title: Meiotic time course of open chromatin as measured by FAIRE

status: Public on Jul 01 2009

first: Sean

last: Hanlon

address: 920 E. 58th Street – CLSC 515E

institute: University of Chicago

summary: To investigate the relationship between chromatin organization and meiotic processes, we used Formaldehyde-Assisted Isolation of Regulatory Elements (FAIRE) to map open chromatin during the transition from mitosis to meiosis in the budding yeast Saccharomyces cerevisiae.

overall_design:
SK1 yeast strain SHy002 (MATa/MATα ho::LYS2/ho::LYS2 leu2::hisG/leu2::hisG lys2/lys2 ura3/ura3).
Meiotic Time Course with samples collected during vegetative growth (YPD) and 0 hr, 1.5hr, and 3hr after transfer to sporulation media (SM).
Regions of open chromatin were mapped using Formaldehyde-Assisted Isolation of Regulatory Elements (FAIRE).

first: Luke

last: Berchowitz

first: Jason

middle: D

last: Lieb

first: Gregory

last: Copenhaver


title: Ror2 gene expression analysis in renal cell carcinoma

status: Public on Jun 04 2009

city: Nashville

first: Kimryn

last: Rathmell

state: TN

address: 2220 Pierce Ave

department: Medicine

country: USA

institute: Vanderbilt

summary:
Renal cell carcinoma (RCC) tumors express varying gene profiles, dependent on varying genetic events.
Here we analyzed a series of RCC tumors for Ror2 expression, in relation to overal gene expression profiles.

Keywords: Patient sample study

overall_design: RNA from 27 RCC tumors was hybridized against the Perou lab RNA standard for gene expression analysis.

first: Tricia

middle: M

last: Wright

first: A

middle: R

last: Brannon

first: John

last: Gordan

first: W

middle: K


title: Down-regulation of SFRP1 in a mammary epithelial cell line

status: Public on Jun 30 2009

city: Chapel Hill

first: Melissa

last: Troester

state: NC

address: 135 Dauer Drive, CB 7435

department: Epidemiology

institute: University of North Carolina at Chapel Hill

summary: Microarray data to accompany Gauger et al. (2009) Cancer Cell International paper

overall_design: A treated X untreated design was used whereby immortalized human mammary epithelial cell lines (TERT cells) were modified to stably express an siRNA that knocked down SFRP1 expression.  These "treated" cells were labeled with Cy5 and four replicate harvests were hybridized to Agilent 4by44k whole genome microarrays, along with a Cy3 labeled untreated control.  The untreated control consisted of 4 pooled harvests of the parent cell line in normal growth conditions at 60-80% confluence.


title: BG02 hESC Exposed to Butyrate

status: Public on Mar 05 2009

city: Seattle

first: Brig

last: Mecham

state: WA

address: 1100 Fairview Ave N

institute: University of Washington

summary: To assess the effect of sodium butyrate exposure on human ESC grown without culture support for self-renewal (I.e. without conditioned medium and added bFGF) in support of data generated on H1 hESC - two groups were compared - BG02 culture in feeder conditioned versus on sodium butyrate - in triplicate and compared on Agilent whole human genome array

overall_design: BG02 hESC were grown under two conitions - A. for 31 passages on Matrigel in feeder conditioned medium and B. for 29 passages on Matrigel in feeder conditioned medium followed by 20 passages in 0.2 mM sodium butyrate without conditioned medium and in human ES cell medium containing no added bFGF

first: Carol

last: Ware

first: Anthony

last: Blau

first: Brigham


title: Aag glycosylase and impact on gene expression changes

status: Public on Feb 04 2009

first: Rebecca

middle: Catherine

last: Fry

address: 1213 MHRC

department: Environmental Sciences and Engineering

institute: UNC-Chapel Hill

summary:
We are investigating the transcriptional response of mice that are wt or null for Aag in response to alkylating agent MMS
We used microarrays to detail the global programme of gene expression response due to MMS exposure in a DNA repair proficient or deficient mouse
Keywords: timepoint

overall_design: Mice (WT and Aag null) were treated with MMS and livers extracted at 6, 12, 24, and 48 hours

first: Lisiane

last: Meira

first: Katherine

last: Pease

first: Peter

last: Svennson

first: Catherine

last: Moroski-Erkul

first: Sanchita

last: Bhattacharya

first: Leona

last: Samson


title: Reprogramming human fat cells into iPS cells

status: Public on Feb 27 2009

city: Stanford

first: Kitchener

middle: D.

last: Wilson

state: CA

address: S140 Grant Bldg

institute: Stanford University

summary: This study determined whether human adipose stem cells (hASCs) could be reprogrammed into induced pluripotent stem (iPS) cells using the 4 factors OCT4, SOX2, KLF4, and cMYC. We showed successfull reprogramming could be achieved in which fat/adipose cells were able to assume embryonic-like phenotypes after lentiviral transduction with the 4 factors. Further, we believe these fat cells are intrinsically better-suited for reprogramming compared to fibroblasts, and result in higher yields of iPS cells.

overall_design: Microarray study was performed in duplicates (hASCs, iPS cells derived from hASCs, and hESCs). Reference control was pooled RNA taken from H9 hESCs, embryoid bodies, and some differentiated cell types such as endothelial cells.


title: The effect of CLA diet on liver gene expression

status: Public on Mar 01 2009

city: Zaragoza

first: Jesus

last: Osada

address: Miguel Servet, 177

country: Spain

institute: Universidad de Zaragoza

summary:
apoE-deficient mice were fed a Western-type diet enriched with linoleic acid (control), cis-9, trans-11-CLA or trans-10, cis-12-CLA (1.0 % wt/wt) for 12 weeks and their hepatic gene expression was analysed using DNA microarrays
Keywords: influence of diet

overall_design: Three experimental designs using different genetic models as well as dietary conditions were carried out. In the first experiment, twenty nine three month-old homozygous apoE knockout male mice with a C57BL/6JxOLA129 genetic background, bred at the Unidad Mixta de Investigación, Zaragoza, were randomly assigned to a control (n=10), c9,t11-CLA-enriched (n=10) or t10,c12-CLA-enriched (n=9) diet.  All mice had similar baseline plasma cholesterol concentrations. The mice were fed the different experimental semi-purified diets for 12 weeks. All three diets were isocaloric and isonitrogenous; fat provided 30% of the energy intake. The control diet contained 1.0 % (wt/wt) linoleic acid while the others contained an equivalent amount of either c9,t11-CLA or t10,c12-CLA, as previously described. All diets were prepared by Unilever (Vlaardingen, The Netherlands) and stored in an N2 atmosphere at –20ºC. Fresh food was provided daily

first: Enda

last: Noone

first: Sergio

last: Acin

first: Maria

middle: A

last: Navarro

first: Carmen

last: Arnal

first: Helen

last: Roche

first: Natalia

last: Guillén


title: Effect of p53 in human iPS cell generation

city: Kyoto

first: Shinya

last: Yamanaka

address: 53 Kawahara-machi, Shogoin, Sakyo-ku

country: Japan

institute: Center for iPS Cell Research and Applicaton (CiRA), Kyoto University

summary: p53 knockdown by shRNA markedly increased efficiency of human iPS cell generation

overall_design:
Gene expression patterns were compared between human ES cells and dermal fibroblasts.
Gene expression patterns were also compared between p53 shRNA-treated fibroblasts and control fibroblasts.


title: Dexamethasone-resistant multiple myeloma cell line OPM1 treated with Dexamethasone and/or DAC

status: Public on Jan 03 2009

city: Tokyo

first: Masanori

last: Nojima

state: Tokyo

address: 4-6-1, Shirokanedai, Minato-ku

department: The Institution of Medical Science

institute: The University of Tokyo

summary: To identify genes responsible for the synergistic effect of DAC with Dex, we performed cDNA microarray analyses using cDNA prepared from Dex-resistant OPM1 cells treated with/without Dex, DAC or DAC+Dex.

overall_design: Cell lines were incubated for 72 h with/without 0.1 µM 5-aza-2'-deoxycytidine (DAC; Sigma), and were then incubated for 24 h with/without 1 µM Dexamethasone (EMD bioscience). The cells were then harvested, and total RNA was extracted for cDNA microarray analysis.

first: Reo

last: Maruyama

first: Hiroshi

last: Yasui

first: Hiromu

last: Suzuki

first: Minoru

last: Toyota

first: Takashi

last: Tokino

first: Yasuhisa

last: Shinomura


title: mutated IGHV3-23 CLL

status: Public on Jun 13 2009

city: Aviano

first: daniela

last: marconi

address: Via franco Gallini 2

country: Italy

institute: CRO AVIANO

summary: Expression of stereotyped B cell receptors (BCR), i.e. non-random combinations of immunoglobulin heavy-chain variable (IGHV) genes, complementarity-determining region-3 (HCDR3), and IGV light chains, identifies discrete clusters and represents a peculiar feature of chronic lymphocytic leukemia (CLL). Expression of IGHV3-23 characterized a CLL subset with peculiar molecular and clinical features.

overall_design: Two-condition experiment, Mutated IGVH3-23 vs. Mutated non-IGVH3-23. Biological replicates: 22 control replicates, 5  Mutated IGVH3-23 replicates. Refrence design

first: Riccardo

last: Bomben

first: Michele

last: Dal Bo

first: Dania

last: Benedetti

first: Daniela

last: Capello

last: Marconi

first: Francesco

last: Bertoni

first: Rossana

last: Maffei

first: Luca

last: Laurenti

first: Davide

last: Rossi

first: Pietro

last: Bulian

first: Massimo

last: Degan

first: Anotonella

last: Zucchetto

first: Roberto

last: Marasca

first: Valter

last: Gattei


title: Effect of tocopherol on caco-2 cells.

status: Public on Jan 27 2009

city: Marseille cedex 05

first: Jean-Francois

last: Landrier

address: 27 Bd Jean Moulin

department: AlimH

country: France

institute: INRA

summary: Caco-2 cells (clone TC7) were cultured for 15 days post confluence on plastic dishes to reach the differentiation, then cells were treated for 24h with alpha or gamma tocopherol enriched mixed micelles, or mixed micelles alone (as control) (Landrier et al Free Radical Research 2008). Cells were rinced with PBS before RNA extraction with Trizol, according the standard protocol of the manufacturer. RNA were checked for integrity with bioanalyser and quantified with Nanodrop. All others steps (labeling, hydridisation, wash and scan) were perfomed with Agilent kits, scanner and dedicated software.

overall_design: 8 samples were analysed, 4 for alpha tocopherol and 4 for gamma tocopherol. dye swap were performed for each conditions.

first: Jean-François

first: Erwan

last: Gouranton


title: Transcriptional Responses in Livers of Adult and Newborn Mice to Aflatoxin B1

status: Public on Jan 01 2009

city: Cambridge

first: Yuriy

middle: O.

