: Pierre

last: Saintigny

first: Li

last: Zhang


title: Expression data from stem samples taken from the base and the first internode of Arabidopsis wildtype and wox4-1 plants

first: Stefanie

last: Suer

address: Dr. Bohr-Gasse 3

institute: Gregor Mendel Institute

summary:
Stem samples of wildtype Columbia plants and the wox4-1 mutant (Gabi_462G01) were analyzed in order to draw a connection between general transcriptomic changes during interfascicular formation in the wildtype and WOX4-dependent gene regulation during this process.
We used microarrays to identify factors downstream of WOX4 in the formation of the interfascicular cambium.

overall_design: Transcriptional profiling, comparing wildtype Columbia and wox4-1 plants. RNA was extracted from 3 biological replicates per plant line and sample type (stem base, first internode), each consisting of a pool of 13-17 stem samples.

first: Thomas

last: Greb


title: MSKCC-B Primary Lung Cancer Specimens

overall_design: 30 primary lung adenocarcinomas and 20 adjacent normal lung controls were analyzed with Affymetrix U133B


title: Gene Expression Patterns that Predict Sensitivity to Epidermal Growth Factor Receptor Tyrosine Kinase Inhibitors in Lung Cancer Cell Lines and Human Lung Tumors

status: Public on Sep 01 2011

city: Lexington

first: Esther

last: Black

state: KY

address: 789 S Limestone

department: Pharmaceutical Sciences

institute: University of Kentucky

summary: Global gene expression data were generated from cultured non small cell lung cancer cell lines (NSCLC), normalized using MAS 5.0, filtered and used to predict response of cells to EGFR inhibition

overall_design:
Gene expression data from additional cell lines and tumors was used to validate the predictive algorithm
Total RNA was prepared from NSCLC cell lines and applied to Affymetric U133 2.0 microarrays

first: Justin

middle: M

last: Balko


title: Whole-transcript expression data for liposarcoma

status: Public on Sep 02 2011

first: Brian

last: Denton

address: 307 E. 63rd Street

department: Epidemiology and Biostatistics

institute: Memorial Sloan-Kettering Cancer Center

summary: Liposarcoma is the most common soft tissue sarcoma, accounting for about 20% of cases. Liposarcoma is classified into 5 histologic subtypes that fall into 3 biological groups characterized by specific genetic alterations. To identify genes that contribute to liposarcomagenesis and to better predict outcome for patients with the disease, we undertook expression profiling of liposarcoma. U133A expression profiling was performed on 140 primary liposarcoma samples, which were randomly split into training set (n=95) and test set (n=45). A multi-gene predictor for distant recurrence-free survival (DRFS) was developed using the supervised principal component method. Expression levels of the 588 genes in the predictor were used to calculate a risk score for each patient. In validation of the predictor in the test set, patients with low risk score had a 3-year DRFS of 83% vs. 45% for high risk score patients (P=0.001). The hazard ratio for high vs. low score, adjusted for histologic subtype, was 4.42 (95% confidence interval 1.26-15.55; P=0.021). The concordance probability for risk score was 0.732.  Genes related to adipogenesis, DNA replication, mitosis, and spindle assembly checkpoint control were all highly represented in the multi-gene predictor. Three genes from the predictor, TOP2A, PTK7, and CHEK1, were found to be overexpressed in liposarcoma samples of all five subtypes and in liposarcoma cell lines. Knockdown of these genes in liposarcoma cell lines reduced proliferation and invasiveness and increased apoptosis. Thus, genes identified from this predictor appear to have roles in liposarcomagenesis and have promise as therapeutic targets. In addition, the multi-gene predictor will improve risk stratification for individual patients with liposarcoma.

overall_design: 140 human liposarcoma specimens were profiled on Affymetrix U133A arrays per manufacturer's instructions.

first: R

last: Gobble

first: L

middle: X

last: Qin

first: E

middle: R

last: Brill

first: C

middle: V

last: Angeles

first: S

last: Ugras

last: O'Connor

first: N

last: Moraco

first: P

last: Decarolis

last: Antonescu

last: Singer


title: The transcriptional modulator H2AFY marks Huntington's disease activity in men and mice

city: Cambridge

first: Bin

last: Zheng

address: 65 Landsdowne Street

department: Center for Neurologic Diseases

institute: Brigham and Women's hospital

summary: To accelerate the development of disease-modifying therapeutics for Huntington’s disease (HD), a dynamic biomarker of disease activity and treatment response is critically needed.

overall_design: Venous cellular whole blood from 8 patients with Huntington's disease (HD) and 6 control subjects were collected in PAXgene tubes (Wiagen, Valencia, CA). RNA was isolated from whole blood using  the PAXgene blood RNA kit (Qiagene) with DNase treatment. The biotinylated complementary RNA was fragmented and hybridized to Affymetrix human genome U133A microarrays. The Affymetrix .CEL files were normalized to “all probe sets” in a standardized matter, and scaled to 100 by the MAS5 5.0 algorithm implemented in the Bioconductor package.

first: Clemens

last: Scherzer

first: Yi

last: Hu

first: Zhixiang

last: Liao


title: Drosophila melanogaster gene expression changes after spaceflight.

