title: Evaluation of lipin-1 effects on gene expression during TLR4 stimulation of macrophages

status: Public on Oct 01 2014

city: Valladolid

first: Maria

middle: A.

last: Balboa

state: Valladolid

address: Sanz y Fores, 3

department: Innate Immunity

institute: Consejo Superior de Investigaciones Cientificas

summary: Lipin-1 affects the expression levels of many genes during TLR4 stimulation of macrophages.

overall_design: Gene expression analysis of peritoneal macrophages from four control (hetorozygotes) mice and four lipin-1 mutant (fatty liver distrophy, fld) mice stimulated with 100 ng/ml LPS for 5 hours.

first: María

middle: A

first: Clara

last: Meana


title: Gene expression analysis of CD11c+ splenic DCs day 7 after allo-HSCT.

status: Public on Sep 19 2014

city: New York

first: Vanessa

middle: Marie

last: Hubbard-Lucey

state: NY

address: 540 First Ave

department: Microbiology

country: USA

institute: NYU School of Medicine

summary: The goal of our study is to determine whether Atg16L1 deficiency leads to differences in the transcriptional profile of CD11c+ Dendritic Cells, ultimately leading to an increased inflammatory phenotype.

overall_design: CD11c+ cell sorted splenic DCs were isolated from 8 week old WT and Atg16L1 hypomorphic mice from spleens of allo-HSCT recipients on day 7 were placed directly into TRIzol LS (Invitrogen). mRNA was isolated, amplified, and hybridized to an Affymetrix GeneChip (MOE430A).

first: Hubbard-Lucey

last: Vanessa

first: Cadwell

last: Ken


title: CD11c+ splenic DCs

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

overall_design: Refer to individual Series


title: Gene expression analysis of CD11c+ splenic DCs.

overall_design: CD11c+ cell sorted splenic DCs were isolated from 8 week old WT and Atg16L1 hypomorphic mice from spleens of untreated mice and  were placed directly into TRIzol LS (Invitrogen). mRNA was isolated, amplified, and hybridized to an Affymetrix GeneChip (MOE430A).

first: V

first: K

last: Cadwell


title: Gene expression data comparing rbf1 mutant and PSC overexpressing Drosophila eye imaginal discs

status: Public on Sep 30 2014

city: Montreal

first: Heather

last: Collins

state: Quebec

address: 1205 Docteur Penfield Avenue

department: Biology

country: Canada

institute: McGill University

summary:
PSC overexpression can cause phenotypes specifically in an rbf1 mutant background, likely due to a sensitization to PSC-induced phenotypes.  The goal of this study is to understand the interaction between rbf1 hypomorphic mutation and the overexpression of Polycomb group gene Posterior sex combs.  We used Drosophila larval eye imaginal discs that were mutant for rbf1 or overexpressing PSC and compared these to control larval eye discs to assess changes in gene expression.
We identified a common set of genes that are deregulated when rbf1 is mutated or when PSC is overexpressed.

overall_design: RNA was extracted from eye imaginal discs dissected from third instar Drosophila larvae.  Samples were amplified and hybridized to Affymetrix Drosophila Genome 2.0 Array.  To better understand the effects of rbf1 mutation and PSC overexpression, we compared the gene expression of rbf1 mutant eye discs and eye discs overexpressing PSC to control eye discs.

first: Nam-Sung

last: Moon


title: Gene expression profiling in murine monocyte-dendritic cell progenitors (MDPs), common monocyte progenitors (cMoPs) and 32Dcl.3 cells transduced with C/EBPalpha and/or IRF8

status: Public on Aug 26 2014

city: Yokohama

first: Tomohiko

last: Tamura

address: 3-9 Fukuura, Kanazawa-ku

department: Department of Immunology

country: Japan

institute: Yokohama City University

summary: To understand the mechanism by which IRF8 inhibits neutrophil differentiation

overall_design: Murine bone marrow MDPs and cMoPs were isolated by cell sorting from wild-type or Irf8 deficient mice.  32Dcl.3 cells were transduced with retroviruses carrying murine C/EBPalpha cDNA and/or murine Irf8 cDNA. Two independent experiments were performed.

first: Daisuke

last: Kurotaki

first: Michio

last: Yamamoto

first: Akira

last: Nishiyama


title: Effect of Sunitinib treatment withdrawal on Immunodeficient mice bearing MDA-MB231 tumors

status: Public on Aug 24 2014

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

summary: Immunodeficient RAG1-/- mice bearing MDA-MB231-LUC+ tumors of 50-70 mm3 were daily administrated by gavage with vehicle (containing, 0.5% carboxymethylcellulose, 1.8 % NaCl, 0.4 % Tween-80, 0.9 %. benzyl alcohol, and ultrapure water adjusted to pH 6.0) or sunitinib (40mg/kg/day) for 30 days followed by treatment withdrawal for 3-4 weeks to allow the tumor regrowth until reaching the same volume as that of the vehicle treated group. Mice were sacrificed when tumor reached the volume of 350-400 mm3 and RNAs of two tumors from two different mice treated with sunitinib or vehicle were extracted.

overall_design: One color experiment with 2  experimental conditions: Sunitinib vs Vehicle (n=2), corresponding to a total of 4 samples.

first: B

last: Mari

first: P

last: Barbry

first: A

last: Noel


title: Expression profiling of Mammary Gland Tumor epithelial cells

status: Public on Sep 15 2014

first: Alain

last: Nepveu

state: Qc

address: 1160 Pine Avenue West

department: Goodman Cancer Centre

summary:
Transcriptional profiling of mammary gland tumors from transgenic mice overexpressing the p110 or p75 isoform of CUX1.
RNA was extracted from epithelial cells isolated using Laser-Capture Microdissection (LCM)

overall_design: 9 tumors from p75-CUX1 transgenic mice and 8 tumors from p110-CUX1 mice. Biological samples were hybridized in technical duplicates with dye swaps between duplicates against a common reference for normalization.

first: Charles

last: Vadnais


title: Continuous requirement for the T cell receptor for regulatory T cell function

status: Public on Sep 08 2014

first: Aaron

last: Arvey

institute: Memorial Sloan-Kettering Cancer Center

summary: Foxp3+ regulatory T cells (Treg cells) maintain immunological tolerance and their deficiency results in fatal multi-organ autoimmunity.  Although heightened T cell receptor (TCR) signaling is critical for the differentiation of Treg cells, the role of TCR signaling in Treg cell function remains largely unknown.  Here we demonstrate inducible ablation of the TCR results in Treg cell dysfunction which cannot be attributed to impaired Foxp3 expression, decreased expression of Treg cell signature genes or altered ability to sense and consume interleukin 2.  Rather, TCR signaling was required for maintaining the expression of a limited subset of genes comprising 25% of the activated Treg cell transcriptional signature.  Our results reveal a critical role for the TCR in Treg cell suppressor capacity.

overall_design: Array expression of Foxp3-CreERT2 CalphaFL/WT mice

first: Andrew

middle: G

last: Levine

first: Wei

last: Jin

first: Alexander

middle: Y

last: Rudensky


title: Microarray analysis of the effects of a γ-tocopherol-rich mixture of tocopherols on global gene expression in the prostates of TRAMP mice

status: Public on Sep 16 2014

city: New Brunswick

first: Tony

last: Kong

state: NJ

address: 160 Frelinghuysen Road

department: Pharmaceutical Science

institute: Rutgers University

summary: We used whole mouse genome microarrays  to the effects of γ-TmT on global gene expression in the prostate

overall_design: TRAMP and age-matched C57BL/6 mice were administered either 600 mg/kg of γ-TmT or a control vehicle via oral gavage. Twelve hours after dosing, prostate tissues were collected for RNA extraction.

first: Ying

last: Huang

first: Zheng-Yuan

last: Su

first: Tien-Yuan

last: Wu

first: Constance

last: Lay-lay Saw

first: Ah-Ng

middle: T


title: Transgenic Eµ-myc mouse lymphoma expression data for test dataset [Mouse430A_2]

status: Public on Sep 10 2014

city: Durham

first: Daphne

middle: R

last: Friedman

state: NC

address: 101 Science Drive, Room 2121, CIEMAS Bldg

institute: Duke University Medical Center

summary: We used gene expression data from Eµ-myc mouse lymphomas to test various genomic signatures and select lymphomas for further study

overall_design: When Eµ-myc mice had evidence of lymphoma and/or ill appearance, they were humanely sacrificed and dissected.  Lymphoma tissue was obtained and flash frozen in liquid nitrogen.  Lymphoma and spleens were dissociated into single cell suspensions, and cell pellets were frozen.  Later, lymphoma tissue or cells were homogenized, and RNA was extracted.  Gene expression microarrays were performed with the isolated RNA.

first: Joseph

last: Nevins


title: Expression data from mouse liver tumor-initiating cells.

city: Los Angeles

first: Keigo

last: Machida

state: CA

address: 2011 Zonal Ave., HMR503C

department: Molecular Microbiology and Immunology

institute: University of Southern California

summary:
We used microarrays to detail the global programme of gene expression underlying cellularisation and identified distinct classes of up-regulated genes during this process.
Goal and objectives: To study the requirement of HCV viral proteins and/or environmental factors (such as alcohol or obesity) in synergistic liver caner development in HCV Core or NS5A Tg mice given alcohol or high-cholesterol high-fat diet, mice were fed alcohol or high-cholesterol high-fat diet and liver tissues from these mice were examined for gene profiles.  Alcohol or obesity contributes to synergistic tumor incidence and HCV Core or Ns5a-induced effects.  Thus, analysis of gene profiling of these transgenic mice will identify the critical pathways to induce synergistic tumor formation caused by alcohol or obesity.

overall_design: Liver samples for RNA extraction and hybridization on Affymetrix microarrays. We sought to obtain gene profiling data in order to increase understanding the pathways. To perform gene array and proteomic analyses, mice were fed alcohol or high-cholesterol high-fat for 12 months and euthanized after 12 months feeding. Livers were collected at the time of euthanasia.

first: Chia-Lin

last: Chen


title: SIRT7 suppresses tumorigenesis by attenuating MYC activity

status: Public on Aug 20 2014

city: Cambridge

middle: Arthur

last: Whittaker

state: MA

institute: Koch Institute

summary: SIRT7 is a member of the mammalian sirtuin family of NAD+ dependent deacylases, and  interacts with RNA polymerase I and UBF to regulate rDNA transcription. Various  studies in mammalian cells and human clinical data have linked SIRT7 to cancer.  However studies differ as to whether SIRT7 is oncogenic or tumor suppressive. Here we  analyzed SIRT7 knockout mice and found SIRT7 deficiency caused sub-Mendelian birth  numbers and a reduction in body size. Moreover, at 18 month of age, roughly 60 % of  the SIRT7 knockout mice develop hepatocellular carcinoma (HCC), in many cases  leading to suspected metastasis. Several HCC associated genes were up-regulated in  livers of mice as young as 6 months of age, particularly targets of the proto-oncogene, c-  MYC. Indeed SIRT7 interacts with MYC at endogenous protein levels and also represses  MYC activity. Our findings thus show that SIRT7 acts as a tumor suppressor in vivo, and  may suggest novel strategies to treat liver cancer.

overall_design: The mRNAs from 3 replicates of mouse Wildtype liver compared to 3 replicates of mouse liver lacking SIRT7

first: Hung-Chun

last: Chang

first: Yun-Chi

last: Tang

first: Eric

middle: O

last: Williams

middle: L

last: Bell

first: Leonard

last: Guarente


title: Expression data from salivary tumor tissues derived from MMTV-ras transgenic mice with wild-type p53, no p53 or gain-of-function mutant p53

status: Public on Aug 15 2014

city: Stanford

first: Dadi

last: Jiang

address: 269 Campus Drive, CCSR-South 1240

institute: Stanford University

summary: Salivary tumors isolated from MMTV-ras transgenic mice expressing wild-type p53, no p53 or p53R172H gain-of-funcion mutant were subjected to genome-wide gene expression profiling to assess the effect of the different p53 status on tumor gene expression.

