title: Expression data from Control diet, Western diet and Western diet + DHA fed rats.

status: Public on Nov 22 2013

city: Fort Collins

first: Kimberly

last: Jeckel

state: CO

address: 1380 Center Avenue

department: Biomedical Sciences

institute: Colorado State University

summary:
LV hypertrophy is associated with Western diet consumption, while intake of n-3 polyunsaturated fatty acids is associated with anti-hypertrophic effects.  We treated rats for 12 weeks with either a Control diet, a Western diet or a Western + DHA diet.  For each of the 3 dietary treatments there were 2 pooled samples of heart tissue (with each pooled sample representing 5 rats) for a total of 6 arrays.  Microarray analysis identified 66 differentially expressed transcripts. Pathways were identified using Ingenuity and DAVID software.
Array results from two pooled samples (5 rats in each pool) for n=10 per treatment group were used for comparisons.  Comparisons between Western vs. Control, Western + DHA vs. Control and Western + DHA vs. Western diets was subjected to analysis to generate log fold changes.

overall_design:
A dietary treatment of 12 weeks was used in an effort to produce LVH while limiting the development of comorbidities.  Microarray analysis was performed on pooled samples, followed by qRT-PCR and Western blot analysis.
Groups were Control, Western and Western + DHA.
Comparisons between groups are expressed as LogFC (i.e. LogFC_WESvCTRL, LogFC_DHAVCTRL, LogFC_DHAvWES), available in Series supplementary files.

first: Jeckel

last: Kimberly

first: Bouma

last: Gerrit

first: Hess

last: Ann

first: Petrilli

last: Erin

first: Spencer

last: Katherine

first: Retana

last: Jessica

first: Frye

last: Melinda


title: Expression data from oligodendroglial cell line

status: Public on Oct 28 2013

city: Aarhus C

first: Christine

middle: Lund

last: Kragh

address: Ole Worms Alle 1.170

department: Biomedicine

country: Denmark

institute: Aarhus University

summary:
Coexpression of alpha-synuclein and p25alpha in an oligodendroglial cell line elicites a degenerative response that relies on aggregation and phosphorylation of alpha-synuclein at Ser129
We used microarray analysis to detail the changes in gene expression caused by alpha-synuclein aggregation followed by cellular degeneration

overall_design: Alpha-synuclein was coexpressed with p25alpha in an oligodendroglial cell line and mRNA was isolated at 8, 12, and 16 hrs after transfection. Gene expression was analyzed by two identical microarray set-ups

middle: L

first: Poul

middle: H

last: Jensen


title: Gene expression of soleus response to simulated microgravity

status: Public on Nov 05 2013

city: Haidian District

first: Zhongquan

last: Dai

state: Beijing

address: No. 26 Beiqing Road

country: China

institute: Astronaut Research and training Center

summary:
Identification of gravisensitive gene expression in rat soleus muscle exposed to 7 and 14 days of Hindlimb suspension (HS) simulated microgravity. Microgravity causes muscle atrophy possibly due to muscle wasting overtake regeneration. Results provide insight into the molecular mechanisms regulating muscle atrophy.
The expression of 787 (373 upregulated and 414 downregulated) and 923 (491 upregulated and 432 downregulated) genes out of 28000 was altered respectively at least 2-fold of 7 and 14 days TS, which represented 397 (233 upregulated and 164 downregulated) genes of common alteration. By using real-time PCR assays, we verified the microarray data using some of the expected genes.

overall_design: The tissue was collected from Sprague-Dawley rats (8 weeks of age) subjected to 7, 14days of TS. mRNA expression profile was determined in three groups: control (CN), TS for 7 days (TS-7), and TS for 14 days (TS-14).Three mRNA microarray chips were analyzed for mixture of four samples of each of the three groups.

first: H

last: Xu

first: F

last: Wu

first: Z

first: Y

last: Li


title: Soleus response to simulated microgravity

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

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

platform_organism:
Rattus norvegicus
synthetic construct

overall_design: Refer to individual Series


title: Geriatric muscle stem cells switch reversible quiescence into senescence (Set 1; Geriatric vs. Young)

status: Public on Dec 31 2013

city: Barcelona

first: Eusebio

last: Perdiguero

address: Dr. Aiguader 88

department: Department of Medicine and Life Sciences

country: Spain

institute: UPF

summary: Regeneration of skeletal muscle depends on a population of adult stem cells (satellite cells) that remain quiescent throughout life. Satellite cell regenerative functions decline with aging. Here we report that geriatric satellite cells, compared to old cells, are incapable of maintaining their normal quiescent state in muscle homeostatic conditions, and this irreversibly affects their intrinsic regenerative and self-renewal capacities.

overall_design: We analyzed the global changes in gene expression occurring within muscle stem cells (satellite cells) in homeostatic conditions during physiological aging.  Pure satellite cell populations from dissociated skeletal muscle from Young (2-3 months) and Geriatric (28-32 months)  mice were isolated using a well-established flow cytometry protocol gating on integrin a7(+)/CD34(+) (positive selection) and Lin- (CD31, CD45, CD11b, Sca1) (negative selection).

first: Pura

last: Munoz-Canoves


title: Toll-like receptor 7 is a primary sensor of malaria infection

status: Public on Sep 21 2013

city: San Francisco

first: Charlie

last: Kim

state: CA

address: 1001 Potrero Ave

department: Medicine

country: USA

institute: University of California, San Francisco

summary: Microarray profiling of amplified total splenic RNA isolated from TLR9-, TLR7-, UNC93b1- or MYD88- deficient mice or their C57BL/6 controls 24h after mock infection or infection with Plasmodium chabaudi.

overall_design: 4 independent replicates collected from each genotype/infection group, RNA isolated and amplified from whole spleen. Hybridized as a one color experiment.

first: Alyssa

last: Baccarella

first: Mary

middle: F

last: Fontana

first: Eunice

last: Chen

first: Charles

middle: C


title: CGH mesurement of DNA replication in wild-type and cdc6-mn replication deficient strains.