city: Moffet Field

first: Sharmila

last: Bhattacharya

state: CA

address: Bldg. 236, Room 213

institute: NASA Ames Research Center

summary: Gene expression levels were determined in 3rd instar and adult Drosophila melanogaster reared during spaceflight, to elucidate the genetic and molecular mechanisms underpinning the effects of microgravity on the immune system.  The goal was to validate the Drosophila model for understanding alterations of innate immune responses in humans due to spaceflight. Five containers of flies, with ten female and five male fruit flies in each container, were housed and bred on the space shuttle (average orbit altitude of 330.35 km) for 12 days and 18.5 hours, with a new generation reared in microgravity.  RNA was extracted on the day of shuttle landing from whole body animals (3rd instar larvae and adults), hybridized to Drosophila 2.0 Affymetrix genome arrays, and the expression level of all genes was normalized against the gene expression level from the corresponding developmental stage animals raised on ground.  Spaceflight altered the expression of larval genes involved in the maturation of plasmatocytes (macrophages) and their phagocytic response, as well as the level of constitutive expression of pattern recognition receptors and opsonins that specifically recognize bacteria, and of lysozymes, antimicrobial peptide pathway and immune stress genes, hallmarks of humoral immunity.

overall_design: Larval microarrays (FL 6 samples) are based on RNA extracted from 6 independent sets of 50 mid 3rd instar larvae reared in microgravity and collected on the day of landing after 12 days and 18.5 hours on the space shuttle and the same number of control larvae raised on ground (GL 6 samples). Adults microarrays (F1 3 samples) are based on RNA from 3 sets of 20 adult females each, that emerged during spaceflight and within 4 hours of landing and the same number of adult females from the corresponding ground control containers (G1 3 samples).

first: Oana

last: Marcu

first: Matthew

last: Lera

first: Max

last: Sanchez

first: Edina

last: Levic

first: Laura

last: Higgins

first: Alena

last: Shmygelska

last: Fahlen

first: Helen

last: Nichol


title: Metronomic doxorubicin blocks HIF-1α-mediated responses in sarcomas and augments the effects of anti-VEGF-A therapy

status: Public on Aug 30 2011

city: Boston

first: Peter

middle: J

last: Park

address: 10 Shattuck St

department: Center for Biomedical Informatics

institute: Harvard Medical School

summary: Increased levels of hypoxia and hypoxia inducible factor 1α (HIF-1α) in human sarcomas correlate with tumor progression and radiation resistance. Prolonged anti-angiogenic therapy of tumors can delay tumor growth but may also increase hypoxia and HIF-1α activity. In our recent clinical trial, treatment with the anti-vascular endothelial growth factor A (VEGF-A) antibody, bevacizumab, followed by a combination of bevacizumab and radiation led to near complete necrosis in nearly half of sarcomas. Gene set enrichment analysis of microarrays from pre-treatment biopsies found the Gene Ontology category “Response to hypoxia” was upregulated in poor responders, and hierarchical clustering based on 140 hypoxia-responsive genes separated poor responders from good responders. The most commonly used chemotherapeutic drug for sarcomas, doxorubicin (Dox), was recently found to block HIF-1α binding to DNA at low metronomic doses. We thus examined Dox treatment in 4 sarcoma cell lines, and found Dox at low concentrations (1-10 uM) blocked HIF-1α induction of VEGF-A by 84-97%, while inhibition of other HIF-1α-target genes including CA9, c-Met and FOXM1 was variable. HT1080 sarcoma xenografts had increased hypoxia and/or HIF-1α activity with increasing tumor size and with anti-VEGF receptor antibody (DC101) treatment. Combining DC101 and metronomic Dox had a synergistic effect in suppressing growth of HT1080 xenografts, primarily via induction of tumor endothelial cell apoptosis. In conclusion, sarcomas respond to increased hypoxia by expressing HIF-1α-target genes which may promote resistance to anti-angiogenic and other therapies. Metronomic Dox can block HIF-1α activation of target genes and works synergistically with anti-VEGF therapy to inhibit sarcomas.

overall_design: Pre-treatment biopsies were collected from 16 human sarcoma.  The gene expression analysis was performed using Illumina platform.

first: Yeo-Jung

last: Kim

first: Hae-June

last: Lee

first: TS

middle: K

last: Eisinger-Mathason

first: Tae-Min

first: Alexia

last: Zhang

first: Daniel

last: Karl

first: Michael

last: Nakazawa

first: Sandra

last: Ryeom

first: M

middle: C

last: Simon

first: Sam

last: Yoon


title: Gene expression response to bacterial phagocytosis by S2 cells (control and eater RNAi knock down)

status: Public on Aug 25 2011

first: Christine

last: Kocks

state: Massachusetts

address: 185 Cambridge St CPZN7.250

department: Pediatrics/Molecular Biology

institute: Massachusetts General Hospital

summary:
The Drosophila phagocytic receptor Eater is expressed specifically in phagocytic hemocytes. It contributes to host immune defense and is required for survival of bacterial infections. Eater is involved in recognition and phagocytosis of bacteria.
We used microarrays to determine whether any gene expression changes after bacterial phagocytosis are dependent on the expression of the phagocytic scavenger receptor Eater. We found transcriptional regulation in response to bacterial internalization, but no significant differences between controls and samples in which eater expression had been diminshed by RNAi eater knock down.

overall_design: Drosophila S2 cells, a hemocyte-derived cell line with phagocytic properties, were exposed to a mixture of Gram-positive and Gram-negative bacteria at conditions of 50% of cell binding. At different time points of synchronized phagocytosis (30, 90 and 180 minutes) total RNA was extracted and subjected to microarray analysis. We compared S2 cells in which Eater expression was decreased by RNA interference with control S2 cells exposed to irrelevant double-stranded (pBR322). Three independent experiments were performed corresponding to three biological replicates. Decreased phagocytosis due to RNAi eater knock down was controlled in all cases.