last: Alekseyev

state: MA

address: 77 Massachusetts ave, bldg. 56-686

department: BE

summary:
Susceptibility to the hepatocarcinogen Aflatoxin B1 (AFB1) varies among species and with age.  Mice are refractory to carcinogenic and toxic effects of AFB1; however, B6C3F1 mice show transient sensitivity if dosed shortly after birth. We compared age-related differences in gene expression and transcriptional responses to AFB1 in livers of newborn (4-day-old) and adult mice.
Keywords: Transcriptional response to  a carcinogen

overall_design: Experiments were carried out under the protocol approved by MIT Animal Care Committee. Pregnant C57BL/6J female mice, mated to C3H/HeJ males, and adult (at least 60 day-old) B6C3F1/J hybrid F1 male mice (C57BL/6J female x C3H/HeJ male) were obtained from Jackson Labs.  They were housed in plastic cages (one per cage) under controlled environmental conditions and 12 h light/dark cycle. Food and water were supplied ad libitum. After female mice gave birth, the male B6C3F1 pups were dosed at 4 days by a single i.p. injection of AFB1 (6 mg/kg body weight) in DMSO (10 ml/kg body weight) or the same volume of just DMSO. The treatments were always performed at the same time of the day and the pups were returned to their mothers until they were sacrificed 4 or 24 h after treatment.  Adult B6C3F1 males were treated with the same doses and volumes of AFB1 or DMSO after an acclimation period of at least two weeks and sacrificed 4 or 24 hours after treatment. We noticed that injection of a volume of 10 ml/kg (whether AFB1 or vehicle alone) is tolerated poorly by adult animals and thus another group of adult animals was added which was treated with the same (6 mg/kg) dose of AFB in lower (5 ml/kg) volume. Corresponding vehicle control animals (5ml/kg DMSO) were also used. In addition, untreated controls were used and sacrificed together with the treated animals. Three independant bilogical replicates were used for each experimental point. Total RNA was isolated from livers and processed according to standard Affymetrix protocol.

middle: O

first: Jeannette

middle: L

last: Fiala

first: Jessica

last: Kosa

first: John

last: Essigmann


title: Transcriptome modulation analysis of cytomegalovirus-infected immature monocyte-derived dendritic cells

status: Public on Jan 22 2009

city: Nantes

first: Franck

last: Halary

address: 30, bd Jean Monnet

department: ITERT - CHU Hotel Dieu

institute: INSERM UMR643

summary:
Analysis of dendritic cells (DCs) at 6h and 48h after infection with cytomegalovirus (CMV) versus non infected. CMV tends to induce immunosuppression followed by lasting immunity. DCs appear to play a role in this effect. Results provide insights into CMV/DC interactions and suggest mechanisms for CMV-regulated early immune response.

Keywords: gene expression array-based, count

overall_design: In the present study, immature monocyte-derived dendritic cells were generated from CMV neg healthy blood donors and infected or not with an endotheliotropic CMV strain. Gene expression modulation by the CMV infection was studied in a time course assay (non-infected - NI - vs 6h or 48h post-infection.  Patient C has no 48h sample

first: Fabienne

last: Haspot

first: Audrey

last: Bihouée

first: Catherine

last: Chevalier

first: Rémi

last: Houlgatte


title: CLL: CD38+CD49d+ vs. CD38-CD49d-

status: Public on Mar 03 2009

first: daniela

last: marconi

summary:
CD38 and CD49d are associated negative prognosticators in chronic lymphocytic leukemia (CLL).
Despite evidence that both molecules are involved in interactions occurring between CLL and normal cells in the context of CLL-involved tissues, a functional link is still missing. Using gene expression profiles comparing CD38+CD49d+ vs. CD38-CD49d- CLL cells, we demonstrated
overexpression of the CCL3 and CCL4 chemokines in cells from the former group. These chemokines were also upregulated by CD38 signals in CLL; moreover, CCL3 was expressed by CLL cells from bone marrow biopsies (BMB) of CD38+CD49d+ but not CD38-CD49d- cases. High levels of CCR1 and, to a lesser extent, CCR5, the receptors for CCL3 and CCL4, were found in CLL-derived monocyte-macrophages. Consistently, CCL3 increased monocyte migration, and CD68+ macrophage infiltration was particularly high in BMB from CD38+CD49d+ CLL.
Conditioned media from CCL3-stimulated macrophages induced endothelial cells to express VCAM-1, the CD49d ligand, likely through TNFα over-production. These effects were apparent in BMB from CD38+CD49d+CLL, where lymphoid infiltrates were characterized by a prominent meshwork of VCAM-1+ stromal/endothelial cells. Lastly, CD49d engagement by VCAM-1-transfectants increased viability of CD38+CD49d+ CLL cells. Altogether, CD38 and CD49d can be thought of as a part of a consecutive chain of events ultimately leading to improved survival of CLL
cells.

overall_design: Dual Color reference design with 26 different patients (15 cd38-cd49d- and 11 cd38+cd49d+)

first: Antonella

first: Dania

last: Benedetti

first: Claudio

last: Tripolo

first: Riccardo

last: Bomben

first: Michele

last: Dal Bo

first: Daniela

last: Marconi

first: Gianluca

last: Gaidano

last: Deagan

first: Fabio

last: Malavasi

first: Debora

last: Lorenzon

first: Francesca

last: Rossi

first: Davide

first: Pietro

first: Vito

last: Franco

first: Giovanni

last: Del Poeta

first: Francesco

last: Tedesco


title: Effect of conditional deletion of S6 ribosomal protein following partial hepatectomy

status: Public on May 01 2009

city: Basel

first: Alessandro

last: Di Cara

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute

summary:
Deletion of the RPS6 gene in mouse liver results in the inhibition of 40S ribosome biogenesis and the failure of hepatocytes to enter S-phase following partial hepatectomy. This microarray experiment was designed to assess the effects of RPS6 deletion on the expression of genes involved in liver regeneration following partial hepatectomy.

Keywords: time course, liver

overall_design: RNA was isolated from mouse livers at different time-points following partial hepatectomy. Conditional deletion of the RPS6 gene was perfomed by injecting polyinosinic-polycytidylic acid in mice harbouring a floxed version of the RPS6 gene and a cre recombinase under the regulation of an interferon responsive promoter (MX-CRE). The mice used a control have also a floxed version of the RPS6 gene but lack the cre recombinaste transgene.

first: Stefano

last: Fumagalli

first: Edward

middle: J

last: Oakeley

first: George

last: Thomas


title: siRNA Administration Against AFP Inhibits Hepatocellular Carcinoma Proliferation in Vitro and Progression in Mice

status: Public on Dec 31 2008

city: Chiba

first: Noboru

last: Mitsuhashi

address: 1-33 Yayoi-cho, Inage-ku

department: Section for Medical Nanotechniques

institute: Research Center for Frontier Medical Engineering, Chiba University

summary:
Increased α-fetoprotein (AFP) levels have been reported to predict a poor prognosis in hepatocellular carcinoma (HCC). We assessed the mechanism of AFP involvement in the progression of HCC and determined whether AFP could be a molecular target. We used human HCC cell lines to assess proliferation and apoptosis response to exogenous AFP. We introduced AFP small interfering RNA (siRNA) into HCC cell lines to examine whether it could inhibit cell proliferation and anti-apoptotic properties. The effects of systemically introduced AFP siRNA were assessed using a tumor xenotransplantation model. The effects of AFP on gene expression in HCC cell lines and human HCC specimens were examined. Exogenous AFP induced cell proliferation dose-dependently and inhibited apoptosis induced by 5-fluorouracil (5-FU) in all cell lines examined. AFP siRNA inhibited the proliferation of AFP-producing HCC cell lines and induced apoptosis in co-cultures with 5-FU. Tumor sizes in mice treated with AFP siRNA were significantly smaller than those in controls. AFP siRNA administration in mice induced a low proliferation index and a high apoptosis index in tumors. cDNA microarray analysis, reverse transcription-polymerase chain reaction (RT-PCR), and Western blot using HepG2 and HLE cells with AFP showed that AFP reduced expression of genes related to apoptosis (DFFB) and tumor suppression (NDRG2). Expression of these molecules was also suppressed in human HCC tissues that overexpress AFP. AFP is not only a passive tumor marker, but also an active tumor stimulator through several mechanisms. AFP siRNA introduction may be of possible therapeutic use for HCC.

Keywords: Genetic modification

overall_design: Two-condition experiment, Control vs. AFP-stimulated cells.

first: Masaru

last: Miyazaki


title: MTB/TRAS short-term induction, tumor, and TGFbeta treated NMuMG cells

status: Public on Dec 22 2008

city: Philadelphia

first: Lewis

middle: A.

last: Chodosh

state: PA

address: 421 curie blvd, BRB II/III 616

department: Cancer Biology

institute: University of Pennsylvania

summary:
To test whether SVD regression is sufficiently sensitive to detect activation of a secondary, endogenous pathway as it occurs following ectopic manipulation of a strong primary pathway by focusing on the relationship between the Ras and TGFβ signaling pathways.

Keywords: Time course, Affymetrix,

overall_design: Bitransgenic MTB/TRAS mice in an FVB/N background were generated by crossing MTB and TRAS mice.  To induce oncogenic v-H-Ras expression, 6-week old MTB/TRAS female mice were administered 2 mg/ml doxycycline with 5% sucrose in their drinking water.  Mammary tissue was harvested at different post-induction time points and snap frozen.  To generate Ras-driven tumors, MTB/TRAS mice were administered 0.012 mg/ml doxycycline in their drinking water and monitored for tumor formation.  Mice were sacrificed when tumors reached ~1 cm and tissue was snap frozen.       The non-transformed murine mammary epithelial cell line, NMuMG, was cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% bovine calf serum, 1% penicillin/streptomycin, and 2 mM L-glutamine.  For TGFβ treatment, cells were cultured in low serum medium (0.5%) overnight followed by treatment with 5 ng/ml TGF-β1 or TGF-β3 (Sigma).  After 24 hr, RNA and protein were harvested for microarray hybridization or biochemical analysis.

first: Zhandong

last: Liu

first: Min

last: Wang

first: James

middle: V

last: Alvarez

first: Megan

middle: E

last: Bonney

first: Chien-chung

last: Chen

first: Celina

last: D'Cruz

first: Tien-chi

last: Pan

first: Mahlet

middle: G

last: Tadesse


title: Gene expression of human primary macrophages induced by carbosilane dendrimer 2G-NN16 complexed with or without siRNA

status: Public on Feb 10 2009

city: Madrid

first: Luis

last: Lopez-Fernandez

address: Dr. Esquerdo 46

department: Pharmacy

institute: Hospital General Universitario Gregorio Marañon

summary:
Purpose: The use of dendrimers for biomedical applications has emerged with promising results. 2G-NN16 is a carbosilane dendrimer with sixteen positive charges per molecule tested to be capable to bind and release antisense oligonucleotides (ODNs) and small interference RNA (siRNA) in vitro. In spite of low cytotoxicity observed for these dendrimers, little is known about cellular changes they produce in cells in general and in immune cells in particular.
Methods: Genomic technologies allow us to identify global gene expression profile changes in macrophages exposed to a non-toxic concentration (5µM) of 2G-NN16, alone or complexed with a random siRNA (dendriplex). Results were confirmed by quantitative real-time RT-PCR.
Results: Exposing macrophages to this dendrimer or dendriplex causes multiple gene expression changes, but no specific action of random siRNA was detected. Pathway analysis of differentially expressed genes shows the altered functions to be immune response, proliferation and transcription regulation. Interleukin 17F (IL17F) was the most regulated gene.
Conclusions: Global gene expression profiles are a highly sensitive method to measure the toxicity degree of a gene delivery vehicle. The strong repression of IL17F, IL23R and IL23A, all of them involved in autoimmune disease, by this particular dendrimer suggests a potential pharmacological application.

overall_design: This experiment was designed to identify changes in gene expression profiles in human macrophages by exposure to carboxilane dendrimer 2G-NN16. Macrophages from three donors were isolated and cultured for 5 hours alone or in the presence of 5µM 2G-NN16 complexed with or without siRNA (Dendriplex). Control samples were labeled with Alexa Fluor 555 and dendrimer and dendriplex samples with Alexa Fluor 647. For each donor, Alexa Fluor 555 and Alexa Fluor 647 were mixed and hybridized to 4x44k whole genome human Agilent microarrays. 3 different microarrays were used and treated as biological replicates for statistical analysis.

first: Rafael

last: Gras

last: Almonacid

first: Paula

last: Ortega

last: Gomez

first: Francisco

last: de la Mata

last: Lopez Fernandez

first: Maria

last: Muñoz-Fernandez


title: Replication and active demethylation represent partially overlapping mechanisms for erasure of H3K4me3 in budding yeast

status: Public on Jan 28 2009

city: Worcester

first: Oliver

last: Rando

address: 364 Plantation St.

institute: UMass Medical School

type: Genome binding/occupancy profiling by genome tiling array

summary:
Histone modifications affect DNA-templated processes ranging from transcription to genomic replication. In this study, we examine the cell cycle dynamics of the trimethylated form of histone H3 lysine 4 (H3K4me3), a mark of active chromatin that is viewed as “long-lived” [1], and that is involved in memory during cell state inheritance in metazoans [2]. We synchronized yeast using two different protocols, then followed
H3K4me3 patterns as yeast passed through subsequent cell cycles. While most H3K4me3 patterns were conserved from one generation to the next, we found that methylation patterns induced by alpha factor or high temperature were erased within one cell cycle, during S phase. Early-replicating regions were erased before late-replicating regions, implicating replication in H3K4me3 loss. However, incomplete H3K4me3 erasure
occurred at the majority of loci even when replication was prevented, suggesting that most erasure results from an active process. Indeed, deletion of the demethylase Jhd2 slowed erasure at most loci. Together, these results indicate overlapping roles for passive dilution and active enzymatic demethylation in erasing ancestral histone methylation states in yeast.