status: Public on Sep 20 2013

city: New York

first: Andreas

last: Hochwagen

state: NY

address: 1009 Silver Center 100 Washington Square East

institute: New York University

type: Genome variation profiling by genome tiling array

summary: Comparative genome hybridization (CGH) was used to measure relative DNA replication after 8 hours in meiosis for wild-type and cdc6-mn cells.

overall_design: We measured DNA replication after 8 hours in meiosis for wild-type and cdc6-mn cells on microarrays using CGH.

first: Hannah

middle: G

last: Blitzblau


title: ChIP-chip of DSB factors in the presence and absence of S phase checkpoint induction

status: Public on Sep 18 2013

type: Genome binding/occupancy profiling by genome tiling array

summary: ChIP-chip was used to compare DSB factor localization in wild-type and checkpoint mutant strains under S phase checkpoint inducing and uninducing conditions.

overall_design: We analyzed the DNA binding of factors associated with meiotic DNA replication and DSB formation by chromatin immunoprecipitation (ChIP), including; the replicative helicase Mcm2-7 and the meiotic DSB factors Mer2, Rec114 and Mre11. Immunoprecipitated and input DNA samples were differentially labeled and cohybridized to a single microarray. We have included 2-3 biological replicates of each experiment, including one dye swap experiment.


title: CREB3L1 is a metastasis suppressor that represses expression of genes regulating metastasis, invasion and angiogenesis

status: Public on Oct 30 2013

city: Saskatoon

first: Deborah

last: Anderson

state: Saskatchewan

address: 107 Wiggins Road

country: Canada

institute: University of Saskatchewan

sample_organism:
Homo sapiens
Rattus norvegicus

platform_organism:
Homo sapiens
Rattus norvegicus

first: Paul

last: Mellor


title: Effects of CREB3L1 on gene expression

status: Public on Oct 26 2013

summary:
The unfolded protein response (UPR) is activated in response to hypoxia-induced stress such as in the tumor microenvironment.  This study examined the role of CREB3L1 (cAMP-responsive element-binding protein 3-like protein 1), a member of the UPR, in breast cancer development and metastasis.  Initial experiments identified the loss of CREB3L1 expression in metastatic breast cancer cell lines compared to low- or non-metastatic cell lines.  When metastatic cells were transfected with CREB3L1 they demonstrated reduced invasion and migration in vitro, as well as a significantly decreased ability to survive under non-adherent or hypoxic conditions.  Interestingly, in an in vivo rat mammary tumor model, CREB3L1 expressing cells not only failed to form metastases compared to CREB3L1 null cells but regression of the primary tumors was seen in 70% of the animals as a result of impaired angiogenesis.  Microarray and ChIP on Chip analyses identified changes in the expression of many genes involved in cancer development and metastasis, including a decrease in those involved in angiogenesis.  These data suggest that CREB3L1 plays an important role in suppressing tumorgenesis and loss of expression is required for the development of a metastatic phenotype.
CREB3L1 is a member of the unfolded protein response family of proteins. CREB3L1 expression is lost from metastatic breast cancer cells. We wanted to determine the effctes CREB3L1 expression had on gene expression.

overall_design: RNA was extracted from LN4D6 rats cells that were either untransfected or transfected with CREB3L1, changes in gene expression following transfection of CREB3l1 were then determined by hybridisation on Affymetrics microarrays.


title: DNA replication and DSB factor binding in the meiotic S-phase checkpoint in budding yeast

summary: During gamete formation, crossover recombination must occur on replicated DNA to ensure proper chromosome segregation in the first meiotic division. We identified a Mec1/ATR-dependent replication checkpoint in budding yeast that prevented the earliest stage of recombination, the programmed induction of DNA double-strand breaks (DSBs), when pre-meiotic DNA replication was delayed. The checkpoint suppressed DSBs through three complementary mechanisms: inhibition of Mer2 phosphorylation by Dbf4-dependent Cdc7 kinase, preclusion of chromosomal loading of Rec114 and Mre11, and lowered abundance of the Spo11 nuclease. Without this checkpoint, cells formed DSBs on partially replicated chromosomes. Importantly, such DSBs frequently failed to be repaired and impeded further DNA synthesis, leading to a rapid loss in cell viability. We conclude that a checkpoint-dependent constraint of DSB formation to duplicated DNA is critical not only for meiotic chromosome assortment, but also to protect genome integrity during gametogenesis.

overall_design: DSB factor association was measured in wild-type and checkpoint mutants strains under non-inducing or replication checkpoint inducing conditions. Additionally, DNA replication and helicase loading were measured in a replication and checkpoint deficient strain (cdc6-mn).


title: Identification and characterization of FGF2-dependent mRNA:microRNA networks during lens fiber cell differentiation