title: Gene expression data from sorted primary human cord blood samples

status: Public on Aug 28 2011

city: Toronto

first: Kolja

last: Eppert

address: 101 College St., rm 8-301

institute: University Health Network

summary: Experiments using xenografts show that some solid tumours and leukemias are organized as cellular hierarchies sustained by cancer stem cells (CSC). Despite promise, the relevance of the CSC model to human disease remains uncertain. Here we show that acute myeloid leukemia (AML) follows a CSC model based on sorting multiple populations from each of 16 primary human AML samples and identifying which contain leukemia stem cells (LSC) using a sensitive xenograft assay. Analysis of gene expression from all functionally validated populations yielded an LSC-specific signature. Similarly, a hematopoietic stem cell (HSC) gene signature was established. Bioinformatic analysis identified a core transcriptional program shared by LSC and HSC, revealing the molecular machinery underlying stemness properties. Both stem cell programs were highly significant independent predictors of patient survival and also found in existing prognostic signatures. Thus, determinants of stemness influence clinical outcome of AML establishing that LSC are clinically relevant and not mere artifacts of xenotransplantation.

overall_design:
Analysis of gene expression in FACS sorted cord blood fractions that were functionally determined to be enriched for HSC or not (6 and 6 respectively).
12 samples were hybridized to Affymetrix HG_U133A microarray [HG_U133A] or Affymetrix HG_U133B microarray [HC_U133B]

first: Katsuto

last: Takenaka

first: John

middle: E

last: Dick


title: Transcriptome analysis of vtc1, abi4-102 and wild type Col 0

status: Public on Aug 26 2011

city: Leeds

first: Pavel

last: Kerchev

address: Faculty of Biological Sciences University of Leeds

country: United Kingdom

institute: University of Leeds

summary: The role of abscisic acid (ABA) signalling in the ascorbic acid (AA)-dependent control of plant growth and defence was determined using the vtc1 and vtc2 mutants, which have impaired ascorbic acid synthesis, and in the abi4 mutant that is impaired in ABA-signalling. ABA levels were increase in the mutants relative to the wild type (Col0). Like vtc1 the vtc2 mutants have a slow growth relative to Col0. However, the wild type phenotype is restored in the abi4vtc2 double mutant. Similarly, the sugar sensing phenotype of in the abi4 is reversed in the abi4vtc2 double mutant. The vtc1 and vtc2 leaf transcriptomes show up to 70 % homology with abi4. Of the transcripts that are altered in the mutants a relative to Col0, only a small number are reversed in the abi4vtc2 double mutants relative to either abi4 or vtc2. We conclude that AA controls growth via an ABA and abi4-dependent signalling pathway. The vtc and abi4 mutants have enhanced glutathione levels and common redox signalling pathways leading to similar gene expression patterns.

overall_design: Rosettes of 42 days old plants were harvested and used to exctract RNA

last: Foyer


title: Transcriptome analysis of vtc2, abi4-102 and the corresponding double mutant abi4 vtc2


title: Ascorbic acid-dependent regulation of growth involves abscisic acid signalling through ABI-4

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

overall_design: Refer to individual Series


title: Prognostic DNA Methylation Patterns in CN-AML; a genome wide methylation and gene expression study

status: Public on Sep 21 2011

first: Stefan

last: Deneberg

type:
Methylation profiling by array
Expression profiling by array

first: Sören

last: Lehmann


title: Expression Data from human Lung tissue of Patients with Non Small Cell Lung Cancer (NSCLC)

city: Bronx

first: Miao

last: Shi

state: NY

address: 1301 Morris Park ave

institute: Albert einstein College of Medicine

summary:
Lung cancers are a heterogeneous group of diseases with respect to biology and clinical behavior. Currently, diagnosis and classification are based on histological morphology and immunohistological methods for discrimination between two main histologic groups: small cell lung cancer (SCLC) and non-small cell lung cancer (NSCLC) which account for 20% and 80% of lung carcinomas, respectively. NSCLCs, which are divided into the three major subtypes adenocarcinoma, squamous cell carcinoma and dedifferentiated large cell carcinoma, show different characteristics such as the expression of certain keratins or production of mucin and lack of neuroedocrine differentiation. The molecular pathogenesis of lung cancer involves the accumulation of genetic und epigenetic alterations including the activation of proto-oncogenes and inactivation of tumor suppressor genes which are different for lung cancer subgroups. The development of microarray technologies opened up the possibility to quantify the expression of a large number of genes simultaneously in a given sample. There are several recent reports on expression profiling on lung cancers but the analysis interpretation of the results might be difficult because of the heterogeneity of cellular components. The methods used for sample selection and processing can have a strong influence on the expression values obtained through microarray profiling. Laser capture microdissection (LCM) provides higher specificity in the selection of target cells compared to traditional bulk tissue selection methods, but at an increased processing cost.
Here we describe the use of an expression microarray study on NSCLC samples and surrounding tissue, comparing macroscopic lung tumor and tissue samples (“grind and bind”), versus tumor and alveolar compartment cells laser capture microdissected (LCM) from the same macroscopic lung samples.
In this study, an initial set of 30 pairs of macroscopic tumor and non-tumor samples (10 pairs squamous-cell carcinoma, 18 pairs adenocarcinoma, 2 pairs adeno-squamous carcinoma) and 2 unpaired samples was selected for bulk/macro sampling. Of these 30 pairs and 2 unpaired samples, 17 pairs and 9 unpaired samples were reanalyzed using laser capture microdissection (LCM) for sampling the cells (7 pairs squamous and 1 unpaired sample, 9 pairs adenocarcinomas and 7 unpaired samples, 1 pair adeno-squamous carcinoma and 1 unpaired sample). For macroscopic samples, 50 to 80 µg of tissue was used to isolate total RNA. Gene expression profile was determined using Affymetrix Human Genome Gene 1.0 ST genechip. For the LCM samples, from representative slides histologically confirmed and mapped by a pathologist, approximately 1000 cells/sample were collected by LCM. cDNA was amplified using Nugen WT-Ovation One-Direct amplification system. In order to validate Nugen amplification bias of WT-Ovation One-Direct amplification system, the total RNA samples of 10 pairs of macroscopic tumor and non-tumor samples were amplified with this amplification system, and their cDNA was used to microarray.