References:

[1] Ng HH, Robert F, Young RA, Struhl K (2003) Targeted recruitment of Set1 histone methylase by elongating Pol II provides a localized mark and memory of recent transcriptional activity. Mol Cell 11: 709-719.

[2] Ringrose L, Paro R (2004) Epigenetic regulation of cellular memory by the Polycomb and Trithorax group proteins. Annu Rev Genet 38: 413-443.

overall_design:
The overall design of the experiment consists of two cell cycle experiments, each consisting of the following subsets:  gene expression, ChIP with anti-H3K4Me3 antibody, and ChIP input.  The experiments are as follows:  CCA - BY4741 bar1- cells synchronized by alpha factor arrest;
CCTS - BY4741 cdc28(ts) cells synchronized by arrest at non-permissive temperature.  The individual time courses are enumerated as follows: CCA gene expression (array title "Synchronized cells, xxx min, cell cycle CCA"), 18 arrays; CCA ChIP for anti-H3K4Me3 (array title "H3K4Me3 ChIP cell cycle CCA, xxx min"), 17 arrays, 1 replicate; CCA ChIP input (array title "ChIP Input cell cycle CCA, xxx min"), 18 arrays, 1 replicate; CCTS gene expression (appears in a different dataset as biological replicate "I"; array title "Synchronized cells, xxx min, biological replicate I"), 18 arrays; CCTS ChIP for anti-H3K4Me3 (array title "H3K4Me3 cell cycle CCTS, xxx min"), 2 technical replicates, 18 arrays per replicate; CCTS ChIP input (array title "ChIP Input cell cycle CCTS, xxx min"), 2 technical replicates, 18 arrays per replicate.  Gene expression arrays were run against a reference of unsynchronized cells, ChIP-chip anti-H3K4Me3 samples were run against an IP (of the same epitope) of unsynchronized cells, and ChIP input samples were run against either a pool of all the time points in the time course (CCTS) or against sonicated DNA isolated from unsynchronized cells (CCA).

Four additional experiments have been performed. They are referred to as series X in the title.

Series 1: anti H3K4me3 CHIP time course of BY4741 bar1 delete cells (wt) synchronized with alpha factor and released in the cell cycle, 9 arrays, 1 replicate.

Series 2: anti H3K4me3 CHIP time course of BY4741 bar1 jhd2 delete cells (jhd2 delete) synchronized with alpha factor and released in the cell cycle, 7 arrays, 1 replicate.

Series 3: anti H3K4me3 CHIP time course of CYM36 cells (cdc7ts) synchronized with alpha factor and released in the cell cycle at the permissive 24C or at the restrictive 37C temperature, 22 arrays, 2 replicates.

Series 4: anti H3K4me3 CHIP time course of BY4741 bar1 delete cells (wt) grown in galactose and  synchronized with alpha factor and either released in the cell cycle in glucose media or alpha factor arrested and switched to glucose media, 6 arrays, 1 replicate.

first: Marta

last: Radman-Livaja

first: Chih

first: Nir

last: Friedman

first: Stuart

last: Schreiber


title: Species difference in gene expression effect of trichloroethylene (TCE) between mouse and rat (rat)

status: Public on Dec 25 2008

city: Shinjyuku-ku

first: Sano

last: Yuri

address: 35 Shinanomachi

department: Department of Preventive Medicine and Public Health

institute: Keio Univ.

summary:
TCE is a non-genotoxic hepatocarcinogen in mouse, but not in rat or human. Extrapolation of data from laboratory animals to humans is difficult due to species-specific differences. To identify molecular pathways and biological changes responsible for species-specific differences in hepatocarcinogenesis, we analyzed gene expression profiles of livers from B6C3F1 mice and SD rats administered TCE by oral gavage once or repeatedly every 24 hrs for 14 days. Gene expression analysis revealed distinct clusters of transcriptional profiles in single- and repeated-dose mice and rats.  Pathway analysis showed differences in biological pathways between single- and repeated-dose mice and rats. Activation of the MAPK signaling cascade and ubiquitin-proteasome inhibitory function, as well as inhibition of TGF-beta signaling, were specific to mice and suggest a role in hepatocyte proliferation. Although pathological analysis showed no evidence of apoptosis, gene expression analysis revealed changes in apoptosis-related genes. In addition to the previously reported suppression of apoptosis, results in repeated-dose mice showed that toxicity induced by TCE in turn induces apoptosis.
Keywords: Response to chemical

sample_organism:
Mus musculus
Rattus norvegicus

platform_organism:
Mus musculus
Rattus norvegicus

overall_design: Eight-week-old B6C3F1 mice and SD rats were administered 1500mg/kgBW TCE (n=4) or with corn oil (n=4) once or every 24h for 2 weeks by oral gavage. The liver tissue were collected 18h after the last dosage. mRNA were extracted from the liver and were hybridized to Affymetrix GeneChip

first: Yuri

last: Sano

first: Hiroshi

last: Nakashima

first: Noriyuki

last: Yoshioka

first: Kazuyuki

last: Omae


title: Immune Responses to Pneumocystis Infection are Robust in Immunocompetent Mice but Absent in CD40 Ligand Deficient Mice

city: Bethesda

first: Joseph

last: Kovacs

state: MD

department: CCMD

institute: NIH

summary:
Pneumocystis is a pathogen of immunocompromised hosts but can also infect healthy hosts, in whom infection is rapidly controlled and cleared. To better understand the immune mechanisms contributing to clearance of infection, microarray methods were used to examine differential gene expression in the lungs of  C57BL/6 and CD40 ligand knock-out (CD40L-KO) mice over time following exposure to Pneumocystis. Immuncompetent C57BL/6 mice, which control and clear infection efficiently, showed a robust response to infection characterized by the upregulation of 349 primarily immune-response associated genes.  Temporal changes in the expression of these genes suggested that there was an early (week 2) primarily innate response, that waned without controlling infection; this were followed by primarily adaptive immune responses that peaked at week 5 and successfully cleared the infection. In conjunction with the latter, there was an increased expression of B cell associated (immunoglobulin) genes at week 6 that persisted through 11 weeks.   In contrast, CD40L-KO mice, which are highly susceptible to developing severe Pneumocystis pneumonia, showed essentially no upregulation of immune-response associated genes at days 35 to 75. Immunohistochemical staining supported these observations by demonstrating an increase in CD4+, CD68+, and CD19+ cells in C57BL/6 but not CD40L-KO mice. Thus, the healthy host demonstrates a robust biphasic response to infection by Pneumocystis; CD40 ligand is an essential upstream regulator of the adaptive immune responses that efficiently control infection and prevent development of progressive pneumonia.
Keywords: Time course response Pneumocystis murina infection wild type versus CD40L-KO mice

overall_design: In experiment 1, C57BL/6 and CD40L-KO mice were co-housed in 2 cages; one cage was exposed to a P. murina-infected seeder, while the second was unexposed. Mice (3 per group) were sacrificed at day 32. Because the initial study demonstrated very little change in gene expression in CD40L-KO mice, only C57BL/6 mice were used for experiments 2 and 3. In Experiment 2,  three cages (10 animals/cage) were set up: 2 cages were exposed to P. murina, and one was unexposed. Animals (5 per cage) were sacrificed at days 34 and 41. In Experiment 3, which focused on gene expression early after exposure to P. murina, five cages (9-10 animals/cage) were set up, of which 3 were exposed and 2 were unexposed. Animals (1-3 per cage) were sacrificed at days 7, 14 and 21 of exposure. Experiment 4 was designed to verify the initial results in CD40L-KO mice, and included 5 unexposed controls and 4 mice exposed for  35 days.

first: Beatriz

last: Hernandez-Novoa

first: Lisa

last: Bishop

first: Carol

last: Logun

first: Peter

last: Munson

first: Eldad

last: Elnekave

first: Zoila

last: Rangel

first: Jennifer

last: Barb

first: Robert

last: Danner


title: Decoy vs Scrambled and siRNA vs Mock Transfected MBA-MD-231 Cell Line

status: Public on Nov 04 2009

city: San Francisco

first: Hani

last: Goodarzi

department: Biochemistry and Biophysics

institute: UCSF

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

overall_design: Refer to individual Series


title: Defining a Chromatin Pattern That Characterizes DNA Hypermethylated Genes in Colon Cancer Cells

status: Public on Jan 20 2009

city: Ghent

first: Leander

last: Van Neste

address: Coupure Links 653

department: Molecular Biotechnology

country: Belgium

institute: Ghent University

summary:
Epigenetic gene regulation is a key determinant of heritable gene expression patterns and is critical for normal cellular function.  Dysregulation of epigenetic transcriptional control is a fundamental feature of cancer, particularly manifesting as increased promoter DNA methylation with associated aberrant gene silencing which plays a significant role in tumor progression.  We now globally map key chromatin parameters for genes with promoter CpG island DNA hypermethylation in colon cancer cells by combining microarray gene expression analyses with ChIP on chip technology.  We first show that the silent state of such genes universally correlates with a broad distribution of a low, but distinct, level of the PcG mediated histone modification, methylation of lysine 27 of histone 3 (H3K27me) and a very low level of the active mark, H3K4me2.  This chromatin pattern, and particularly H3K4me2 levels, crisply separates DNA hypermethylated genes from those where histone deacetylation is responsible for transcriptional silencing.  Moreover, the chromatin pattern can markedly enhance identification of truly silent and DNA hypermethylated genes.  We additionally find that when DNA hypermethylated genes are de-methylated and re-expressed, they adopt a “bivalent” chromatin pattern which is associated with the poised gene expression state of a large group of ES cell genes, and is characterized by an increase in levels of both the H3K27me3 and H3K4me2 marks.  Our data have great relevance for the increasing interest in re-expression of DNA hypermethylated genes for the treatment of cancer.
Keywords: DNA methylation, chromatin, histone modifications, cancer, epigenetic, ChIP-chip, expression microarray, hypermethylome, DNA-hypermethylation, DAC, TSA, colorectal cancer

overall_design:
Cell Culture.  HCT116 and DKO cells were maintained in McCoy’s 5A modified medium supplemented with 10% fetal bovine serum (Gemini Bio-Products) and 1% penicillin/streptomycin (Invitrogen) and grown at 37°C in 5% CO2 atmosphere.
ChIP-chip.  Chromatin immunoprecipitation was combined with DNA microarray analysis results (Schuebel KE et al., PLoS Genetics, 2007) on HCT116 colorectal cancer cells and DKO cells in duplicate using antibodies specific for H3K27me3 (Perez-Burgos L et al., Methods Enzymol, 2004), H3K4me2 (Upstate) or an IgG control (Upstate).  Using 5 x 10^7 cells per experiment, chromatin immunoprecipitation, DNA amplification, labeling, and array hybridization were performed as previously described (Boyer LA et al., Cell, 2005).  Independent batches of HCT116 and DKO cells were used to perform independent ChIP experiments and ChIPs for each antibody were hybridized to independent Agilent array sets.  Whole genome expanded promoter 244K arrays from Agilent Technologies that span roughly 5 Kb upstream to 2 Kb downstream from gene transcription start sites were used.
Analyses.  The data preprocessing for the tiling arrays was performed according to the manufacturers recommendations using the Agilent® ChIP Analytics 1.3 software, i.e. a median blanks subtraction followed by an inter-array median normalization and a dye-bias median normalization.  The data was imported into R for downstream analysis.  The expression arrays were preprocessed as previously described (Schuebel KE et al., PLoS Genetics, 2007).