overall_design: A total of 12 spontaneous salivary tumors from MMTV-ras/p53+/+, MMTV-ras/p53-/- or MMTV-ras/p53R172H/R172H mice (4 tumors per genotype) were analyzed using Affymetric GeneChip for gene expression profiling. The multi-class comparison function of Significance Analysis of Microarray (SAM) with an FDR of 1%  was used to identify genes that are differentially regulated across the three genotypic groups.

first: Dad

last: i Jiang

first: Jolene

middle: J

last: Windle


title: Murine Liver Cells: Control B6 males vs. little (GH-deficient) and Tfm (AR-null) males

status: Public on Aug 09 2014

city: Madison

first: Christopher

last: Oberley

state: Wisconsin

address: 3809 Hillcrest Dr.

department: Oncology

institute: University of Wisconsin-Madison

summary:
Transcriptional profiling of mouse whole liver comparing control WT B6 mice with B6 growth hormone-deficient little, B6 androgen receptor-null Tfm mice, and STAT5b KOs normalized to WT on B6 and BALB/c backgrounds. All animals were 10-week-old males initiated with DEN.
Oberley et al. Molecular carcinogenesis 2014 May 17. doi: 10.1002/mc.22165.

overall_design: Three-condition experiment, WT vs. little and Tfm livers. Biological replicates: 3 control replicates, 3 mutant replicates. Little and Tfm normalized to WTa, B6 STAT5b KO

first: Norman

last: Drinkwater


title: Transcriptional response to stress in serum deprived mouse fibroblasts

status: Public on Aug 12 2014

city: Goettingen

first: Anna

last: Sawicka

address: Am Fassberg 11

department: Dep. of Molecular Biology

country: Germany

institute: Max Planck Institure for Biophysical Chemistry

summary: We have employed gene expression profiling in order to identify targets of transcriptional response to stress in mouse Swiss 3T3 fibroblasts, where we induced p38/MAP kinase pathway using anisomycin.

overall_design: Serum starved (72 h) mouse 3T3 cells were treated with anisomycin (188.5 nM) for 1, 3, and 6 h (in triplicates). Untreated, serum-starved cells were used as a control. RNA was collected and gene expression profiling using mouse Agilent expression array (4x44k) was performed.

first: Christian

last: Seiser


title: HEXIM knockdown triggers apoptosis-induced proliferation and deregulates Hedgehog signaling

status: Public on Jul 31 2014

city: Orsay

first: Patricia

last: Uguen

address: Rue des Adèles

department: Biologie

institute: Université Paris Sud

summary: We address the function of HEXIM, an inhibitor of the general transcriptional elongation regulator P-TEFb which regulates the transcriptional status of many developmental genes, during Drosophila development. We showed that HEXIM knockdown mutants display organs development failure. In the wing disc, it induces apoptosis and affects Hh signaling. The continuous death of proliferative cells is compensated by apoptosis-induced cell proliferation, in a manner similar to that of differentiated cells, together with high levels of Hh and Ci. We completed this analysis with microarrays to characterize the molecular phenotype of HEXIM knockdown during eye differentiation.

overall_design: HEXIM knockdown during eye differentiation was carried out with a UAS-Hexim-RNAi strain crossed with a GMR-Gal4 driver strain (Bloomington stock center)). Adult GMR>RNAi Hexim flies display slightly smaller, rough and often necrosed eyes. Total RNA were collected from isolated heads. We then used microarray to compare the transcriptome of HEXIM knockdown mutant with that of wild type flies.

first: Duy

last: Nguyen

first: Nicolas

last: Buisine


title: Expression analysis of circadian light response in Drosophila

status: Public on Jul 23 2014

city: Leicester

first: Eran

last: Tauber

address: University Road

department: Genetics

country: United Kingdom

institute: University of Leicester

summary:
Light is a strong environmental cue that resets the circadian clock rhythm. We have used Affymetrix microarrays to profile the Drosophila  head transcriptome response following a brief light pulse during the early night.
Comparison of control (un-pulsed) and experimental flies reveal large number of differentially expressed transcripts underlying the process of light entrainment of the clock.

overall_design: Wild type flies exposed to light pulse at ZT15 compared to control group (no pulse)

first: Adeolu

last: Adewoye


title: Partial phenotypic rescue of the Sesb1 mitochondrial ANT1 disease model in Drosophila

status: Public on Aug 11 2014

city: Tampere

first: Suvi

last: Vartiainen

address: Biokatu 6

department: Institute of Biomedical Technology

country: Finland

institute: University of Tampere

summary: Study of gene expression patterns of Drosophila melanogaster Sesb1 mutants compared to wild type

overall_design: Inbreeding under stressful conditions inevitably results in the selection of compensatory alleles of many genes. In order to avoid such issues, and thus determine the global effects on gene expression of the Sesb1 mutation in a truly unselected and 'wild-type' background, we outbred Sesb1 over more than 10 generations by back-crossing to each of two commonly used wild-type strains, Canton S and Oregon R. Subsequent to this backcrossing, Sesb1 was maintained in each background using a balancer chromosome. These stocks were then used to generate a Sesb1 mutant F1 generation, by crossing virgin Canton S Sesb1.  homozygous mutant females with Oregon R Sesb1 males. For comparison, we generated otherwise isogenic wild-type F1 progeny by crossing virgin Canton S wild-type females with Oregon R wild-type males. Progeny was collected on the day of eclosion and aged for one day after which the RNA was isolated with Trizol. The quality of the RNA was analyzed with a spectrophotometer.

first: Shanjun

last: Chen

first: Tea

last: Tuomela

first: Kaisa

last: Luoto

first: Kevin

last: O'Dell

first: Howard

last: Jacobs


title: Comparison of gene expression in wild-type Drosophila testes with tbrd-1 mutant testes

status: Public on Aug 08 2014

city: Giessen

first: Marek

last: Bartkuhn

state: Hessen

address: Aulweg 132

department: Biomedical Informatics and Systems Medicine

institute: Justus-Liebig-University Giessen

summary: Gene expression is tightly linked to histone acetylation on lysine residues that can be recognized by bromodomains. The testis-specific bromodomain protein tBRD-1 is essential for male fertility and might act as a co-factor of testis-specifc TAFs. Here, we perform microarray analyses and demonstrate that tBRD-1 selectively controls gene expression in male germ cells

overall_design: Testes were dissected from 0-2 day old Drosophila males. The wild-type control sample was w1118. The tbrd-1 mutant is described in Leser et al., 2012 (Leser K, Awe S, Barckmann B, Renkawitz-Pohl R, Rathke C. 2012. The bromodomain-containing protein tBRD-1 is specifically expressed in spermatocytes and is essential for male fertility. Biology Open 1: 597-606)

first: Christina

last: Rathke


title: Mouse Liver: Tumors vs Two Week Transgene Expression vs Normal

first: Ly

last: Pham

state: WI

address: 2015 Linden Drive

department: Pathobiological Sciences

institute: UW-Madison

summary:
Transcriptional Profiling of mouse liver tissues comparing normal tissues, tissues with two weeks expression of transgene, and tumors arising from transgene expression after hepatocy transplantation using the comparative hepatocyte growth assay
Experimental groups: Control (hPAP marker gene); Normal Liver Expressing Transgene for Two Weeks; Liver Tumors Expressing Transgene

overall_design: Twenty-Conditon Experiment: 1 Control Group (hPAP marker transgene); 10 Groups of  Normal Liver Expressing Different Transgene for 2 weeks; 9 Groups of Tumors Arising from Different Transgene

last: Boley

first: Eric

last: P. Sandgren


title: Gene expression profiling of mouse prostate over-expressing the Notch1 intracellular domain.

status: Public on Aug 07 2014

city: Houston

first: Chad

last: Creighton

state: TX

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

summary: Molecular signaling that regulates differentiation, survival and proliferation of the prostate luminal epithelial cells has not been thoroughly understood. Herein, we show that increased canonical Notch1 activity suppresses terminal differentiation of prostate luminal epithelial cells but is insufficient to transform. Augmented Notch1 activity delays anoikis of luminal epithelial cells by augmenting NF-κB activity independent of Hes-1, stimulates luminal cell proliferation by potentiating the PI3K-AKT signaling, and rescues the capacities of a fraction of prostate luminal epithelial cells for unipotent differentiation in vivo and short-term self-renewal in vitro. Epithelial cell-autonomous AR signaling is dispensable for the Notch-mediated cellular survival and proliferation. This study reveals a previously unappreciated role of Notch in prostatic luminal epithelial cell differentiation, supports the presence of a lineage hierarchy within the prostate luminal epithelial cells, and implies a pro-metastatic function of Notch signaling during prostate cancer progression.

overall_design: Two group comparison (WT and Mut)

first: Oh-Joon

last: Kwon

first: Li

last: Xin

first: Yiqun

last: Zhang


title: Altered mRNA expression profile of GW4064 treated mouse livers compared to vehicle control

status: Public on Jul 24 2014

city: Piscataway

first: Le

last: Zhan

address: 170 Frelinghuysen Rd

department: Pharmacology and Toxicology

summary:
Farnesoid X receptor (FXR) is a ligand activated nuclear receptor belonging to the nuclear receptor superfamily. Bile acids (BAs) are the endogenous ligand for FXR. FXR is a master regulator of BA homestasis, including BA synthesis, metabolism, transport, and enterohepatic circulation of BAs. Besides, FXR is involved in regulating diverse physioligical function in both humans and mice.
GW4064 is a synthetic FXR agonist which selectively activates FXR and induce the transcription of FXR target genes.

overall_design: In this study, we treated wild type C57BL/6J mice with GW4064 at 100mg per kg body weight or vehicle control. Mice were treated three times, first dose at 8 am, second dose at 6 pm, third dose at 8 am the second day. Mice were sacrificed 2 hours after the last dose, and liver tissues were harvested for analysis. Animal protocols and procedures were approved by the Institutional Animal Care and Use Committee (IACUC) at the University of Kansas Medical Center. Total RNA from livers was prepared with TRIzol Reagent (Invitrogen, CA), and the whole transcription expression levels were determined using Mouse Gene 1.0 ST Array system manufactured by Affymetrix, Inc..

first: Grace

last: Guo

first: Bo

last: Kong


title: Polysomes from DENR knockdown cells

status: Public on Jun 30 2014

city: Heidelberg

first: Aurelio

last: Teleman

address: Im Neuenheimer Feld 580

institute: German Cancer Research Center (DKFZ)

summary:
The aim was to identify transcripts that are poorly translated upon knockdown of DENR. Lysates from control (GFP) and DENR knockdown S2 cells were run on polysome gradients.
RNA from the (80S peak + polysome peaks) was isolated and analyzed by microarrays. In parallel, total RNA from the cells was also profiled as a normalization control and profiled.
The 'translation score' of translated mRNA to total RNA was then calculated for control and DENR knockdown cells.

overall_design: Two biological replicates for DENR knockdown and GFP knockdown were performed. For each sample, (80S+polysomes) and total RNA were profiled, leading to 8 samples in total.

first: Sibylle

last: Schleich

first: Katrin

last: Strassburger

first: Philipp

middle: C

last: Janiesch

first: Tatyana

last: Koledachkina

first: Katharine

middle: K

last: Miller

first: Katharina

last: Haneke

first: Yong-Sheng

last: Cheng

last: Kuechler

first: Georg

last: Stoecklin

first: Kent

middle: E

last: Duncan


title: Mouse Liver: Tumors vs livers with transgene turned off for 4 weeks vs livers with transgene turned off for 12 weeks vs Normal

status: Public on Jul 15 2014

first: Ly

last: Pham

summary:
Transcriptional Profiling of mouse liver tissues comparing normal tissues, livers arising from transgene expression after hepatocy transplantation using the comparative hepatocyte growth assay, and livers with transgene turned off for 4 and 12 weeks.
Experimental groups: Control normal liver; Endstage liver tumors, livers with transgene turned off for 4 weeks, and livers with transgene turned off for 12 weeks.