first: G

last: Marquardt

first: N

last: Mullapudi

first: J

last: Lin

first: T

last: Wang

last: Locker

first: S

last: Keller

last: Spivack


title: The inflammasome is a central player in the induction of obesity and insulin resistance

status: Public on Aug 21 2011

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

summary:
Inflammation plays a key role in the pathogenesis of obesity. Chronic overfeeding leads to macrophage infiltration in the adipose tissue, resulting in pro-inflammatory cytokine production. Both microbial and endogenous danger signals trigger assembly of the intracellular innate immune sensor Nlrp3 [NLR family, pyrin domain containing 3] resulting in caspase-1 activation and production of pro-inflammatory cytokines interleukin (IL)-1beta and IL-18. Here, we showed that mice deficient in Nlrp3, ASC [apoptosis-associated speck-like protein containing a CARD; a.k.a PYCARD (PYD and CARD domain containing)] and caspase-1 were resistant to the development of high fat diet-induced obesity, which correlated with protection from obesity-induced insulin resistance. Detailed metabolic and molecular phenotyping demonstrated that the inflammasome controls energy expenditure and adipogenic gene expression during chronic overfeeding. These findings reveal a critical function of the inflammasome in obesity and insulin resistance and suggest inhibition of the inflammasome as a potential therapeutic strategy.

Keywords: Expression profiling by array

overall_design: Wild-type (WT), ASC-null and Casp1-null mice were subjected to high fat diet feeding for 16 weeks. After the diet intervention period, the animals were killed and epididymal white adipose tissue was removed. Total RNA was isolated and subjected to gene expression profiling.

first: Rinke

last: Stienstra

first: Janna

middle: A

last: van Diepen

first: Cees

last: Tack

first: Mohammad

last: Zaki

first: Frank

last: van de Veerdonk

first: Deshani

last: Perera

first: Geoff

last: Neal

first: Anneke

last: Hijmans

first: Irene

middle: O

last: Vroegrijk

first: Sjoerd

last: van den Berg

first: Johannes

last: Romijn

first: Patrick

last: Rensen

first: Leo

last: Joosten

first: Mihai

last: Netea

first: Thirumala-Devi

last: Kanneganti


title: CYTOKININ HYPERSENSITIVE1 (CKH1) and CKH2 affect to cytokinin responses in tissue culture

status: Public on Aug 17 2011

city: Okazaki

first: Minoru

last: Kubo

state: Aichi

address: 38NIshigonaka, Myoudaiji

department: ERATO

country: Japan

institute: JST

summary: Analysis of calli derived from the wild type (Ler), the ckh1 and ckh2 mutants cultured on media in the absence of cytokinin (control), in the presence of low (25 ng/ml kinetin) or high (200 ng/ml kinetin) levels of cytokinin, or in the presence of Trichostatin A (TSA). In these conditions, a constant 2,4-dichlorophenoxyacetic acid (2,4-D) was included as an auxin.

overall_design: Hypocotyl segments of the wild type (Ler), ckh1-1 and ckh2-1 mutants were cultured for 3 days on media containing 100 ng/ml 2,4-D in the absence of kinetin or in the presence of low (25 ng/ml) or high (200 ng/ml) kinetin or 100ng/ml TSA, and then collected and rapidly frozen by liquid nitrogen. Total RNA was extracted by using an RNeasy plant kit (Qiagen; USA), and 10 µg of total RNA was used for target preparation by using

first: Kaoru

last: Furuta

first: Taku

last: Demura

first: Tatsuo

last: Kakimoto


title: Transcriptomic and phenotypic variation for salt stress response in Arabidopsis

status: Public on Aug 16 2011

city: Wuhan

first: Zhulong

last: Chan

address: Wuchang District, Moshan

institute: Wuhan Botanic Garden, Chinese Academy of Sciences

summary:
Transcriptional variation, also called expression level polymorphism (ELP), contributes to intra-specific phenotypic variation in many organisms. Differentially expressed transcripts are typically enriched for stress-related genes, suggesting that differences in response to the environment are a particularly common point of divergence among gentoypes. Analysis of ELPs also has been suggested as a way to assess unintended consequences of transgene introduction; however, it is important that interpretation of transcriptional changes be performed within the context of potential fitness effects.  In these studies we sought to examine differential gene expression in response to salinity for two widely used Arabidopsis thaliana ecotypes, Wassilewskija (Ws) and Columbia (Col), and a single gene mutation (glabrous, gl1-1) in the Col background (Col(gl)), in relation to genetic, phenotypic, and fitness differences.
Growth analyses were performed with seedlings germinated on culture media and growth chamber-grown plants carried through the full life cycle. Transcriptome analyses were performed with salt treated and control growth-chamber grown plants six days post initiation of salt stress. Ws plants had the least salt injury and highest dry matter accumulation and seed production in salt stressed conditions. ELPs among genoytypes and in response to 100 mM NaCl were enriched for genes associated with response to stress, including stress-associated transcription factors, heat shock and redox metabolism genes, and R genes. Application of salt resulted in many more transcripts up- or down-regulated in Col and Ws than in Col(gl).  Many of the transcripts influenced by salt in Col were already altered in gl1-1 plants in the absence of salt, although Col(gl) plants did not show any detectable signs of stress, or effects on fecundity in the absence of salt treatment.  The majority of salt-induced transcriptional changes that occurred in Ws also occurred in Col, suggesting common salt stress responses in these two ecotypes. Many more genes were affected by salt in Col than Ws, however, possibly reflecting the greater salt injury observed for Col. There was minimal overlap between the transcripts that differed for Ws and Col prior to salt treatment and those that were subsequently affected by salt stress.  Thus, many genes conferring comparative salt stress tolerance in Ws likely differ from those whose expression levels are modified in response to salt stress. These studies demonstrate transcriptional variation among Arabidopsis genotypes in response to salt stress.  Greater transcriptome differences did not necessarily correspond with greater genetic difference or phenotypic differences in morphology, fecundity, and resistance to salt stress.  These results suggest that depending on circumstance, transcriptional changes can reflect response to injury, facilitate adaptive expression of fitness-associated traits, or allow for phenotypic buffering to minimize the impact of genetic changes.

