title: The effect of knocking down miR-27b on DIV14 mouse cortical neurons

status: Public on Sep 22 2015

city: Singapore

first: Vivian

middle: Y

last: Poon

state: SINGAPORE

address: 8 College Road

institute: Duke-NUS Graduate Medical School

summary: To understand the effect of reducing miR-27b levels on genome-wide expression in cortical neurons and identify potential targets of miR-27b, we generated dissociated cortical neuron cultures and treated them with lentivirus to knock down miR-27b.

overall_design: 2 treatment conditions (control lentivirus or lentivirus to knock down miR-27b); 3 neuronal preparations of dissociated mouse cortical neurons; total of 6 samples

first: Marc

last: Fivaz


title: Pten cell autonomously regulates HSC mobilization and function via G-CSF independent mechanisms

city: St Louis

first: Jeffery

last: Magee

state: Missouri

address: 660 S Euclid Ave.

department: Internal Medicine - Cardiovascular Division

country: USA

institute: Washington University School of Medicine

summary: gene expression in control, Pten deficient and G-CSF mobilized hematiopoietic stem cells

overall_design: HSCs isolated from control bone marrow, Pten deficient spleens and G-CSF treated spleens

first: Jeffrey


title: Foxp3 is a key downstream regulator of p53-mediated cellular senescence

status: Public on Aug 13 2015

city: Seoul

first: Dong-Hoon

last: Jin

address: 88 Olympicro-43gil, Songpa-gu

country: South Korea

institute: Asan Medical Center

summary: The downstream events and target genes of p53 in the process of senescence are not fully understood. Here, we report a novel function of the forkhead transcription factor Foxp3, which is a key player in mediating T cell inhibitory functions, in p53-mediated cellular senescence. The overexpression of Foxp3 in mouse embryonic fibroblasts (MEFs) accelerates senescence, whereas Foxp3 knockdown leads to escape from p53-mediated senescence in p53-expressing MEFs. Consistent with these results, Foxp3 expression resulted in the induction of senescence in epithelial cancer cells, including MCF7 and HCT116 cells. Foxp3 overexpression also increased the intracellular levels of reactive oxygen species (ROS). The ROS inhibitor N-acetyl-L-cysteine rescued cells from Foxp3-expression-induced senescence. Furthermore, the elevated ROS levels that accompanied Foxp3 overexpression were paralleled by an increase in p21 expression. Knockdown of p21 in Foxp3-expressing MEFs abrogated the Foxp3-dependent increase in ROS levels, indicating that Foxp3 acts through the induction of p21 and the subsequent ROS elevation to trigger senescence. Collectively, these results suggest that Foxp3 is a downstream target of p53 that is sufficient to induce p21 expression and ROS production and is necessary for p53-mediated senescence.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: control and treated samples (human), young passage (p3) or old passage (p7) samples (mouse). Young passage (p3) or senescent passage (p11) samples (mouse)


title: Transcriptomics Modeling of the Late-Gestation Fetal Pituitary Response to Transient Hypoxia

status: Public on Oct 01 2015

city: GAINESVILLE

first: Charles

middle: Evans

last: Wood

state: Florida

address: 1345 Center Drive/Room M552

department: Physiology and Functional Genomics

institute: University of Florida

summary: The late-gestation fetal sheep responds to hypoxia with physiological, neuroendocrine, and cellular responses that aid in fetal survival .  The response of the fetus to hypoxia represents a coordinated effort to maximize oxygen transfer from the mother and minimize wasteful oxygen consumption by the fetus.  While there have been many studies aimed at investigating the coordinated physiological and endocrine responses to hypoxia, and while immunohistochemical or in situ hybridization studies have revealed pathways supporting the endocrine function of the pituitary, there is little known about the coordinated cellular response of the pituitary to the hypoxia.   The objective of this study was to use transcriptomics and systems analysis to determine significantly altered biological processes in the late gestation ovine fetal pituitary one hour after a 30 minute period of hypoxia, produced by lowering the inspired oxygen content in the maternal inspired gas.  We found that the acute response to 30 min of transient hypoxia in the late-gestation fetus results in reduced cellular metabolism and a pattern of gene expression that is consistent with cellular oxygen and ATP starvation. The response is not consistent with gene regulation by HIF1A .

overall_design: Chronically catheterized late gestation fetal sheep were subjected to 30 min hypoxia (n=4) or normoxia (n=4). Fetuses were euthanized 60 min after the onset of hypoxia or normoxia and pituitaries removed for microarray analysis.  Gene expression was measured using Agilent 15k ovine microarrays.

middle: E

first: Eileen

middle: I

last: Chang

first: Elaine

middle: M

last: Richards

first: Maria

middle: B

last: Rabaglino

first: Maureen

last: Keller-Wood


title: Genomics of the ovine heart ontogeny during the perinatal period

status: Public on Jul 30 2015

city: Utrecht

middle: Belen

address: Yalelaan 7

department: Population Health Science

country: Netherlands

institute: Utrecht University

summary: The period of development from the last two weeks of gestation through the first two weeks of life spans a period of great functional and metabolic challenge to the fetal and neonatal lamb heart. Important changes in gene expression occur to meet these challenges. On this study, septa from sheep hearts at 130 days gestation (n=6), term (n=8, gestational lenght is around 145 days) and 14-days-old lambs (n=8) were used to model the changes in gene expression patterns during the perinatal period using Agilent 15k ovine microarrays. Weighted gene co-expression network analysis (WGCNA) determined five major patterns of co-expressed and functionally related genes during this critical period of cardiac transition.

overall_design: Septum samples from the heart were collected from non-treated fetuses at 130 days of gestational age (GA130d, n=6) and term (n=8); and from naturally born 14-days-old lambs (Lamb, n=8). None of the ewes suffered gestational diseases or showed signs of impending labor.

first: Andrew

last: Antolic


title: Gene expression profile of rice shoot in response to macronutrient deficiency

status: Public on Aug 12 2015

city: Tsukuba

first: Yutaka

last: Sato

state: Ibaraki

address: 2-1-2 Kannondai

country: Japan

institute: National Institute of Agrobiological Sciences

summary: Macronutrients are pivotal elements for proper plant growth and development. We performed microarray analysis of rice shoot under nitrogen (N), phosphorus (P), and potassium (K) deficiency conditions to obtain a global view of gene regulations associated with plant response to essential nutrients.

overall_design: We performed microarray analysis of rice shoot under N, P and K deficiency conditions (1/4, 1/16 and 1/64 of normal concentration) and control for each nutrient. We collected a total of 36 microarray data corresponding to 12 samples with 3 replicates.

first: Hinako

last: Takehisa

first: Baltazar

last: Antonio

first: Yoshiaki

last: Nagamura


title: The contained self-reactive peripheral T cell repertoire: size, diversity and cellular composition

status: Public on Aug 04 2015

city: Mainz

first: Michael

last: Delacher

state: Rhineland-Palatinate

address: Langenbeckstrasse 1

department: Institute for Immunology

country: Germany

institute: University Medical Center of the Johannes Gutenberg-University Mainz

summary: To further characterize the self-reactive T cell population and determine if there are sub-compartments within the naïve T cell pool that are more likely to respond in the absence of Treg cell-mediated control, we focused on CD5. CD5 is a membrane protein that is associated with the TCR and its expression is correlated with higher signaling intensity, presumably due to higher TCR self-MHC/peptide affinity, during positive selection. FACS was used to purify three distinct populations of naïve CD4+ T cells from the bottom, middle and top 10 percent based on CD5 expression; CD5low, CD5int and CD5high.

overall_design: Naïve (CD44low/int CD62Lhigh) CD4+ CD5low, CD5int and CD5high T cell populations were FACS purified from spleens from three female (Fe) and three male (Ma) mice, to account for possible gender differences. RNA was extracted using the RNEasy Plus Micro Kit (Qiagen).

first: David

first: Ann-Cathrin

last: Hofer

first: Markus

last: Feuerer


title: Systems genetics analysis of a recombinant inbred mouse cell culture panel reveals Wnt pathway member Lrp6 as a regulator of adult hippocampal precursor cell proliferation

status: Public on Jul 29 2015

city: Dresden

first: Gerd

last: Kempermann

state: Saxony

address: Tatzberg 41

institute: German Center for Neurodegenerative Diseases (DZNE)

summary: Stem/precursor cells were isolated from the hippocampal subgranular zone of adult mice and maintained as adherent cultures. Cultures from 20 different strains of the BXD recombinant inbred poulation were established in this study. For each cell line (strain), cells from 3 different passages were hybridised to Illumina Mouse-6 microarrays (1 replicate (strain/passage) per array).

overall_design: A total of 60 proliferating cell cultures on 60 arrays

first: Suresh

last: Kannan

first: Rupert

middle: W

last: Overall

first: Giannino

last: Patone

first: Kathrin

last: Saar

first: Norbert

last: Hübner


title: Gene expression profile of mouse embryonic stem cells derived cardiomyocytes following the knockdown of ErbB4

status: Public on Sep 11 2015

city: Tainan

first: Desy

middle: S

last: Lee

address: University Road

country: Taiwan

institute: NCKU

summary: To identify the potential target genes that were affected by the expression of ErbB4 in mouse embryonic stem cells-derived cardiomyocytes

overall_design: Embryonic Stem Cells-Derived Cardiomyocytes were transfected with si-ErbB4 for 48 hours

first: Patrick

middle: C

last: Hsieh


title: Placental changes caused by food restriction during early pregnancy in mice are reversible

status: Public on Jun 18 2015

city: Columbia

first: Laura

middle: Clamon

last: Schulz

state: MO

address: 1 Hospital Dr.

department: Obstetrics, Gynecology and Women's Health

institute: University of Missouri

summary: In a previous study, 50% calorie restriction in mice from days 1.5-11.5 of pregnancy resulted in reduced placental weights and areas, relatively sparing of labyrinth zone area compared to junctional zone area, and dramatic changes in global gene expression profiles. Here we examined placental gene expression at day 18.5, after the return to normal feeding to see whether differences were reversible

overall_design: Mice were randomized to 2 treatment groups on day 1.5 of pregnancy: (1) ad libitum fed (control) (2) 50% food restriction (restricted). Mice were returned to ad libitum feed on d11.5, sacrificed on d18.5 and placentas were collected.


title: Comparison of mRNA expression pattern between wild-type regulatory T (Treg) cells and Nr4a-deficient Treg cells

status: Public on Jun 27 2015

city: Ichikawa

first: Takashi

last: Sekiya

state: Chiba

address: 1-7-1 Kohnodai

institute: National Center for Global Health and Medicine

summary: Regulatory T (Treg) cells, as central mediators of immune suppression, play crucial roles in many aspects of immune system physiology and pathophysiology. Treg cells are characterized by a distinct pattern of gene expression, including upregulation of immune-suppressive genes and silencing of inflammatory cytokine genes. However, the molecular mechanisms that establish and/or maintain such gene regulation in Treg cells remain largely unknown. We recently reported that Nr4a family nuclear orphan receptors are essential for the development of Treg cells. The fact that Treg cells maintain high levels of expression of all Nr4a family components suggests that they may also play critical roles beyond Treg cell development. Thus, we compared mRNA expression pattern between wild-type Treg cells and Nr4a-deficietn Treg cells. As a result, we found that expression of 'Treg-signature genes' were globally down regulated in Nr4a-deficient Treg cells.