status: Public on Sep 06 2013

city: LYON

first: Jiri

last: ZAVADIL

state: Other

address: 150 COURS ALBERT THOMAS

country: France

institute: IARC WHO

summary:
Background: FGF signaling controls numerous processes during cell lineage specification, organogenesis and terminal differentiation. In lens, FGF signaling was implicated as the key pathway that controls lens fiber cell differentiation, but little is known about its full range and spectrum of regulated genes. Results: Herein, we employed rat lens epithelial explant system and performed RNA and microRNA expression profiling in cells induced to differentiate by FGF2. The primary data were collected at explants grown overnight in the presence of 5 ng/ml of FGF2, followed by a treatment with 100 ng/ml of FGF2 and collection of samples at 2, 4, 12 and 24 hours. Global analysis identified extensive FGF2-regulated cellular responses that were both independent and dependent on microRNAs (miRNAs). We identified a total number of 131 FGF2-regulated miRNAs. Forty-four of these microRNAs had at least two predicted and inversely regulated target RNA molecules. The genes regulated by the highest number of miRs include Nfib, Nfat5, c-Maf, Ets1 and N-Myc, all encoding DNA-binding transcription factors. Analysis of RNA data revealed that activated FGF signaling influenced other major signaling pathways known to regulate lens differentiation including BMP/TGF-β, Notch, and Wnt signaling. In the “early” response phase (2-4 hours), miRNAs targeted expression of batteries of genes that control transcription, cell death, cell proliferation, cell junction, and protein serine/threonine kinase activity. In “late” stages (12-24 hours), the main miRNA targets included regulators of cell cycle arrest and cellular differentiation. Specific miRNA:mRNA interaction networks were identified for c-Maf, N-Myc, and Nfib (DNA-binding transcription factors); Cnot6, Dicer1, Fbx33 and Wdr47 (RNA processing); Ash1l, Med1/PBP and Kdm5b (chromatin remodeling); and c-Maf, Ets1 and Stc1 (FGF signaling). MicroRNAs including miR-9, -143, -155, -455 and -543 downregulated expression of c-Maf in the 3’-UTR luciferase reporter asssays. The functional requirement for miRNAs in lens was further demonstrated via disrupted lens fiber cell differentiation in lenses with inactivated Dicer1. Conclusions: These studies demonstrate for the first time global impact of activated FGF signaling in lens cell culture system and identified novel gene regulatory networks (GRNs) connected by multiple miRNAs.
Differential gene expression of FGF2-treated lens cell cultures was analyzed at 0, 2, 4, 12 and 24 hours following the treatment.

overall_design: Two biological replicate experiments were performed.

first: Louise

middle: V

last: Wolf

first: Chun

middle: S

last: Gao

first: Karen

last: Gueta

first: Qing

last: Xie

first: Tiphaine

last: Chevalier

first: Nikhil

middle: R

last: Podduturi

first: Jian

last: Sun

first: Ivan

last: Conte

first: Peggy

last: Zelenka

first: Ruth

last: Ashery-Padan

last: Zavadil

first: Ales

last: Cvekl


title: Gene expression of thymic settling progenitors from embryos at E13 compared to E18

status: Public on Sep 17 2013

city: Paris

first: Ana

last: Cumano

address: 25 Rue du Dr. Roux

department: Immunology

institute: Pasteur Institute

summary: We used whole genome transcriptome as gene discovery to further understand the differential behaviour of the first (embryonic) and second waves of thymic settling progenitors in the murine embryo.

overall_design: Mouse embryos at days 13 and 18 of gestation were isolated and the thymic lobes were dissected. Single cell suspension was prepared and treated with biotinilated antibodies to CD3, CD4, CD8, TER119, Gr1, CD25, CD19, NK1.1 and CD11c. Cell suspensions were then incubated with streptavidin Miltenyi Macs beads. Lineage negative thymocytes were recovered in Macs columns. Cell suspensions were then incubated with antibodies against CD135, CD117, CD44, CD24 and Streptavidin bound to PECy7. Lin-, CD117+, CD44+, CD24low, CD135+ cells were then isolated by cell sorting. 3 biological replicates of each sample were isolated with 104-3x104 cells


title: Temporal Transcriptomic Signatures Associated with Post-viral Bronchiolitis Sequelae in Rats

status: Public on Oct 01 2013

city: San Diego

first: Xin

address: 9500 Gilman Dr., CMME, Room 1055

department: Department of Pediatrics, Department of Biological Sciences

institute: UNIVERSITY OF CALIFORNIA AT SAN DIEGO

summary: Early life respiratory viral infections and atopic characteristics are significant risk factors for the development of childhood asthma. It is hypothesized that repeated respiratory viral infections might induce structural remodeling by interfering with the normal process of lung maturation; however, the specific molecular processes that mediate these developments are not understood. To define relevant molecular pathways, we used a well-established Sendai virus infection model in weanling rats to compare transcriptome signatures between a post-infection asthma prone susceptible strain (BN) and a post-infection asthma resistant strain (F344). Specific to this weanling model and not described in adult models, Sendai virus infection in the susceptible strain resulted in morphological abnormalities in distal airways that persist into adulthood, suggesting a disruption of normal lung growth. Gene expression data from infected and control lungs across five time points indicated that specific features of the immune response following viral infection were heightened and prolonged in lungs from BN compared with F344 rats. These features included an increase in macrophage cell number and related gene expression, which then transitioned to an increase in mast cell number and related gene expression. In contrast to the heightened immune response in infected BN lungs, infected F344 lungs displayed more efficient re-epithelialization. We conclude that the structural defects that developed and persisted in infected BN but not F344 lungs were preceded by a pronounced macrophage and mast cell response to viral infection acting in parallel with an inadequate re-epithelialization.

overall_design: For each of the five time points, one array was run for each of the four conditions (F344 control, BN control, F344 virus, BN virus) with 15 individual smaples pooled on each array.

first: Elizabeth

middle: A

last: Hines


title: Gene expression analysis of cultured adipocytes treated with different types of asbestos fibers

status: Public on Sep 03 2013

city: Nagoya

first: Shinya

last: Toyokuni

state: Aichi

address: 65 Tsuruma-Cho, Showa-Ku

department: Pathology

country: Japan

institute: Nagoya University

summary: We hypothesized that adipocytes can be triggered by asbestos fibers to produce an inflammatory response. Microarray-based gene expression analysis was thus carried out to identify potential inflammation-related candidates with altered expression in adipocytes following asbestos exposure. We found changes in the expression of some inflammation-related genes in adipocytes treated with the different types of asbestos fibers

overall_design: Cultured adipocytes were treated with 3 different types of asbestos fibers: chrysotile, crocidolite and amosite fibers at 10 mg/cm2 for 72 hours. Physiological saline was used as a control. Microarray was performed with duplicate for each sample.

first: Toyokuni

last: Shinya

first: Chew

last: Shan-Hwu

first: Okazaki

last: Yasumasa

first: Akatsuka


title: Global gene expression profiling of mesotheliomas from vehicle control and VDC-exposed male F344N rats