overall_design: Three Arabidopsis genotypes were grown in the growth chamber in the absence and presence of salt stress. Plants from 20 days after sowing (6 days after salt treatment) were used for RNA extraction and hybridization on Affymetrix microarrays. There were two biological replicates for each genotype and salt treatment combination.

first: Wayne

last: Loescher

first: Rebecca

last: Grumet


title: Mulcom: a multiple comparison statistical test for microarray data in Bioconductor (Affymetrix)

status: Public on Aug 10 2011

first: Enzo

last: Medico

address: Strada Prov. 142, km 3,95

institute: Candiolo Cancer Institute, University of Torino

summary:
Background
Many microarray experiments search for genes with differential expression between a common “reference” group and multiple test groups, like in the case of time-course designs or of various treatments versus a control condition. In such cases, currently employed statistical approaches based on t-test or close derivatives have limited efficacy, mostly because estimation of noise is done on only two groups at time. Alternative approaches based on ANOVA correctly capture noise from all the groups, but then do not confront single test groups with the reference. We therefore conceived a statistical test for pairwise comparisons between the reference group and each test group that uses within-group variance calculated from all the groups.

Results
We implemented an R-Bioconductor package named Mulcom, with a statistical test derived from the Dunnett’s test, designed to compare multiple experimental groups against a common reference. In addition to the basic Dunnett’s t value, the package includes an optional minimal fold-change threshold, m. Thanks to automated, permutation-based estimation of False Discovery Rate (FDR), the package also permits fast optimization of the test, to obtain the maximum number of significant genes at a given FDR value. When applied on a time-course experiment profiled in parallel on two microarray platforms, and compared with currently used tests, Mulcom displayed higher concordance of significant genes in the two array platforms, and higher enrichment in functional annotation to categories related to the biology of the experiment.

Conclusions
The Mulcom package provides a fast and powerful tool for the identification of differentially expressed genes when several experimental conditions are compared with a common reference. We found that Mulcom leads to lists of differentially expressed genes that are particularly consistent across microarray platforms and enriched in significant classes of genes. In our opinion, the main reasons for these good performances are three: (i) within-group variability is estimated from all experimental groups even if only two of them are compared each time; (ii) the optional fold-change threshold m avoids false positives due to aberrantly low within-group variability; (iii) automated test optimization allows maximizing sensitivity without compromising specificity.

overall_design: Ten MDA-MB-435 samples, biological duplicates of each condition (untreated, integrin Beta4 treatment, hepatocyte growth factor treatment for 1 hr, 6 hrs, or 24 hrs).

first: Claudio

last: Isella


title: Expression data from third instar larval eye discs

city: Chicago

first: Mary

last: Truscott

state: IL

address: 900 S Ashland Ave, room 2356

department: Biochemistry and Molecular Genetics

institute: University of Illinois at Chicago

summary:
Expression of dE2F1 induces proliferation and apoptosis. We sought to perform an unbiased analysis of the effect of co-expression of miR-11
We used microarrays to identify differentially regulated genes following expression of dE2F1 and/or dme-miR-11 using the GMR-Gal4 driver

overall_design: Drosophila third instar larvae were selected for RNA extraction and hybridization on Affymetrix microarrays. The GMR-Gal4 driver induces expression posterior to the morphogenetic furrow. We compared the gene expression profiles following induction of expression of dE2F1 + dDP and/or dme-miR-11.

first: Maxim

last: Frolov


title: Expression data from Arabidopsis thaliana under dark and far-red light

status: Public on Aug 02 2011

city: Shenzhen

first: Bosheng

last: Li

state: Guangdong

address: SUStech Huiyuan #1 406

department: MCDB

institute: SUSTC (current, may different with previous institution )

summary: FAR-RED ELONGATED HYPOCOTYL 3 (FHY3) and its homolog FAR-RED IMPAIRED RESPONSE 1 (FAR1) are two transposase-derived transcription factors initially identified as the key components in phytochrome A signaling and recently shown to function in the circadian clock. However, whether FHY3 and FAR1 are involved in other processes of plant development remains largely unknown. Here, we explored chromatin immunoprecipitation-based sequencing (ChIP-seq) analysis to identify 1745 and 1171 FHY3 direct binding target genes in darkness and far-red light conditions, respectively in the Arabidopsis thaliana genome. This analysis revealed that FHY3 preferentially binds to the gene promoters through the previously identified typical FHY3/FAR1 binding motif. Interestingly, FHY3 also binds to two novel motifs in the 178-bp repeats of the Arabidopsis centromere regions in vivo. Comparison between the ChIP-seq and microarray data indicates that FHY3 regulates the expression of 196 and 85 genes in dark and far-red respectively by directly binding to their promoters. FHY3 also co-regulates a number of common target genes with PHYTOCHROME INTERACTING FACTOR 3-LIKE 5 (PIL5) and ELONGATED HYPOCOTYL 5 (HY5). Moreover, our genome-wide identification of FHY3 direct target genes ultimately led to the discovery and validation of a new role of FHY3 in controlling chloroplast development, by directly activating the expression of ACCUMULATION AND REPLICATION OF CHLOROPLASTS5 (ARC5), a key gene regulating chloroplast constriction and division. Taken together, our data suggest that FHY3 is involved in regulating multiple facets of plant development, thus providing new insights into the functions of this type of transposase-derived transcription factors.