overall_design: mRNA from wild-type and Nr4a-deficient Treg cells were analyzed.

first: Akihiko

last: Yoshimura


title: Effect of 90Sr internal emitter on gene expression in mouse blood

status: Public on Jun 25 2015

city: New York

first: Shanaz

middle: Adi

last: Ghandhi

state: NY

address: 630, W 168th street

department: Center for Radiological Research

institute: Columbia University Medical Center

summary:
Background The radioactive isotope Strontium-90 (90Sr) may be released as a component of fallout from nuclear accidents, or in the event of a radiological incident such as detonation of an improvised nuclear device, and if ingested poses a significant health risk to exposed individuals. In order to better understand the response to 90Sr, using an easily attainable and standard biodosimetry sample fluid, we analyzed the global transcriptomic response of blood cells in an in vivo model system.
Methods We injected C57BL/6 mice with a solution of 90SrCl2 and followed them over a 30-day period. At days 4, 7, 9, 25 and 30, we collected blood and isolated RNA for microarray analyses. These days corresponded to target doses in a range from 1 to 5 Gy. We investigated changes in mRNA levels using microarrays, and changes in specific microRNA (miRNA) predicted to be involved in the response using qRT-PCR.
Results We identified 8082 differentially expressed genes in the blood of mice exposed to 90Sr compared with controls. Common biological functions were affected throughout the study, including apoptosis of B and T lymphocytes, and atrophy of lymphoid organs. Cellular functions such as RNA degradation and lipid metabolism were also affected during the study. The broad down regulation of genes observed in our study suggested a potential role for miRNA in gene regulation. We tested candidate miRNAs, mmu-miR-16, mmu-miR-124, mmu-miR-125 and mmu-mir-21; and found that all were induced at the earliest time point, day 4.
Conclusions Our study is the first to report the transcriptomic response of blood cells to the internal emitter 90Sr in mouse and a possible role for microRNA in gene regulation after 90Sr exposure. The most dramatic effect was observed on gene expression related to B-cell development and RNA maintenance. These functions were affected by genes that were down regulated throughout the study, suggesting severely compromised antigen response, which may be a result of the deposition of the radioisotope proximal to the hematopoietic compartment in bone.

overall_design: Radiation induced gene expression in mouse blood  was measured at 4, 7, 9, 25 and 30 days after 90Sr injection.  Six independent experiments were performed at each time point.

middle: A

first: Sally

last: Amundson


title: Gene expression profiling of splenic monocytes from TCL1-AT mice and WT controls

status: Public on Jul 01 2015

city: Heidelberg

first: Bola

last: Hanna

address: Im Neuenheimer Feld 280

institute: German Cancer Research Center

summary: Analysis of the effect of CLL development on differentation and gene expression of splenic monocytes.

overall_design: C57BL/6 mice were transplanted with murine CLL cells from Eµ-TCL1 mice and after 6 weeks total RNA was isolated from splenic monocytes from leukemic mice and matched WT controls.


title: The effect of whole-glucan particles on the gene expression of polarized M2 bone-derived macrophages

city: Louisville

first: Sabrin

middle: H

last: Albeituni

state: KY

address: 505 S Hancock St

department: Microbiology and Immunulogy

institute: University of Louisville

summary: Bone-marrow macrophages polarized to M2 phenotype are immunosuppressive. Interestingly, treatment with whole-glucan particles converts M2 macrophages to M1 phenotype with an anti-tumor phenotype. In this study, the effect of WGP treatment for 6 hours on the gene expression of M2 macrophages was assessed.

overall_design: Polarized M2 bone-marrow derived macrophages were incubated for 6 hours in media with or without WGP, followed by RNA extraction.

first: Min

last: Liu


title: Wild type and ATG5-KO mouse dendritic cells exposed to interleukin-4 (IL4) and/or lipopolisaccharyde (LPS)

status: Public on Jun 16 2015

city: Marseille

first: Philippe

last: Pierre

address: Avenue de Luminy

country: France

institute: Centre d’Immunologie de Marseille-Luminy

summary: Male C57BL/6 normal and ATG5-KO mouse dendritic cells exposed to interleukin-4 (IL4) and/or lipopolisaccharyde (LPS)

overall_design: 24 samples representing the different biological combinations between wild type and ko cells exposed to IL4 and LPS (three replicates for each)

first: Rodrigo

last: Santamaría


title: Gene expression in zebrafish following knockdown of pitx2 or tbx5

status: Public on Jul 14 2015

city: Boston

first: Gabriel

last: Musso

state: MA

address: 75 Francis St, Thorn 1123

department: Medicine

institute: Harvard Medical School

summary:
Key regulators of septum formation between the left and right ventricle in mammals, including the transcription factors TXB5 and PITX2, feature loss-of-function phenotypes that affect development of the two-chambered zebrafish heart, suggesting
uncharacterized primordial functions of these septation regulators prior to the evolution of any physical boundaries between heart chambers. Data is as published in Mosimann & Panakova et al (Nature Communications, 2015)

overall_design: Samples for tbx5a versus pitx2ab MO comparison were collected from three independent experiments of MO-injected siblings and uninjected wildtype controls at 56hpf by morphology.

first: Leonard

last: Zon

first: Christian

last: Mosimann


status: Public on Jun 02 2015

city: South San Francisco

first: Matthew

last: Brauer

state: California

address: 1 DNA Way

department: Bioinformatics

institute: Genentech, Inc.

summary:
Gene expression of liver tissue from db/db untreated (6x replicates) and db/db treated with 5mg/kg of 3c7.v44 mAb (6x replicates).
Anti-GCGR antibody treatment in db/db mice: fig 2b in Solloway et al.

overall_design: db/db mice, untreated compared to treated with 5mg/kg of 3c7.v44 mAb (6x replicates).

middle: J

first: Mark

last: Solloway


title: Wnt/b-catenin signaling regulates sequential fate decisions of murine cortical precursor cells

status: Public on Jun 23 2015

city: Zurich

first: Lukas

last: Sommer

address: Winterthurerstr 190

department: Anatomy

country: Switzerland

institute: University of Zurich

summary: In order to compare expression changes upon Wnt/b-catenin signaling inactivation in the forebrain of mouse embryos, we have isolated dorso-medial pallium from E11.5 mutant and control embryos and performed microarray analysis.

overall_design: Dorso-medial pallium from E11.5 control and mutant embryos was dissected and snap-frozen. RNA isolation on single embryo brains was performed with RNAeasy kit with on-column Dnase digestion.

first: Kalina

last: Draganova

first: Martina

last: Zemke

first: Luis

last: Zurkirchen

first: Tomas

last: Valenta

first: Claudio

last: Cantu

first: Michal

last: Okoniewski

first: Marie-Theres

last: Schmid

first: Raymond

last: Hoffmans

first: Magdalena

last: Götz

first: Konrad

last: Basler


summary:
Glucagon receptor deficient liver during postnatal development: fig S5a-S5c in Solloway et al.
livers from ko and wt GCGR mice at various developmental stages

overall_design: Gene expression profiling of livers from WT and and GCGR KO mice at the following ages E18.5, P2.5, P7.5, P19 and 3 month.


title: Brown Adipose Tissue Harbors a distinct subpopulation of regulatory T cells

first: Michael

last: Delacher

summary: Regulatory T (Treg) cells are critical determinants of both immune responses and metabolic control. Here we show that systemic ablation of Treg cells compromised the adaptation of whole-body energy expenditure to cold exposure, correlating with impairment in thermogenic marker gene expression and massive invasion of pro-inflammatory macrophages in brown adipose tissue (BAT). Indeed, BAT harbored a unique sub-set of Treg cells characterized by a unique gene signature. As these Treg cells respond to BAT activation upon cold exposure, this study defines a BAT-specific Treg sub-set with direct implications for the regulation of energy homeostasis in response to environmental stress.

overall_design: We isolated regulatory and conventional T cells from brown-adipose tissue of warm-conditioned or cold-conditioned mice. As controls, we harvested spleen-Treg and Tconv cells from warm-treated mice. Cells were isolated pooled organs and target cells purified by FACS. RNA was extracted and gene expression measured.

first: Dasa

last: Medrikova

first: David

last: Richards

first: Markus

last: Feuerer

first: Stephan

last: Herzig


title: Comparison of gene expression in sams-1(RNAi) and sbp-1(RNAi) adult C. elegans

status: Public on Aug 27 2015

city: Worcester

first: Amy

middle: K

last: Walker

address: 373 Plantation Street

department: Program in Molecular Medicine

institute: UMASS Medical School

summary: Gene expression was compared from adult C. elegans after RNAi

overall_design: Triplicate control RNAi (Empty vector), sbp-1(RNAi) and sams-1(RNAi) animals were grown to young adulthood and RNA was extracted


title: Hematopoietic Kit Deficiency, but not lack of mast cells, protects mice from onesity and insulin resistancel

status: Public on Jun 01 2015

first: Dario

middle: Alejandro

last: Gutierrez

state: BW

department: Cellular Immunology

institute: German Cancer Research center

summary: Analysis of epididymal AT transcriptome between Kit-deficient mast cell-deficient mice and Kit Wild-type mast cell deficient mice after 16 weeks of HFD feeding

overall_design: Total RNA was isolated from epididymal AT WBB6F1.KitW/Wv mice, WBB6F1.Cpa3Cre/+ and WBB6F1.Cpa3+/+ mice that were fed a HFD (60% kcal from fat) or chow diet (6% fat) for 12 weeks

first: Hans-Reimer

last: Rodewald


title: Change of gene expression in mouse heart after permanent occlusion of the left anterior descending artery

city: Fukuoka

first: Michio

last: Nakaya

state: Fukuoka

address: 3-1-1 Maidashi, Higashi-ku

department: Department of Pharmacology and Toxicology

institute: Kyushu University Graduate School of Pharmaceutical Science

summary: We have employed whole genome microarray expression profiling as a discovery platform to identify genes with the potential to influence the pathogenesis after myocardial infarction.   Male mice (8 weeks old) were anesthetized  and subjected to permanent occlusion of the left coronary artery [Myocardial infarction (MI) model].

overall_design: Gene expression in wild-type mouse heart was measured at 3 days after the MI-surgery.

first: Hitoshi

last: Kurose


title: Expression data at drug-sensitive and drug-resistant phases of canine B-cell lymphoma

city: Tokyo

first: Hirotaka

last: Tomiyasu

state: Not Applicable

address: 1-1-1 Yayoi, Bunkyo-ku

department: Veterinary Internal Medicine

institute: the University of Tokyo

summary: Multidrug resistance (MDR) is one of the major obstacles during the chemotherapy in lymphoma patients. Although there have been various molecules associated with acquisition of MDR phenotype in human tumor cells, MDR of tumor cells have not been successfully overcome. Canine lymphoma is thought to be a spontaneous animal model of human lymphoma because it shares many similarities with human non-Hodgkin’s lymphoma. We conducted a comprehensive analysis of changes in gene expression profiles of canine lymphoma cells by microarray analysis using tumor cell samples at drug-sensitive and drug-resistant phases in 4 dogs. It was revealed that expression of the molecules related to chemotaxis and inflammation were down regulated in MDR phases of all of the 4 dogs.

overall_design: We isolated RNA from tumor cell samples at drug-sensitive and drug-resistant phases of 4 dogs and detected changes in gene expression profiles between 2 phases of each dog using microarrays.