overall_design: Ten Condition Experiment: ES vs Control, 4wks vs ES, 12wks vs ES; Control normal liver (3 replicate); Endstage(ES) liver tumors, 3 groups(c-Myc (7), TGFa (3), TGFa and c-Myc(3)); livers with transgene turned off for 4 weeks, 3 groups (c-Myc (3), TGFa (3), TGFa and c-Myc(3)); and livers with transgene turned off for 12 weeks, 3 groups (c-Myc (3), TGFa (3), TGFa and c-Myc(3)).

first: Patricia

last: Boley

first: Eric

middle: P

last: Sandgren


title: M-CSF priming of osteoclast precursors can cause osteoclastogenesis-insensitivity, which can be prevented and overcome on bone

status: Public on Jun 02 2014

city: Amsterdam

first: Teun

middle: J.

last: de Vries

address: Gustav Mahlerlaan 3004

department: Periodontology

country: Netherlands

institute: Academic Centre for Dentistry Amsterdam (ACTA), University of Amsterdam and VU University

summary:
Comparison of gene expression of the osteoclast precursor myeloid blast seeded on plastic and on bone, primed with M-CSF for 4 days and culture with M-CSF and RANKL for 1 day.
Osteoclasts and macrophages share progenitors that must receive decisive lineage signals driving them into their respective differentiation routes. Macrophage colony stimulation factor M-CSF is a common factor; bone is likely the stimulus for osteoclast differentiation. To elucidate the effect of both, shared mouse bone marrow precursor myeloid blast was pre-cultured with M-CSF on plastic and on bone. M-CSF priming prior to stimulation with M-CSF and osteoclast differentiation factor RANKL resulted in a complete loss of osteoclastogenic potential without bone. This coincided with a steeply decreased expression of osteoclast genes TRACP and DC-STAMP, but an increased expression of the macrophage markers F4/80 and CD11b. Compellingly, M-CSF priming on bone accelerated the osteoclastogenic potential: M-CSF primed cells that had received only one day M-CSF and RANKL and were grown on bone already expressed an array of genes that are associated with osteoclast differentiation and these cells differentiated into osteoclasts within 2 days. This implies that adhesion to bone dictates the fate of osteoclast precursors. Common macrophage-osteoclast precursors may become insensitive to differentiate into osteoclasts and regain osteoclastogenesis when bound to bone or when in the vicinity of bone.

overall_design: Two conditions: Osteoclast precursors on plastic and on bone, n=4, dye swap

first: Ton

last: Schoenmaker

first: David

last: Aerts

first: Lilyanne

last: Grevers

first: Pedro

last: Souza

first: Kamran

last: Nazmi

first: Mark

last: van de Wiel

first: Bauke

last: Ylstra

first: Peter

last: van Lent

first: Pieter

last: Leenen

first: Vincent

last: Everts


title: Expression data from skeletal muscles of flies with muscle-specific overexpression of Foxo or Mnt

status: Public on Jul 02 2014

city: Boston

first: William

last: Swindell

address: 77 Avenue Louis Pasteur

institute: Harvard University

summary:
Skeletal muscle senescence influences whole organism aging, yet little is known on the relay of pro-longevity signals from muscles to other tissues. We performed an RNAi screen in Drosophila for muscle-released cytokines (?myokines?) regulating lifespan and identified Myoglianin, the homolog of human Myostatin. Myoglianin is induced in skeletal muscles by the transcription factor Mnt and together they constitute an inter-organ signaling module that regulates lifespan, age-related muscle dysfunction, and protein synthesis across aging tissues. Both Mnt and Myoglianin activate already in young age the protective decline in protein synthesis that is typical of old age, while knock-down of Myoglianin impairs this process. Mechanistically, Mnt decreases the expression of nucleolar components in muscles while also decreasing nucleolar size in distant tissues via Myostatin/p38 MAPK signaling. Our results highlight a myokine-dependent inter-organ longevity pathway that coordinates nucleolar function and protein synthesis across aging tissues.
Affymetrix microarrays were used to evaluate genome-wide expression in skeletal muscles of flies with muscle-specific overexpression of FOXO or Mnt (Affymetrix Drosophila Genome 2.0 Array).  This design allowed us to identify genes and pathways induced by overexpression of FOXO and/or Mnt, and enabled us to address the degree to which FOXO-induced pathways were independent of those induced by Mnt.

overall_design: Three independent biological replicates from each of three groups (control, UAS-Foxo and UAS-Mnt)

first: Fabio

last: Demontis

first: Vishal

last: Patel

first: Norbert

last: Perrimon


title: Liver Transcriptomics data from mouse model with Features of Post-traumatic Stress Disorder

status: Public on Jun 07 2014

city: Fort Detrick

first: Meskerem

last: Jibitu

address: 568 Doughten Drive

department: Integrative Systems Biology

institute: US Army Center for Environmental Health Research

summary:
We have used a social defeat (SD) mouse model of post-traumatic stress disorder (PTSD) that is based on a brief exposure of a mouse to the aggressor mice for either 5 d or 10 d stress periods.
Mice simulating aspects of posttraumatic stress disorder exhibit behavioral changes, body weight gain, increased body temperature, and inflammatory and fibrotic histopathologies and transcriptomic changes of heart tissue. Liver tissue of these mice was subjected to mRNA analysis. Transcriptomic analysis of liver indicated chronic toxicities and metabolic alterations in aggressor-exposed mice that possibly contributed to the persistent metabolic disturbance

overall_design: Two-condition experiment, C57BL6/J mice Biological replicates: 4-6 control replicates, 5-6 stressed replicates.

first: Aarti

last: Gautam

last: D’Arpa

first: Duncan

last: Donohue

first: Seid

last: Muhie

first: Stacy-Ann

last: Miller

first: Nabarun

last: Chakraborty

first: Rasha

last: Hammamieh

first: Marti

last: Jett


title: Dietary switch reveals fast coordinated gene expression changes in Drosophila melanogaster.

status: Public on Jun 01 2014

city: Providence

first: M. Pilar

last: Gil

state: Rhode Island

address: 75 Waterman St

institute: Brown University

summary: Dietary restriction (DR) is one of the most studied interventions known to extend life span. The robustness of its effect across species suggests the existence of conserved mechanisms to reduce mortality rates and increase longevity. However, because DR elicits a large number of physiological changes, many of which are unrelated to the longevity response, it has been difficult to identify these specific mechanisms. Whole-genome gene expression studies have typically reported several hundreds to thousands of differentially expressed genes in response to DR. The fruit fly Drosophila melanogaster shows a remarkable response to a change in diet: after a switch to DR, food mortality rates drop within 2-4 days to the same level as cohorts continuously on DR. Based on this observation, we utilized a novel experimental design to enrich for genes directly associated with the longevity response. By profiling gene expression in a cohort of fruit flies that were switched from normal food to DR we were able to partition genes in several classes with distinct patterns of expression.

overall_design: Canton-S flies were kept at 25˚C in a temperature-controlled incubator at 50% humidity with a 12 hour on/off light cycle. The flies were sorted into vials at a density of 25 males and 25 females per vial, randomly divided into treatment groups and passed every day on either Control Food (CF, 150 g/L sucrose, 150 g/L autolysed yeast, and 20 g/L agar, all w/v) or Restricted Food (RF, 50 g/L sucrose, 50 g/L autolysed yeast, and 20 g/L agar, all w/v) and the number of dead flies recorded. On day 40, half of the flies on Control Food were switched to the Restricted Food. During the course of the experiment, age-specific instantaneous mortality rate was analyzed and the separation of mortality rate between the food conditions was verified before the switch. Flies were sorted under light CO2 and collected at fixed time intervals during (0 = time of switch), and after (2, 4, 6, 8, 12, 18, 24, 32, 40, 48, 56, 72 hours after) the switch time point via snap freezing in liquid nitrogen and were stored at −80°C. Heads and thorax of female flies were collected for microarray experiments.

first: M

first: Nicola

last: Neretti


title: Expression data from TFIIA-non-cleavable mouse fetal liver hematopoietic stem cells

status: Public on May 28 2014

city: New York

first: Hidetaka

last: Niizuma

address: 1275 York Ave

department: HOPP

institute: Memorial Sloan Kettering Cancer Center

summary:
During embryogenesis, development of hematopoietic stem cells (HSC) occurs in the fetal liver and involves coordinate programs of transcription. Taspase1, a highly conserved threonine protease, directly cleaves and regulates the TFIIA families of transcription factors. We discovered that loss of Taspase1 (Tasp1-/-) or non-cleavage of TFIIAα−β (TFIIAα-βnc/nc) leads to a severe fetal liver developmental retardation that is associated with impaired HSC self-renewal and loss of HSC quiescence.
We used microarray to elucidate the mechanism(s) by which TFIIA regulates fetal liver hematopoiesis, and expression of targets of HoxA9 was found to be altered by gene set enrichment analyses.

overall_design: Embryonic day 14.5 fetal liver HSCs (defined as Lineage-Sca-1+c-Kit+CD150+cells) of wild-type (n = 4) and TFIIAα-βnc/nc (n = 3) were analyzed.


title: Expression data from RCAS PDGFB/Nestin tv-A glioma cells within Ptprd+/+p16-/- (n=2), Ptprd+/-p16-/- (n=2), and Ptrpd-/-p16-/- (n=3) mice.

first: Timothy

last: Chan

address: 1275 York Avenue

department: Human Oncology and Pathogenesis Program

institute: Memorial Sloan-Kettering Cancer Center

summary:
PTPRD is a tumor suppressor of glioma that is frequently co-deleted with CDKN2A/p16. We show that Ptprd and p16 cooperate to promote gliomagenesis in the RCAS PDGFB / Nestin tv-A glioma mouse model.
We found unique gene expression changes within tumor cells of Ptprd+/-p16-/- vs. Ptprd+/+p16-/- and Ptprd-/-p16-/- tumor cells.

overall_design:
Neonatal mice were injected with RCAS PDGFB GFP. At symptoms, or at 12 weeks post injection, GFP+DAPI- tumor cells were sorted for RNA extraction and hybridization on Affymetrix microarrays.