overall_design: We used the FHY3p:FHY3-GR fhy3-4 transgenic lines expressing FHY3-glucocorticoid receptor (GR) fusion proteins under the control of the FHY3 native promoter, in which, without dexamethasone (DEX), the GR-fusion proteins localize in the cytoplasm, whereas, when treated with DEX, the fusion proteins translocate into the nucleus. The seedlings were grown in D or continuous FR light for 4 days, then treated with DEX or mock (equal volume of ethanol), and grown in the same conditions for a further 2 hours before the samples were harvested. RNA samples were extracted from these samples, and then hybridized with Affymetrix Arabidopsis ATH1 genome arrays. Four independent biological replicates for each treatment were used for the microarray analysis.

first: Xinhao

last: Ouyang

first: Jigang

first: Gang

first: Huaishun

last: Shen

first: Xi

last: Huang

first: Xiaorong

last: Mo

first: Xiangyuan

last: Wan

first: Rongcheng

last: Lin

first: Shigui

first: Haiyang

last: Wang

first: Xingwang

last: Deng


title: Transcriptomic characterization of a synergistic genetic interaction during carpel margin meristem development in Arabidopsis thaliana

status: Public on Aug 01 2011

city: Raleigh

first: April

middle: N

last: Wynn

state: NC

address: Campus Box 7614

department: Genetics

institute: NC State University

summary: We are interested in examining the transcriptional hierarchies that are required for proper formation and function of the carpel margin meristem in Arabidopsis thaliana. The carpel margin meristem (CMM) gives rise to the ovule primorida (which begin to form around flower stage 8).  We know that the loss of the seuss-3 (seu-3) and aintegumenta-1(ant-1) separately leads to a mild disruption of ovule formation, while the loss of both causes a complete loss of ovule formation. In this study we wanted to examine expression levels changed between each single mutant and the double mutant. We dissected out stage 8-10 carpel of each of the four genotypes (seu-3, ant-1, Col-0, seu-3 ant-1) pooling 15-25 carpels into one biological replicate. Then using 16 ATH1 arrays we hybridized, amplified and labeled cDNA to 16 arrays (4 replicates for each genotype). We then analyzed our data to reveal transcripts that went down in the double compared to either single mutant, and transcripts that went down more than additively in the double mutant compared to added level of the decrease of the single mutant levels.

overall_design: 16 arrays: 4 seuss-3, 4 aintegumenta-1, 4 Col-0, 4 seuss-3 aintegumenta-1.  Each biological replicate was a sample of 15-25 pooled stage 8-10 carpels manually dissected by hand.

first: Robert

last: Franks


title: Mulcom: a multiple comparison statistical test for microarray data in Bioconductor

city: Candiolo

first: Enzo


title: Microarray expression analysis of patients Dupuytren´s contracture (DC)

status: Public on Aug 13 2011

city: Rijeka

first: Ivana

last: Ratkaj

address: Trga brace Mazuranica 10

department: Department of Biotechnology

country: Croatia

institute: University of Rijeka

summary: We used a high-throughput technology, DNA microarray, to screen the entire genome for the changes in gene expression in diseased tissue to characterize Dupuytren's contracture at a molecular level and find genes that are involved in development of the disease.

overall_design: Primary cell cultures were established from surgically removed diseased (D) and healthy (ND) tissue from 3 patients. Total we had 6 samples, 3 diseased and 3 healthy patient-matched samples.  Total RNA was isolated by RNeasy mini kit (Qiagen) and further used for microarray expression analysis (HG-U133A array, Affymetrix).  Raw data, CEL. files were analysed with software MAS5, GeneSpring and GENEMAPP.

first: Mirela

middle: B

last: Loncar


title: Evidence of mechanism how rs7575840 influences apolipoprotein B containing lipid particles

city: Los Angeles

first: Blake

middle: Edwin

last: Haas

address: 695 Charles E. Young Drive South

institute: UCLA

summary: Objective: Recent genome-wide association studies (GWAS) identified a variant rs7575840 in the apolipoprotein B (APOB) gene region to be associated with LDL-C. However, the underlying functional mechanism of this variant that resides 6.5 kb upstream of APOB has remained unknown. Our objective was to investigate rs7575840 for association with refined apoB containing lipid particles; for replication in a non-Caucasian Mexican population; and for underlying functional mechanism.   Methods and Results  Our data show that rs7575840 is associated with serum apoB levels (P=4.85x10-10) and apoB containing lipid particles, very small VLDL, IDL and LDL particles (P=2x10-5 - 9x10-7) in the Finnish METSIM study sample (n=7,710). Fine mapping of the APOB region using 43 SNPs replicated the association of rs7575840 with apoB in a Mexican study sample (n=2,666, P=3.33x10-05). Furthermore, our transcript analyses of adipose RNA samples from 175 Finnish METSIM subjects indicate that rs7575840 alters expression of APOB (P=1.13x10-10) and a regional non-coding RNA (BU630349) (P=7.86x10-6) in adipose tissue.    Conclusions  It has been difficult to convert GWAS associations into mechanistic insights. Our data show that rs7575840 is associated with serum apoB levels and apoB containing lipid particles as well as influences expression of APOB and a regional transcript BU630349 in adipose tissue. We thus provide evidence how a common genome-wide significant SNP rs7575840 may affect serum apoB, LDL-C, and TC levels.