first: Manabu

last: Watanabe


title: The rat lncRNA microarray analysis of the 8 samples from control and NNK treatment group

status: Public on May 19 2015

city: Guangzhou

first: Jianjun

last: Wu

address: Xinzao Town, Panyu District

department: School of Public Health

country: China

institute: Guangzhou Medical University

summary: In order to assess the alteration in lncRNA expression in rat lung carcinogenesis induced by NNK, we determined the lncRNA expression profiles in 3 rat lung tumor samples and matched normal lung tissues and 2 blood samples from the control and NNK treatment group in the 95th week using Arraystar Rat lncRNA Microarray.

overall_design: We induced lung cancer using 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK) in a rat model and determined the lncRNA expression profiles in lung cancer tissues and rat blood samples.

first: Yiguo

last: Jiang


title: Gene expression Tet-mev-1 mouse fed either normal diet or high fat high sucrose diet compared with wild type mouse

status: Public on May 07 2015

city: Isehara

first: Yutaka

last: Inagaki

state: Kanagawa

address: Shimokasuya 143

department: Regenerative Medicine

institute: Tokai University School of Medicine

summary: To assess the effect of steatosis and oxidative stress on progression of liver fibrosis, we have employed whole genome microarray expression profiling as a discovery platform to identify genes that are related with oxidative stress- and steatosis-induced hepatic fibrogenesis. When wild type mice were fed high-fat/high-sucrose diet for 24 weeks, expression of 69 genes was changed more than 10-fold compared with wild type animals fed normal diet, 11 of which were categorized to lipid metabolic process. Moreover, expression of 208 genes showed more than 5-fold changes in Tet-mev-1 mice fed high-fat/high-sucrose diet compared with the same transgenic animals fed normal diet, and gene ontology analyses indicated significant changes in chemokine activity and chemokine receptor binding as well as defense and immune responses.

overall_design: oxidative stress and high fat high calorie induced gene expression in wild type or Tet-mev-1 mouse liver tissue. wild type and Tet-mev-1 mice were fed either normal diet or high fat high sucrose diet for 4 months, and have been given doxycycline-containing water from embryo. Each group were perfomed by duplicate.

first: Tadashi

last: Moro

first: Sachie

last: Nakao

first: Hideaki

last: Sumiyoshi

first: Takamasa

last: Ishii

first: Masaki

last: Miyazawa

first: Naoaki

first: Tadayuki

last: Sato

first: Yumi

last: Iida

first: Yoshinori

last: Okada

first: Masayuki

last: Tanaka

first: Hideki

last: Hayashi

first: Satoshi

last: Ueha

first: Kouji

last: Matsushima


title: Zebrafish developmental hypoxia

status: Public on May 02 2015

city: La Jolla

first: Farhad

middle: Bryan

last: Imam

state: CA

address: 9500 Gilman Drive #0734

department: Pediatrics

institute: University of California, San Diego

summary: Study of hypoxia-induced differential expression during zebrafish development at gastrulation (shield) and segmentation (8-somite) stages

overall_design: An 8-chip study with 2 biological replicates from +/- hypoxia at 2 different stages of development. Each sample is prepared from 12-15 dechorionated, hand-selected, developmentally synchronized embryos exposed to 1-2 hours of hypoxia.


title: Expression profiles in alcohol-associated hepatocellular carcinoma

status: Public on May 05 2015

city: Verona

first: Alberto

last: Ferrarini

state: Veneto

address: Strada le Grazie, 15

department: Scientific and Technological Department

country: Italy

institute: University of Verona

summary: Alcohol is a major risk factor for hepatocellular carcinoma (HCC) although the mechanisms underlying the alcohol-related liver carcinogenesis are still poorly understood. Alcohol is known to increase hepatocarcinogenesis possibly by inducing aberrant DNA methylation through the reduced provision of methyl groups within the hepatic one-carbon metabolism. Whether the epigenetically-regulated pathways in alcohol-associated HCC can be reversible or modifiable by nutritional factors is unknown.   The aim of the present study was to investigate the genome wide promoter DNA methylation profiles along with array-based, gene expression profiles in non-viral, alcohol-associated HCC. From eight HCC patients the methylation status and transcriptional levels of all annotated genes were compared by analyzing HCC tissue and the cancer-free surrounding liver tissue, following curative surgery.   After merging both the DNA methylation and gene expression data, we identified 159 hypermethylated-repressed, 30 hypomethylated-induced, 49 hypermethylated-induced and 56 hypomethylated-repressed genes. A number of potentially novel candidate tumor-suppressor genes (FAM107A, IGFALS, MT1G, MT1H, RNF180) demonstrated promoter hypermethylation and transcriptional repression in alcohol-associated HCC. Notably, promoter DNA methylation appeared as the regulatory mechanism for the transcriptional repression of genes controlling the retinol metabolic pathway (ADH1A, ADH1B, ADH6, CYP3A43, CYP4A22, RDH16) and SHMT1, a key gene within one-carbon metabolism.   A genome-wide DNA methylation approach linked up with array-based gene expression profiles allowed identifying a number of novel, epigenetically-regulated candidate tumor-suppressor genes in alcohol-associated hepatocarcinogenesis. Retinol metabolism genes and SHMT1 are also epigenetically-regulated through promoter DNA methylation in alcohol-associated hepatocarcinogenesis.

overall_design: 16 samples (8 control samples from non-neoplastic liver tissue, 8 test samples from hepatocellular carcinoma) from 8 patients affected from hepatocellular carcinoma were analyzed.

first: Silvia

last: Udali

first: Patrizia

last: Guarini

first: Andrea

last: Ruzzenente

first: Alfredo

last: Guglielmi

first: Valentina

last: Lotto

first: Paola

last: Tononi

last: Pattini

first: Sara

last: Moruzzi

first: Tommaso

last: Campagnaro

first: Simone

last: Conci

first: Oliviero

last: Olivieri

first: Roberto

last: Corrocher

first: Massimo

last: Delledonne

first: Sang

last: Choi

first: Simonetta

last: Friso


title: Microarray analysis of mouse gene expression in metronomic cyclophosphamide-treated human glioma U251 xenografts implanted in scid mice

status: Public on May 04 2015

first: David

middle: J.

last: Waxman

address: 5 Cummington Mall

department: Department of Biology and Bioinformatics Program

institute: Boston University

summary: Cyclophosphamide (CPA) treatment on a six-day repeating metronomic schedule induces a dramatic, innate immune cell-dependent regression of implanted gliomas. However, little is known about the underlying mechanisms of innate immune cell mobilization and recruitment, or about the role of DNA damage and cell stress response pathways in eliciting the anti-tumor immune responses linked to tumor regression. To address these questions, we compared untreated and 6-day metronomic cyclophosphamide-treated human U251 glioblastoma xenografts by mouse microarray analysis to identify responsive mouse (host) cell-specific factors.

overall_design: Human glioma U251 tumors were implanted sc in scid immunodeficient mice then treated with cyclophosphamide at 140 mg/kg every 6 days. Tumors were collected 6 days after the second cyclophosphamide treatment and also 6 days after the third cyclophosphamide treatment. Tumor RNA was then analyzed on two color Agilent mouse expression microarrays comparing cyclophosphamide-treated RNA to untreated control tumor RNA.

first: Joshua

last: Doloff


title: Microarray analysis of mouse gene expression in metronomic cyclophosphamide-treated rat glioma 9L xenografts implanted in scid mice

summary: Cyclophosphamide (CPA) treatment on a six-day repeating metronomic schedule induces a dramatic, innate immune cell-dependent regression of implanted gliomas. However, little is known about the underlying mechanisms of innate immune cell mobilization and recruitment, or about the role of DNA damage and cell stress response pathways in eliciting the anti-tumor immune responses linked to tumor regression. To address these questions, we compared untreated and 6-day metronomic cyclophosphamide-treated rat 9L gliosarcoma xenografts by mouse microarray analysis to identify responsive mouse (host) cell-specific factors.

overall_design: Rat glioma 9L tumors were implanted sc in scid immunodeficient mice then treated with cyclophosphamide at 140 mg/kg every 6 days. Tumors were collected 6 days after the fourth cyclophosphamide treatment. Tumor RNA was then analyzed on two color Agilent mouse expression microarrays comparing cyclophosphamide-treated RNA to untreated control tumor RNA.


title: Expression and DNA methylation profiles in alcohol-associated hepatocellular carcinoma

first: Alberto

last: Ferrarini

type: Genome binding/occupancy profiling by array

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

overall_design: Refer to individual Series


title: Virus-Induced Airway Disease in Mice (C57BL/6J, d3)

status: Public on Mar 27 2015

city: St. Louis

first: Anand

middle: Champak

last: Patel

address: Campus Box 8116, 660 S. Euclid Ave.

department: Pulmonary/Critical Care Medicine

institute: Washington University School of Medicine

summary:
Analysis of gene expression in lungs of C57BL/6J mice that develop chronic airway disease phenotypes after a single Sendai virus infection, compared with mice treated with UV-inactivated virus.
Keywords: disease state analysis

overall_design: Whole lung RNA was analyzed from 3 mice per condition per time point 3 days post infection, Sendai virus versus UV-inactivated virus, C57BL/6J mouse strain.

first: Kangyun

last: Wu

first: Derek

middle: E

last: Byers

first: Xiaohua

last: Jin

first: Eugene

last: Agapov

first: Jennifer

last: Alexander-Brett

first: Maria

last: Cella

first: Susan

last: Gilfilan

first: Marco

last: Colonna

first: Daniel

middle: L

last: Kober

first: Tom

last: Brett

first: Michael

last: Holtzman


title: Transcriptional profiling of small intestinal crypts from mice treated with Notch blocking antibodies or Notch blocking antibodies in combination with an Lrp6 blocking antibody.

status: Public on Mar 11 2015

first: Brian

last: Biehs

institute: Genentech

summary: The goal of this study was to identify genes that are differentially expressed during a 24 hour Notch blockade and whether a Wnt antagonist (anti-Lrp6) could block this effect.

overall_design: 3 condition experiment, Control untreated compared to N1N2 treated, and N1N2 treated compared to N1N2_Lrp6 treated. 5 biological replicates per condition.


title: Egress of mature murine regulatory T cells from the thymus requires RelA

status: Public on Mar 04 2015

city: Nankoku

first: Taro

last: Fukazawa

state: Kochi

address: Kohasu, Oko-cho

department: Department of Immunology

institute: Kochi Medical School

summary: The mechanism of egress of mature regulatory T cells (Tregs) from the thymus to the periphery remains enigmatic, as does the nature of those factors expressed in the thymic environment. Here, we examined the fate of thymic Tregs in TNFα/RelA double-knockout (TA-KO) mice, because TA-KO mice retain a Treg population in the thymus but have only a small Treg population at the periphery. Transplantation of whole TA-KO thymus to under the kidney capsule of Rag1 null mice failed to induce the production of donor-derived splenic Tregs expressing neuropilin-1 (Nrp1), which was reported to be a marker of naturally occurring Tregs, indicating that TA-KO thymic Tregs either do not leave the thymus or are lost at the periphery. We next transplanted enriched TA-KO thymic Tregs to the peripheries of TA-KO mice and traced mouse survival. Transplantation of TA-KO thymic Tregs rescued the lethality in TA-KO mice, demonstrating that TA-KO thymic Tregs remain functional at the periphery. The TA-KO thymic Treg population had highly demethylated CpG motifs in the foxp3 locus, indicating that the cells were arrested at a late-mature stage. Also, the population included a large subpopulation of Tregs expressing IL-7Rα, which is a possible marker of late-mature Tregs. Finally, TA-KO fetal liver chimeric mice developed an Nrp1+ splenic Treg population from TA-KO cells, suggesting that Treg arrest is caused by a lack of RelA in the thymic environment. Together, these results suggest that egress of mature Tregs from the thymus depends on RelA in the thymic environment.