first: Kelly

last: McGarvey

first: Leslie

last: Cope

first: Joyce

last: Ohm

first: James

last: Herman

first: Wim

last: Van Criekinge

first: Kornel

last: Schuebel

first: Stephen

middle: B

last: Baylin


title: Expression profile of PITX2 overexpressed HEK293 cells

city: Huntington

last: Denvir

state: WV

address: One John Marshall Drive

department: Biochemistry and Microbiology

institute: Marshall University School of Medicine

summary: PITX2 is a homeodomain transcription factor that has a substantial role in cell proliferation and differentiation in various tissues. In this study we have characterized PITX2-regulating genes. These data provide an insightful perspective for further studying PITX2 function and mechanism of action.

overall_design: Two condition experiment comparing HEK293 cells transfected with pEGFP-NFLAG-PITX2c (sample) to HEK293 cells transfected with pEGFP-N1 (control). Balanced-block design (each array has one sample replicate and one control replicate) with dye-swap, with 4 biological replicates.

first: Yue

last: Huang

first: Kan

first: Goran

last: Boskovic

first: Yulia

last: Dementieva

first: Guo-Zhang

last: Zhu


title: Response of p53 isogenic colorectal cancer panel to 12 Gy gamma irradiation

status: Public on Dec 11 2008

first: Raymond

middle: Anthony

last: Pagliarini

address: 250 Massachusetts Ave. Room 3C-292

department: Oncology

institute: NIBRI

summary:
Though targeted homologous recombination, we developed a panel of matched colorectal cancer cell lines that differ only with respect to their endogenous TP53 status.  We then used these lines to define the genes whose expression was altered following DNA damage induced by ionizing radiation.    Transcriptome analyses revealed a consistent upregulation of polo-like kinase I (PLK1) as well as other genes controlling the G2/M transition in the cells whose TP53 genes were inactivated compared to those with wild type (wt ) TP53 genes.

Keywords: Genetic Modification, Stress Response

overall_design: Two-condition experiment, with or without 12 Gy gamma radiation; these conditions are on the same array.  No replicates included


title: Effect of L1CAM Knockout on Gene Expression in the Cerebellum

status: Public on Dec 17 2008

city: Miami

first: Vance

middle: P

last: Lemmon

state: FL

address: 1095 NW 14th Terrace

department: Miami Project to Cure Paralysis

institute: University of Miami

summary: Cerebellum from post-natal day 11 L1 knockout mice on the 129Sv background were compared to wild type littermates.  The original goal of the study was to determine if there was compensation from other L1 family members or alterations in cell survival or apoptosis.  Interestingly no major changes were detected in those families or pathways.

overall_design: The microarray experiment was conducted by extracting total RNA from the cerebellums of three postnatal day 11 congenic 129Sv L1 knock outs and three of their wild type siblings utilizing Qiagen's RNeasy Mini kit (# 74104). Therefore, each genotype, L1KO and wildtype, had three replicates. Samples were processed at the Case Western Reserve University Cancer Center Gene Expression Array Core Facility and hybridized to Affymetrix Murine Genome U74AV2 gene chips.

first: Robin

last: Smith

first: Yoshimasa

last: Kamei

first: Alexis

last: Tapanes-Castillo


title: The Repertoire and Dynamics of Evolutionary Adaptations to Controlled Nutrient-Limited Environments in Yeast

status: Public on Nov 08 2008

city: Seattle

first: Maitreya

middle: J.

last: Dunham

address: Foege Building, S403B, Box 355065

department: Genome Sciences

institute: University of Washington

type:
Expression profiling by array
Genome variation profiling by array

summary:
The experimental evolution of laboratory populations of microbes provides an opportunity to observe the evolutionary dynamics of adaptation in real time.Until very recently, however, such studies have been limited by our inability to systematically find mutations in evolved organisms.We overcome this limitation by using a variety of DNA microarray-based techniques to characterize genetic changes, including point mutations, structural changes, and insertion variation, that resulted from the experimental adaptation of 24 haploid and diploid cultures of Saccharomyces cerevisiae to growth in glucose-, sulfate, or phosphate-limited chemostats for ~ 200 generations.We identified frequent genomic amplifications and rearrangements as well as novel retrotransposition events associated with adaptation.Global mutation detection in 10 clonal isolates identified 32 point mutations. On the basis of mutation frequencies, we infer that these mutations and the subsequent dynamics of adaptation are determined by the batch phase of growth prior to initiation of continuous phase in the chemostat.We relate these genotypic changes to phenotypic outcomes, namely global patterns of gene expression, and to increases in fitness by 5-50%. We found that the spectrum of available mutations in glucose or phosphate-limited environments combined with the batch phase population dynamics early in our experiments to allow several distinct genotypic and phenotypic evolutionary pathways in response to these nutrient limitations. By contrast, sulfate-limited populations were much more constrained in both genotypic and phenotypic outcomes.Thus, the reproducibility of evolution varies with specific selective pressures reflecting the constraints inherent in the system-level organization of metabolic processes in the cell.We were able to relate some of the observed adaptive mutations (e.g. transporter gene amplifications) to known features of the relevant metabolic pathways, but many of the mutations pointed to genes not previously associated with the relevant physiology. Thus, in addition to answering basic mechanistic questions about evolutionary mechanisms our work suggests that experimental evolution can also shed light on the function and regulation of individual metabolic pathways.

Keywords: gene expression, CGH, and TSE analysis

overall_design:
consult individual records for details of analysis
This Dataset consists of several experiments:

Gene expression experiments found in Figure 1a of paper:
Design: RNA from each evolved clone or population grown in chemostat culture is compared to RNA from matching ancestor strains grown in the same conditions.
Samples: GSM339025-GSM339088

CGH experiments found in Figure 2A, Figure 3, and Table S2:
Experiment design: DNA from each evolved clone or population is hybridized vs DNA from the matched ancestor strain
Samples: GSM339089-GSM339146

CGH experiments found in Table S3:
Experiment design: DNA from each segregant derived from an evolved strain is hybridized vs DNA from the matched ancestor strain
Samples: GSM339147-GSM339158

Gel band CGH experiments found in Figure S1:
Experiment design: Chromosomes from evolved strains were run on a gel and excised.  DNA from the bands is hybridized vs matched ancestor genomic DNA
Samples: GSM339159-GSM339184

TSE CGH experiments found in Table S4:
Experiment design: DNA linked to Ty1/Ty2 sequences was extracted from evolved strains and ancestor strains, and compared to ancestral extracted or genomic DNA as indicated.
Samples: GSM339185-GSM339212

CGH experiments for experiments in Figure S7:
Experiment design: DNA from 2 strains transformed with a SUL1 plasmid hybridized vs DNA from the matched ancestor strain
Samples: GSM339213 and GSM339214

first: David

last: Gresham

first: Michael

middle: M

last: Desai

first: Cheryl

last: Tucker

first: Harry

middle: T

last: Jenq

first: Dave

last: Pai

first: Alexandra

last: Ward

first: Christopher

last: DeSevo

last: Botstein


title: TNFa-stimulation of XIAP -/- MEF

status: Public on Nov 12 2008

city: Vienna

first: Rainer

last: de Martin

address: Schwarzspanierstr. 17

department: Vascular Biology

country: Austria

institute: Medical University of Vienna

summary:
XIAP (X chromosome-linked inhibitor of apoptosis; ILP, BIRC4) is involved not only in apoptosis, but also in signal tranduction in the NF-kappaB, TGF-beta, bone morphogenic protein, and JNK signalling pathways. We have analyzed whether XIAP deletion leads to changes in gene expression, particularly after inflammatory stimulation.
Keywords: genetic modification, inflammatory response

overall_design: Fibroblasts from wild-type and XIAP knockout mice were analyzed with and without TNFa stimulation (4 hours) using Affymetrix U74Av2 arrays.

first: Gabriele

last: Winsauer

first: Renate

last: Hofer-Warbinek

first: Martin

last: Bilban


title: Gene expression data from murine liver samples comparing hormone sensitive lipase (HSL) knockout mice vs. wildtype mice

status: Public on Jan 03 2009

city: Lund

first: Céline

last: Fernandez

address: BMC C11

department: Experimental Medical Science

country: Sweden

institute: Medical Faculty, Lund University

summary:
HSL is a key enzyme in in the mobilization of fatty acids from the triglyceride stores of white adipose tissue. In addition, it is expressed in mice liver.  In the present microarray study, changes in the transcript profile of murine liver samples due to global HSL knockout were investigated.
Keywords: genetic modification

overall_design:
Genetic modification to analyze the impact of a general knockout of the HSL gene on liver metabolism.
HSL knockout (ko) mice versus wildtype (wt) mice. Mice fed a normal diet (ND) versus mice fed a high fat diet (FD) for 6 months. Equal amounts of liver samples from six mice were pooled and total RNA was extracted, except for HSL-null mice on FD were only 4 livers were pooled.

first: Cecilia

last: Holm


title: Meiotic DNA double strand breaks in wild-type and set1∆ cells

status: Public on Nov 01 2008

city: New York

first: Nicolas

last: Robine

state: NY

address: 101 Avenue of the Americas

department: Bioinformatics

institute: New York Genome Center

summary: In relation with the study of the meiotic dynamic of H3K4 methylation, we determined the meiotic Double Strand Breaks (DSB) profiles of wild-type and set1∆ cells.

overall_design: We profiled the DSB sites by immunoprecipitating Rfa1 in dmc1∆ cells, at 5h for the wild-type experiment and at 7h for the set1∆ cells.

first: Valerie

last: Borde

first: Vincent

last: Geli

first: Alain

last: Nicolas


title: Meiotic time course of Histone H3 occupancy in a mutant Spo11F

summary:
To study the meiotic dynamic of the methylation of H3K4, in relation with the transcriptomic regulation, we determine the meiotic time-course of H3 occupancy by ChIP-chip in a mutant Spo11F.
Keywords: ChIP-chip, meiotic time course, histone modification

overall_design:
Strain ORD7341
meiotic time-course from 0 to 6h.
Immunoprecipitation with rabbit polyclonal anti H3Cter (Abcam #1791)

first: Valérie

first: Waka

last: Lin

first: Sandrine

last: Bonfils

last: Géli


title: Meiotic time course of the trimethylation of the Lysine 4 of Histone H3 (H3K4me3)

summary:
To study the meiotic dynamic of the methylation of H3K4, in relation with the transcriptomic regulation, we determine the meiotic time-course of H3K4me3 by ChIP-chip.
Keywords: ChIP-chip, meiotic time course, histone modification

overall_design:
Strain ORD7339
meiotic time-course from 0 to 6h.
Immunoprecipitation with rabbit polyclonal anti-triMe H3K4 (Abcam #Ab8580).