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

summary: A recent two-year NTP cancer bioassay showed a marked increase in the incidence of malignant mesothelioma arising from the tunica vaginalis in male Fischer 344/N rats exposed to Vinylidene chloride (VDC). Aged male F344/N rats are prone to developing spontaneous peritoneal mesotheliomas, which also arise predominantly from the tunica vaginalis of the testes. A definitive mechanism for the observed increased incidence in VDC-exposed rats is unknown. Investigation of the molecular alterations that occur in mesotheliomas from vehicle control and VDC-exposed rats may provide insight into their pathogenesis, as well enable a better understanding regarding the mechanisms underlying chemically induced mesothelioma in rodents. Mesothelial cell function represents a complex interplay of pathways related to host defense mechanisms and maintenance of cellular homeostasis.  Global gene expression profiles of spontaneous mesotheliomas from vehicle control male F344/N rats from various two-year National Toxicology Program carcinogenicity bioassays were compared to mesotheliomas from VDC-exposed rats to characterize the molecular features that are present in mesotheliomas from VDC-exposed animals, and to elucidate tumor-specific gene expression profiles. The resulting gene expression pattern showed that mesotheliomas from VDC-exposed animals are genomically very different from spontaneous tumors; while both tumor types are characterized by alterations in gene expression associated with carcinogenic pathways (oncogenes, tumor suppressor genes, growth factors, etc.), mesotheliomas from VDC-exposed animals are associated with increased dysreguation of immune pathways and inflammatory mediators. Alterations in these pathways may suggest a pro-inflammatory and immune dysfunction signature as one mechanism in the observed increased incidence of these tumors in VDC-exposed animals.

overall_design: Five spontaneous malignant mesotheliomas from two-year-old F344/N rats, eight mesotheliomas from VDC-exposed two-year-old F344/N rats, and six normal Fred-PE mesothelial cell culture samples (as controls).

first: Pamela

last: Blackshear

first: Arun

last: Pandiri

first: Tai-Vu

last: Ton

first: Natasha

middle: P

last: Clayton

first: Keith

last: Shockley

first: Shyamal

middle: D

last: Peddada

first: Kevin

middle: E

last: Gerrish

first: Robert

last: Sills

first: Mark

middle: J

last: Hoenerhoff


title: Gene expression in the spleen; effect of maternal exposure to carbon black nanoparticle

status: Public on Aug 30 2013

city: Noda

first: Masakazu

last: Umezawa

state: Chiba

address: 2641 Yamazaki

department: Department of Hygienic Chemistry, Faculty of Pharmaceutical Sciences

institute: Tokyo University of Science

summary: The aim of this study was to investigate the effects of administration of carbon black nanoparticle (CB-NP) to pregnant mice on the development of lymphoid tissues in infantile mice. Pregnant ICR mice were treated with a suspension of CB-NP 95 microg/kg/time) by intranasal instillation, twice, on gestational day 5 and 9. Spleen and thymus were collected from offspring mice at 5 days post-partum.

overall_design: RNA sample was taken from spleen of 5-day-old mouse prenatally received carbon black nanoparticle, while control RNA was taken from control counterpart prenatally received distilled water. Comparisons among groups were made by one-color method with normalized data from Cy3 channels for data analysis.

first: Ryuhei

last: Shimizu

first: Ken

last: Takeda


title: Pdx-1 activates islet α- and β-cell proliferation via a TRPC3/6- and ERK 1/2-regulated mechanism

status: Public on Sep 01 2013

city: Durham

first: Heather

middle: L.

last: Hayes

address: 4321 Medical Park Dr., Ste. 200

department: Sarah W. Stedman Nutrition and Metabolism Center

institute: Duke University

summary:
The homeodomain transcription factor, Pdx-1, has important roles in pancreatic development and β-cell function and survival. In the present study, we demonstrate that adenovirus-mediated overexpression of Pdx-1 in rat or human islets also stimulates cell replication. Moreover, co-overexpression of Pdx-1 with another homeodomain transcription factor, Nkx6.1, has an additive effect on proliferation compared to either factor alone, implying discrete activating mechanisms. Consistent with this, Nkx6.1 stimulates mainly β-cell proliferation, whereas Pdx-1 stimulates both α- and β-cell proliferation. Furthermore, cyclins D1/D2 are upregulated by Pdx-1 but not by Nkx6.1, and inhibition of cdk4 blocks Pdx-1- but not Nkx6.1-stimulated islet cell proliferation. Genes regulated by Pdx-1 and not Nkx6.1 were identified by microarray analysis. Two members of the transient receptor potential cation (TRPC) channel family, TRPC3 and TRPC6, are upregulated by Pdx-1 overexpression, and siRNA-mediated knockdown of TRPC3/6 or TRPC6 alone inhibits Pdx-1-induced but not Nkx6.1-induced islet cell proliferation. Pdx-1 also stimulates ERK1/2 phosphorylation, an effect partially blocked by knockdown of TRPC3/6, and blockade of ERK1/2 activation with a MEK1/2 inhibitor partially impairs Pdx-1-stimulated proliferation. These studies define a pathway by which overexpression of Pdx-1 activates islet cell proliferation that is distinct from and additive to a pathway activated by Nkx6.1.
We identified genes that were upregulated or downregulated at 48 h with Pdx-1 overexpression as compared to untreated and βgal controls.

overall_design: We set up a microarray using primary rat islets that were left untreated or transduced with adenoviruses overexpressing βgal or Pdx-1 for 48 h.