overall_design: For the isolation of thymic Tregs, CD4+CD8α-CD25hi thymocytes were isolated from five 1.5- to 2-week-old TNFα-KO or TA-KO mice by using a FACSAria cell sorter. For the isolation of thymic stromal cells, 10 thymi from 1.5- to 2-week-old TNFα-KO or TA-KO mice were minced with scissors and treated with RPMI 1640 supplemented with 2% FCS, 0.2 mg/ml collagenase (Roche, Basel, Switzerland), 0.2 mg/ml dispase I (Roche), and 100 U/ml DNase I (Life Technologies) for 30 min with stirring. Digested thymi were centrifuged in a Percoll (GE Healthcare Bio-Sciences, Piscataway, NJ, USA) gradient (density, 1.115, 1.065, and PBS) at 1400g for 30 min. Cells in the upper layer were collected, and the CD45-EpCAM+ (thymic epithelial cells) and CD45+EpCAM- populations (enriched thymic stromal cells containing macrophages or dendritic cells) were sorted.


title: Effects of shear stress on cells of the aorta-gonad-mesonephros (AGM)

status: Public on Apr 05 2015

city: Houston

first: Pamela

last: Wenzel

state: TX

address: 6431 Fannin St, MSB 4.130

department: Integrative Biology & Pharmacology

institute: University of Texas Health Science Center at Houston

summary:
Blood flow promotes emergence of definitive hematopoietic stem cells (HSCs) in the developing embryo, yet the signals generated by hemodynamic forces that influence hematopoietic potential remain poorly defined. In transplantation assays of hematopoietic reconstitution, we find that fluid shear stress endows long-term multilineage engraftment potential upon early hematopoietic tissues at E9.5 not previously described to harbor HSCs. Effects on hematopoiesis appear to be mediated in part by prostaglandin E2 (PGE2) and the cyclic AMP-protein kinase A (cAMP-PKA) signaling axis. Studies of Ncx1 cardiac mutants corroborate that blood flow is required for sufficient COX2 levels and phosphorylation of CREB. Further implicating PGE2 in mediating the effects of shear stress, we find that E10.5 and E11.5 AGM treated transiently with the synthetic analog dmPGE2 engraft more robustly and contribute to greater lymphoid reconstitution. These data provide a mechanism by which biomechanical forces induced by blood flow modulate hematopoietic potential.
-

overall_design: AGM from C57BL/6J embryos at 10.5 days gestation (E10.5) were isolated by microdissection from uteri of pregnant dams, following by gentle dissociation by Accutase with agitation at room temperature for 20 minutes. Single cell suspension was seeded on microfluidic IBIDI VI^0.4 6-channel slides (0.8 to 1x10^7 cells per channel) and permitted to attach for 8 hours. Fluid movement was then applied to each channel using a Harvard Apparatus PHD ULTRA programmable syringe pump for manangement of M5300 Myelocult medium. Cells were exposed either to static/low flow (0.0001 dyne/cm^2) or wall shear stress (WSS) of 5 dyne/cm^2 for 6 hours or 36 hours. In addition, some cells were treated with 10 uM indomethacin (indo) to inhibit COX2 activity and PGE2 synthesis. Upon collection of cells with RLT lysis buffer (QIAGEN RNeasy kit), six channels of identical treatment were pooled to comprise a single sample. 24 samples total are included in this study. 12 samples were collected after 6 hours and 12 after 36 hours. In detail, samples included at 6 hours: 3 static, 3 static with indo, 3 WSS, 3 WSS with indo; and at 36 hours: 3 static, 3 static with indo, 3 WSS, 3 WSS with indo. Sample labels begin with the timepoint collected and end with the replicate number, i.e., 06WSS1 for the 6 hour collection of the first replicate of the WSS sample.


title: Transcriptome analysis of CD4+ T cells in experimental autoimmune encephalitomyelitis

status: Public on Feb 26 2015

city: Mainz

first: Volker

last: Siffrin

address: Langenbeckstrasse 1

department: Department of Neurology

institute: University Medical Center of the Johannes Gutenberg-University Mainz, Germany

summary: In this study we determined whole genome gene expression of murine naive CD4+ T cells, in vitro differentiated Th17 cells, and CD4+ T cells isolated from experimental autoimmune encephalitomyelitis (EAE)-affected animals either after adoptive transfer of Th17 cells or after immunization with MOG35-55-peptide. The overall goal was to identify candidate genes involved in T cell pathology, encephalitogenicity and plasticity. These findings could then be correlated to multiple sclerosis pathology.

overall_design: Naive CD4+ T cells were isolated from B6.2d2 transgenic mice with MOG-specific T cell receptors and differentiated in vitro into Th17 cells. These Th17 cells were adoptively transferred into lymphopenic RAG1-/- mice to induce EAE. Further, EAE was induced by immunizing wild-type C57BL/6 mice with MOG35-55 peptide. RNA was extracted from naive CD4+ T cells, Th17 cells, and from CD4+ T cells isolated from the CNS of EAE-affected mice for gene expression analysis. Replicates from three independent experiments were analyzed.

first: Nicola

last: Hoppmann

first: Christiane

last: Graetz

first: Magdalena

last: Paterka

first: Laura

last: Poisa-Beiro

first: Catherine

last: Larochelle

first: Maruf

last: Hasan

first: Christina

middle: M

last: Lill

first: Frauke

last: Zipp


title: Transcriptome of CD4+ T cell subsets

status: Public on Dec 31 2014

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

institute: HCI - Helmholtz Centre for Infection Research

summary: We compared the transcriptome of ex vivo-isolated murine naive CD4+ T cells, Th1 cells and Th17 cells by microarray.

overall_design: CD4+ T effector cells were prepared ex vivo, stimulated with PMA/Ionomycin, subjected to a comercially available cytokine secretion kit (IL-17A and IFNg), stained by adding fluorescence-labeled antibodies against CD3, CD4 and CD45RB and sorted by flow cytometry. We sorted naive CD4+ T cells (CD3+CD4+CD45RB_high), Th1 cells (CD3+CD4+CD45RB_low_IFNg+IL17A-) and Th17 cells (CD3+CD4+CD45RB_low_IFNg-IL17A+).

first: Stefan

last: Floess

first: Bi-Huei

last: Yang


title: Whole genome expression signature of SWCNT sub-chronically exposed to human bronchial epithelial cells

status: Public on Mar 05 2015

city: Morgantown

first: Todd

last: Stueckle

state: WV

address: 1095 Willowdale Road

department: Health Effects Laboratory Division

institute: National Institute for Occupational Safety and Health

summary: Carcinogenicity of carbon nanotubes is a major concern but has not been well addressed due to the lack of experimental models. Here, we show that chronic exposure to single-walled carbon nanotubes causes malignant transformation of human lung epithelial cells. The transformed cells induce tumorigenesis in mice and exhibit an apoptosis resistant phenotype characteristic of cancer cells. In addition, cancer stem cells (CSCs), a subpopulation that drives tumor growth and progression, may represent targets for carcinogenic initiation by chemical and environmental agents.  Transformed B-SWCNT also exhibited emergence of lung CSCs, as indicated by the induction of CSC tumor spheres and side population (SP). These CSCs, which were found to overexpress tumor promoter caveolin-1 (Cav-1), displayed aggressive cancer phenotypes of apoptosis resistance and enhanced cell invasion and migration compared with their non-CSC counterpart. Using gene manipulation strategies, we reveal for the first time that Cav-1 plays an essential role in CSC regulation and aggressiveness of SWCNT-transformed cells partly through p53 dysregulation. Overexpression of Cav-1 resulted in p53 inactivation, while its inhibition by shRNA activated the p53. The role of Cav-1 in tumorigenesis and metastasis of the transformed cells was evaluated in a xenograft mouse model using luciferase-labeled SWCNT-transformed cells. Our data demonstrate that Cav-1 not only promoted tumor formation but also metastasis of the transformed cells to neighboring tissues. Since CSCs are crucial to the initiation and early development of carcinogenesis, our findings on the induction of CSCs by SWCNTs and their regulation by Cav-1 could aid in the early detection and risk assessment of the disease.

overall_design: Whole genome expression profiling was conducted on human immortalized bronchial epithelial cells (BEAS2B) following 6 month in vitro sub-chronic single-walled carbon nanotube (SWCNT) exposure to assess tumorigenesis signaling.  Dispersed SWCNT-exposed (B-SWCNT) were compared to Survanta® dispersant (B-Cont) passage control cells.  Each treatment possessed 3 biological cDNA replicates.  One technical replicate was performed per biological sample.

first: Liying

last: Rojanasakul

first: Sudjit

last: Luanpitpong


title: Identifying interferon-stimulated genes enriched in multiple tissues of Irgm1-/- mice

status: Public on Jan 03 2015

city: Saint Louis

first: Lulu

last: Sun

address: 4940 Parkview Place, 1020 CSRB-NTA

department: Pathology and Immunology

institute: Washington University in St. Louis

summary: We observed enhanced epithelial proliferation secondary to elevated Type I IFNs in multiple tissues of Irgm1-/- mice. We discovered that Type I IFNs signaled through macrophages to promote this epithelial hyperproliferation. To determine candidate factors that could play a role in this process, we performed whole genome microarray analysis of salivary gland, small intestine, and isolated colonic macrophages of Irgm1-/- mice and C57BL/6 WT controls. Genes enriched in at least 2 of the 3 sample sources were then screened for the ability to augment epithelial proliferation in vitro.

overall_design: RNA was extracted from three (small intestine and isolated colonic macrophage samples) or four (salivary gland samples) mice of each genotype (Irgm1-/- and WT). Both male and female six to nine week-old mice were used.

first: Thaddeus

last: Stappenbeck


title: Gene expression profile of murine Flvcr-deleted and control CD4+CD8+ double-positive (DP) thymocytes

status: Public on Feb 17 2015

city: Nashville

first: Mary

last: Philip

state: TN

address: 777 PRB, 2220 Pierce Ave

department: Medicine

institute: Vanderbilt University Medical Center

summary:
Genomewide microaarray analysis of murine DP thymocytes to determine the genes whose expression was altered by FLVCR loss
Gene signatures from Flvcr+/+ DP thymocytes was compared to gene signatures from Flvcr-/- DP thymocytes

overall_design: Total RNA obtained from sort-purified Flvcr-/- and Flvcr+/+ DP thymocytes

first: Janis

last: Abkowitz

first: Jeffrey

last: Delrow

first: Ryan

last: Basom


title: A "developmental hourglass" in fungi

status: Public on Mar 01 2015

city: Shatin

first: Xuanjin

last: Cheng

address: Rm 386, Science Center South Block

department: School of Life Sciences

country: Hong Kong

institute: The Chinese University of Hong Kong

summary: The "developmental hourglass" concept suggests that intermediate developmental stages are most resistant to evolutionary changes and that differences between species arise through divergence later in development. This high conservation during middevelopment is illustrated by the "waist" of the hourglass and it represents a low probability of evolutionary change. Earlier molecular surveys both on animals and on plants have shown that the genes expressed at the waist stage are more ancient and more conserved in their expression. The existence of such a developmental hourglass has not been explored in fungi, another eukaryotic kingdom. In this study, we generated a series of transcriptomic data covering the entire lifecycle of a model mushroom-forming fungus, Coprinopsis cinerea, and we observed a molecular hourglass over its development. The "young fruiting body" is the stage that expresses the evolutionarily oldest (lowest transcriptome age index) transcriptome and gives the strongest signal of purifying selection (lowest transcriptome divergence index). We also demonstrated that all three kingdoms-animals, plants, and fungi-display high expression levels of genes in "information storage and processing" at the waist stages, whereas the genes in "metabolism" become more highly expressed later. Besides, the three kingdoms all show underrepresented "signal transduction mechanisms" at the waist stages. The synchronic existence of a molecular "hourglass" across the three kingdoms reveals a mutual strategy for eukaryotes to incorporate evolutionary innovations.