status: Public on Dec 06 2008

city: Kyoto

first: Akira

last: Watanabe

state: Kyoto

address: Rm504, Miyako Bldg, 233, Isa-cho, kamigyo-ku

institute: CyberomiX Inc

summary:
The immune system sustains inflammation, and can occasionally inhibit tumor development. Conversely, chronic inflammation positively contributes to the development of cancer. Furthermore, it was revealed that the large number of macrophages and haematopoietic progenitor cells accumulate in response to primary tumors in pre-metastatic lungs. However, the relationship between the inflammation-like state induced by primary tumors in pre-metastatic phase and the migration of tumor cells in metastasis is not well understood. Here we analyzed transcriptional change of the lungs by pre-metastatic stimuli.
Keywords: Gene expression analysis of pre-metastatic lungs

overall_design: We examined the lungs derived from mice that had been injected with tumor cells into the back subcutaneously. This model mimics pre-metastatic lungs responding to a primary tumor before tumor cells reach the lungs.

first: Sachie

last: Hiratsuka

first: Sachiko

last: Akashi

first: Kensuke

last: Miyake

first: Shizuo

last: Akira

first: Hiroyuki

last: Aburatani

first: Yoshiro

last: Maru


title: Molecular characterization of novel peroxisome proliferator-activated receptor alpha agonists

status: Public on Nov 25 2008

city: Groton

first: James

last: Fischer

state: CT

department: Exploratory Medicinal Sciences

institute: Pfizer, Inc

summary:
The nuclear receptor PPARalpha is recognized as the primary target of the fibrate class of hypolipidemic drugs and mediates lipid lowering in part by activating a transcriptional cascade that induces genes involved in the catabolism of lipids.  We report here the characterization of three novel PPARalpha agonists with therapeutic potential for treating dyslipidemia.  These structurally related compounds display potent and selective binding to human PPARalpha and support robust recruitment of coactivator peptides in vitro.  These compounds markedly potentiate chimeric transcription systems in cell-based assays and strikingly lower serum triglycerides in vivo.  The transcription networks induced by these selective PPARalpha agonists were assessed by transcriptional profiling of mouse liver after acute and chronic treatment.  The induction of several known PPARalpha target genes involved with fatty acid metabolism were observed, reflecting the expected pharmacology associated with PPARalpha activation.  We also noted the downregulation of a number of genes related to immune cell function, the acute phase response, and glucose metabolism; suggesting that these compounds may have anti-inflammatory action in the mammalian liver. Taken together, these studies articulate the therapeutic promise of a selective PPARalpha agonist.

Keywords: acute versus chronic treatment of piperidine PPARalpha agonists

overall_design: Male C57Bl/6 mice (n=4 for all except 5 day treatment of 146-02 was n=2) were treated with the piperidine agonists for 24hr or 5 days at 1mg/kg/day, or water (vehicle) as control.

first: Christopher

middle: D

last: Kane

first: Kimberly

last: Stevens

first: Mehrdad

last: Haghpassand

first: Lori

last: Royer

first: Charles

last: Aldinger

first: Katherine

last: Landschulz

first: Panayiotis

last: Zagouras

first: Scott

middle: W

last: Bagley

first: William

last: Hada

first: Robert

last: Dullea

first: Cheryl

last: Hayward

first: Omar

last: Francone


title: Transcriptional Profiling of Human Embryonic Stem Cell-Derived Cardiomyocytes

city: Stanford

first: Kitchener

middle: D.

last: Wilson

address: S140 Grant Bldg

institute: Stanford University

summary:
Myocardial infarction is a major cause of morbidity and mortality worldwide. The limited ability of the surviving cardiac cells to proliferate following an ischemic attack renders the damaged heart susceptible to unfavorable remodeling processes and heart failure. Currently, pharmaceutical and implantable device management of heart failure seek only to preserve existing viable myocardium after an ischemic attack, and thus merely slows the progression of cardiac dysfunction. Ultimately, heart transplantation is the only viable treatment option for end-stage heart failure patients. To “regenerate” the heart and not only preserve cardiac function but also recover lost or diseased muscle, stem cell therapy has emerged as a promising therapy for heart disease because it can provide a virtually unlimited source of cardiomyocytes, endothelial cells, and other differentiated cell types. The hope is to use these cells to replace diseased myocardium that would otherwise progress to outright failure and regenerate the heart to its former, healthy self.

Recently, human embryonic stem cells (hESCs) have generated much interest because of their capacity for self-renewal and pluripotency. In practical terms, hESCs can be cultured indefinitely ex vivo, and can differentiate into virtually any cell type in the adult body. hESCs are thus an attractive source for the derivation of large numbers of cells to be used in various tissue repair and cell replacement therapies. However, upon transplantation into living organisms, undifferentiated hESCs can spontaneously differentiate into rapidly proliferating teratomas, which are disordered amalgams of all three germs layers. Nevertheless, under the appropriate conditions, ex vivo hESCs can be directed to differentiate into beating cardiomyocytes via an embryoid body (EB) intermediate. Subsequently, the cardiomyocyte sub-population is enriched several-fold using discontinuous density gradient separation. Therefore, coaxing hESCs into cardiomyocytes for therapeutic applications is an innovative and feasible strategy that can minimize the risk of cellular misbehavior and teratoma formation.

In order to define at a molecular level the changes occurring at each stage of hESC differentiation into cardiomyocytes, we performed transcriptional profiling of the cells using whole human genome microarrays.  This allowed us to examine the activation of specific genes as well as broader developmental processes during the progression from hESC to fetal cardiomyocyte, and to identify novel genes that are potentially important in mediating differentiation and development as well as potential novel markers of each stage.  In the future, such genes may prove vital in efforts to more closely direct and assess differentiation of potential therapeutic pre-cardiomyocytes or cardiomyocytes in the repair of injured cardiac tissues.

In our microarray analysis, we observed high expression of pluripotency-related genes involved in the core hESC regulatory circuitry, including OCT4, SOX2, and NANOG, as well as CRYPTO 1 and 3, LCK, and HESX1. Differentiation into beating EBs was accompanied by mesodermal differentiation and dramatic activation of TWIST1, TBX5, and MEOX transcription, as well as the very clear induction of nearly all of the early cardiogenic genes, including FOXC1, ISL2, HAND1, GATA4, 5, and 6, FOXH1, and MEF2C. While it is clear that other developmental lineages are still present in the EB population, it is also clear from the high levels of cardiac gene expression that this population is significantly enriched for the cardiac lineage even at an early stage. The transcriptional analysis of the final differentiation and selection of the hESC-derived CMs indicates that this enrichment continues, with the CM population expressing differentiated cardiomyocyte genes at levels similar to our more advanced FH cells. Importantly, because of the cell type heterogeneity in the fetal heart, we specifically isolated cardiomyocytes from the fetal left ventricles for microarray analysis.

In summary, hESC-CMs hold potential promise for treatment of cardiovascular disease. The molecular processes that control stem cell pluripotency, differentiation, and proliferation are complex, justifying the need for a broad investigation that integrates systems biological tools for transcriptome analysis. We found that the enriched hESC-CMs expresses cardiomyocyte genes at levels similar to 20-week fetal heart cells, making this population a good source of potential replacement cells in the in vivo setting.

overall_design: Each group was performed in biological quadruplicates. Pooled RNA from all samples used as reference control.

first: Feng

last: Cao

first: Roger

middle: A

last: Wagner

first: Xiaoyan

last: Xie

first: Ji-Dong

last: Fu

first: Micha

last: Drukker

first: Andrew

last: Lee

first: Ronald

last: Li

first: Sanjiv

middle: S

last: Gambhir

first: Irving

last: Weissman

middle: C

last: Robbins

first: Joseph

last: Wu


title: Adipose Tissue Expression Profiles of Mice that Vary in Adiposity and Insulin Sensitivity

first: Anthony

last: Ferrante

address: 1150 St. Nicholas Ave. Rm. 243

department: Medicine

institute: Columbia University

summary:
Adipose tissue gene expression was profiled from perigonadal adipose tissue of mice whose body mass and insulin sensitivity varied as a function of diet, gender, monogenic mutations and insulin sensitizing therapies.  Mice were 22-24 weeks of age and sacrificed between 2-3 hours into the light portion of a 12/12 dark-light cycle.  The goal was to identify transcripts whose adipose tissue expression is correlated with adiposity, insulin sensitivity and other measures of metabolic function.
Keywords: population

overall_design: Mice on the C57BL/6J strain were housed in groups of 3-5 and fed ad libitum.  2-4 days prior to collection of adipose tissue fasting blood glucose and serum insulin concentrations were measured. Mice were sacrificed 2-3 hours into the light cycle. RNA was extracted from perigonadal adipose tissue and used to generate labed cRNA for hybridization to Affymetrix Mu74Av2 microarrays.

first: Stuart

last: Weisberg

first: Daniel

last: McCann


title: Hypoxic shock in DLD-1 cells

status: Public on Dec 20 2008

city: Minatoku

first: Yutaka

last: Suzuki

email: ysuzuki@k.u-tokyo.ac.jp, ysuzuki@hgc.jp

address: 4-6-1, Shirokanedai

institute: University of Tokyo

summary: Combining our full-length cDNA method and the massively-parallel sequencing technology, we developed a simple method to collect precise positional information of transcriptional start sites (TSSs) together with digital information of the gene expression levels in a high throughput manner. We applied this method to observe gene expression changes in a colon cancer cell line cultured in normoxic and hypoxic conditions. We generated more than 100 million 36-base TSS-tag sequences and revealed comprehensive features of hypoxia responsive alterations in the transcriptional landscape of the human genome. The features include presence of inducible hot regions in 54 genomic regions, 220 novel hypoxia inducible promoters that may drive non-protein-coding transcripts, 191 hypoxia responsive alternative promoters and detailed views of 120 novel as well as known hypoxia responsive genes. We further analyzed hypoxic response of different cells using additional 60 million TSS-tags and found that the degree of the gene expression changes were different among cell lines, possibly reflecting cellular robustness against hypoxia. The novel dynamic figure of the human gene transcriptome will deepen our understanding of the transcriptional program of the human genome as well as bringing new insights into the biology of cancer cells in hypoxia.

overall_design: Gene expression changes were observed in DLD-1 cells in response to hypoxic shock (1% O2).

first: Y


title: Expression data from mouse aorta-gonad-mesonephros(AGM) derived stromal cells

status: Public on Oct 10 2008

city: Machida-shi

first: Kenji

last: Nagao

address: 3-6-6, Asahi-machi,

department: Innovative Drug Research Laboratories

institute: Kyowa Hakko Kirin Co., Ltd.

summary:
A mouse AGM-derived cell line, AGM-s3, was shown to support the development of hematopoietic stem cells. To elucidate the molecular mechanisms regulating early hematopoiesis, we obtained subclones from AGM-s3, some of which were hematopoiesis supportive (s3-A9) and others which were non-supportive (s3-A7), and we analyzed the gene expression profiles by gene chip analysis.