first: Larry

last: Moss

first: Jonathan

last: Schisler

middle: M

last: Haldeman

first: Zhushan

last: Zhang

first: Paul

middle: B

last: Rosenberg

first: Christopher

last: Newgard

first: Hans

last: Hohmeier


title: Rat mammary cancer (spontaneous, radiation, MNU, PhIP, radiation + MNU, radiation + PhIP) (high corn oil diet)

status: Public on Aug 29 2013

city: Chiba

first: Tatsuhiko

last: Imaoka

address: 4-9-1 Anagawa, Inage-ku

department: National Institute of Radiological Sciences

institute: National Institutes for Quantum and Radiological Science and Technology

summary: Although various mechanisms have been inferred for combinatorial actions of multiple carcinogens, these mechanisms have not been well demonstrated in experimental carcinogenesis models. We evaluated mammary carcinogenesis initiated by combined exposure to various doses of radiation and chemical carcinogens. Female rats at 7 weeks of age were γ-irradiated (0.2–2 Gy) and/or exposed to 1-methyl-1-nitrosourea (20 or 40 mg/kg, single intraperitoneal injection) or 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (40 mg/kg/day by gavage for 10 days) and were observed until 50 weeks of age. The incidence of mammary carcinoma increased steadily as a function of radiation dose in the absence of chemicals; mathematical analysis supported an additive increase when radiation was combined with a chemical carcinogen, irrespective of the chemical species and its dose. Hras mutations were characteristic of carcinomas that developed after chemical carcinogen treatments and were overrepresented in carcinomas induced by the combination of radiation and MNU (but not PhIP), indicating an interaction of radiation and MNU at the level of initiation. The expression profiles of seven classifier genes, previously shown to distinguish two classes of rat mammary carcinomas, categorized almost all examined carcinomas that developed after individual or combined treatments with radiation (1 Gy) and chemicals as belonging to a single class; more comprehensive screening using microarrays and a separate test sample set failed to identify differences in gene expression profiles among these carcinomas. These results suggest that a complex, multilevel interaction underlies the combinatorial action of radiation and chemical carcinogens in the experimental model.

overall_design: Mammary cancers were from untreated rats (n = 3) and rats treated with radiation (1 Gy; n = 4), MNU (40 mg/kg; H-ras–mutated cancers, n = 5; H-ras–nonmutated cancers, n = 4), PhIP (H-ras–mutated, n = 1; H-ras–nonmutated, n = 3), radiation 1 Gy plus MNU (40 mg/kg; H-ras–mutated, n = 5; H-ras–nonmutated, n = 4) and radiation 1 Gy plus PhIP (H-ras–nonmutated , n = 4). Normal mammary tissues were from untreated rats (n = 3).

first: Mayumi

last: Nishimura

first: Kazutaka

last: Doi

first: Shusuke

last: Tani

first: Ken-ichi

last: Ishikawa

first: Satoshi

last: Yamashita

first: Toshikazu

last: Ushijima

first: Takashi

last: Imai

first: Yoshiya

last: Shimada


title: Gene expression in spinal cord neurons grown on polyornithine or on carbon nanotube (CNT)-based substrates

status: Public on Aug 05 2013

city: Trieste

first: Paola

last: Roncaglia

state: TS

address: via Bonomea 265

department: Neurobiology

country: Italy

institute: SISSA/ISAS (International School for Advanced Studies)

summary:
Carbon nanotubes are cylindrically-shaped carbon nanostructures, made up of layers of graphene rolled onto themselves, with diameters similar to those of neuronal processes. In the last decade, CNT have been used as biocompatible growing substrates for neuronal attachment, differentiation and growth. In the perspective of  new developments in tissue engineering, and in particular in  spinal cord repair strategies, based on the use of CNTs, our aim is to clarify the biophysical interactions between CNTs and spinal cord neurons, studying the development of the morphological and functional characteristics of spinal neurons grown on CNT-based interfaces.
In this context, we used microarrays to show whether cultured dissociated spinal neurons show a difference in gene expression when grown in control conditions (polyornithine-covered substrates) or on CNT-based substrates.

overall_design: Gene expression profiling was evaluated from 3 replicates each of neurons grown on nanotubes and control conditions.

first: Antonella

last: Sucapane

first: Alessandra

last: Fabbro

first: Claudia

last: Carrieri

first: Stefano

last: Gustincich

first: Laura

last: Ballerini


title: Comparison of gene expression between SDR and HHR mammary glands tissue

status: Public on Aug 21 2013

city: Aomori

first: Naoki

last: Nanashima

state: Aomori

address: 58-1 Mase, Hamadate

department: Department of Nutrition

institute: Aomori University of Health and Welfare

summary: To examine whether factors responsible for early involution of HHR mammary gland are different from those involved in physiologic involution of the SDR tissue, gene expression profiles of HHR tissue at lactation day 1 and SDR tissue at involution day 1 were evaluated by microarray analysis

overall_design: Microarray results of the mammary glands of SDR, heterozygous HHR and homozygous HHR at lactation.

first: Shigeki

last: Tsuchida


title: Gestational high salt stressed new born BdkrB2 knockout collecting duct cells vs BdkrB2 wild type collecting duct cells

status: Public on Aug 08 2013

city: NEW ORLEANS

first: Lei

last: Yan

state: LA

address: 1430 Tulane Ave #SL37

department: Pediatrics

institute: Tulane University

summary: Transcriptional profiling of new born mouse kidney collecting duct (CD) cells comparing the infuence of gestational high salt stress on gene expression remolding of BdkrB2 receptor knockout CD cells with that of BdkrB2 receptor wild type CD cells. The BdkrB2 receptor has been shown to be playing a role in renal vascular tone, kidney secretion and reabsorption function, normal kidney development, while impaired BdkrB2 receptor in kidney shown being associated with renal agenesis and renal dysplasia. Goal was to determine the effects of BdkrB2 receptor knockout together with gestational high salt stress on collecting duct gene expression pattern.

overall_design: Single color microarray experiment, BdkrB2 knockout new born mouse CD cells vs. BdkrB2 WT mosue CD cells with both on gestational high salt stress. Biological replicates: 3 BdkrB2 null replicates, 3 BdkrB2 WT replicates. Expression level of each sample was normalized to WT1 replicate.