overall_design: NimbleGen custom microarray with total RNAs extracted from two biological replicates for each stage of mycelium, fruiting initials (~2mm tall), stage 2 primordium (~1cm tall), young fruiting body (~2cm tall) and the fully-expanded cap of the mature fruiting body (~4cm tall). Mycelia from 5 agar plates were collected and pooled to form one replicate. For the other stages, 4-5 independent structures were isolated and their RNA extracted as one replicate sample.

first: Ho

last: Hui

first: Yung

middle: Y

last: Lee

first: Tik

last: Law

first: Hoi

last: Kwan


title: Genome-wide analysis of the TEC-specific Hipk2 gene knockout  in mouse medullary thymic epithelial cells (mTECs)

status: Public on Jan 05 2015

city: Heidelberg

first: Kristin

last: Rattay

address: Im Neuenheimer Feld 280

institute: German Cancer Research Center

summary: Analysis of the role of Hipk2 in regulating gene expression in medullary thymic epithelial cells. The whole genome gene signatures of purified mTEC subsets (CD80 low, CD80 high) from TEC-specific Hipk2 knockout mice were compared to mating wildtype control mice (floxed, Cre-). Results provide the up- or down-regulated genes, affected by the Hipk2 gene knockout.

overall_design: Total RNA obtained from isolated CD80 low and CD80 high mTECs of TEC-specific Hipk2 knockout mice compared to control mice mTEC subsets

first: Bruno

last: Kyewski


title: G2/M transition for stabilizing mouse haploid ESCs

status: Public on Nov 07 2014

first: Saori

last: Takahashi

address: 1-5-45 Yushima Bunkyo-ku, Tokyo

department: Epigenetics

institute: Tokyo Medical and Dental University

type: Genome variation profiling by genome tiling array


title: Prolyl-4-hydroxylase domain 3 (PHD3) is a critical terminator for cell survival of  macrophages under stress conditions

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

institute: Universitaetsmedizin Goettingen

summary: On molecular level cells sense changes in oxygen availability through the prolyl-4-hydroxylase domain enzymes (PHDs), which regulate the protein stability of the α-subunit of the transcription factor hypoxia inducible factor (HIF). Especially PHD3 has been additionally associated with apoptotic cell death. We hypothesized that PHD3 plays a role in cell-fate decisions in macrophages. Therefore myeloid-specific PHD3 knock out mice (PHD3-/-) were created and analysed. PHD3-deficient bone marrow-derived macrophages (BMDM) showed no altered HIF-1alpha or HIF-2alpha stabilization or increased HIF target genes expression in normoxia or hypoxia. Macrophage M1 and M2-polarization was unchanged likewise. Compared to macrophages from wild type littermates PHD3-/- BMDM exhibited a significant reduction in TUNEL positive cells after serum withdrawal or treatment with staurosporine and s-nitroso-N-acetylpenicillamine (SNAP). Under the same conditions PHD3-/- BMDM also showed less Annexin V staining which is representative for membrane disruption and indicated a reduced early apoptosis. In an unbiased transcriptome screen we found that angiopoietin like protein 2 (Angptl2) expression was reduced in PHD3-/- BMDM under stress conditions. Addition of recombinant Angptl2 rescued the anti-apoptotic phenotype demonstrating that it is involved in the PHD3-mediated response towards apoptotic stimuli in macrophages.

overall_design: 3 mice each for control wildtype and knockout mice, low/normal oxygen concentration, starved/normal feeding

first: Lija

last: Swain

first: Marieke

last: Wottawa

first: Annette

last: Hillemann

first: Angelika

last: Beneke

first: Haruki

last: Odagiri

first: Kazutoyo

last: Terada

first: Motoyoshi

last: Endo

first: Yuichi

last: Oike

first: Katja

last: Farhat

first: Dörthe

last: Katschinski


title: G2/M transition for stabilizing mouse haploid ESCs: Gene Expression

summary: To compare the gene expression profiles between haploid ESCs and diploid ESCs, we examined the gene expression profile using DNA microarray analysis using G1 phase cells collected by FACS.

overall_design: Two independent experiments were performed at each cell type (haploid or diploid).

first: Jiyoung

last: Lee

first: Takashi

last: Kohda

first: Miyuri

last: Kawasumi

first: Masami

last: Kanai-Azuma

first: Tomoko

last: Kaneko-Ishino

first: Fumitoshi

last: Ishino


title: Induced CD103+ Dendritic Cells

first: Robert

last: Geffers

summary:
Multiple subsets of FLT3L-dependent dendritic cells (DCs) control T cell tolerance and immunity. In mouse tissues, CD8α-like DCs are identified by CD103 expression. This DC subset efficiently enters lymph nodes and cross-presents antigens, rendering CD103+ DCs promising targets for therapeutic tolerance induction or vaccination. However, only limited numbers of CD103+ DCs can be isolated with current methods. Moreover, bone marrow cultures with FLT3L produce complex mixtures of DC subsets. We developed a novel method for generating large numbers of Batf3-dependent CD103+ DCs.
We used microarray analysis to compare in vitro generated CD103+ and CD103- DCs and correlated their expression patterns to published profiles and signatures of DC subsets.

overall_design: We generated iCD103 DCs according to our new method. We sorted CD11c+B220-CD103hi and CD11c+B220-CD103- DC subsets and processed these populations for RNA extraction and hybridization to Agilent microarrays.

first: Christian

middle: T

last: Mayer

first: Tim

last: Sparwasser


title: Murine bone marrow derived macrophages: wildtype Vs. CDK5R1 knockout

status: Public on Nov 20 2014

city: Seoul

first: Yi Rang

address: 101, daehak-ro Jongro-gu

department: Microbiology and Immunology

institute: Seoul National University College of Medicine

summary: Transcriptional profiling of mouse bone marrow derived macrophages comparing wildtype with CDK5R1 knockout. CDK5R1 is an activating parter for CDK5 and synthesized upon TLRs stimaultion. Activated CDK5 has various target substrates, and functions as a key singnaling regulator in macrophages.

overall_design: Two condition experiments: basal state and LPS-stimulated macrophages for 6 hours. Two biological replicates.

first: Yi-Rang

first: Seung

last: Seok


title: Genome-wide identification of rat long non-coding RNAs (microarray)

status: Public on Dec 10 2014

city: Toledo

first: Bina

last: Joe

state: Ohio

address: Block Health Science Bldg, 3000 Arlington Ave

department: Department of Physiology and Pharmacology

institute: University of Toledo, College of Medicine and Life Sciences

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

summary: In the current study, we have focused on a distinct group of non-coding elements, lncRNA, and profiled renal tissues from three different inbred rat strains. We chose the three strains S, SHR and R for the main purpose of cataloging lncRNA annotations from  the most widely used rat models of cardiovascular and renal disease.

overall_design: Identification of lncRNAs on the rat genome by Microarray

first: Kathirvel

last: Gopalakrishnan


title: Epigenetic regulations in the IFNγ signalling pathway: IFNγ-mediated MHC class I upregulation on tumour cells is associated with DNA demethylation of antigen-presenting machinery genes [TC1A9_IFN]

status: Public on Dec 08 2014

city: Prague

first: Milan

last: Reinis

address: Videnska 1083

country: Czech Republic

institute: Institute of Molecular Genetics of the ASCR, v. v. i.

summary: Reversible MHC class I deficiency on tumour cells is commonly caused by coordinated silencing of antigen-presenting machinery genes and restorable by IFNγ. Here we describe association of  DNA demethylation of selected antigen-presenting machinery gene regulatory regions located in the MHC genomic locus (TAP-1, TAP-2, LMP-2, LMP-7) upon IFNγ treatment with MHC class I upregulation on tumour cells. Our novel findings demonstrate that IFNγ acts as an epigenetic modifier upregulating the expression of antigen-presenting machinery genes through DNA demethylation.  Our data also cast more light on the role of DNA methylation in tumour cell escape from specific immunity.

overall_design: TC-1/A9 cultured cells treated with IFN gama or nothing. 3 biological replicates per condition.

first: Veronika

last: Vlková

first: Ivan

last: Štěpánek

last: Hrušková

first: Filip

last: Šenigl

last: Mayerová

first: Jana

last: Šímová

last: Bieblová

first: Marie

last: Indrová

first: Tomas

last: Hejhal

first: Nicolas

last: Dérian

first: David

last: Klatzmann

first: Adrien

last: Six

last: Reiniš


title: Gene expression profile on wt and mdx mice treated or untreated with Tadalafil

status: Public on Oct 24 2014

city: Rome

first: Lucia

last: Monaco

address: Piazzale Aldo Moro 5

department: Dept. di Fisiologia e Farmacologia

institute: Universita degli Studi di Roma Sapienza

summary: Microarray-based genomic analysis to assess the pattern of gene expression in muscle samples obtained from animals treated with tadalafil. This scrutiny allowed us to identify several classes of modulated genes that may provide hints for the identification of common factors underlying the improvement of muscle performance.

overall_design: The pharmacological treatments were started before birth by oral administration  and continued after birth until 16 weeks of age.

first: V

last: De Arcangelis

first: G

last: Strimpakos

first: F

last: Gabanella

first: N

last: Corbi

first: S

last: Luvisetto

first: A

last: Magrelli

last: Onori

first: C

last: Passananti

last: Pisani

last: Rome

last: Severini

last: Naro

first: E

last: Mattei

first: M

middle: G

last: Di Certo

first: L


title: Gene expression in E9.5 trunks comparing wt with Arid3b-null embryos

status: Public on Oct 07 2014

city: Madrid

first: Juan Jose

last: Sanz-Ezquerro

address: Darwin, 3

department: Biologia Molecular y Celular

country: Spain

institute: Centro Nacional dde Biotecnologia

summary: We have analysed and compared mRNA expression between wt embryos and embryos deficient for Arid3b in E9.5 trunks, with the aim of identifying differentially expressed genes that could give us a clue to the functions of Arid3b during development.

overall_design: Trunks were dissected from E9.5 embryos (including the body from the otic vesicle to somite 15 and forelimbs). Four wild-type and four mutant embryos were collected and pooled for each of the microarray triplicates.

first: Verónica

last: Uribe

first: Juan


title: Arid3b is required for heart development

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

overall_design: Refer to individual Series


title: Gene expression in E9.5 heads comparing wt with Arid3b-null embryos

summary: We have analysed and compared mRNA expression between wt embryos and embryos deficient for Arid3b in E9.5 heads, with the aim of identifying differentially expressed genes that could give us a clue to the functions of Arid3b during development.