overall_design: 175 samples, no replicates

first: Daphna

last: Weissglas-Volkov

first: Carlos

last: Aguilar-Salinas

first: Elina

last: Nikkola

first: Laurent

last: Vergnes

first: Ivette

last: Cruz-Bautista

first: Laura

last: Riba

first: Alena

last: Stancakova

first: Johanna

last: Kuusisto

first: Pasi

last: Soininen

first: Antti

last: Kangas

first: Mika

last: Ala-Korpela

first: Teresa

last: Tusie-Luna

first: Markku

last: Laakso

first: Paivi

last: Pajukanta


title: Human Hematopoietic and Leukemic Stem Cell Gene Expression Profiles

first: Kolja

last: Eppert


title: Differences in subcutaneous adipose tissue gene expression between obese African Americans and Hispanic Youths

first: Swapna

last: Mahurkar

address: 2250 Alcazar St

department: Preventive Medicine, Keck School of Medicine

institute: University of Southern California

summary: Obesity is a major risk factor for several chronic diseases including diabetes, fatty liver disease and cancer. Despite similar propensities for obesity, Hispanics and African Americans exhibit unique and distinct differences in obesity related outcomes such as greater risk of, obesity-related cancers in AA and non alcoholic fatty liver disease (NAFLD) in Hispanics. This study was aimed to determine whether differences in subcutaneous adipose tissue (SAT) gene expression in obese, Hispanic and AA young adults might explain ethnic differences in obesity-related phenotypes.

overall_design: cross-sectional study design to compare subcutaneous adipose tissue gene expression profiles of 19 Hispanic and 17 African American young adults

first: Michael

middle: I

last: Goran


title: Isolation of single human hematopoietic stem cells capable of long-term multilineage engraftment

first: Sergei

last: Doulatov

address: 101 College Street, TMDT 8-301

department: Division of Stem Cell and Developmental Biology

institute: Campbell Family Institute for Cancer  Research/Ontario Cancer Institute

summary: Gene expression profiling was used to investigate the relationship between human cord blood hematopoietic stem cells (HSC) and multipotent progenitors described in the study. Genes more highly expressed in HSC may be associated with stem cell function and self-renewal.

overall_design: Total RNA was obtained from flow-sorted populations based on the cell surface expression of CD34, CD38, CD45RA, Thy1, and CD49f.

first: Faiyaz

last: Notta

first: Elisa

last: Laurenti

first: Armando

last: Poeppl

first: Igor

last: Jurisica


title: Calorie/Dietary Restriction and Resveratrol in Female Drosophila Melanogaster Head/Thorax

status: Public on Jul 21 2011

city: Providence

last: Antosh

state: RI

address: Brown University Box 1843

institute: Michael Antosh

summary: Feeding resveratrol to Drosophila melanogaster extends lifespan. Studies of microarray show similarities between calorie/dietary restriction and resveratrol on both a gene expression and biological pathway level.

overall_design: 9 samples: 3 biological replicates each of normal diet, restricted diet and normal diet plus resveratrol

middle: P

first: Stephen

last: Helfand


title: Genome-wide mRNA profiling of adult human pancreatic beta and duct cells in comparison to other human tissues

city: Brussels

first: Geert

middle: A.

last: Martens

address: Laarbeeklaan 103

department: Diabetes Research Center

country: Belgium

institute: Vrije Universiteit Brussel

summary: Aims: establishment of reference samples to investigate gene expression selective for endocrine or ductal-exocrine cells within the adult human pancreas. To this end, human islet endocrine cells, FACS-enriched in insulin+ cells, (n=3) and human exocrine ductal cells (n=2) are compared on Affymetrix HG133A platform with duplicate hybridizations of a panel of other primary human tissues.

overall_design:
The microarray analysis was performed on 3 pools of human beta cell-enriched cell fractions, isolated from 10 non-selected donor organs, and 2 pools of duct cell-enriched fractions obtained from 6 non-selected donor pancreases. The cells were suspension-cultured for 2-3 weeks along standard procedures and with no specific treatment prior to FACS-sorting and RNA extraction.  The average composition of human beta cell-preparations was 55 ± 13% insulin+ cells, 13±8% glucagon+ cells and 21 ±7% non-granulated cells. Pancreatic duct cells-enriched preparations contained 85 ±7% cytokeratin 19+ cells with 4 ± 1% insulin+ cells and 6 ±4% glucagon+ cells and were isolated as described by Heimberg H. et al.( Diabetes 2001,49: 571-579 ).
Pancreatic cell mRNA profiles were compared to those of a panel of other human primary tissues (n=2 biological replicates).

first: Zhidong

last: Ling

first: Daniel

last: Pipeleers

first: Harry

last: Heimberg


title: Identification of Gene Networks and Pathways Associated with Guillain-Barre Syndrome

status: Public on Jul 28 2011

city: Taoyuan

first: Kuo Hsuan

last: Chang

address: No. 5,  No.5, Fusing Street, Gueishan Township

department: Department of Neurology

country: Taiwan

institute: Chang Gung Memorial Hospital

summary: The underlying change of gene network expression of Guillain-Barre syndrome (GBS) remains elusive. We sought to identify GBS-associated gene networks and signalling pathways by analyzing the transcriptional profile of leukocytes in the patients with GBS.

overall_design: Quantitative global gene expression microarray analysis of peripheral blood leukocytes was performed on 7 patients with GBS and 7 healthy controls.