first: Zubaida

last: Saifudeen

first: Samir

last: El-Dahr


title: Genome-wide mRNA expression profiles of FACS-enriched rat beta cells freshly isolated from neonatal (postnatal day 2-3) and adult (10 weeks-old) Wistar rats

status: Public on Aug 20 2013

city: Brussels

first: Geert

middle: A.

last: Martens

address: Laarbeeklaan 103

department: Diabetes Research Center

country: Belgium

institute: Vrije Universiteit Brussel

summary:
The lower glucose-responsiveness of neonatal beta cells is generally considered a sign of endocrine immaturity. We compared mRNA profiles of neonatal and 10-weeks old rat beta cells to see how their gene expression changes with functional maturation.  Neonatal beta cells showed a lower glucose-inducible increment in insulin production than adult cells. This was in part explained by basal protein synthetic hyperactivity of neonatal cells: while at 2.5mM glucose 80% of neonatal beta cells were recruited into active protein synthesis, 10 mM glucose was required to achieve a similar fraction of active adult beta cells. Besides this progressive recruitment, glucose exerted in both age groups an additional amplifying effect in the recruited cells, but clearly more so in adult beta cells that showed a higher maximal synthetic capacity/cell. Neonatal beta cells balanced an advanced endocrine differentiation as judged by their mRNA expression of conserved beta cell marker genes, with higher expression of genes involved in cell cycle and development.  One example, Delta-like 1 homolog (DLK1) was used to investigate if neonatal beta cells with basal hyperactivity corresponded to a more immature subset, as marked by high DLK1. Neonatal pancreas contained distinct subsets of DLK1high and DLK1low insulin-expressing cells, but both showed equal hyperactivity.  We conclude that neonatal beta cells combine advanced endocrine maturation with traits of residual developmental immaturity. If DLK1 is used as marker for the latter, the basal hyperactivity which proved to be a cardinal feature of neonatal beta cells is not a direct reflection of their residual immaturity.
A genome-wide view on postnatal maturation/differentiation of the rat beta cells

overall_design: The study compares Affymetrix RG230.20 expression profiles of 3 cell subsets: (1) HSSC: a population of cells isolated from post natal day 2-3 rat pancreas that is enriched (65-70%) in insulin cells (n=3), (2) LSSC:  a population of cells isolated from postnatal day 2-3 rat pancreas that is mostly devoid of endocrine cells, and selected by its low side scatter (n=3); and (3) adult beta: a reference population of FACS-purified adult rat beta cells (>90% insulin+) freshly isolated from pancreas of 10 weeks-old rats (n=5). RNA was extracted from the cells immediately after isolation, without further treatment or  culture. Details of the isolation procedure and extensive microscopic characterization of the preps are described in the accompanying scientific paper by Martens GA et al.

first: Daniel

last: Pipeleers


title: Expression data from Tet2-hypomorph (knockdown) and/or Ezh2-null Lineage-Sca-1+c-Kit+ (LSK) cells and granulocyte-macrophage progenitors (GMPs)

status: Public on Aug 01 2013

first: ATSUSHI

last: IWAMA

address: 1-8-1 Inohana, Chuo-ku

department: Department of Cellular and Molecular Medicine

institute: Graduate School of Medicine, Chiba University

summary: PcG proteins form the polycomb repressive complexes (PRC) 1 and 2, functioning as transcriptional repressors through histone modifications. They have been implicated in the maintenance of self-renewing somatic and cancer stem cells. PcG genes have been characterized as tumor suppressor genes as exemplified by somatic inactivating mutations of EZH2, a gene encoding histone methyltransferase in PRC2, in myeloid malignancy. Mice deficient for Tet2 have been reported to recapitulate some aspects of myeloid malignancies. We evaluated the Ezh2-deficient mice and also tested the impact of concurrent depletion of Ezh2 and Tet2 on hematopoiesis.

overall_design: Purified LSK cells and GMPs from BM of recipient mice repopulated with wild-type, Tet2KD/KD, Ezh2-/- and Tet2KD/KDEzh2-/- fetal liver cells were subjected to RNA extraction and hybridization on Agilent microarrays.

first: Atsushi

last: Iwama

first: Tomoya

last: Muto


title: SetD8 Knockdown in ß-estradiol-treated (24 h) G1E-ER-GATA-1 cells

status: Public on Jul 24 2013

city: Madison

first: Andrew

last: DeVilbiss

state: WI

address: 1111 Highland Ave, WIMR 4028

department: Cell and Regenerative Biology

institute: UW-Madison

summary: The establishment and maintenance of cell type-specific transcriptional programs require an ensemble of broadly expressed chromatin remodeling and modifying enzymes. Many questions remain unanswered regarding the contributions of these enzymes to specialized genetic networks that control critical processes such as lineage commitment and cellular differentiation. We have been addressing this problem in the context of erythrocyte development driven by the transcription factor GATA-1 and its coregulator Friend of GATA-1 (FOG-1). As certain GATA-1 target genes have little to no FOG-1 requirement for expression, presumably additional coregulators can mediate GATA-1 function. Using a genetic complementation assay and RNA interference in GATA-1-null cells, we demonstrate a vital link between GATA-1 and the histone H4 lysine 20 methyltransferase PR-Set7/SetD8 (SetD8). GATA-1 selectively induced H4 monomethylated lysine 20 at repressed, but not activated, loci, and endogenous SetD8 mediated GATA-1-dependent repression of a cohort of its target genes. GATA-1 utilized different combinations of SetD8, FOG-1, and the FOG-1-interacting Nucleosome Remodeling and Deacetylase (NuRD) complex component Mi2b to repress distinct target genes. Implicating SetD8 as a context-dependent GATA-1 corepressor expands the repertoire of coregulators mediating establishment/maintenance of the erythroid cell genetic network and provides a biological framework for dissecting the cell type-specific functions of this important coregulator. We propose a coregulator matrix model in which distinct combinations of chromatin regulators are required at different GATA-1 target genes, and the unique attributes of the target loci mandate these combinations.