Keywords: cell type comparison

overall_design: Genome-wide gene expression was examined using Affymetrix GeneChip array. Assays were performed according to the manufacturer's protocol. Total RNA was isolated from each stromal cell lines. We analysed 3 cell lines, AGM-s3-A9, AGM-s3-A7 and OP9. AGM-s3-A9 and OP9 are hematopoiesis supportive cell lines. AGM-s3-A7 is a hematopoiesis non-supportive cell line.

first: Yoshiaki

last: Sohma

first: Takashi

last: Yoneya


title: Gene expression profiling of peripheral T-cell lymphoma including gamma delta T-cell lymphoma

status: Public on Oct 15 2008

city: Tsu

first: Kana

last: Miyazaki

state: Mie

address: 2-174 Edobashi

department: Department of Hematology and Oncology

institute: Mie University

summary: We performed gene expression profiling in 34 peripheral T-cell lymphoma, including 7 cases of gamma delta T-cell lymphoma to identify a unique T-cell receptor signature gene set for classification of gamma delta T-cell lymphoma and alpha beta T-cell lymphoma.

overall_design: Lymphoma tissue RNA from 34 patients was extracted for target preparation and hybridization onto Agilent microarrays.

first: Motoko

last: Yamaguchi


title: Gene expression analysis in renal cell carcinoma

status: Public on Oct 18 2008

city: Nashville

first: Kimryn

last: Rathmell

address: 2220 Pierce Ave

institute: Vanderbilt

summary:
Renal cell carcinoma (RCC) tumors express varying gene profiles, dependent on VHL and HIF status, as well as other events.
Here we analyzed a series of RCC tumors for HIF-alpha expression and VHL genotype, in relation to overal gene expression profiles.

Keywords: Patient sample study

overall_design: RNA from 12 RCC tumors was hybridized against the Perou lab RNA standard for gene expression analysis. DNA was genotyped for VHL mutation status, and tumor sections were stained for HIF-1alpha and HIF-2alpha expression.

first: John

last: Gordan

first: W

middle: K

first: M

last: Simon


title: Glioblastoma microvesicles transport RNA and proteins

status: Public on Nov 16 2008

city: Charlestown

first: Johan

last: Skog

address: 149 13th street

department: Molecular Neurogenetics

institute: Massachusetts General Hospital

summary: Glioblastoma tumour cells release microvesicles (exosomes) containing mRNA, miRNA and angiogenic proteins. These microvesicles are taken up by normal host cells, such as brain microvascular endothelial cells. By incorporating an mRNA for a reporter protein into these microvesicles, we demonstrate that messages delivered by microvesicles are translated by recipient cells. These microvesicles are also enriched in angiogenic proteins and stimulate tubule formation by endothelial cells. Tumour-derived microvesicles therefore serve as a means of delivering genetic information and proteins to recipient cells in the tumour environment. Glioblastoma microvesicles also stimulated proliferation of a human glioma cell line, indicating a self-promoting aspect. Messenger RNA mutant/variants and miRNAs characteristic of gliomas could be detected in serum microvesicles of glioblastoma patients. The tumour-specific EGFRvIII was detected in serum microvesicles from 7 out of 25 glioblastoma patients. Thus, tumour-derived microvesicles may provide diagnostic information and aid in therapeutic decisions for cancer patients through a blood test.

overall_design: The glioblastoma cell and exosome RNA was analyzed on two dual color arrays.

first: Thomas

last: Wurdinger

first: Sjoerd

last: van Rijn

first: Dimphna

last: Meijer

first: Laura

last: Gainche

first: Miguel

last: Sena-Esteves

first: William

last: Curry

first: Bob

last: Carter

first: Anna

last: Krichevsky

first: Xandra

middle: O

last: Breakefield


title: Glycogen Synthase Kinase-3-beta Regulates Glucocorticoid Signaling by Phosphorylating the Glucocorticoid Receptor

status: Public on Nov 24 2008

city: RTP

first: NIEHS

last: Microarray Core

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

summary:
Glucocorticoids (GCs) bind to the glucocorticoid receptor (GR) to regulate diverse biological functions from cell growth to apoptosis. Drugs that mimic their action are the most commonly prescribed therapeutic agents in the world and are currently used for the treatment of many diseases including asthma, autoimmune disorders, and some cancers. However, the mechanisms by which one hormone, via one receptor, modulates such diverse biological functions remain unclear. We hypothesized that epigenetic alteration to the GR may contribute to its signaling diversity, and here we demonstrate that Glycogen Synthase Kinase-3-beta phosphorylates GR on Serine 404 in a glucocorticoid-dependent manner. U-2 OS cells expressing a mutant GR that is incapable of Ser404 phosphorylation have enhanced global transcriptional responses, stronger NF-kappaB transrepression, and enhanced cell death in response to dexamethasone. Conversely, presence of Ser404 phosphorylation on the GR inhibits glucocorticoid-dependent NF-kappaB transrepression and cell death of these osteoblasts. Collectively, our results describe a novel convergence point of the GSK-3-beta pathway with the GR resulting in altered glucocorticoid regulated signaling. Our results also provide a mechanism by which the phosphorylation status of Ser404 in GR can dictate how cells will ultimately respond to GCs.
Keywords: Glucocorticoid Receptor; GSK-3-beta; NF-kappaB Transrepression; Phosphorylation

overall_design: U-2 OS cells with stable WT- or S404A-GR expression were treated, in triplicate, with either vehicle or 100nM Dex for 6 hrs and cytoplasmic RNA was harvested (QIAGEN, Valencia, CA). Gene expression analysis was conducted using Agilent Whole Genome Genome 4x44 multiplex format oligo arrays (014850) (Agilent Technologies, Santa Clara, CA) following the Agilent 1-color microarray-based gene expression analysis protocol. Starting with 500ng of total RNA, Cy3 labeled cRNA was produced according to manufacturer’s protocol. For each sample, 1.65ug of Cy3 labeled cRNAs were fragmented and hybridized for 17 hours in a rotating hybridization oven. Slides were washed and then scanned with an Agilent Scanner. Data was obtained using the Agilent Feature Extraction software (v9.5), using the 1-color defaults for all parameters. The Agilent Feature Extraction Software performed error modeling, adjusting for additive and multiplicative noise.

first: Amy

middle: J

last: Galliher-Beckley

first: Jason

last: Williams

first: Jennifer

last: Collins

last: Cidlowski


title: Direct contact with mesenchymal stromal cells impacts CD133+ hematopoietic stem cells during ex-vivo expansion

status: Public on Nov 13 2008

city: Dresden

first: Nael

last: Alakel

address: Fetscherstrasse 74

country: Germany

institute: university hospital Dresden

summary:
Direct contact with mesenchymal stromal impacts on migratory behavior and gene expression profile of CD133+ hematopoietic stem cells during ex-vivo expansion
Objective: To investigate the impact of direct contact between mesenchymal stromal cells (MSCs) and CD133+ hematopoietic stem cells (HSCs) in terms of expansion potential differentiation, migratory capacity and gene expression profile.  Methods: CD133+ purified HSCs were cultured for 7 days on subconfluent MSCs supplemented with growth factor containing medium. After ex-vivo expansion, non-adherent and adherent cells were collected and analyzed separately. Results: The adherent cells were found to have a more immature phenotype compared to the non-adherent fraction. CXCR4 was up regulated in the adherent fraction which was associated with a higher migration capacity towards a SDF-1 gradient. CFU-GM and LTC-IC assays demonstrated a higher clonogenicity and repopulating capacity of the adherent fraction. Genes involved in adhesion, cell cycle control, motility, self-renewal and apoptosis were expressed at a higher level in the adherent fraction.  Conclusion: Adhesion and direct cell-cell contact with a MSC feeder layer supports ex-vivo expansion, migratory potential and stemness of CD133+ HSCs.

Keywords: co-culture hematopoietic stem cells (HSCs) on mesenchymal stromal cells (MSCs)

overall_design: Non-adherent and adherent fractions from three independent experiments were isolated and collected. Cells were stabilized in PreProtct™ buffer (Miltenyi Biotec, Germany) and stored at -80ºC. Samples were shipped to Miltenyi Biotec (Bergisch Gladbach, Germany) a Whole Human Genome expression analysis. Briefly RNA was extracted and overall quality of total RNA samples was checked via the Agilent 2100 Bioanalyzer platform (Agilent Technologies). RNA samples were amplified and labelled using the Agilent Low RNA Input Linear Amp Kit (Agilent Technologies). Non-adherent samples were pooled as “Non-adherent pool” and adherent samples were pooled as “adherent pool” and labelled with Cy3 and Cy5, respectively. Fluorescence signals of the hybridized Agilent Oligo Microarrays were detected using Agilent’s DNA microarray scanner and the microarray image files were processed with The Agilent Feature Extraction Software (FES).

first: Duohui

last: Jing

first: Katrin

last: Muller

first: Martin

last: Bornhauser

first: Gerhard

last: Ehninger

first: Rainer

last: Ordemann


title: Influence of CFTR on Lipid Metabolism Gene Expression in Marrow Derived Dendritic Cells infected with P. aeruginosa

status: Public on Oct 01 2008

first: Stefan

last: Worgall

address: 515 East 71st Street

department: Genetic Medicine

institute: Weill Cornell Medical College

summary:
Dysfunction of the cystic fibrosis transmembrane regulator (CFTR) in cystic fibrosis (CF) results in exaggerated and chronic inflammation as well as increased susceptibility to chronic pulmonary infections, in particular with Pseudomonas aeruginosa. Based on the concept that host immune responses do not seem to be adequate to eradicate P.aeruginosa from the lungs of CF patients and that dendritic cells (DC) play an important role in initiating and shaping adaptive immune responses, this study analyzed the role of CFTR in bone marrow-derived murine DC from CFTR knockout (CF) mice with and without exposure to P.aeruginosa. DC expressed CFTR mRNA and protein, although at much lower levels compared to whole lung. Microarray analysis of gene expression levels in DC generated from CF and wild type (WT) mice revealed significantly different expression of 16 genes in CF DC compared to WT DC. Among the genes with lower expression in CF DC was Caveolin-1, a membrane lipid raft protein. Messenger RNA and protein levels of Caveolin-1 were decreased in the CF DC compared to WT DC. Consistently, the active form of sterol-responsive element binding protein (SREBP), a negative regulator of Caveolin-1 expression, was increased in CF DC. Following exposure to P.aeruginosa, gene expression levels in CF and WT DC changed for 912 genes involved in inflammation, chemotaxis, signaling, cell cycling and apoptosis more than 1.5-fold. Among the genes that showed a different response between WT and CF DC infected with P.aeruginosa, were 3β-hydroxysterol-Δ7 reductase (Dhcr7) and stearoyl-CoA desaturase 2 (Scd2), two enzymes involved in the lipid metabolism that are also regulated by SREBP. These results suggest that CFTR dysfunction in non-epithelial cells results in changes in the expression of genes encoding factors involved in membrane structure and lipid-metabolism. These membrane alterations in immune cells may contribute to the abnormal inflammatory and immune response characteristic of CF.
Keywords: CF control vs CF PAK vs WT control vs WT PAK

overall_design: comparison of gene expression in dendritic cells of cystic fibrosis mice without or with Pseudosmonas aeruginosa infection vs wild type dendritic cell controls

first: Yaqin

last: Xu

first: Christine

last: Tertilt

first: Luis

last: Quadri

first: Ronald

last: Crystal


title: Meiotic time course of the trimethylation of the Lysine 4 of Histone H3 (H3K4me3) in a mutant clb5Delta-clb6Delta

first: Nicolas

last: Robine

summary:
To study the meiotic dynamic of the methylation of H3K4, in relation with the transcriptomic regulation, we determine the meiotic time-course of H3K4me3 by ChIP-chip in a mutant deficient for DSB formation in a mutant clb5Delta-clb6Delta
Keywords: ChIP-chip, meiotic time course, histone modification

overall_design:
Strain ORD6830
meiotic time-course from 0 to 6h.
Immunoprecipitation with rabbit polyclonal anti-triMe H3K4 (Abcam #Ab8580).