first: Kuo-Hsuan

first: Chiung-Mei

last: Chen


title: A Gene Expression-Based Risk Stratification Model for Newly Diagnosed Multiple Myeloma

status: Public on Aug 20 2011

city: Little Rock

first: Yiming

last: Zhou

state: AR

address: 4301 West Markham St., Slot 776

institute: Myeloma Institute for Research and Therapy

summary:
We recently defined a gene expression-based signature of high-risk multiple myeloma; this predictive signature was developed with and independently validated for newly diagnosed patients treated with high dose therapy and stem cell rescue.  Here we use Phase 3 clinical trial data to show that this signature also predicts short survival in relapsed disease treated with single agent bortezomib or high dose dexamethasone.  In addition, a survival signature derived with relapsed myeloma samples identified newly diagnosed patients with short survival.  Taken together these data suggest that a similar biology underlies poor outcome in both newly diagnosed and relapsed myeloma and provide strong evidence that the high-risk signature is a powerful tool to identify patients who are candidates for new therapeutic regimens.
Keywords: Model validation

overall_design: See above (Series_summary)

first: John

middle: D

last: Shaughnessy Jr


title: Gene expression profiling in the leukemic stem cell-enriched CD34+ fraction identifies target genes that predict prognosis in normal karyotype AML

status: Public on Jul 19 2011

city: Groningen

first: JJ

last: Schuringa

address: Hanzeplein 1

department: Experimental Hematology

institute: UMCG

summary: Mononuclear cells from AML patients (n=46) were sorted into CD34+ and CD34- subfractions and genome-wide expression analysis was performed using Illumina BeadChip Arrays (HT12 v3). Of 2 AML samples only the CD34+ fraction could be analyzed. AML CD34+ and CD34- gene expression was compared to a large group of normal CD34+ bone marrow cells (n=31).

overall_design: Mononuclear cells from AML patients (n=46) were sorted into CD34+ (46) and CD34- (44) subfractions and genome-wide expression analysis was performed using Illumina BeadChip Arrays (HT12 v3). AML CD34+ and CD34- gene expression was compared to a large group of normal CD34+ bone marrow cells (n=31).

first: Hendrik

last: de Jonge

first: Carolien

middle: M

last: Woolthuis

first: Annet

middle: Z

last: Vos

first: Andre

last: Mulder

first: Eva

last: van den Berg

first: Philip

last: Kluin

first: Karen

last: van der Weide

first: Eveline

middle: S

last: de Bont

first: Gerwin

last: Huls

first: Edo

last: Vellenga

first: Jan


title: Y-linked rDNA deletions in Drosophila melanogaster

city: Cambridge

first: Bernardo

last: Lemos

state: MA

address: 16 Divinity Avenue, Room 2105

institute: Harvard University

summary: Please see publication. These experiments were performed to ascertain the contribution of Y-linked rDNA copy number variation in the modulation of gene expression. Males (XY) and female (XXY) genotypes were probed.

overall_design: Dye swaps and direct comparisons within each sex

first: Silvana

last: Paredes

first: Alan

middle: T

last: Branco


title: DNA methylation and expression profiling study for prostate cancer

status: Public on Jul 25 2011

city: Daejeon

first: Seon-Kyu

last: Kim

address: 125 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Korea

department: Personalized Genomic Medicine Research Center

country: South Korea

institute: Korea Research Institutue of Bioscience & Biotechnology

type:
Expression profiling by array
Methylation profiling by array

summary: Microarray-based DNA methylation and gene expression profiling was carried out using a panel of prostate cancer cell lines (LNCaP-FGC, DU-145, and PC-3) and the control normal prostate RWPE1 cell line. The identification of prostate cancer-specific methylation markers was based on the following criteria: a difference in DNA methylation level (β) of at least 0.5, and at least a 2-fold difference in expression level between cancer and control cells. Using highly stringent selection criteria, we identified novel hypermethylated genes whose expression was silenced in prostate cancer cells.

overall_design: Genomic DNA was extracted by standard methods using the Wizard Genomic DNA Purification System (Promega, Madison, WI). Total RNA was extracted with TRIzol reagent (Life Technologies, NY) according to the manufacturer’s protocol. Methylation patterns were assayed using the genome-wide Illumina Infinium HumanMethylation27 BeadChip array (Illumina Inc., San Diego, CA). Methylation assays were carried out according to the manufacturer’s protocol. Bisulfite conversion of genomic DNA was performed using the EZ DNA Methylation Kit (Zymo Research, Orange, CA). Fluorescence signals corresponding to C or T nucleotides were measured and the data were used to assign a quantitative measure of methylation level (β value). The β value is a quantitative measure of DNA methylation levels of specific CpGs and ranges from 0 for completely unmethylated to 1 for completely methylated. For the integrated analysis of global methylation status and gene expression levels, we used the genome-wide HumanHT-12 Gene Expression BeadChip (Illumina Inc., San Diego, CA). Gene expression analysis was performed according to the manufacturer’s protocol. Five hundred nanograms of total RNA were used for labeling hybridization according to the manufacturer’s protocol. Arrays were scanned with an Illumina Bead Array Reader confocal scanner (BeadStation 500GXDW; Illumina Inc., San Diego, CA), according to the manufacturer's instructions. Initial microarray gene expression data were obtained using the gene expression analysis module of Bead Studio software (version 3.1.3, Illumina Inc., San Diego, CA).

first: Yong-June

first: Wun-Jae


title: High content analysis of estrogen receptor activity: a mechanism-driven approach to compound testing

status: Public on Jul 14 2011

city: Houston

first: David

last: Loose

address: 6431 Fannin St, MSB 4.130

department: Integrative Biology & Pharm

institute: University of Texas

summary: Analysis of the genome-wide response of the ER:PRL-HeLa cell line to treatment with estrogen receptor ligands estradiol, 4H-tamoxifen and bisphenol-A.

overall_design: Total RNA obtained from ER:PRL-HeLa cells treated for 4 hours with estradiol, 4H-tamoxifen or bisphenol -A is compared to vehicle treated controls

first: Felicity

last: Ashcroft