The mouse strain used was a mixed background of C57/BL6 and FVB/N. Ptprd mice were from Uetani et al. 2000 and p16/Nestin-tvA mice were from Tchouganouva et al. 2007.

first: Berenice

last: Ortiz


title: INO80 complex in the core regulatory network governing ESC self-renewal [728_subunits]

status: Public on May 16 2014

city: Durham

first: Li

last: Wang

address: 111 T.W. Alexander Dr

institute: NIH

summary: Embryonic stem cell (ESC) self-renewal and pluripotency is controlled by the coordinated action of transcription factors and chromatin regulators. Compared to the pluripotency transcription factors, the function of the chromatin regulators, especially the ATP-dependent chromatin remodelers, remains poorly understood in ESCs. Here, we show that INO80, a SWI/SNF family chromatin remodeling complex, is essential for ESC self-renewal, pluripotency, somatic cell reprogramming, and embryonic development. Ino80, the ATPase of the complex, forms an auto-regulatory loop with the ESC master transcription factors Oct4, Nanog, and Sox2. More importantly, it co-occupies the enhancer regions of most key pluripotency genes with the master transcription factors, and positively regulates their expression by maintaining an open chromatin structure. Our data suggests that INO80 is an integral component of the pluripotency transcription network, and plays a critical role in both the maintenance and establishment of pluripotency

overall_design:
Mouse J1 cells were transfected with non-targeting (NT), Ino80, Ino80b, Ino80c or Ino80e siRNAs, and RNA was isolated 96 hours after transfection.
agent: non-targeting siRNA: Mock_1, Mock_2
agent: Ino80 siRNA: Ino80a_1, Ino80a_2
agent: Ino80b siRNA: Ino80b_1, Ino80b_2
agent: Ino80c siRNA: Ino80c_1, Ino80c_2
agent: Ino80e siRNA: Ino80e_1, Ino80e_2
cell line: mouse J1 ESC: Mock_1, Mock_2, Ino80a_1, Ino80a_2, Ino80b_1, Ino80b_2, Ino80c_1, Ino80c_2, Ino80e_1, Ino80e_2
time: 96 hours: Mock_1, Mock_2, Ino80a_1, Ino80a_2, Ino80b_1, Ino80b_2, Ino80c_1, Ino80c_2, Ino80e_1, Ino80e_2
biological replicate: Ino80a_1, Ino80a_2
biological replicate: Ino80b_1, Ino80b_2
biological replicate: Ino80c_1, Ino80c_2
biological replicate: Ino80e_1, Ino80e_2
biological replicate: Mock_1, Mock_2

first: Guang

last: Hu

first: James

middle: M

last: Ward


title: INO80 complex in the core regulatory network governing ESC self-renewal [771_timecourse]

overall_design:
Mouse  J1 cells were infected with lentiviral-shNT or lentiviral-Ino80, RNA was extracted at 2, 4 or 6 days after infection.
agent: non-targeting shRNA: NS_Day_2_1, NS_Day_2_2, NS_Day_4_1, NS_Day_4_2, NS_Day_6_1, NS_Day_6_2
agent: Ino80 shRNA: shIno80_Day_2_1, shIno80_Day_2_2, shIno80_Day_4_1, shIno80_Day_4_2, shIno80_Day_6_1, shIno80_Day_6_2
time: 48 hours: NS_Day_2_1, NS_Day_2_2, shIno80_Day_2_1, shIno80_Day_2_2
time: 96 hours: NS_Day_4_1, NS_Day_4_2, shIno80_Day_4_1, shIno80_Day_4_2
time: 144 hours: NS_Day_6_1, NS_Day_6_2, shIno80_Day_6_1, shIno80_Day_6_2
cell line: mouse J1 ESC: NS_Day_2_1, NS_Day_2_2, shIno80_Day_2_1, shIno80_Day_2_2, NS_Day_4_1, NS_Day_4_2, shIno80_Day_4_1, shIno80_Day_4_2, NS_Day_6_1, NS_Day_6_2, shIno80_Day_6_1, shIno80_Day_6_2
biological replicate: shIno80_Day_2_1, shIno80_Day_2_2
biological replicate: shIno80_Day_4_1, shIno80_Day_4_2
biological replicate: shIno80_Day_6_1, shIno80_Day_6_2
biological replicate: NS_Day_2_1, NS_Day_2_2
biological replicate: NS_Day_4_1, NS_Day_4_2
biological replicate: NS_Day_6_1, NS_Day_6_2


title: Transgenic SCLC induced by E6/E7 oncoproteins vs normal controls

status: Public on May 27 2014

city: Baronissi (SA)

first: Rosanna

last: Martinelli

address: Via Allende

department: Medicine and Surgery

country: Italy

institute: Salerno University

summary: The human papillomavirus virus (HPV) is a proven cause of most human cervical cancers, and might have a role in other malignancies including vulva, skin, oesophagus, head and neck cancer. HPV has also been speculated to have a role in the pathogenesis of lung cancer. To validate the hypothesis of HPV involvement in small cell lung cancer pathogenesis we performed gene expression profile of transgenic mouse model of SCLC induced by HPV-16 E6/E7 oncoproteins.

overall_design: Gene expression profile of SCLC has been performed using Agilent whole mouse genome (4x44k) representing ~ 41000 genes and mouse transcripts. Samples were obtained from two HPV16-E6/E7 transgenic mouse model and from littermate’s normal lung.

first: Tonia

last: Buonomo


title: Gene expression in intestinal stem cells

status: Public on Jun 16 2014

city: Worcester

first: Thomas

last: Greenough

address: 373 Plantation Street

department: Program in Molecular Medicine

institute: University of Massachusetts Medical School

summary: Genetic Manipulation to increase number of ISC (intestinal stem cells) and gene expression profiling to identify ISC regulators

overall_design: Fly midguts were disected from wild type and transgenic animals

first: Tony

last: Ip


title: Hippocampal expression data from FTY720- and vehicle-treated SCID mice following fear consolidation testing

status: Public on May 12 2014

city: Richmond

first: Michael

last: Miles

state: VA

institute: Virginia Commonwealth Univ.

summary:
FTY720/Fingolimod, an FDA-approved drug for treatment of multiple sclerosis, has beneficial effects in the CNS that are not yet well understood, independent of its effects on immune cell trafficking. Here we show that FTY720 enters the nucleus where it is phosphorylated by sphingosine kinase 2 (SphK2) and nuclear FTY720-P that accumulates there, binds and inhibits class I histone deacetylases (HDACs) enhancing specific histone acetylations. FTY720 is also phosphorylated in mice and accumulates in various brain regions, including hippocampus, inhibits HDACs and enhances histone acetylation and gene expression programs associated with memory and learning leading to improvement of memory impairment independently of its immunosuppressive actions. Our data suggest that sphingosine-1-phosphate and SphK2 play specific roles in memory functions and that FTY720 may be a useful adjuvant therapy to facilitate extinction of aversive memories.
Microarrays were used to survey the effect of FTY720 treatment during contextual fear conditioning on hippocampal gene expression.

overall_design: Total RNA was isolated from individual hippocampi of SCID mice 1 hour following fear consolidation testing after the third day of FTY720 or saline treatment. Eight arrays were run in total: 4 FTY720-treated mice and 4 saline-treated control mice.

middle: F

first: Megan

last: O'Brien


title: Expression Data from Fluorescently Sorted Muscle Subsets

status: Public on Jun 23 2014

first: Mary

middle: K.

last: Baylies

department: Developmental Biology

summary:
Skeletal muscles are formed in a variety of shapes and sizes, and this diversity impacts muscle function and disease susceptibility. To understand how muscle diversity is generated, we performed gene expression profiling of muscle subsets from Drosophila embryos. By comparing the transcriptional profiles of two muscle subsets, we identified a core group of founder cell-enriched genes. We screened mutant embryos for muscle defects and identified Sin3A and 10 other transcription and chromatin regulators as having novel functions in the Drosophila embryonic somatic musculature. Sin3A is required for the morphogenesis of a subset of muscles, and Sin3A mutants display muscle loss and misattachment. Additionally, misexpression of identity gene transcription factors in Sin3A heterozygous embryos leads to direct transformations of one muscle into another, while overexpression of Sin3A results in the reverse transformation. Our data implicate Sin3A as a key buffer controlling muscle responsiveness to transcription factors in the formation of muscle identity, thereby generating tissue diversity.
We used microarray analysis to look for changes in gene expression between different musle founder cell subsets

overall_design: Flies expressing GFP or RFP transgenes were maintained at 25° C on a 12-hour light/12-hour dark cycle in an incubator and fed with yeast paste spread on apple juice agar plates. After a 2-hour pre-lay, flies were allowed to lay for 2 hours; these plates were removed and aged for an additional 8 hours. Embryos were dissociated by dounce homogenization into a single cell suspension as previously described (Dobi et al., 2011). Cells were sorted using standard methods on a Beckton-Dickson FACS Aria Cell Sorter (Estrada and Michelson, 2008). Total cellular RNA from each sample was prepared from sorted cells using TRIzol LS Reagent without amplification (Invitrogen). Total cellular RNA was labeled and hybridized to Drosophila Affymetrix GeneChip 2.0 arrays according to the manufacturers instructions. Three independent sorts were made for each transgene, and each RNA sample was independently labeled and hybridized.    For apME-GFP, we sorted 1,000,000 GFP-positive cells from 4 X 108 starting cells, a positive-rate of 0.03%, which yielded 1 μg of RNA. The purity upon resort of the cells was 74%. The purity of S59ME-RFP and twiprom-actin-GFP was 87% and 95%, respectively, with positive-rates and yields also correspondingly higher.   Affymetrix microarray data was normalized and compared using Partek Genomics Suite Software. apterousME-GFP and slouchME-RFP-positive cells were compared to twiprom-actin-GFP-expressing cells to generate lists of differentially regulated genes, fold change ≥ 1.7, p-value < 0.05. The Database for Annotation, Visualization and Integrated Discovery (DAVID) v6.7 was used to assign Gene Ontology classifications to the genes identified by the array (Huang et al., 2009a; 2009b). Default parameters were used to perform Functional Annotation of gene lists, p-value < 0.05.

first: Krista

last: Dobi

first: Marc

middle: S

last: Halfon


title: Sex-specific mRNA and miRNA expression data from Drosophila larvae, pupae and adults [mRNA]

status: Public on May 07 2014

city: Falmer

first: Fiona

last: Ingleby

address: John Maynard Smith Building

department: School of Biology

institute: University of Sussex

summary:
Sex differences in gene expression throughout development are poorly understood, especially sex-specific expression of micro RNAs. However these patterns of gene expression could have important implications in our understanding of the underlying mechanics of sex differentiation and sexual conflict.
We extract mRNA and miRNA from male and female Drosophila melanogaster from three developmental timepoints, third larval instar, pupae and adults, and examine gene expression using microarrays. We found a large number of sex-biased mRNA transcripts at each stage of development, whereas sex-biased miRNA expression was low in larvae and pupae and more prevalent in adults.

overall_design: We isolated 2 biological replicates of each sex at each of the three developmental timepoints and extracted mRNA and miRNA from each sample, creating 12 samples of each type of RNA which were ran on GeneChip Drosophila Genome 2.0 Affymetrix microarrays to examine mRNA expression, and GeneChip miRNA 3.0 Affymetrix microarrays to examine miRNA expression.

first: Ilona

last: Flis

first: Edward

middle: H

last: Morrow


title: IKKα promotes intestinal tumorigenesis

city: Erlangen

first: Roland

last: Lang

address: Wasserturmstr. 3-5

institute: University Hospital Erlangen

summary: Depending on the tumor type IκB kinase α (IKKα) can act as tumor promoter or tumor suppressor in various malignancies. Here we demonstrate a key function of IKKα in the suppression of a tumoricidal microenvironment during intestinal carcinogenesis. Mice deficient in IKKα kinase activity are largely protected from intestinal tumor development that is dependent on the enhanced recruitment of IFNγ expressing M1-like myeloid cells. In IKKα mutant mice M1-like polarization is not controlled in a cell autonomous manner but depends rather on the interplay of both IKKα mutant tumor epithelia and immune cells.

overall_design: Tamoxifen-inducible β-catc.a. mice comprise an excellent model to study Wnt-dependent tumor initiation. These mice are characterized by IEC-restricted stabilization of β-catenin causing rapid expansion of intestinal crypts and loss of differentiated IEC. To further explore the underlying IKKα controlled pro-proliferative mechanism, we performed a microarray analysis comparing RNA isolated from wildtype, IkkαAA/AA, β-catc.a. or β-catc.a./IkkαAA/AA IEC 15 days after the first tamoxifen administration. and within 4 weeks β-catc.a. mice succumb to this marked crypt hyperproliferation

first: Florian

last: Greten


title: Compare gene expression patterns in Chsy-1 wt and ko mouse 13.5 days embryo forelimbs

city: South San Francisco

first: Li

last: Li

address: 1 DNA Way

institute: Genentech, Inc

summary: Transcriptional profiling of 13.5 day mouse embryo forelimbs. Gene expression comparison done between wild type and Chsy-1 gene knockout mice.

overall_design: Two-condition experiment, control (wild type) vs. test (Chsy-1 knockout). Biological replicates: 9 control replicates, 13 test replicates.

first: Deanna

last: Grant

first: Zora

last: Modrusan


title: Mutant IDH inhibits HNF4a to disrupt hepatocyte differentiation and promote cholangiocarcinoma.