overall_design: 3 SetD8 knockdown samples were compared to 3 control samples

middle: W

first: Emery

last: Bresnick


title: Gene expression data from HD mutant and wild type ST14A cells, differentiated for 24 hours and treated with vehicle (DMSO) or with 5µM MIND4

city: Irvine

first: Leslie

last: Thompson

address: Biological Sciences III

institute: University of California, Irvine

summary:
Activation of cellular responses through the NRF2/KEAP1/ARE pathway is a promising therapeutic strategy to counter neurodegeneration. The present study identified a novel lead compound, MIND4, which induces canonical NRF2-dependent responses and is protective in primary neurons, neuronal slice cultures and a Drosophila model of Huntington’s disease (HD). In accord with the known anti-inflammatory effects of NRF2 activation, MIND4 and its structural analog, potently repressed an expression of inflammatory markers in activated microglial cells.
MIND4 treatment significantly reduced levels of TNF-alpha in the cortex of symptomatic HD mice, demonstrating the neuroprotective anti-inflammatory potential of NRF2 activator in the CNS. A high affinity reversible binding of MIND4 ligands to the NRF2 inhibitor, KEAP1, was identified by a docking model and confirmed by mechanistic studies, suggesting a novel approach to activating the NRF2 pathway. The results offer a new therapeutic path for HD and other human diseases.

overall_design: A total of 8 samples, HD mutant and wild type ST14A cells, stably expressing either a mutant expanded repeat (128Q) or wild type (26Q) 546 amino acid huntingtin fragment (a generous gift of E. Cattaneo) (Ehrlich et al., 2001)), 4 HD & 4 control, were used for drug treatment and array-based gene expression analysis. 4 samples, 2 HD and 2 Contol, were treated with 5µM MIND4 with each pair ran as replicates. The other 4 samples, 2 HD and 2 Contol, were treated with DMSO with each pair ran as replicates.

first: L


title: The change of gene expression profile of primary rat hepatocytes after treatment with interferon alpha.

status: Public on Jul 15 2013

city: Kiev

first: Andrii

last: Droni

address: Zabolotnogo 150

country: Ukraine

institute: IMBG

summary:
The transcriptional response to interferon alpha is cell type specific. To data, majority of investigations of interferon alpha induced gene expression have been made using immortalized or transformed cell lines underlining interferon's importance for treatment of cancer but omitting physiological relevance. Here in we have determined gene expression change in primary culture of hepatocytes after interferon alpha treatment.
We used Affymetrix Rat Genome 230 2 microarrays to determine gene expression profiles in primary rat hepatocytes after interferon alpha treatment and untreated cells.

overall_design: Primary hepatocytes were chosen because they are most relevant to physiological state in intact liver. Hepatocytes was isolated from rat liver using collagenase treatment procedure and purified on percoll gradient. Next day after isolation primary hepatocytes culture was cultivated with (or without) 250u/ml rat interferon alpha for 3 and 6 hours. Experiment was performed in 3 biological replicates. cRNA preparation was performed according manufacturer's recommendation from 5ug of total RNA and gene expression profiles were determined.

last: Kuklin

first: Bogdan

last: Tokovenko

first: Nataliya

last: Makogon

first: Jarząb

last: Barbara

first: Maria

last: Obolenskaya


title: BET Bromodomains Mediate Transcriptional Pause Release in Heart Failure [NRVM Expression]

status: Public on Aug 06 2013

city: Boston

first: James

last: Bradner

state: MA

address: 450 Brookline

department: Medical Oncology

institute: Dana-Farber Cancer Institute

summary: Heart failure (HF) is driven via interplay between master regulatory transcription factors and dynamic alterations in chromatin structure. While pathologic gene transactivation in this context is known to be associated with recruitment of histone acetyl-transferases and local chromatin hyperacetylation, the role of epigenetic reader proteins in cardiac biology is unknown. We therefore undertook a first study of acetyl-lysine reader proteins, or bromodomains, in HF. Using a chemical genetic approach, we establish a central role for BET-family bromodomain proteins in gene control during HF pathogenesis. BET inhibition potently suppresses cardiomyocyte hypertrophy in vitro and pathologic cardiac remodeling in vivo. Integrative transcriptional and epigenomic analyses reveal that BET proteins function mechanistically as pause-release factors critical to activation of canonical master regulators and effectors that are central to HF pathogenesis and relevant to the pathobiology of failing human hearts. This study implicates epigenetic readers in cardiac biology and identifies BET co-activator proteins as therapeutic targets in HF.

overall_design: Gene expression analysis of neonatal rat ventricular mycotes (NRVM) subjected to phenylephrine (PE) treatment followed by treatment with vehicle (DMSO) or the BET bromodomain inhibitor JQ1

first: Priti

last: Anand

first: Jonathan

last: Brown

first: Charles

middle: Y

last: Lin

first: Jun

last: Qi

first: Madeleine

last: Lemieux

first: Saptarsi

last: Haldar


title: Gene expression data from brain central nucleus of amygdala (CeA) following binge-like alcohol drinking by adolescent alcohol-preferring rats