overall_design: Heads were dissected from E9.5 embryos (including head and first branchial arch). Four wild-type and four mutant embryos were collected and pooled for each of the microarray triplicates.


title: Gene expression in E9.5 hearts comparing wt with Arid3b-null embryos

summary: We have analysed and compared mRNA expression between wt embryos and embryos deficient for Arid3b in E9.5 hearts, with the aim of identifying differentially expressed genes that could give us a clue to the functions of Arid3b during development.

overall_design: Hearts were dissected from E9.5 embryos (including the heart tube and the pharyngeal mesoderm and endoderm located beneath). Four wild-type and four mutant embryos were collected and pooled for each of the microarray triplicates.


title: Distinct distributions of histone marks shape cell identities of murine hepatic progenitors and adult hepatocytes

status: Public on Jul 01 2014

city: Yokohama City

first: Yasuharu

last: Ueno

address: 3-9  Fuku-ura, Kanazawa-ku

department: Graduate School of Medicine

institute: Yokohama City University

summary: The present study revealed dynamic reposition of localizations of silencing histone marks including H3K27me3 in hepatocyte differentiation, of which target genes reflect the cell identities in connection to the cellular functions. Our results shed light on the process of hepatocyte terminal differentiation regulated by epigenetic mechanisms.

overall_design: Comparison of gene expression in E13.5 liver cells from WT and Ezh2 KO mice.

first: Hiroyuki

last: Koike


title: Effects of Myb shRNA on Airway Epithelial Cells

status: Public on Aug 12 2014

city: St. Louis

first: Anand

last: Patel

state: MO

address: Campus Box 8116, 660 S. Euclid Ave.

institute: Washington University School of Medicine

summary:
The epithelium of the pulmonary airway is specially differentiated to provide defense against environmental insults, but also subject to dysregulated differentiation that results in lung disease. The current paradigm for airway epithelial differentiation is a one-step program whereby a p63+ basal epithelial progenitor cell generates a ciliated or secretory cell lineage, but the cue for this transition and whether there are intermediate steps is poorly defined. Here we identify transcription factor Myb as a key regulator that permits early multilineage differentiation of airway epithelial cells. Myb+ cells were identified as p63– and therefore distinct from basal progenitor cells, but were still negative for markers of differentiation.
Myb RNAi treatment of primary-culture airway epithelial cells and Myb gene deletion in mice resulted in a p63– population with failed maturation of Foxj1+ ciliated cells, as well as Scbg1a1+ and Muc5ac+ secretory cells. Consistent with these findings, analysis of whole genome expression of Myb-deficient cells identified Myb-dependent programs for ciliated and secretory cell differentiation. Myb+ cells were rare in human airways but were increased in regions of ciliated cells and mucous cell hyperplasia in samples from subjects with chronic obstructive pulmonary disease. Together, the results show that a p63– Myb+ population of airway epithelial cells represents a distinct intermediate stage of differentiation that is required under normal conditions and may be heightened in airway disease.

overall_design: 12 samples, 2x2 factorial design, factor 1: time (days post-ALI), factor 2:shRNA (Myb vs Scrambled Control), performed in triplicate (biological replicates)

first: Jie-hong

last: Pan

first: Tracy

last: Adair-Kirk

middle: C

first: Tao

last: Huang

first: Nicholas

middle: S

last: Yozamp

first: Jian

last: Xu

middle: P

last: Reddy

first: Derek

last: Byers

first: Richard

last: Pierce

first: Michael

last: Holtzman

first: Steven

last: Brody


title: Expression analysis of murine splenic B-cells after retroviral transduction with a constitutively active variant of IRF5 (IRF5-4D)

status: Public on Sep 24 2014

city: Berlin

first: Karl

last: Koechert

address: Robert-Roessle-Str. 10

institute: Max-Delbrueck-Centre for Molecular Medicine

summary: Genome-wide gene expression analysis of murine splenic B-cells following retroviral transduction with a constitutively active IRF5 (IRF5-4D)

overall_design: Illumina WG-6 v2.0 arrays were hybridized to determine the gene expression profile of murine splenic B-cells following retroviral transduction with i) control virus (MSCV-IRES-CFP) or ii) IRF5-4D virus (MSCV-IRF5-4D-CFP). All hybridizations were done in biological triplicates.

first: S

last: Kreher

first: K

last: Köchert

last: Mathas

first: M

last: Janz


title: Highly sensitive amplicon-based transcript quantification by semi-conductor sequencing

status: Public on Jul 15 2014

city: Basel

first: Jitao David

last: Zhang

address: Grenzacherstrasse 124

department: Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel

institute: F. Hoffmann-La Roche

type: Expression profiling by high throughput sequencing

summary: We have adapted a commercial assay that employs mRNA quantification based on the frequency of PCR amplicons determined by next-generation to a high-throughput semi-conductor sequencing platform (Ion-Torrent Proton). We show parallel amplification of pathway derived transcript sets/genes in 12 reference RNA samples followed by sequence-based quantification covering a dynamic range of five orders of magnitude with low technical variation.

overall_design: Expression of selected genes were profiled at four time points (0d, 10d, 20d, and 60d) during differentiation of induced pluripotent stem cells into cardiomyocytes, with three independent biological replicates at each time point.

first: Jitao

middle: D

first: Tobias

last: Schindler

first: Erich

last: Küng

first: Martin

last: Ebeling

first: Ulrich

last: Certa


title: Expression analysis of colorectal cancer cell line SW480 expressing  FOXC2

status: Public on Jul 02 2014

city: Guangzhou

first: Yan-Qing

last: Ding

address: 1838#, Northern Guangzhou Dadao Road

institute: Southern Medical University

summary:
Investigation of whole genome gene expression level changes in a colorectal cancer cell line SW480  expressing FOXC2, compared to the pBabe control cells.  Genes associated with metastasis regulated by FOXC2 in colorectal cancer were analysed.
The role of FOXC2 in breast cancer metastasis are further described in Mani SA, Yang J et al. Mesenchyme Forkhead 1 (FOXC2) plays a key role in metastasis and is associated with aggressive basal-like breast cancers. PNAS  2007; 104: 10069-10074 .

overall_design: A six chip study using total RNA recovered from three separate  cultures of SW480/pBabe and  three separate cultures of SW480/FOXC2.  Each chip measures the expression level of 45033 genes from SW480/pBabe or SW480/FOXC2.

first: Yan-Mei

last: Cui

first: Wen-Ting

last: Liao


title: Myb permits multilineage airway epithelial cell differentiation

status: Public on Aug 13 2014

first: Anand

last: Patel

department: Pulmonary/Critical Care Medicine


title: Copper Metabolism Domain-Containing 1 Represses Genes That Promote Inflammation and Protects Mice From Colitis and Colitis-Associated Cancer

status: Public on May 19 2014

city: Hannover

first: Oliver

last: Dittrich-Breiholz

address: Carl-Neuberg-Str. 1

department: Research Core Unit Genomics

institute: Medical School Hannover

summary:
Background & Aims

Activation of the transcription factor nuclear factor-κB (NF-κB) has been associated with the development of inflammatory bowel disease (IBD). Copper metabolism MURR1 domain containing 1 (COMMD1), a regulator of various transport pathways, has been shown to limit NF-κB activation. We investigated the roles of COMMD1 in the pathogenesis of colitis in mice and IBD in human beings.

overall_design: Bone marrow derived macrophages (BMDM) were isolated from two individual wildtype - and two Commd1 knockout mice. Cells from individual mice were splitted and were treated with LPS for 3h, 24h, or, were left untreated. The corresponding 12 cell samples were subjected to total RNA preparation and subsequently used for Single-Color-based Microarray Analysis (Agilent Technologies).

first: Haiying

last: Li

first: Axel

last: Weber

last: Kracht

first: Schneider

last: Heike

first: Bart

last: van de Sluis

first: Ezra

last: Burstein


title: Effect of Gnas knockout on mouse skin

status: Public on Jun 28 2014

city: Bethesda

first: Ramiro

last: Iglesias-Bartolome

address: 37 Convent Drive

department: LCMB

institute: NIH/NCI

summary: Analysis of skin lesions from adult mice with epidermal conditional deletion of heterotrimeric G protein Galpha s in cytokeratin 14 positive cells, compared with control mouse skin. Epidermal Gnas ablation leads to skin defects, including basal cell carcinoma (BCC). Results provide insight into role of Galpha s in the regulation of stem cells from the skin.

overall_design: Changes in gene expression following Gnas deletion from the mouse epidermis were analyzed. Skin from four independent mice of each wild type (control) and Gnas epidermal knockout (Gnas eKO) were analyzed.

first: Daniela

last: Torres

first: Romina

last: Marone

first: Xiaodong

last: Feng

first: Daniel

last: Martin

first: Min

last: Chen

first: Lee

last: Weinstein

first: Susan

last: Taylor

first: Alfredo

middle: A

last: Molinolo

first: J

last: Gutkind


title: Genome-wide analysis of High glucose-induced gene expression by Ninjurin1 siRNA

status: Public on May 20 2014

city: Shinheung- Dong, Jung-Gu Incheon

first: GUO NAN

last: YIN

address: 7-206, 3rd ST B dong, 3 floor room 307-2

department: Urology

institute: Inha university hospital

summary: Transcriptional profiling of Mouse cavernous primary endothelial cells (MCECs) in comparing normal glucose condition with high glucose condition or Ninjurin1 siRNA transfection condition. Objective was to determine the effect of ninjurin1 on high glucose conditioned cells on global gene expression.

overall_design: Total RNA obtained from MCECs, which were treated with High glucose (HG) condition or (HG+ninjurin1 siRNA). Biological replicates: 1 control replicates, 1 HG replicates, 1 (HG+ninjurin1 siRNA) replicates.

first: Guo

middle: N

last: Yin

first: Ji-Kan

last: Ryu

first: Jun-Kyu

last: Suh


title: Whole genome profiling of whole liver lysates of vehicle and Sorafenib-treated iAST mice

status: Public on Jun 20 2014

first: Anja

last: Runge

summary: Analysis of changes in gene expression upon Sorafenib treatment. Looking for candidates, that could potentially be up- or down-regulated upon Sorefanib treatment.

overall_design: Total RNA were optained from whole liver lysates of vehicle 14d-, Sorafenib 14d- and LT Sorafenib-treated iAST mice

first: Hellmut

last: Augustin


title: Analysis of gene expression in ALK5Ctrl and ALK5CA mouse hippocampus

status: Public on May 25 2014

city: Stanford

first: Yingbo

last: He

address: Stanford University

institute: Stanford University

summary: Activation of TGF-β signaling in ALK5CA mouse induces changes in gene expression, which are involved in brain development, cell death and migration, cell cycle, and neurologic diseases, processes and functions that are in line with the effects on neurogenesis.