status: Public on Apr 30 2014

first: Kenneth

middle: N

last: Ross

address: 450 Brookline Ave., Rm M640

department: Pediatric Oncology

institute: Dana-Farber Cancer Institute

summary:
Gene expression of mouse hepatoblasts (HBs) expressing IDH1 WT, IDH1 R132C, IDH2 WT, R172K and empty vector controls (N=2 cultures for each condition) grown on collagen-coated plates and IDH1 R132C and empty vector controls on uncoated plates were evaluated using Affymetrix Mouse 430Av2 DNA microarrays that were processed at the Dana-Farber Cancer Institute core facility (http://macf-web.dfci.harvard.edu/) using their standard protocol.
Mutations in Isocitrate dehydrogenase 1 (IDH1) and IDH2 are among the most  common genetic alterations in intrahepatic cholangiocarcinoma (IHCC), a deadly primary liver cancer. Mutant IDH proteins in IHCC and other malignancies acquire an abnormal enzymatic activity allowing them to convert alphaketoglutarate (aKG) to 2-hydroxyglutarate (2HG), which inhibits the activity of multiple aKG-dependent dioxygenases, and results in alterations in cell differentiation, survival, and extracellular matrix maturation. However, the molecular pathways by which IDH mutations lead to tumour formation remain unclear. Here we show that mutant IDH blocks primary liver progenitor cells from undergoing hepatocyte differentiation through the production of 2HG and suppression of HNF4a, a master regulator of hepatocyte identity and quiescence. Correspondingly, genetically engineered mouse models (GEMMs) expressing mutant IDH in the adult liver show aberrant response to hepatic injury, characterized by HNF4a silencing, impaired hepatocyte differentiation and markedly elevated levels of cell proliferation. Moreover, mutant IDH and activated Kras, genetic alterations that co-exist in a subset of human IHCCs, cooperate to drive the expansion of liver progenitor cells, development of premalignant biliary lesions, and progression to metastatic IHCC. These studies provide a functional link between IDH mutations, hepatic cell fate, and IHCC pathogenesis and present a novel GEMM of IDH-driven malignancy.

overall_design: Gene expression of HBs expressing IDH1 WT, IDH1 R132C, IDH2 WT, IDH2 R172K and empty vector controls under a doxycycline-inducible system (N=2 cultures for each condition) grown on collagen-coated plates and IDH1 R132C and empty vector controls on uncoated plates were evaluated using Affymetrix Mouse 430Av2 DNA microarrays.

first: Supriya

last: Saha

first: Christine

middle: A

last: Parachoniak

first: Nabeel

last: Bardeesy


title: ASC deficiency suppresses proliferation and prevents medulloblastoma incidence

status: Public on May 23 2014

city: Chapel Hill

first: Mohanish

last: Deshmukh

address: 7109E Neuroscience Research Building, 105 Mason Farm Road

department: Cell Biology and Physiology

institute: University of North Carolina

summary: Apoptosis-associated speck-like protein containing a caspase recruitment domain (ASC) is silenced by promoter methylation in many types of tumors, yet ASC's role in most cancers remains unknown. Here, we show that ASC is highly expressed in a model of medulloblastoma, the most common malignant pediatric brain cancer; ASC is also expressed in human medulloblastomas. Importantly, while ASC deficiency did not affect normal cerebellar development, ASC knockout mice on the Smoothened (ND2:SmoA1) transgenic model of medulloblastoma exhibited a profound reduction in medulloblastoma incidence and a delayed tumor onset. A similar decrease in tumorigenesis with ASC deficiency was also seen in the hGFAP-Cre:SmoM2 mouse model of medulloblastoma. Interestingly, hyperproliferation of the external granule layer (EGL) was comparable at P20 in both wild-type and ASC-deficient SmoA1 mice. However, while the apoptosis and differentiation markers remained unchanged at this age, proliferation makers were decreased, and the EGL was reduced in thickness and area by P60. This reduction in proliferation with ASC deficiency was also seen in isolated SmoA1 cerebellar granule precursor cells in vitro, indicating that the effect of ASC deletion on proliferation was cell autonomous. Interestingly, ASC-deficient SmoA1 cerebella exhibited disrupted expression of genes in the transforming growth factor-β pathway and increased level of nuclear Smad3. Taken together, these results demonstrate an unexpected role for ASC in Sonic hedgehog-driven medulloblastoma tumorigenesis, thus identifying ASC as a promising novel target for antitumor therapy.

overall_design: reference x sample

first: Elizabeth

middle: R

last: Knight


title: Expression data from dexamethasone treated mouse embryonic neural progenitor/stem cells isolated from wild type C57Bl/6 or caveolin-1 knockout mice

status: Public on May 21 2014

city: Pittsburgh

first: Uma

last: Chandran

state: PA

address: 5150 Center Ave

department: BioMedical Informatics

institute: University of Pittsburgh

summary:
Neurosphere cultures prepared from E14.5 mouse cerebral cortex at passage 3 were treated for 4 hours with 100 nM dexamethasone
We used microarrays to detail the global program of dexamethasone regulated gene expression  in embryonic neural progenitor/stem cells

overall_design: Cerebral cortex was isolated from E14.5 mouse fetuses and cultured as neurospheres for 3 passages prior to treatment with 100 nM dexamethasone or ethanol vehicle for 4 hours

first: Donald

middle: B

last: DeFranco


title: Cdk8, Cyclin C, Med12 or Med13 depletion effect on gene expression in Drosophila S2 cells

status: Public on Apr 29 2014

city: Helsinki

first: Emilia

last: Kuuluvainen

address: Viikinkaari 9

department: Institute of Biotechnology

institute: University of Helsinki

summary: Expression profiling following depletion of Mediator Cdk8 module subunits Cdk8, Cyclin C (CycC), Med12 and Med13 72 hours after dsRNA treatment of Drosophila melanogaster S2 cells. Results provide insight into the role of individual Cdk8 module subunits in regulation of transcription.

overall_design: 22 samples. 2 Cdk8 dsRNA, 4 CycC dsRNA, 4 Med12 dsRNA, 4 Med13 dsRNA, 8 control samples including 4 Luciferase (Luc) dsRNA and 4 GFP dsRNA

first: E

first: T

last: Mäkelä


title: A mechanistic rationale for targeting the unfolded protein response in pre-B acute lymphoblastic leukemia [array]

status: Public on Apr 24 2014

city: San Francisco

first: Huimin

last: Geng

address: 513 Parnassus Ave., MSB HSW 1201

department: Department of Laboratory Medicine

institute: UCSF

summary: The plasma cell transcription factor XBP1 is critical for terminal differentiation of B cells into plasma cells but has no known role at earlier stages of B-cell development. Here we show that XBP1 is not only important during early B-cell development and for survival of pre-B cells but also protects pre-B ALL cells. Among pre-B ALL subset, XBP1 was hypomethylated and highest expressed in the Ph+ ALL subset. Cre-mediated deletion of XBP1 in a mouse model of Ph+ ALL compromised proliferation and viability and prolonged survival of leukemia-bearing mice. Interestingly, XBP1 expression levels were positively transcriptionally regulated by STAT5 and negatively by BACH2 and BCL6. High XBP1 expression in high risk ALL patients at the time of diagnosis predicted poor outcome in two clinical trials. Clinically, small-molecule inhibition of IRE1-dependent XBP1-activation caused cell death of patient-derived pre-B ALL cells and affected leukemia-initiation in transplant recipient mice. Collectively, these studies identify XBP1 as an important survival factor and as a potential therapeutic target to overcome drug-resistance in pre-B ALL.

overall_design: Genome-wide profiling of mRNA levels in BCR-ABL1 transduced murine Grp78 fl/fl pre-B cells with an empty vector (Grp78 wild type, MIG-1,2,3) and Cre  (Grp78 deletion, CRE-1,2,3).

first: Behzad

last: Masouleh

first: Misook

last: Chang

first: Markus

last: Muschen


title: Expression profile of bcl11b-deficient NAÏVE CD8+ T cells versus wild type

status: Public on Apr 22 2014

city: Albany

first: Dorina

last: Avram

address: 43 New Scotland Avenue

department: Center for Immunology and Microbial Disease

institute: Albany Medical Center

summary: Naïve CD44low CD25low CD8+ T cells from Bcl11bF/F/dLck-iCre and wild type mice at steady state were sorted at 90% purity, RNA was extracted and profile for mRNA expression to identify mRNAs differentially expressed in Bcl11b-/- naïve CD8+ T cells versus wild type.

overall_design: Naïve CD44low CD25low CD8+ T cells purified from Bcl11bF/F/dLck-iCre and wild type mice and investigated for mRNA expression


title: Co-regulation analysis of CP190 and CG9740 [expression]

status: Public on Apr 18 2014

city: Barcelona

first: M Lluisa

last: Espinas

address: Baldiri Reixac 10

country: Spain

institute: IBMB-CSIC

summary: Gene expression in S2 cells after CG9740 or CP190 RNAi

overall_design: Two biological replicates for each RNAi condition are analyzed including LacZ RNAi as control.

first: Maria


title: MicroRNA miR-223 constrains lethal inflammation during Mycobacterium tuberculosis infection

status: Public on Apr 21 2014

city: Berlin

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

institute: Max-Planck-Institute for Infection Biology

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

summary: The molecular mechanisms that control innate cell recruitment during chronic infection and inflammation, such as tuberculosis (TB), are incompletely understood. During TB, myeloid cells infiltrate the lung and sustain local inflammation. We identified microRNA (miR)-223 as one of the most abundant noncoding RNAs in lung parenchyma of TB patients and susceptible mice. MiR-223 controlled lung recruitment of myeloid cells, and consequently, neutrophil-driven lethal inflammation, by directly targeting the chemoattractants CXCL2, CCL3 and IL-6. Our study reveals an essential role for a single miR in TB. Moreover, we identify new targets for and assign novel biological functions to miR-223. By regulating leukocyte chemotaxis via chemoattractants, miR223 is critical for control of TB and probably other nonresolving inflammatory diseases.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: MicroRNAs expression analysis in whole blood from 8 TB and 8 TST+ subjects. The samples were collected at Makerere University in Kampala, Uganda. Gene expression analysis of whole blood and lung tissue of C57/BL6 and miR-223-/- mouse strains (8-12 weeks of age) after Mtb aerosol infection. Samples were collected at 7, 14 and 21 days post infection.

first: Anca

last: Dorhoi

first: Marco

last: Iannaccone

first: Stefan

last: Kaufmann


title: Expression profile of bcl11b-deficient cd8 T cells during immune response

status: Public on Apr 12 2014

summary: Review on the role of Bcl11b in thymus and periphery and impact on immune diseases

overall_design: CD8+ T cells purified from bcl11bf/flckd-cre and wild type mice were infected with Listeria monocytogenes and on day 6 mice were sacrificed and Cd8+ T cells were purified at more than 90% purity. The RNA was purified with trizol and submitted for generation of library and microarrays to establish genes which are regulated in infected KO versus WT cytotoxic T cells.


title: Expression profile of bcl11b-/- preselected DP thymocytes

summary: Review on the role of Bcl11b in thymus and periphery and impact on diseases

overall_design:
RNA was extracted from DP thymocytes of bcl11bf/fCd4cre/tcra-/- and tcra-/- mice. Tcra-/- mice only have preselected DP thymocytes. Such mice were used to determine the role of Bcl11b before selection, considering the defective positive selection in bcl11bf/fcd4cre mice.
RNA was isolated and submitted for library generation and microarray analysis to determine expression profile of bcl11b-/- preselected DP thymocytes.


title: Effect of prolactin and actinomycin D on gene expression in murine AML12 and Hepa 1-6 hepatocytes

status: Public on Apr 25 2014

city: North Grafton

first: Arlin

last: Rogers

address: 200 Westoboro Road

department: Biomedical Sciences

institute: Tufts Cummings School of Vet Med

summary: Transcriptional profiling of murine hepatocyte gene expression following exposure to prolactin or actinomycin D

overall_design: Prolactin or actinomycin D-treated versus serum-free control cells: AML12 and Hepa 1-6. Biological replicates: 2 per cell line per treatment protocol.