first: Valérie

last: Borde

first: Waka

last: Lin

first: Sandrine

last: Bonfils

first: Vincent

last: Géli

first: Alain

last: Nicolas


title: Meiotic time course of the trimethylation of the Lysine 4 of Histone H3 (H3K4me3) in a mutant Spo11F

summary:
To study the meiotic dynamic of the methylation of H3K4, in relation with the transcriptomic regulation, we determine the meiotic time-course of H3K4me3 by ChIP-chip in a mutant deficient for DSB formation.
Keywords: ChIP-chip, meiotic time course, histone modification

overall_design:
Strain ORD7341
meiotic time-course from 0 to 6h.
Immunoprecipitation with rabbit polyclonal anti-triMe H3K4 (Abcam #Ab8580).


title: Response of the adipose tissue transcriptome to dihydrotestosterone in mice

status: Public on Aug 26 2008

city: Quebec

first: Ezequiel

middle: L

last: Calvo

state: Quebec

address: 2705 Boul. Laurier

department: Molecular Endocrinilogy

country: Canada

institute: CRCHUL

summary:
Androgens have been postulated to be important modulators of adipose tissue metabolism and fat cell function. In the present study, we investigated the response of male and female mice retroperitoneal adipose tissue to the non-aromatizable androgen dihydrotestosterone (DHT). Adipose tissue samples were obtained in gonadectomized (GDX) animals treated with vehicle (control group), or injected with 0.1mg DHT at 1, 3, 6, 12, 18 and 24h prior to necropsy. Transcripts which were significantly modulated were considered as androgen-responsive genes. Quantitative real-time RT-PCR was used to confirm results from the microarry analysis in a subset of 46 probe sets in male mice and 98 probe sets in female mice. Using both methods and considering peak time versus control, 74.5% and 61.2% of the modulated genes were confirmed by PCR in males and females, respectively. Four genes were significantly stimulated in a similar manner by DHT in both sexes, namely metallothionein 1 (Mt1), growth arrest and DNA-damage-inducible 45 gamma (Gadd45g), cyclin-dependent kinase inhibitor 1A (Cdkn1a), and fk506-binding protein 5 (Fkbp5). All these genes appear to be associated with a down-regulation of adipocyte differentiation/proliferation and adipogenesis. In conclusion, this study which evaluated the transcriptome response of adipose tissue to DHT in male and female mice suggests that DHT consistently modulates genes involved in the regulation of adipogenesis in retroperitoneal adipose tissue of both male and female animals.
Keywords: time course

overall_design: Retroperitoneal adipose tissue samples were obtained in gonadectomized (GDX) animals treated with vehicle (control group), or injected with 0.1mg DHT at 1, 3, 6, 12, 18 and 24h prior to necropsy.

first: Yonghua

last: Zhang

first: Céline

last: Martel

first: Van

last: Luu-The

first: Fernand

last: Labrie

first: André

last: Tchernof


title: Mouse Mammary Gland Development

status: Public on Aug 01 2008

city: Glasgow

first: Torsten

last: Stein

address: College of MVLS

department: School of Medicine

country: United Kingdom

institute: University of Glasgow

summary:
The mammary gland develops mainly postnatally, when during pregnancy the epithelium grows out into the mammary fat pad and forms a network of epithelial ducts. During pregnancy, these ducts branch and  bud to form alveoli. These alveoli produce the milk during lactation. After 7 days of lactation, involution was induced by force weaning the pups. The newly formed epithelium undergoes apoptosis and is removed from the tissue by neighbouring epithelial cells. Tissue remodelling leads to a morphology resembling a gland of a pre-pregnant mouse. Microarray analysis was used to measure mRNA expression of genes during puberty, pregnancy, lactation and involution in a Balb/c mouse strain.

Keywords: developmental time course

overall_design: Total RNA was extracted from the 4th (inguinal) gland after removal of the lymph node. Individual samples represent RNA from one gland of one mouse. Samples were taken in triplicate (i.e. three mice per triplicate) for 18 time points of development.

first: Barry

last: Gusterson

first: Joanna

last: Morris

first: Marie-Anne

last: Duffy (Pringle)

first: Claire

last: Davies


title: Transcriptomic regulation and methylation of the Lysine4 of Histone H3 during meiosis

first: Nicolas

last: Robine

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

overall_design: Refer to individual Series


title: The role of the central region of Ada2 in gene regulation

status: Public on Nov 11 2008

city: London

first: Christopher

last: Brandl

state: Ontario

address: 1151 Richmond St.

department: Biochemistry

institute: University of Western Ontario

type: Expression profiling by genome tiling array

summary:
The SAGA complex of Saccharomyces cerevisiae contains greater than 20 components that acetylate and deubiquitylate nucleosomal histones. Its acetyltransferase, Gcn5 preferentially acetylates histones H3 and H2B and is regulated through interactions with Ada2 and Ngg1/Ada3. The N-terminal region of Ada2 contains a SANT domain that contacts Gcn5 near its catalytic site. Sequence alignments of Ada2 homologues indicate a conserved ~120 amino acid residue central region that interacts with Ngg1.To examine the function of this central region, we constructed ada2 alleles with mutations of clustered conserved residues. One of these alleles, ada2-RLR, resulted in a ~3-fold reduction in transcriptional activation of the PHO5 gene and growth changes that parallel deletion of ada2. Microarray analyses further revealed that ada2-RLR  alters expression of a subset of those genes affected by deletion of ada2.
Keywords: yeast, Ada2, SAGA complex, gene expression, genetic modification

overall_design: Three dye-swapped, biological replicate experiments were performed for BY4842 (ada2delta) with reference to BY4741 (wt).  Similarly, in the BY4842 (ada2delta) strain background three dye-swapped, biological replicate experiments were performed for a strain expressing a mutant ada2 allele from a plasmid with reference to a strain expressing wild-type ada2 from a plasmid.

first: Stephen

last: Hoke

first: Julie

last: Genereaux

first: Ana

middle: I

last: Mutiu

first: Gaoyang

last: Liang


title: Transcriptional Profiling of Responses to Estrogen and Progesterone in Mammary Gland

status: Public on Jul 31 2008

city: Amherst

first: D.

middle: Joseph

last: Jerry

address: 161 Holdsworth Way

department: Veterinary & Animal Scineces

institute: University of Massachusetts

summary:
Epidemiological studies have shown that a full-term pregnancy at early age can decrease the breast cancer risk up to one-half.  Pregnancy has been shown to prevent carcinogen-induced mammary tumors in rodents as well.  The protective effect of pregnancy can be mimicked by administration of estrogen and progesterone to nulliparous rodents in amounts that are similar to those during pregnancy and alters responsiveness of p53 to DNA damage.
Ovariectomized mice were treated with estrogen (E), progesterone (P), both estrogen and progesterone (E + P), or vehicle (V) alone and global expression profiles was analyzed to identify the mechanisms by which estrogen and progesterone combine to sensitize p53 function.
Keywords: comparative hormone treatment

overall_design: Twenty ovariectomized animals were used for examine transcriptional effects of hormones by microarray.  The hormones were administered by daily i.p. injection for 4 days.Treatment groups included: 4 animals receiving 2ug 17-beta-estrogen (E), 4 animals receiving 1mg progesterone (P), 5 animals receiving both estrogen and progesterone (E+P) and 4 animals receiving 100ul sesame oil (V). Epithelial-free fat pads from 3 animals receiving E+P were also analyzed to distinguish responses to E+P in the stroma (E+P CFP).  Lymph nodes were removed from mammary glands at the time of collection.

first: S

last: Lu

first: K

last: Becker

first: L

last: Minter

first: A

last: Roberts

last: Mathews

last: Schneider

first: O

last: Loureiro

last: Guo

first: H

last: Siegelmann

last: MacBeth

first: P

last: Sebastiani

last: Tirrell

first: D


title: Normal human prostate (NHP) epithelial cells: Senescent and immortalized cells compared to young progenitors

status: Public on Oct 09 2008

city: Smithville

first: Dean

middle: G

last: Tang

state: TX

address: 1808 Park road 1C

department: Carcinogenesis

institute: U.T M. D. Anderson Cancer Center

summary:
Normal human prostate (NHP) epithelial cells undergo senescence in vitro and in vivo, but the underlying molecular mechanisms remain incompletely understood. Here we first show that multiple primary strains of NHP cells are all immunophenotyped as CK5+/CK18+CD44+α2β1+p63+hTERT+ progenitor cells, which gradually lose progenitor markers as they lose proliferative capacity. NHP cell senescence involves loss of telomerase expression, upregulation of p16, and activation of p53. Using genetically defined manipulations of these three signaling pathways, we show that p16 is the primary determinant of the NHP cell proliferative capacity and hTERT is required for unlimited proliferative lifespan. Hence, suppression of 16 alone significantly extends NHP cell lifespan but both p16 inhibition and hTERT are required to immortalize NHP cells. Importantly, the immortalized NHP cells are normal progenitors that possess the ability to differentiate into functional prostatic glands containing both basal and luminal cells and, frequently, neuroendocrine cells. The immortalized NHP cells possess gene expression profiles characteristic of proliferating progenitor cells. Our studies shed light on the molecular mechanisms regulating the proliferative lifespan of NHP progenitor cells and provide direct evidence that basal-like progenitor cells can regenerate the entire prostatic glands in vivo. The availability of these cells should facilitate future studies of prostate cancer development.

Further processed data linked below as Supplementary files.

TestvsControl: corresponding GSM#
3vs1: GSM266720, 721, 722
4vs1: GSM266727, 730, 731
5vs1: GSM266732, 733, 734
7avs1: GSM266735, 736, 737
9vs1: GSM266772, 773, 812
11vs1: GSM266813, 816, 823
13vs1: GSM266824, 826, 828

Note: The 'TestvsControl' comparisons report the top 100 up- or down-regulated genes. The numeric designations (1 to 13) are used in the corresponding manuscript. The 'SignificantGenes' lists were used in clustering analysis.
Keywords: Cell type comparison (senscent and immortalized NHP cells compared to young NHP progenitors)

overall_design: Total 7 sets of two color arrays with 3 technical replicates in each set (total 21 individual arrays) were performed and each individual array included a test sample (experimental condition) and a control (young NHP progenitors) sample.

first: Bobby

last: Bhatia

first: Ming

last: Jiang

first: Lubna

last: Patrawala

first: Mark

last: Badeaux

first: Robin

last: Schneider Broussard

first: Asha

last: Multani

first: Collene

middle: R

last: Jeter

first: Mahipal

middle: V

last: Suraneni

first: Tammy

last: Calhoun Davis

first: Limei

last: Hu

first: Jianhua

first: Spiridon

last: Tsavachidis

first: Wei

last: Zhang

first: Sandy

last: Chang

first: Simon

last: Hayward


title: Noise-Induced Changes in Gene Expression in the Cochleae of Mice Differing in Their Susceptibility to Noise Damage

status: Public on Sep 01 2008

city: Davis

first: Ana

middle: Elena

last: Vazquez

address: 1515 Newton Court

department: Otolaryngology-Head and Neck Surgery

institute: University of California, Davis

summary:
The molecular mechanisms underlying the great differences in susceptibility to noise-induced hearing loss (NIHL) exhibited by both humans and laboratory animals are unknown. Using microarray technology, the present study demonstrates that the effects of noise overexposure on the expression of molecules likely to be important to the development of NIHL differ among inbred mice that have distinctive susceptibilities to NIHL including B6.CAST, 129X1/SvJ, and 129S1/SvImJ. The noise-exposure protocol produced, on average, a permanent loss of about 40 dB in sensitivity for auditory brainstem responses in susceptible B6.CAST mice, but no threshold elevations for the two resistant 129S1/SvImJ and 129X1/SvJ substrains. Measurements of noise-induced gene expression changes 6 h after the noise exposure revealed significant alterations in the expression levels of 48 genes in the resistant mice, while by these same criteria, there were seven differentially expressed genes in the susceptible B6.CAST mice. Differentially expressed genes in both groups of mice included subsets of transcription factors. However, only in the resistant mice was there a significant induction of proteins involved in cell-survival pathways such as HSP70, HSP40, p21, GADD45beta, Ier3, and Nf-kappaB. Moreover, increased expression of three of these factors after noise was confirmed at the protein level. Drastically enhanced HSP70, GADD45beta, and p21 immunostaining were detected 6 h after the noise exposure in subsets of cells of the lateral wall, spiral limbus, and organ of Corti as well as in cochlear nerve fibers. Upregulation of these proteins after noise exposure likely contributes to the prevalence of survival cellular pathways and thus to the resistance to NIHL that is characteristic of the 129X1/SvJ mice.
Keywords: effects of noise exposure in distinct inbred mice

overall_design: Female 10-wk-old mice of the B6.CAST and 129X1/SvJ strains were divided randomly into non-noise control and noise-exposure groups. The non-noise mice served as controls in the gene-profiling experiments to control for the stress induced by experimenter handling and/or confinement of the mice in the noise-exposure chamber that was not directly related to the noise. This mice were in the noise chamber for a sham exposure. In contrast, the ‘noise’ groups were exposed to a 105-dB SPL, 10-kHz octave band of noise for 1 h and sacrificed 6 h after the exposure. Of each of these major groups, eight mice were used for each of three 129X1/SvJ control and three noise-exposed 129X1/SvJ arrays and two B6.CAST control and two noise-exposed B6.CAST arrays. Consequently within each subgroup the arrays are biological replicates.