overall_design: Total RNA obtained from hippocampi of ALK5CA mice compared to those of ALK5Ctrl mice


title: Maternal age effect on mouse oocytes: new biological insight from proteomic analysis

status: Public on Apr 15 2014

city: Rostock

first: Marcin

last: Siatkowski

address: Ernst-Heydemann-Str. 8

institute: IBIMA

summary: The long-standing view of 'immortal germ line versus mortal soma' poses a fundamental question in biology concerning how oocytes age in molecular terms. A mainstream hypothesis is that maternal aging of oocytes has its roots in gene transcription. Investigating the proteins resulting from mRNA translation would reveal how far the levels of functionally available proteins correlate with mRNAs, and would offer novel insight into the changes oocytes undergo during maternal aging. Gene ontology semantic analysis reveals the high similarity of the detected proteome (2,324 proteins) to the transcriptome (22,334 mRNAs), though not all proteins have a cognate mRNA. Concerning their dynamics, 4-fold changes of abundance are more frequent in the proteome (3%) than the transcriptome (0.05%), with correlation. Whereas proteins associated with the nucleus (e.g. structural maintenance of chromosomes, spindle-assembly checkpoints) are largely represented among those that change in oocytes during maternal aging; proteins associated with oxidative stress/damage (e.g. superoxide dismutase) are infrequent. These quantitative alterations are either impoverishing or enriching. Using gene ontology analysis, these alterations do not relate in any simple way to the classic signature of aging known from somatic tissues. We conclude that proteome analysis of mouse oocytes may not be surrogated with transcriptome analysis, given the lack of correlation. Furthermore, we conclude that the classic features of aging may not be transposed from somatic tissues to oocytes in a one-to-one fashion. Overall, there is more to the maternal aging of oocytes than mere cellular deterioration exemplified by the notorious increase of meiotic aneuploidy.

overall_design: Three pools of 20 zona-enclosed B6C3F1 oocytes from each age group were subjected for experiment.

first: Caroline

last: Schwarzer

first: Martin

middle: J

last: Pfeiffer

first: Nicole

last: Bäumer

first: Hannes

last: Drexler

first: Georg

last: Fuellen

first: Michele

last: Boiani


title: Cell competition regulates thymocyte turnover

status: Public on May 16 2014

city: Heidelberg

first: Vera

middle: C.

last: Martins

address: Im Neuenheimer Feld 280

department: Division of Cellular Immunology

institute: German Cancer Research Center

summary: Wild type thymi were transplanted into a competitive (wild type hosts), or non-competitive (Rag2-/-γc-/-KitW/Wv hosts) environment. Triple negative 2 and 3 (TN2/3) stages were sorted 14 days afetr transplantation and separated for cells of host or donor origin.

overall_design: Global gene expression data for TN2/3 cells, that were young, old with, and old without competition were compared.

first: Hans-Reimer

last: Rodewald


title: Intrathymic origins of T-ALL

summary: Leukemia cells are considered developmentally 'frozen', and their phenotype is thought to reflect their stage of origin. To gain insights into the cell population from which T-ALL arises, we compared by global gene expression profiling T-ALL samples (n = 10) to different stages of T cell development, following the order from early thymic progenitor (ETP), to triple negative (TN) TN2, to TN3, to TN4, to immature single positive (ISP), to double positive (DP) thymocytes.

overall_design: Comparison of global gene expression between T-ALL samples and various stages of T cell development.

first: Katrin

last: Busch

first: Thomas

last: Hielscher


title: Genomics of the ovine fetal brain ontogeny during the last stage of gestation

status: Public on Jun 30 2014

city: Utrecht

first: Maria

middle: Belen

last: Rabaglino

address: Yalelaan 7

department: Population Health Science

institute: Utrecht University

summary: Normal development in the brain requires temporal changes in gene expression. A better understanding of the genomics of the fetal brain during late gestation can help to improve our understanding of the molecular events that enable the newborn to survive extra-uterine life.  The purpose of the present study is to model changes and coherence of gene expression in cerebral cortex, brainstem, hippocampus, and hypothalamus throughout the second half of gestation. We used the sheep as an animal model to identify co-expressed genes in different regions of the ovine fetal brain, from mid-gestation (80 days) to one day of postnatal life. In the ewe, gestation length varies from 142 to 152 days, with an average of 147 days. Using a newly-available ovine array and weighted gene co-expression network analysis (WGCNA), we tested the hypothesis that the resulting products of genes expressed in a similar pattern through the last stage of gestation in different brain regions are functionally related and could play an important role in the normal fetal development.

overall_design: Tissues from cortex, brainstem, hippocampus and hypothalamus were collected from non treated fetuses at 80 (80d, n=4), 96–100 (100d, n=4), 120 (120d, n=4), 130 (130d, n=4), and 142–144 (145d, n=4) days of gestation and on the first (1d, n=4) day after delivery. Each group included one set of twin fetuses. None of the ewes showed any signs of impending labor.

middle: B

first: Elaine

last: Richards

first: Nancy

last: Denslow

first: Maureen

last: Keller-Wood

first: Charles

last: Wood


title: Cell competition is a tumor suppressor mechanism in the thymus.

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

overall_design: Refer to individual Series


title: Toxicogenomics in the 3T3-L1 cell line, a new approach for screening of obesogenic compounds

status: Public on May 01 2014

city: Antwerp

first: Anna

last: Pereira-Fernandes

address: Groenenborgerlaan 171

department: Biology

country: Belgium

institute: University of Antwerp

summary:
The obesogen hypothesis states that exposure to environmental compounds early in life or throughout lifetime might have an influence on obesity development. In this paper a new approach for obesogen screening is proposed, namely the use of transcriptomics in the 3T3-L1 pre-adipocyte cell line. Based on the data from a previous study of our group using a lipid accumulation based adipocyte differentiation assay, several humanly relevant obesogenic compounds were selected: reference obesogens [Rosiglitazone (ROSI), Tributyltin (TBT)], test obesogens [Butylbenzyl phthalate (BBP), butylparaben (BP), propylparaben (PP), Bisphenol A (BPA)] and non-obesogens [Ethylene Brassylate (EB), Bis (2-ethylhexyl)phthalate (DEHP)].
In this paper, the high stability and reproducibility of the 3T3-L1 gene transcription patterns over different experiments and cell batches was shown. Obesogens and non-obesogen gene transcription profiles were clearly distinguished using hierarchical clustering. Furthermore, a gradual distinction corresponding to differences in induction of lipid accumulation could be made between test and reference obesogens based on transcription patterns, indicating the potential use of this strategy for classification of obesogens. Marker genes that are able to distinguish between non, test and reference obesogens were identified. Well known genes involved in adipocyte differentiation, as well as genes with unknown functions were selected, implying a potential adipocyte related function of the latter. Cell physiological lipid accumulation was well predicted based on transcription levels of the marker genes, indicating the biological relevance of omics data.
In conclusion, this study shows the high relevance and reproducibility of this 3T3-L1 based in vitro toxicogenomics tool for classification of obesogens and biomarker discovery.

overall_design: The hybridization design was a reference design (reference sample was a mixture of equal aliquots from control and exposed samples), recommended for class discovery purposes (Knapen et al. 2009). The reference sample was labeled with Cy5, and the exposed samples with Cy3. Three biological replicates were measured for every condition.

last: Vanparys

first: Tine

last: Hectors

first: Lucia

last: Vergauwen

first: Dries

last: Knapen

first: Philippe

last: Jorens

first: Ronny

last: Blust


title: Transcriptome analyses during disease progression

summary: Transcriptome was assessed in the transitions from the normal thymus (with regular progenitor turnover), to a thymus devoid of extrinsic progenitor competition for 10 weeks, to fully malignant T cell acute lymphoblastic leukemia (T-ALL).

overall_design: Comparison of global gene expression between normal thymus, to thymus grafts with autonomous thymopoiesis, and T-ALL


title: Six2GFPE15.5 110309

status: Public on Mar 24 2014

city: Kumamoto

first: Ryuichi

last: Nishinakamura

address: Honjo 2-2-1

department: IMEG

institute: Kumamoto Univ.

summary: We have employed whole genome microarray expression profiling to identify genes  regulated by Sall1 in the kidney.

overall_design: Six2GFP-positive nephron progenitors and Six2GFP-negative cells were collected from the embryonic kidneys at E15.5  (2 set) , and their expression profiles were compared.


title: Gene expression analysis of GzmB-/- hematopoietic stem cells (HSC).

status: Public on Apr 11 2014

city: Macclesfield

first: Larissa

last: Carnevalli

state: Cheshire

address: Mereside, Alderley Park

country: United Kingdom

institute: Astrazeneca

summary: This study aimed to compare the  expression profile of GzmB deficient HSCs and their WT counterparts in order to understand their phenotype in bone marrow in vivo reconstitution assays.

overall_design: GzmB-/- HSC mRNA expression was compared to WT counterparts. Samples of 3 biological replicates (pool of 3 mice per replicate) of each group has been used for the array.

first: L


title: Transcriptomic analysis of midbrain and individual hindbrain rhombomeres in the chick embryo

status: Public on Jun 25 2014

city: London

first: David

last: Chambers

state: London

address: Guy's Campus

department: Wolfson CARD

institute: King's College Londonn

summary:
A systematic survey of the transcriptional status of individual segments of the developing chick hindbrain (r1-5) and the adjacent region of the embryonic midbrain (m) during the HH11 stage of chick development
Affymetrix Chicken GeneChip Expression Study

overall_design: Paralell comparison of defined regions of the neural tube during early chick development


title: Genome-wide RNAi screen reveals factors needed at the transition steps of induced reprogramming

status: Public on Aug 01 2014

city: La Jolla

first: Tariq

last: Rana

address: 9500 Gilman Drive, MC 0602

department: Pediatrics

institute: University of California, San Diego

summary: Analysis of step-wise transcriptome changes of reprogrammed cells in different stages during induced reprogramming.

overall_design: Total RNA obtained from sorted cells representing four stages of induced reprogramming. The mRNA expression changes among these four sorted cell populations will reveal important transcription signatures for the cell-fate transitions.

first: Chao-Shun

last: Yang


title: TAp73 is essential for germ cell adhesion and maturation in testis

status: Public on Mar 07 2014

city: Goettingen

first: Gabriela

last: Salinas

address: Kreuzbergring 57

department: Department of Pathology

institute: Universitaetsmedizin Goettingen

summary: A core evolutionary function of the p53 family is to protect the genomic integrity of gametes. However, the role of p73 in the male germline is unknown. Here we uncover that TAp73 unexpectedly functions as adhesion and maturation factor of the seminiferous epithelium orchestrating spermiogenesis. TAp73KO and p73KO mice, but not ΔNp73KO mice, display a ‘near-empty seminiferous tubule’ phenotype due to massive premature loss of immature germ cells. Its cellular basis are defective cell-cell adhesions of developing germ cells to Sertoli nurse cells, with secondary degeneration of Sertoli cells including the blood-testis-barrier, thereby disrupting the adhesive integrity and maturation of the germ epithelium. At the molecular level, TAp73, produced in germ cells, controls a coordinated transcriptional program of adhesion- and migration-related proteins including peptidase inhibitors, proteases, receptors and integrins required for germ-Sertoli cell adhesion and dynamic junctional restructuring. Thus, the testis emerges as unique organ with strict division of labor among all family members: p63 and p53 safeguard germline fidelity, while TAp73 ensures fertility by enabling sperm maturation.

overall_design: 3 mice each for control wildtype and TAp73 knockout mice

first: Lena

last: Holembowski

first: Daniela

last: Kramer

first: Dietmar

last: Riedel

first: Raffaella

last: Sordella

first: Matthias

last: Dobbelstein

first: Ute

last: Moll

first: Alice

last: Nemajerova


title: Microarray analysis of colon tissue of DSS colitis STAP-2 KO mice

status: Public on Apr 17 2014

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

summary: To identify STAP-2 regulating genes modulated intestine inflammation, we conducted microarray analyses using colon tissue from pooled WT (n=3) or STAP-2-/- mice (n=3) treated with DSS for 3 days. Bioinformatic analyses revealed that STAP-2 deletion mediates insufficient immune and inflammatory reaction through altering a series of associated gene expression.