title: Gene expression signature induced by 8 weeks of cigarette smoke exposure in the lung of BALB/c mice

status: Public on Apr 01 2014

city: Hamilton

first: Mathieu

last: Morissette

state: Ontario

address: 1280 Main St W

department: Pathology and Molecular Biology

institute: McMaster University

summary: To investigate the impact of cigarette smoke on lung gene expression, female BALB/c mice were obtained from Charles River at 6-8 weeks of age. Using a whole body exposure system (SIU48, PROMECH LAB AB, Vintrie, Sweden), mice (5 per group) were exposed to room air or the mainstream cigarette smoke of twelve 3R4F reference cigarettes (University of Kentucky, Lexington, USA) with filters removed 5 days per week, twice daily for 50 minutes/exposure for 8 weeks, as previously described. Control animals were exposed to room air only. Lungs were collected and stored in RNALater at -80°C prior to RNA extraction.

overall_design: Impact of an 8 week cigarette smoke exposure on BALB/c mouse lung gene expression was assessed.

first: Maxime

last: Lamontagne

first: Jean-Christophe

last: Bérubé

first: Gordon

last: Gaschler

first: Sabina

last: Halappanavar

first: Martin

last: Stampfli

first: Yohan

last: Bossé


title: Ba/F3 cells expressing ETV6-PDGFRb and FIP1L1-PDGFRa treated or not with Glivec

status: Public on Mar 21 2014

city: Brussels

first: Jean-Baptiste

last: Demoulin

address: av Hippocrate 75, B1.74.05

department: de Duve Institute

country: Belgium

institute: Université catholique de Louvain

summary: Gene expression profiles in Ba/F3 cells expressing ETV6-PDGFRB, FIP1L1-PDGFRA or a control vector, treated or not with imatinib (Glivec)

overall_design:
Ba/F3 cells expressing FIP1L1-PDGFRA or ETV6-PDGFRB were cultured in the presence or absence of imatinib for 4 hours before RNA extraction followed by hybridization on Affymetrix microarrays.
In a control condition Ba/F3 cells were cultured in the presence of IL3  in the absence or in the presence of imatinib for 4 hours before RNA extraction.
4 hours treatment with imatinib in Ba/F3 cells expressing  ETV6-PDGFRB, FIP1L1-PDGFRA or a control vector

first: Toffalini

last: Federica

first: Demoulin

last: Jean-Baptiste

first: Essaghir

last: Ahmed


title: Expression data from the mushroom bodies of Drosophila-PKA activity dependent manner

status: Public on Mar 25 2014

city: Daejeon

first: Jongkyun

last: Kang

address: 335 Gwahangro, Yuseong-gu

country: South Korea

institute: KAIST

summary:
Temperature preference behavior in Drosophila depends on the level of PKA signaling in the mushroom bodies.
To identify new components downstream to PKA, we carried out a genome-wide screen for genes regulated by PKA signaling in the mushroom bodies.

overall_design: Using the Gal4-UAS system, we increased or decreased PKA activity in the mushroom bodies by expressing dominant-negative (UAS-PKADN) or constitutively active PKA (UAS-PKACA), respectively. Expression of PKA transgenes was targeted to the mushroom bodies using the mushroom body-specific MB247-Gal4 driver. PKA expression was induced for 12-16 hours in three-day-old adults by inactivating the temperature-sensitive Gal80 at the restrictive temperature. We then analyzed gene-expression profiles to identify the genes showing altered expression levels in response to the high or low PKA activity.

first: Jaeseob

last: Kim

first: Kwang-Wook

last: Choi


title: Expression data from Adult Drosophila with controled microbiota

status: Public on Mar 26 2014

city: Lyon

first: François

last: Leulier

address: 46, allée d'Italie

institute: Institut of Functional Genomics Lyon

summary:
The microbial population that live within the gut of animals influences their physiology. We used axenic and recolonized flies to identify genes whose expression is modulated by the presence of a bacterial flora in the gut.
We identified several up regulated genes, most of which are described as enriched in the midgut, and related either to immunity or to metabolism. This work also suggests that most microbiota regulated genes are Relish dependent.

overall_design: We raised axenic Flies and either : (1) kept them germ free or (2) recolonized their environment with a set of 4 known commensal bacteria of lab-raised drosophila (Commensalibacter intestini, Lactobacillus plantarum, Lactobacillus brevis, Acetobacter pomorum). Flies were maintained in their respective (axenic or recolonized) environment from emergence to 7 days of age. Then females were collected, and total RNA extraction was performed on groups of 20 whole bodies.

first: Berra

last: Combe

first: Arnaud

last: Defaye

first: Noémie

last: Bozonnet

first: Denis

last: Puthier

first: Julien

last: Royet


title: Hippocampal neuronal dematuration as a common effect of antidepressant treatments

city: Tokyo

first: Eri

last: Segi-Nishida

state: Tokyo

address: Niijuku 6-3-1

institute: Tokyo University of Science

summary: The dentate gyrus (DG) of the hippocampus is one of major targets for antidepressant treatments. Our recent research has revealed that selective serotonin reuptake inhibitor (SSRI) treatment causes a long-lasting change in the phenotypes of mature dentate granule neurons to immature state in adult mouse DG. However, it is unknown whether this “dematuration” of DG is a common effect of antidepressant treatments and what mechanisms underlie it. Using electroconvulsive stimulation (ECS), a model of highly effective and fast-acting antidepressant therapy, here we show that neural stimulation via ECS induces rapid and lasting dematuration of granule neurons in DG. A single or few times of stimulation transiently reduced mature marker expression and mature synaptic functions. Repetitive stimulation converted this transient dematuration into a stable form lasting more than 1 month. Dematured granule neurons showed higher excitability, and an increase in GABA-mediated inhibition by the benzodiazepine diazepam prevented the lasting maintenance phase of dematuration without affecting the initial induction phase. Our study suggests that dematuration of DG is a common cellular mechanism underlying effects of different types of antidepressant treatments, and demonstrate a novel role for excitation/inhibition balance in bidirectional regulation of the state of neuronal maturation in the adult brain.

overall_design: Mice were decapitated after the 11 times of ECS (or Sham) or 4 weeks treatment of fluoxetine (or vehicle) at a dose of 22 mg/kg. The brains were sliced and the frequency facilitation of mossy fiber synapse was measured in each sample. The samples which exhibited low frequency facilitation were selected to be used as dematured DG (n = 3) and the dentate gyrus was dissected from each sample. Total RNA was extracted by using an RNeasy micro kit (Qiagen) and the samples of the same groups were put together. From each group, 100 ng of total RNA was amplified with 3’IVT Express kit (Affymetrix, Inc., Santa Clara, CA, USA). All samples were hybridized to the GeneChip mouse genome 430A 2.0 array (Affymetrix, Inc.), and the microarray suite 5.0 of the Affymetrix gene chip operating software was used for the analysis of the GeneChip data.

first: Yuki

last: Imoto

first: Katsunori

last: Kobayashi


title: Transcriptional analysis of live and hybridized iPSCs

status: Public on Mar 20 2014

city: Cambridge

first: Sandy

last: Klemm

address: 31 Ames St.

department: Biology

institute: MIT

summary: Mouse induced pluripotent stem cells (iPSCs) were derived from embryonic fibroblasts by overexpressing the Yamanaka factors Oct4, Sox2, Klf4 and c-Myc, and then grown in standard 2i/serum media conditions. Hybridized iPSCs were fixed with 4% paraformaldehyde; permeabilized in 70% ethanol for over 12 hours; incubated for 12 hours at 30C in an RNA preserving hybridization buffer (300 mM Sodium chloride, 30mM Sodium citrate, 2.1M Ammonium sulfate, 25% formamide, 10 mM EDTA, 1 mg/ml E. Coli tRNA, 500 μg/ml BSA); and reverse cross-linked for 1 hour at 50C with Sodium dodecyl sulfate (SDS) and Proteinase K (100 mM NaCl, 10 mM Tris pH 8.0, 1 mM EDTA, 0.5% SDS, 500 μg/ml Proteinase K).

overall_design: RNA was extracted and compared for live and hybridized iPSCs (1 sample each).

first: Alexander

last: van Oudenaarden


title: Transcriptional analysis of iPSCs during cellular reprogramming using RNA FACS

summary: Mouse induced pluripotent stem cells (iPSCs) were derived from embryonic fibroblasts by overexpressing the Yamanaka factors Oct4, Sox2, Klf4 and c-Myc for 32 consecutive days. iPSCs were isolated by RNA FACS (for endogenous Sox2) from a heterogeneous reprogramming culture and transcriptionally compared with (1) iPSCs stabilized in 2i medium (iPS-2i) and (2) iPSCs stabilized in co-culture with mouse embryonic fibroblasts (iPS-MEF)

overall_design: n = 2 replicates for each sample/condition

last: klemm


title: Effect of Oleanolic acid on liver transcriptome of mice lacking apolipoprotein E

city: Zaragoza

first: Jesus

last: Osada

address: Miguel Servet, 177

institute: Universidad de Zaragoza

summary:
The hypothesis that the oleanolic acid of olive oil might influence hepatic gene expression in an apoE was tested in mice.
Gene expression was analyzed using DNA microarrays in male apoE-deficient mice that received 10 mg/kg/day of oleanolic acid for 11 weeks.

overall_design: As initial screening of potential candidate genes involved in a differential response, only genes with remarkably modified expression (signal log2 ratio > 1.5 or < -1.5) were further considered

first: Clara

last: Gabás-Rivera

first: Roberto

last: Martínez-Beamonte

first: María

last: Navarro

first: Carmen

last: Arnal

first: Joaquín

last: Surra

first: Valentina

last: Ruiz-Gutierrez

first: Jesús


title: Functional genomic analysis of the periodic transcriptome in the developing Drosophila wing [Affymetrix]

status: Public on Mar 15 2014

city: Kansas City

first: Chris

middle: W

last: Seidel

state: MO

department: Genomics

institute: Stowers Institute

summary: The eukaryotic cell cycle, driven by both transcriptional and post-translational mechanisms, is the central molecular oscillator underlying tissue growth throughout animals.  While genome-wide studies have investigated cell cycle-associated transcription in unicellular systems, global patterns of periodic transcription in multicellular tissues remain largely unexplored.  Here we define the cell cycle-associated transcriptome of the developing Drosophila wing epithelium and compare it with that of cultured Drosophila S2 cells, revealing a core set of periodic genes as well as a surprising degree of context-specificity in periodic transcription.  We further employ RNAi-mediated phenotypic profiling to define functional requirements for over 300 periodic genes, with a focus on those required for cell proliferation in vivo.  Finally, we investigate the role of novel genes required for interkinetic nuclear migration. Combined, these findings provide a global perspective on cell cycle control in vivo, and highlight a critical need to understand the context-specific regulation of cell proliferation.

overall_design: Cells from developing Drosophila wing epithelium, and cultured S2 cells are FACS sorted into G1 and G2 populations based on DNA content and compared in triplicate on Affymetrix microarrays to identify differences in the transcriptional program of the cell cycle by cell type.

first: Liang

last: Liang

first: Jeff

last: Haug

first: Matthew

last: Gibson


title: Expression data from E18.5 Igf1 -/- (homozygous mutant) and Igf1+/+ (normal wild type control) mouse lungs

status: Public on Mar 31 2014

city: Salamanca

first: Javier

last: De Las Rivas

address: Campus Miguel de Unamuno

department: CSIC and University of Salamanca

institute: Cancer Research Center (CiC-IBMCC)

summary: Insight into the role of Insulin-like Growth Factor (IGF) in development of lungs has come from the study of genetically modified mice. IGF1 is a key factor during lung development. IGF1 deficiency in the neonatal mouse causes respiratory failure collapsed alveoli and altered alveolar septa. To further characterize IGF1 function during lung development we analyzed Igf1-/- mouse prenatal lungs in a C57Bl/6 genetic background. Mutant lungs showed disproportional hypoplasia, disorganized extracellular matrix and dilated alveolar capillaries. IGF1 target genes during lung maturation were identified by analyzing RNA differential expression in Igf1-/- lungs using microarrays.