first: Michael

last: Gratton

first: Jerel

last: Garcia

first: Esteban

last: Verduzco

first: Glen

last: Martin

first: Brenda

last: Lonsbury–Martin

first: Anna

last: Eleftheriadou

middle: E

last: Vázquez


title: Meiotic time course of Histone H3 occupancy

status: Public on Nov 01 2008

city: New York

first: Nicolas

last: Robine

address: 101 Avenue of the Americas

institute: New York Genome Center

summary:
To study the meiotic dynamic of the methylation of H3K4, in relation with the transcriptomic regulation, we determine the meiotic time-course of H3 occupancy by ChIP-chip.
Keywords: ChIP-chip, meiotic time course, histone modification

overall_design:
Strain ORD7339
meiotic time-course from 0 to 6h.
Immunoprecipitation with rabbit polyclonal anti H3Cter (Abcam #1791)

first: Valérie

last: Borde

first: Waka

last: Lin

first: Sandrine

last: Bonfils

first: Vincent

last: Géli

first: Alain

last: Nicolas


title: Untreated 32Dcl3 cell lines expressing oncogenic tyrosine kinases or cells treated with small molecule inhibitors

status: Public on Jul 12 2008

city: Boston

first: Winnie

middle: F

last: Tam

address: 1 Blackfan Circle

department: Hematology

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

summary:
Oncogenic tyrosine kinases, such as BCR-ABL, TEL-ABL, TEL-PDGF-beta-R and FLT3-ITD, play a major role in the development of hematopoietic malignancy.  They activate many of the same signal transduction pathways.
To identify the critical target genes required for transformation in hematopoietic cells, we used a comparative gene expression strategy in which selective small molecules were applied to 32Dcl3 cells that had been transformed to factor-independent growth by these respective oncogenic alleles.

Keywords: comparative gene expression analysis

overall_design: In our microarray study, we have total 22 samples from four different cell lines expressing BCR-ABL, TEL-ABL, FLT3-ITD or TEL-PDGF-betaR.  Each cell line was treated with specific small molecule inhibitors for 4 hours, then RNA was extracted and cRNA was hybridized to Affymetrix U74 oligonucleotide arrays. Untreated cells or cells treated with unrelated inhibitors were used as controls or references.  We have three replicates and six references obtained from three independent experiments for cells expressing BCR-ABL or FLT3-ITD.  We have one treated and one untreated sample for each cell line expressing TEL-ABL or TEL-PDGF-beta-R.

first: Ting

last: L Gu

first: Jing

last: Chen

first: Benjamin

middle: H

last: Lee

first: Lars

last: Bullinger

first: Stefan

last: Frohling

first: Andrew

last: Wang

first: Stefano

last: Monti

first: Todd

last: Golub

first: D

last: Gilliland


title: Comparison of rapidly vs. slowly dividing CD8 T cells during acute homeostatic proliferation

status: Public on Jul 25 2008

city: Worcester

first: Raymond

middle: M

last: Welsh

address: 55 Lake Ave. North

department: Pathology

institute: UMASS Medical School

summary:
Our earlier study demonstrated that when CFSE-labeled LCMV-or Pichinde virus-immune spleen leukocytes were transferred into T cell-deficient hosts, the bona fide virus-specific memory cells underwent relatively limited cell division and were substantially diluted in frequency by other more extensively proliferating cells originating from that donor cell population. We questioned how the slowly dividing population, which contained bona fide memory cells, differed from the rapidly dividing cells, which contained “memory-like” cells. As a preliminary screen we performed a comparative genome-wide microarray analysis of genes expressed on sorted rapidly proliferating (CFSE-low) and slowly proliferating (CFSE-high) CD8 cell populations
Keywords: Division profile comparison

overall_design: 2x10^7 CFSE-labeled, Ly5.1+, LCMV-Immune splenocytes were adoptively transferred into congenic T cell ko hosts.  Splenocytes were harvested 12 days post-transfer and stained with anti-CD8 Ab, anti-Ly5.1 Ab and 7AAD. 7AAD negative cells were gated, and CFSE-low (> eight divisions) and CFSE-high (0-6 divisions) cells were sorted by flow cytometry using a FACStarPLUS sorter (BD Bioscience, Mountain View, CA). Total RNA was extracted from both CFSE-low and CFSE-high CD8+Ly5.1+ donor populations to compare rapidly vs. slowly dividing CD8 T cells during acute homeostatic proliferation via Affymetrix gene analysis.

first: SuChen


title: Normal human fibroblast cell line bystander effects by Carbon ion irradiation

status: Public on Sep 02 2008

city: Chiba

first: Kaori

last: Imadome

state: Chiba

address: Anagawa 4-9-1

department: Research Center of Charged Particle Therapy

institute: National institute of radiological sciences

summary:
We have recently investigated the response of irradiated and bystander fibroblasts to heavy ions in confluent cultures exposed randomly to broadbeam and selectively to precision microbeam that target a predefined fraction of cells with counted number of particle(s), respectively, and found the difference in the time course of apoptosis induction and p53 phosphorylation between irradiated and bystander cells [Hamada MR2008]. In the present investigation, to further scrutinize the underpinnings of their temporally distinct responses, we set out to examine the gene expression changes in irradiated and bystander fibroblasts at a genome-wide level with the microarray analysis under the same experimental condition. We demonstrate that the gene expression profiles of bystander cells are substantially different from those of heavy ion-irradiated cells.
Keywords: bystander effect, hour-time course cell number dependency, irradiation-dose response

overall_design: 36 samples ; Broadbeam control A, Broadbeam control B, Broadbeam sham 2 h A, Broadbeam sham 2 h B, Broadbeam sham 6 h A, Broadbeam sham 6 h B, Broadbeam D 2 h A, Broadbeam D 2 h B, Broadbeam D 6 h A, Broadbeam D 6 h B, Broadbeam 0.1D 2 h A, Broadbeam 0.1D 2 h B, Broadbeam 0.1D 6 h A, Broadbeam 0.1D 6 h B, Broadbeam 0.01D 2 h A, Broadbeam 0.01D 2 h B, Broadbeam 0.01D 6 h A, Broadbeam 0.01D 6 h B, Microbeam Control A, Microbeam Control B, Microbeam sham 2 h A, Microbeam sham 2 h B, Microbeam sham 6 h A, Microbeam sham 6 h B, Microbeam 1c 2 h A, Microbeam 1c 2 h B, Microbeam 1c 6 h A, Microbeam 1c 6 h B, Microbeam 5c 2 h A, Microbeam 5c 2 h B, Microbeam 5c 6 h A, Microbeam 5c 6 h B, Microbeam 25c 2 h A, Microbeam 25c 2 h B, Microbeam 25c 6 h A, Microbeam 25c 6 h B.

first: Mayumi

last: Iwakawa

first: Nobuyuki

last: Hamada


title: Gene expression data from NECA (5/-N-ethylcarboxamidoadenosine) treated murine pituitary folliculostellate cells(TtT/GF)

status: Public on Apr 08 2009

city: Cardiff

first: jack

last: ham

address: Heath Park

department: Centre for Endocrine and Diabetes Sciences

institute: Cardiff University

summary: Folliculostellate cells constitute as much as 10% of the cells within the anterior pituitary gland; they however do not secrete any of the classical hormones but do express cytokines and growth factors. The endogenous nucleoside adenosine can be either pro- or anti-inflammatory depending on receptor expression and the activation of one or more receptors A1, A2a, A2b and A3. Adenosine stimulates the secretion of immune molecules from folliculostellate; these cells appear to mediate communication between the endocrine and immune systems.

overall_design: Replicate (x3) cultures of TtT/GF cells were treated with 10µM NECA (5/-N-ethylcarboxamidoadenosine) for 30 and 120 minutes. RNA was extracted, cRNA prepared and hybridized to murine MG_U74A v2 GeneChip (Affymetrix), changes in expression were compared with untreated controls.

first: Jack

last: Ham


title: Fine temporal analysis of DHT transcriptional modulation of the ATM/Gadd45g signaling pathways in the mouse uterus.

status: Public on Aug 05 2008

first: Ezequiel

last: Calvo

summary:
In rodents, the uterus of a mature
female undergoes changes during the uterine cycle,
under the control of steroid hormones. 5a-Dihydrotestosterone
(DHT) is recognized to play an important
role in the regulation of androgen action in normal
endometrium. Using microarray technology, a screening
analysis of genes responding to DHT in the uterus
of ovariectomized mice, has allowed us to highlight
multiple genes of the ATM/Gadd45g pathway that
are modulated following exposure to DHT. Two phases
of regulation were identified. In the early phase, the
expression of genes involved in the G2/M arrest is
rapidly increased, followed by the repression of genes
of the G1/S checkpoint, and by the induction of
transcriptional regulators. Later, i.e. from 12 to 24 hr,
genes involved in G2/M transition, cytoarchitectural
and lipid-related genes are stimulated by DHT while
immunity-related genes appear to be differentially
regulated by the hormone. These results show that a
physiological dose of DHT induces the transcription of
genes promoting the cell cycle progression in mice.
Profile determination of temporal uterine gene expression
at the transcriptional level enables us to suggest
that the DHT modulation of genes involved in ATM/
Gadd45g signaling in an ATM- or p53-independent
manner, could play an important role in the cyclical
changes of uterine cells in the mouse uterus.
Keywords: DHT time course

overall_design: Ten 10-11 weeks old C57Bl/6 mice were gonadectomized under isoflurane-induced anesthesia and sacrified seven days after GDX.  Mice  were injected s.c with DHT (0.1mg/mice) or vehicle, at 0.5, 1, 3, 6, 12 or 24 h before sacrifice. Uteri was removed and pooled before total RNA extraction. Samples was hybridized to U74Av2 Genechips (Affymetrix).

first: Francine

last: Durocher

first: Mahinè

last: Ivanga

first: Yvan

last: Labrie

first: Fernand


title: Expression data from postnatal day (P) 14, 28, 60 mouse visual cortex (V1)

status: Public on Jun 12 2008

city: Brighton

first: alvin

last: lyckman

address: 736 Cambridge St

institute: St Eliz Med Ctr

summary:
Analysis of gene expression before (P14), during (P28), and after (P60) the critical period for ocular dominance plasticity.

Keywords: time course

overall_design: V1 from litters of mice were microdissected and processed for RNA extraction.

first: Alvin

last: Lyckman