overall_design: The DSS-treated colons derived from WT (n=3) and STAP-2 KO (n=3) mice were examined. Each strain was run in biological duplicate.

first: Natsuko

last: Fujita


title: Genome-wide expression kinetics of children with T1D-associated autoantibodies compared to healthy matched controls I

status: Public on Feb 20 2014

city: Turku

first: Henna

last: Kallionpää

address: P.O. Box 123

department: Turku Centre for Biotechnology

country: Finland

institute: University of Turku

summary: To unravel genes and molecular pathways involved in the pathogenesis of type 1 diabetes (T1D), we performed genome-wide gene expression profiling of prospective venous blood samples from children developing T1D-associated autoantibodies or progressing towards clinical diagnosis.

overall_design: 63 peripheral blood RNA samples from 6 autoantibody-positive children (Case) and their matched controls (Control) were analyzed with Illumina Sentrix WG-6 v2 genome-wide arrays, in order to study the gene expression changes occuring during the pathogenesis of Type 1 diabetes (T1D). Each case child (positive for T1D-specific autoantibodies) was matched with a persistently autoantibody-negative control child, with the same HLA-DQB1 risk category, gender, and place and date of birth. Seroconversion is determined as the first detection of T1D-specific autoantibody/autoantibodies (ICA titre >4 JDFU, IAA >3.47 RU, GADA >5.4 RU, IA-2A >0.43 RU, ZnT8A >0.61 RU).

first: Laura

last: Elo

first: Juha

last: Mykkänen

first: Essi

last: Laajala

first: Matti

last: Vaarma

first: Teemu

first: Heikki

last: Hyöty

first: Jorma

last: Ilonen

first: Riitta

last: Veijola

first: Tuula

last: Simell

first: Mikael

last: Knip

first: Harri

last: Lähdesmäki

first: Olli

last: Lahesmaa

first: Isis

last: Ricaño-Ponce

first: Wijmenga

last: Cisca


title: Genome-wide expression kinetics of children with T1D-associated autoantibodies compared to healthy matched controls II

overall_design: 58 peripheral blood RNA samples from 4 autoantibody-positive children and their matched controls were analyzed with Illumina Sentrix WG-6 v2 genome-wide arrays, in order to study the gene expression changes occuring during the pathogenesis of Type 1 diabetes (T1D). Each case child (positive for T1D-specific autoantibodies) was matched with a persistently autoantibody-negative control child, with the same HLA-DQB1 risk category, gender, and place and date of birth. Seroconversion is determined as the first detection of T1D-specific autoantibody/autoantibodies (ICA titre >4 JDFU, IAA >3.47 RU, GADA >5.4 RU, IA-2A >0.43 RU, ZnT8A >0.61 RU).

first: Cisca

last: Wijmenga


title: B-myb is Essential Regulator of Hematopoietic Stem Cell and Myeloid Progenitor Cell Development

status: Public on Feb 12 2014

city: New York

first: Stacey

last: Baker

state: NY

address: One Gustave L. Levy Place, Box 1130

department: Oncological Sciences

institute: Icahn School of Medicine at Mount Sinai

summary:
The B-myb (MYBL2) gene is a member of the MYB family of transcription factors and is involved in cell cycle regulation, DNA replication and maintenance of genomic integrity. However, its function during adult development and hematopoiesis is unknown. We show here that conditional inactivation of B-myb in vivo results in depletion of the HSC pool, leading to profound reductions in mature lymphoid, erythroid and myeloid cells. This defect is autonomous to the bone marrow and is first evident in the HSCs, which accumulate in the S and G2/M phases. B-myb inactivation also causes defects in the myeloid progenitor compartment and results in an accumulation of GMPs. Microarray studies indicate that B-myb null LKS+ cells differentially express genes that direct myeloid lineage development and commitment, suggesting that B-myb is a key player in controlling cell fate. Collectively, these studies demonstrate that B-myb is essential for HSC and progenitor maintenance and survival during hematopoiesis.
Total RNA was isolated from FACS purified LKS+ cells isolated from pIpC-treated control and B-myb floxed-MxCre mice.

overall_design: Each sample is derived from a pool of 3-5 mice. 2 samples were analyzed for each genotype.

first: E

last: Reddy


title: Transcriptional regulation of cellular processes important in control of skeletal myogenesis by interferon-γ

status: Public on Feb 05 2014

city: Warsaw

first: Zofia

last: Wicik

state: mazovia

address: Pawinskiego 5

department: Department of Human Epigenetics

country: Poland

institute: Mossakowski Medical Research Center

summary:
The purpose of the study was to investigate the effect of IFN-γ on transcriptomic profile of differentiating mouse C2C12 myogenic cells. Global gene expression was evaluated using the oligonucleotide whole mouse genome microarrays and was validated with real-time PCR method. Exogenous IFN-γ (1 ng/ml) increased myoblast proliferation, but decreased cell viability, the fusion index and the cellular content of myosin heavy chain, MyHC in C2C12 cultures on the 3rd day of differentiation. IFN-γ up-regulated genes were mainly involved in biological processes such as: cell cycle, regulation of cell proliferation, programmed cell death, inflammatory, vasculature development, regulation of cytokine, transmembrane receptor protein tyrosine kinase signaling pathway, and chemotaxis, whereas down-regulated genes contributed mainly to: regulation of transcription, cell-cell signaling, nitrogen compound biosynthetic process, transmembrane receptor protein ser/thr protein kinase signaling pathway, and regulation of Wnt receptor signaling pathway.  IFN-γ up-regulated the expression of cytokines/growth factors controlling cell proliferation (Cxcl10, Il15, Ccl2, Fgf7, Figf, Csf1, Vegfc, Hgf). Moreover, IFN-γ: i) down-regulated genes encoding factors that are anabolic for muscle cells (Fst, Igf-1); ii) inhibited pro-myogenic transcription (via Mef2a, Nfkb1, and Pparg); iii) decreased expression of genes controlling cell adhesion and sarcolemma/cytoskeleton organization; and iv) activated the proteolytic pathways: proteasomes and catepsins, leading to protein degradation and impaired myotube growth. Our data suggest that the effect of IFN-γ on mygenesis is, at least partly, associated with the regulation of muscle cell secretom at the transcriptional level.

To whom the correspondence should be addressed: Dr K. Grzelkowska-Kowalczyk; e-mail: k_grzel_kow@poczta.fm, tel/fax: (48 22) 847 24 52

overall_design: After scanning of hybridized microarrays, quantitation of slide images was performed using Feature Extraction Software (Agilent) using default parameters and the raw data were exported to GeneSpring GX 12 (Agilent, Santa Clara, CA) and log2 transformed. For identification of genes significantly altered in cell compared with the control normal gene set, total detected entities were filtered by flags (detected, non detected) to remove very low signal entities and to select reproducible signal values of entities among the replicated experiments, respectively. In statistical analysis, separated for experiment with myoblasts treated with  IFNG (IFNG vs CTRL 1-4) was used t-test unpaired (p < 0.05) with multiple testing correction: Benjamini-Hochberg <0.05, all significant changes over fold change 2 were selected. Analysis of GO, GSEA and signaling pathway was carried out using GeneSpring GX 12 (Agilent) and the DAVID Classification System (p<0.05).

first: Katarzyna

last: Grzelkowska-Kowalczyk

first: Alicja

last: Majewska

first: Justyna

last: Tokarska

first: Kamil

last: Grabiec

first: Marcin

last: Kozlowski

first: M

last: Milewska

last: Blaszczyk


title: Transcriptional analysis of live and hybridized J1 and NIH-3T3 cells

status: Public on Mar 20 2014

city: Cambridge

first: Sandy

last: Klemm

state: MA

address: 31 Ames St.

country: USA

institute: MIT

summary: J1 mouse embryonic stem cells (mESCs) and NIH-3T3 fibroblasts were grown in standard media conditions. Hybridized cells were fixed with 4% paraformaldehyde; permeabilized in 70% ethanol; incubated for 12 hours at 30C in an RNA preserving hybridization (RPH) 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: The fold change between J1 and NIH-3T3 cells was compared for live and hybridized samples (one replicate per sample).

first: Alexander

last: van Oudenaarden


title: Gene expression in cardiac macrophages

status: Public on Jan 18 2014

city: Toronto

first: Slava

last: Epelman

state: Ontario

address: 101 College St

department: Medicine

country: Canada

institute: University of Toronto

summary: Three cardiac macrophage subsets and blood ly6chi monocytes were sorted to compare gene expression at steady state.

overall_design: 4 samples (CCR2+ Mac, MHC-IIlo Mac, MHC-IIHi Mac, Ly6cHi Mono), with 4 replicates of each sample.


title: TAp73 is a trophic factor essential for sperm cell adhesion and maturation in testis

status: Public on Dec 31 2013

first: Gabriela

last: Salinas

overall_design: 3 mice each for control wildtype and TAp73 knockout mice.

first: Lena

last: Holembowski

first: Daniela

last: Kramer

first: Dietmar

last: Riedel

first: Matthias

last: Dobbelstein

first: Ute

last: Moll

first: Raffaella

last: Sordella

first: Alice

last: Nemajerova


title: Immunomagnetic purification of mES derived neuronal precursors increases neuronal migration and differentiation in vivo

status: Public on Dec 21 2013

city: Bergisch-Gladbach

first: Stefan

last: Tomiuk

address: Friedrich-Ebert-Str. 68

department: Bioinformatics

institute: Miltenyi Biotec GmbH

summary: All established protocols for differentiation of mouse and human pluripotent stem cells into specific neural subpopulations generate a considerable cellular heterogeneity that hampers experimental and clinical progress. In order to obtain a homogenous population of neuronal precursor cells and to streamline the differentiation of embryonic stem cells (ESCs), we assessed PSA-NCAM, a surface glycoprotein that is specifically expressed on immature neurons. We developed an optimized strategy for magnetic isolation of PSA-NCAM positive neuronal precursors from differentiated ESC cultures and characterized their neuronal differentiation potential in vitro. PSA-NCAM enrichment at an early step of neural differentiation increased the number of ES cell derived neurons and reduced cellular diversity. Gene expression analysis revealed that mainly genes involved in neuronal activity were over-represented after purification. The in vivo potential of in vitro derived PSA-NCAM+ enriched precursors was functionally characterized by grafting into the forebrain of adult mice. Analysis for several neuronal and glia markers at 10 or 40 days post graft showed a distinct differentiation pattern. While unsorted control cells gave rise to a mixed population composed of immature precursors, early postmitotic neurons or glial cells, the majority of PSA-NCAM+ enriched cells differentiated into NeuN positive neurons. Furthermore, when in contact with the rostral migratory stream, higher numbers of cells integrated into the stream and migrated towards the olfactory bulb when the PSA-NCAM enriched population was grafted. Thus, enrichment of neuronal precursors based on PSA-NCAM expression represents a general and straightforward approach to narrow cellular heterogeneity during neuronal differentiation of pluripotent cells.

overall_design: Two conditions (step 4, step 5), each represented by three biological replicates of control and enriched cells (Cy5); mESC was used as common reference (Cy3)

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