overall_design: Lungs from E18.5 were isolated from both Igf1+/+ wild type and Igf1-/- null mice and pooled to obtain RNA. Heterozygous male and female with a genetic background C57BL/6J were mated to obtain embryos at embrionic (E) stage 18.5 days post coitum (E18.5). 3 biological replicates per genotype.

first: Jose

middle: G

last: Pichel


title: Differential Kinetics of Antigen Dependency of CD4+ and CD8+ T Cells

status: Public on Feb 28 2014

city: Neuherberg

first: Martin

last: Irmler

state: Bayern

address: Ingolstaedter Landstrasse 1

department: Institute of Experimental Genetics

institute: Helmholtz Zentrum München GmbH

summary: Ag recognition via the TCR is necessary for the expansion of specific T cells that then contribute to adaptive immunity as effector and memory cells. Because CD4+ and CD8+ T cells differ in terms of their priming APCs and MHC ligands we compared their requirements of Ag persistence during their expansion phase side by side. Proliferation and effector differentiation of TCR transgenic and polyclonal mouse T cells were thus analyzed after transient and continuous TCR signals. Following equally strong stimulation, CD4+ T cell proliferation depended on prolonged Ag presence, whereas CD8+ T cells were able to divide and differentiate into effector cells despite discontinued Ag presentation. CD4+ T cell proliferation was neither affected by Th lineage or memory differentiation nor blocked by coinhibitory signals or missing inflammatory stimuli. Continued CD8+ T cell proliferation was truly independent of self-peptide/MHC-derived signals. The subset divergence was also illustrated by surprisingly broad transcriptional differences supporting a stronger propensity of CD8+ T cells to programmed expansion. These T cell data indicate an intrinsic difference between CD4+ and CD8+ T cells regarding the processing of TCR signals for proliferation. We also found that the presentation of a MHC class II–restricted peptide is more efficiently prolonged by dendritic cell activation in vivo than a class I bound one. In summary, our data demonstrate that CD4+ T cells require continuous stimulation for clonal expansion, whereas CD8+ T cells can divide following a much shorter TCR signal.

overall_design:
Samples 1-12: Analysis on day 2. Purified CD4+ AND-TCR transgenic cells and CD8+ OT1-TCR transgenic cells were separately stimulated with anti-CD3 and anti-CD28 antibodies. 48 hours later, the cells were sorted again to a purity of >99 %. Extracted total RNA was amplified twice and hybridized on Affymetrix Mouse 430A2 microarrays. First, we analysed the changes of the CD4+ and CD8+ T cells after stimulation. Second, we compared the differences of the changes between the two cell types after stimulation. For each of the four groups (CD4+ and CD8+, stimulated and unstimulated), we analysed three independent biological replicates.
Samples 13-28: Analysis on day 5. AND and OT1 TCR-transgenic T cells were prepared as described before, but transferred into mice that do not or do present their respective antigens. 72 hours later, the cells were FACS-sorted twice to >99 % purity, directly into Trizol. For each of the six groups (CD4+ and CD8+, unstimulated, transient (2 days) and continuous (5 days) stimulation), three independent biological replicates were analyzed, except for CD4+ unstimulated and CD4+ transient, with two replicates each.

first: Johannes

last: Beckers

first: Marion

last: Horsch


title: Cerebellar RNA in Grid2 deficient mice.

status: Public on Feb 26 2014

city: Ibaraki

first: Hiroshi

last: Takemori

state: Osaka

address: 7-6-8, Saito-Asagi

institute: National Institute of Biomedical Innovation

summary: Downsream of GRID2 in the mouse cerebellum.

overall_design: Control mice N=3 and Grid2 deficient mouse N=3


title: Microarray analysis of gene expression in CD4+CD8+ double pos (DP) thymocytes upon depletion of Ubiquitin specific protease 8

status: Public on Mar 04 2014

city: Freiburg im Breisgau

first: Klaus-Peter

last: Knobeloch

address: Breisacher Str. 64

department: Inst. for Neuropathology

institute: University Freiburg

summary: T-cell-specific deletion of USP8 (USP8ffCD4Cre) revealed that USP8 is required for thymocyte transition to the CD4+ and CD8+ single positive (SP) stages. To evaluate underlying mechanisms, gene expression profilling was performed in CD4+CD8+ double pos thymocytes derived from control (USP8ff and USP8ffCD4Cre) mice.

overall_design: Microarray analysis of two groups of USP8fl/fl and USP8fl/flCD4Cre thymocytes. Material from two mice was combined for each group (eight mice in total).

first: Almut

last: Dufner


title: Prolactin Prevents Hepatocellular Carcinoma by Restricting Innate Immune Activation of c-Myc in Mice

status: Public on Mar 07 2014

first: Arlin

last: Rogers

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

overall_design: Refer to individual Series


title: Gene expression profiles of irradiated lung tissue in three mouse strains

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: The aim of our research is to clarify the mechanisms generating heterogeneity in response to C-ion irradiation that arise from individual genetic variations in humans. In this study, we performed whole lung C-ion irradiation using three different strains of mice to examine whether strain-dependent differences in radiation effects occur in high-LET C-ion thoracic irradiation. Murine strain-variance was evaluated by histopathological examination of intra-alveolar hemorrhage that is likely to occur during the early phase after irradiation, and of lung fibrosis during the late phase, occurring more than three months after irradiation. We also performed microarray analysis to identify the key genes that are differentially regulated in different mouse strains after C-ion irradiation and to determine the mechanism of strain-dependent pulmonary damage after high-LET C-ion irradiation.

overall_design: Eight-week old female inbred C3H/He Slc, C57BL/6J Jms Slc and A/J Jms Slc mice (3 kinds of mice) were used. The whole thorax of three mice was locally irradiated at 10 Gy with C-ion beams, with a reference beam, 137Cs gamma-rays (2 kinds of beam). Three mice of each strain (3 mice) were sacrificed, and immediately dissected for lung extraction at 6 h (6h sample). Lungs for three mice of each strain without irradiation were extracted at the same time as control samples (control sample). Hybridization to microarrays (Whole Mouse Genome 4x44K OligoMicroarray Kit, single color, Cyamine 3-CTP) consisting of 44,000 total spots was conducted using an Agilent Gene Expression hybridization kit. The arrays from three independent replicates for each sample (3 arrays) were scanned on an Agilent dual-laser Microarray Scanner (all from Agilent Technologies) following the manufacturer's instructions. A total of 108 samples were analyzed. 3 replicate arrays x 3 mice x 3 strains x 2 timing for sampling x 2 kinds of beam.

first: Mayumi

last: Iwakawa


title: Expression data from adult Drosophila females [normoxia]

status: Public on Feb 04 2014

city: LA JOLLA

first: Erilynn

last: Heinrichsen

address: 9500 Gilman Dr, MC0735

institute: UC-San Diego

summary:
High-fat diet (HFD) in normoxia causes a worsened phenotype in adult female flies compared to regular diet (RD).
We used microarrays to examine the transcriptional changes occuring on a HFD compared to RD in normoxia.

overall_design: Adult female Drosophila were collected at d3-5 and placed on RD or HFD and in normoxia for 1 week. Following this week,flies were immediately frozen on dry ice, RNA was extracted and hybridized on Affymetrix microarrays.

middle: T

first: Gabriel

last: Haddad


title: Mouse liver: Control versus IL1-beta challenge, male and female

status: Public on Feb 01 2014

summary: Transcriptional profiling of liver gene expression following IL1-beta challenge comparing male versus female mice

overall_design: IL1-beta versus no cytokine control, male and female. Biological replicates: 2 per sex per treatment protocol.


title: Role of interleukin-4 in the licensing of dendritic cells for the induction of Th2 responses

status: Public on Feb 19 2014

city: Cantoblanco

first: Juan

middle: Carlos

last: Oliveros

state: Madrid

address: Darwin 3

institute: CNB, CSIC


title: Mouse liver transcription profiling by array

status: Public on Feb 21 2014

city: San Diego

first: Dawn

last: Applegate

address: 9855 Towne Centre Drive

institute: RegeneMed, Inc.

summary: Analysis of livers of male and female B6C3F1 mice exposed to prototype treatments from five classes of model hepatotoxicants.  These hepatotoxicants include compounds that activate the peroxisome proliferator-activated receptor (PPAR), induce the inflammatory response, activate the constitutive androstane receptor (CAR), stimulate the hypoxia signal transduction pathway, and activate the aryl-hydrocarbon receptor (AHR).  The results provide insights into the shared and unique pathways that are activated across these model hepatotoxicants.

overall_design: Exposures of mice of  both sexes were initiated at 7 weeks of age. Matched vehicle controls were run concurrently with each exposure and gene expression levels in liver tissue compared between exposed and control animals.


title: Transcription profiling of liver from farnesoid X receptor knockout mice

status: Public on Jan 31 2014

city: Piscataway

first: Grace

last: Guo

state: NJ

address: 170 Frelinghuysen Road

institute: Rutgers University

summary: Expression profiling of whole body (WB) FXR knockout (KO) mice (FXR WB KO), liver-specific FXR KO mice (AFXR Cre+) and enterocyte specific FXR KO mice (VFXR Cre+) on a C57BL/6J genetic background

overall_design: Whole body (WB) FXR knockout (KO) mice (FXR WB KO), liver-specific FXR KO mice (AFXR Cre+) and enterocyte specific FXR KO mice (VFXR Cre+) on a C57BL/6J genetic background were bred and maintained in the laboratory animal research facility at the University of Kansas Medical Center in rooms under a 12-hour light-dark cycle.  All experiments used 10-16 week-old male mice.  FXR was activated by treatment with the FXR synthetic agonist, GW4064, at 150 mg/kg. GW4064 or vehicle was administered by oral gavage at 6 p.m., followed by a second administration at 8 a.m. the next morning.  Two hours later, the liver was harvested.

first: G


title: Expression data from multiple mouse adipose depots

status: Public on Jan 16 2014

city: Boston

first: Paul

last: Cohen

address: 450 Brookline Ave, CLSB11118

institute: Dana-Farber Cancer Institute

summary: Comparing gene expression profiles of murine subcutaneous vs. visceral adipose tissue. Gene expression was analyzed in two subcutaneous depots (inguinal and axillary) and two visceral depots (epididymal and mesenteric) from male C57Bl/6 mice.

overall_design: 4 samples were analyzed as two groups: inguinal and axillary (subcutaneous) and epididymal and mesenteric (visceral). Each sample was derived by pooling RNA from the relevant fat depot from 3 age-matched, male C57Bl6 mice.

first: P

first: J

middle: D

last: Levy

first: Y

last: Zhang

first: A

last: Frontini

first: D

last: Kolodin

first: K

last: Svensson

middle: C

last: Lo

first: X

last: Zeng

first: L

last: Ye

first: M

middle: K

last: Khandekar

last: Wu

first: S

last: Gunawardana

last: Banks

last: Camporez

middle: J

last: Jurczak

last: Kajimura

last: Piston

last: Mathis

last: Cinti

middle: I

last: Shulman

last: Seale

first: B

last: Spiegelman


title: Expression profiling of mouse fetal liver late erythroblasts after knockdown of Xpo7

status: Public on Jan 29 2014

city: New Haven

first: Shilpa

last: Hattangadi

state: CT

address: 333 Cedar Street LMP 2073

department: Pediatric Hematology-Oncology

institute: Yale School of Medicine

summary:
To determine the transcriptional function (if any) of the presumed nuclear export protein Xpo7 or RanBP16
Murine fetal liver erythroid precursors (Ter119-negative cells) were isolated from C57Bl6 E14.5 embryos by magnetic depletion and infected with retroviruses containing shRNA constructs against Xpo7.  They were then cultured in Epo-containing media (2U/mL) for 36hrs until they were fully differentiated and then sorted by FACS for GFP+ (infected) cells in order to isolate total RNA to be used for the profiling.

overall_design: Expression profiling in late cultured mouse erythroblasts before and after knockdown of gene Xpo7.

first: Karly

last: Burke


title: Post-mating expression of female D. melanogaster genomes experimentally evolved under different post-copulatory sexual selection regimes

status: Public on Jan 15 2014

city: Uppsala

first: Paolo

last: Innocenti

address: Norbyvägen 18D

department: Dept. of Animal Ecology

country: Sweden

institute: Uppsala university

summary: By combining an experimental evolution approach with genomic techniques, we investigated the effects of seminal fluid on female gene expression. In our study, we experimentally manipulated the mating system in replicate populations of D. melanogaster, by removing post-copulatory sexual selection, with the aim of testing differences in short term post-mating reaction of females evolved under different mating strategies. We show that monogamous females suffer decreased fecundity, regardless of the type of male they were mated with, and that their post-mating gene expression profiles differ significantly from promiscuous females, involving 1141 transcripts (9% of the genes tested). These transcripts are active in several tissues, mainly ovaries, neural tissues, midgut and spermathecae, and are involved in metabolic processes, reproduction and signaling pathways. Our results provide a list of candidate genes responsible for the decrease in female fecundity in the absence of post-copulatory sexual selection, and demonstrate how the female post-mating response can evolve under different mating systems over relatively short time frames.

overall_design: From a LHM base population, we created 8 replicate populations and maintained them under experimental evolution: 4 populations were allowed to mate only once every generation (monogamy), and the other 4 were kept under the standard mating protocol (promiscuous). After 46 generation, we crossed males and females within the same population and with individuals of the opposite treatment. Mated female flies were frozen 6 h after mating and RNA extracted. Two biological replicates per cross per population (2x2x8=32 samples).

first: Edward

last: Morrow


title: Interactions between Jag1 and Ddr1 in mouse liver

status: Public on Jan 13 2014

city: London

first: Reiner

last: Schulz

address: 8th floor Guy's Tower

department: Medical & Molecular Genetics

institute: King's College London

summary: Microarray gene expression experiments to identify differentially expressed genes and pathways in Jag1 conditional/null livers reveal up-regulation of many genes related to fibrosis and ECM interactions.

overall_design: 3 Jag1 conditional/null mutant mice versus 3 littermate wildtype control mice.

first: Lara

last: Silvis

first: Erikka

last: Carr

first: Anthony

last: Nelson

first: Matthew

last: Ryan

first: Kathleen

middle: M

last: Loomes


title: Murine host body reactions to implanted scaffolds: non-coat polystyrene scaffold vs. collagen- or PMB-coated scaffold

status: Public on Jan 23 2014

city: Kobe

first: Tomo

last: EHASHI

address: 1-1 Rokkodai, Nada

institute: Kobe University

summary: This study investigated early host reactions to implanted materials to predict successful tissue regeneration with implant. Three kinds of scaffold, i.e., non-coat, collagen-coated, and PMB-coated porous polystylene scaffolds were implanted subcutaneously in mice dorsal area. Those scaffolds were used as bio-incomopatible materials, appropriate materials for tissue regeneration (bio active), and inappropriate to regenration (bio-inert) scaffolds. Seven days after implantation, scaffolds were explanted and total RNA was isolated from infiltrated host cells into scaffold by laser microdissection. Gene expressions of cells in collagen-  and PMB-coated scaffold were normalized using results of non coat scaffold. Genes with more than 2-fold difference between collagen and PMB were picked up and narrowed to related keywords; inflammation, angiogenesis, wound healing, and mcrophage polarization. Among those genes, interluekin (IL)-1beta which promote both inflammation and wound healing was up-regulated in collagen-coated scaffold. On the other hand, IL-10 which suppress both inflammation and wound healing was up-regulated in PMB-coated scaffold. Angiogenesis-promoting genes were up-regulated and angiogenesis suppressve genes were suppressed in collagen. Up-regulation of IL-1b and the angiogenesis-relating genes inside the porous scaffolds are the possibly important factors for controlling tissue regeneration.

overall_design: Three-condition experiment, host cells infiltrated in non coat (reference), collagen-coated, and PMB-coated scaffolds. Two-microarray condition experiments, collagen vs. non coat and PMB coat vs. non coat. Hybridization: 2 replicates. Scanning: 3 replicates. Biological experiments: once.

first: Taro

last: Takemura

first: Nobutaka

last: Hangata

first: Takashi

last: Minowa

first: Hisatoshi

last: Kobayashi

first: Kazuhiko

last: Ishihara

first: Tetsuji

last: Yamaoka


title: Expression data from 18h-fasted WT versus KLF15-null mice: heart

status: Public on Jan 09 2014

city: Cleveland

first: Mukesh

last: Jain

state: OH

address: 2103 Cornell Road

department: Medicine

institute: Case Western Reserve University

summary: We used microarray analysis to identify differences in gene expression levels in heart following an 18h (overnight) fast in WT control and KLF15-null mice

overall_design: Heart tissue was isolated from 3-4 month old, 18h-fasted WT and KLF15-null male mice for RNA extraction and hydridization on Affymetrix microarrays

first: D

last: Prosdocimo

first: M


title: Hes1 and Liver Glucocorticoid Signaling

status: Public on Jan 08 2014

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

summary: To investigate the role of HES1 during glucocorticoid signaling in the liver, we employed whole-genome microarray expressions in liver mRNA extracted from control and Hes1-liver knockout male mice (HESKOL) that had been adrenalectomized to remove endogenous glucocorticoids.

overall_design: RNA isolated from the liver of control and HESKOL animals either untreated or treated with 1mg/kg of synthetic glucocorticoid (dexamethasone) for 6hours. Each group had an n of 3 mice.

first: Javier

last: Revollo

first: John

last: Cidlowski


title: C57BL6/J livers exposed to low fat and high fat diet, wild-type vs Cyp1b1 null

city: Madison

first: Justin

last: Bushkofsky

address: 2500 Overlook Terrace

department: Medicine Endocrinology, Diabetes and Metabolism

institute: University of Wisconsin Madison

summary: Investigating the transcriptional changes in mouse livers exposed to low and high fat diets for 11 weeks. Determine what gene changes in the Cyp1b1 null livers may be contributing to prevention of increased adiposity when givin a high fat diet.

overall_design: Three Comparison experiment. Comparing wild-type low fat vs Cyp1b1 null low fat, wild-type high fat vs Cyp1b1 null high fat and low fat vs high in wild-type mice. Sample size is 3 per group. Limma analysis data provided in Series supplementary file (Normalized log2 ratio of (Cy3/Cy5) representing test group/control group).


title: HES1 Is a Master Regulator of Glucocorticoid Receptor-Dependent Gene Expression


title: Gene expression profiles (stroma and epithelium) of prostate cancer mouse models (JOCK1, Pro-Cat × JOCK1, Ubi-Cat × JOCK1)

status: Public on Jan 07 2014

city: Houston

first: Chad

last: Creighton

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

summary: The fibroblast growth factor receptor (FGFR) and canonical Wnt signaling pathways are important regulators of carcinogenesis; however, the interaction between these two pathways in the context of prostate cancer (PCa) has not been fully elucidated. Using novel transgenic mouse models, we describe Wnt-induced synergistic acceleration of FGFR1-driven adenocarcinoma; largely due to pronounced fibroblastic reactive stroma (RS) activation surrounding prostatic intraepithelial neoplasia (PIN) lesions in endogenous and reconstitution assays. Finally, both mouse and human RS are characterized by increases in TGF-β signaling heterogeneity immediately adjacent to PIN lesions; however, heterogeneity is lost during later stages of progression, likely contributing to tissue invasion. These studies confirm the importance of the FGFR1-Wnt-TGF-β signaling axes as driving forces behind reactive stroma and aggressive adenocarcinoma.

overall_design: To elucidate the mechanism behind the Wnt-accelerated FGFR1 adenocarcinoma, we performed laser capture microdissection (LCM) to separate pre-cancerous (hyperplasia and PIN) epithelia and adjacent reactive-stroma cells. We utilized frozen samples from specific time points (JOCK1, 40 weeks, Pro-Cat × JOCK1 and Ubi-Cat × JOCK1, 24 weeks) and performed gene expression profiling on the respective tissues.

first: David

last: Spencer

last: Rowley

first: Julienne

last: Carstens


title: Gene expression in intestinal epithelial crypt and villus cell populations

status: Public on Jan 06 2014

first: Fugen

last: Li

state: MA

address: 450 Brookline Ave

summary: We analyzed gene expression profiles in isolated mouse LGR5+ intestinal stem cells, lineage-specific enterocyte and secretory progenitors, and terminally differentiated villus enterocytes. Gene Ontology analyses of cell type-specific transcripts indicated their expected biological functions.

overall_design: We hybridized Affmetrix 430A 2.0 mouse microarrays with processed RNA isolated from purified Lgr5+ intestinal stem cells, secretory (Sec-Pro) and enterocyte (Ent-Pro) crypt progenitors, and mature villus enterocytes (ENT).

first: Tae-Hee

last: Kim

first: Li-Lun

last: Ho

first: Kodandaramireddy

last: Nalapareddy

first: Ramesh

last: Shivdasani


title: Post-mating expression of female Drosophila melanogaster genomes experimentally evolved under different post-copulatory sexual selection regimes

status: Public on Jan 01 2014

city: Brighton

first: Edward

last: Morrrow

address: Science Park Road

department: Life Sciences

institute: University of Sussex

overall_design: From an LHM base population, we created 8 replicate populations and maintained them under experimental evolution: 4 populations were allowed to mate only once every generation (monogamy), and the other 4 were kept under the standard mating protocol (promiscuous). After 46 generations, we crossed males and females within the same population and with individuals of the opposite treatment. Mated female flies were frozen 6 h after mating and RNA extracted. Two biological replicates per cross per population (2x2x8=32 samples).

first: Paolo

last: Innocenti

last: Morrow


title: Expression Data from Normal or Tumor Fibroblasts With or Without Ets2

status: Public on Mar 19 2014

city: Columbus

first: Julie

last: Wallace

address: 460 W. 12th Ave 840 BRT

institute: OSUCCC

summary:
The mechanisms involved in epithelium-stroma interactions remain poorly understood, despite the importance of the microenvironment during tumorigenesis.  Here, we studied the role of the Ets2 transcription factor in tumor-associated fibroblasts in the MMTV-PyMT mammary tumor model.  Inactivation of Ets2 specifically in fibroblasts using Fsp-cre significantly reduced tumor growth, in contrast to Ets2 inactivation in epithelium, in which no differences in tumor growth were observed.
Microarray analysis on isolated fibroblasts demonstrated the important role of Ets2 in remodeling of the extracellular matrix and angiogenesis in these cells.  At the molecular level, Ets2 regulated Mmp9 expression through direct binding to the promoter region.  Tumors lacking Ets2 in fibroblasts had diminished blood vessels.  We also found a significant correlation between phosphorylation of ETS2 and MMP9 levels in stroma of human breast cancer samples.  Collectively, our results suggest Ets2 uniquely contributes to angiogenesis from fibroblasts in the tumor microenvironment.

overall_design: Primary mammary fibroblasts were isolated from mice without the PyMT oncogene with or without Ets2, and from mice with the PyMT oncogene with or without Ets2. RNA was extracted and samples were submitted for Affymetrix gene expression arrays.

first: Carmen

middle: Z

last: Stone

first: Karl

last: Kornacker

first: Michael

last: Ostrowski