status: Public on Jul 20 2013

city: Westfield

first: Mark

middle: William

last: Kimpel

state: IN

address: 15032 Hunter Court

department: Psychiatry

institute: Indiana University

summary: The objective of this study was to determine changes in gene expression within the extended amygdala following binge-like alcohol drinking by adolescent alcohol-preferring (P) rats. Starting at 28 days of age, P rats were given concurrent access to 15 and 30 % ethanol for 3 one-h sessions for 5 consecutive days each week until they were 49 days old. Rats were killed by decapitation 3 h after the first ethanol access session on the 15th day of drinking. RNA was prepared from micropunch samples of the nucleus accumbens shell (Acb-sh) and central nucleus of the amygdala (CeA). Ethanol intakes were 2.5 – 3.0 g/kg/session. There were 154 and 182 unique named genes that significantly differed (FDR = 0.2) between the water and ethanol group in the Acb-sh and CeA, respectively. Gene Ontology (GO) analyses indicated that adolescent binge drinking produced changes in the in biological processes involved in cell proliferation and regulation of cellular structure in the Acb-sh, and in neuron projection and positive regulation of cellular organization in the CeA. Ingenuity Pathway Analysis indicated that, in the Acb-sh, there were several major intracellular signaling pathways (e.g., cAMP-mediated and protein kinase A signaling pathways) altered by adolescent drinking, with 3-fold more genes up-regulated than down-regulated in the alcohol group. The cAMP-mediated signaling system was also up-regulated in the CeA of the alcohol group. Weighted gene co-expression network analysis (WGCNA) indicated significant G-protein coupled receptor signaling and transmembrane receptor protein kinase signaling categories in the Acb-sh and CeA, respectively. Overall, the results of this study indicated that binge-like alcohol drinking by adolescent P rats is differentially altering the expression of genes in the Acb-sh and CeA, some of which are involved in intracellular signaling pathways and may produce long-term changes in neuronal function.

overall_design: Differences in gene expression in the central nucleus of the amygdala (CeA) were compared in two groups of alcohol-preferring (P) rats, one given water only and the other given access to 15 & 30% ethanol during adolescence.

first: William

last: McBride

first: Jeanette

middle: N

last: McClintick

first: Zheng-Ming

last: Ding

first: Howard

last: Edenberg

first: Tiebing

last: Liang

first: Zachary

last: Rodd

first: Richard

middle: L

last: Bell


title: Changes in Gene Expression within the Extended Amygdala Following Binge-Like Alcohol Drinking by Adolescent Alcohol-Preferring (P) Rats

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

overall_design: Refer to individual Series


title: Actinonin induced changes in gene expression profiles in MEFs

status: Public on Jul 05 2013

city: Tampere

first: Dario

last: Greco

address: Arvo ylpön Katu 34

department: Faculty of Medicine and Health Technology

country: Finland

institute: Tampere University

summary: Retrograde signaling induced remodelling of nuclear gene expression from mitochondrial ribosomal dysfunction was analyzed. Global expression profile changes in mouse embryonic fibroblasts were assesed under actinonin treatment 6, 24, 48 and 72 hours post drug addiction.

overall_design: Control and four different time points with two labels and two replicates each

first: Uwe

last: Richter

first: Brendan

last: Battersby


title: Gene expression data from brain nucleus accumbens shell (Acb-sh) following binge-like alcohol drinking by adolescent alcohol-preferring rats

overall_design: Differences in gene expression in brain nucleus accumbens shell (Acb-sh) were compared in two groups of alcohol-preferring (P) rats, one given water only and the other given access to 15 & 30% ethanol during adolescence.


title: Mi2ß knockdown in ß-estradiol-treated (24 h) G1E-ER-GATA-1 cells

status: Public on Jul 04 2013

first: Andrew

last: DeVilbiss

summary: Objective: To determine the extent to which GATA-1 utilizes Mi2ß to regulate gene transcription in the context of G1E-ER-GATA-1 cells.

overall_design: 3 Mi2ß knockdown samples were compared to 3 control samples.

first: Emery

middle: H

last: Bresnick


title: Lack of hepatic response of microRNA in mice following DB[a,h]A exposure (Agilent expression)

status: Public on Jul 02 2013

city: Ottawa

last: Williams

state: ON

address: 50 Columbine

institute: Health Canada

summary: Dibenzo[a,h]anthracene  DB[a,h]A is a polycyclic aromatic hydrocarbon potent carcinogen. Few studies have investigated the role of DB[a,h]A on mRNA and miRNA expression. In this study a 10-week old male MutaTM Mouse were exposed to 6.25, 12.5,  and  25  mg/kg/day  DB[a,h]A by oral gavage for 28 consecutive days. DNA adducts were detected in the livers at each  DB[a,h]A  dose  tested,  and a dose-dependent increase in lacZ mutants was observed in the same samples. MAANOVA analysis  revealed  minor  changes  in  the  mRNA  expression  for the two lowest doses. Differential expression of 19 up-regulated  and  22 down-regulated transcripts with fold-change > 1.5 (FDR-adjusted P < 0.05) were identified in the 6.25  mg/kg/day  DB[a,h]A treatment group. For the 12.5 mg/kg/day treatment group 13 transcripts were up-regulated and 32  down-regulated  (FDR-adjusted  P  <  0.05  and  fold-change  > 1.5). Major effect on mRNA expression resulted from exposure  to  the  highest  dose  (25  mg/kg/day)  of DB[a,h]A with 135 up-regulated and 104 down-regulated genes with fold-change  >  1.5  (FDR-adjusted P < 0.05). The significantly regulated genes are involved in circadian rhythm, drug metabolism,  glucose  metabolism, cholestrol and lipid metabolism, immune response, cell cycle, and apoptosis. We also investigated  miRNA  response to the three doses of DB[a,h]A. MiRNA expression was relatively unaffected. Only miR-34a showed significant (FDR-adjusted P < 0.05) up-regulation with a fold change above 1.3-fold.

overall_design:
Individual total RNA (200 ng) from 4-5 mice per treatment group (control, 6.25 mg/kg, 12.5mg/kg, and 25mg/kg) and universal reference total RNA (Stratagene, Mississauga, ON, Canada) was used to synthesize double stranded cDNA.
Agilent mouse 8 x 60 K oligonucleotide microarrays were used to assess global gene expression in response to 6.25, 12.50, and 25 mg/kg DB[a,h]A treatment

first: Amal

middle: I

last: Malik

first: Andrea

last: Rowan-Carroll

first: Christine

first: Paul

last: White

first: Carole

last: Yauk


title: Transcriptional profiles of psychostimulant reinforcement in rats

status: Public on Jun 27 2013

city: Seoul

first: Minsoo

last: Noh

address: 1 Gwanak-ro, Gwanak-gu

department: Pharmacy

country: South Korea

institute: Seoul National University

summary: Drug-induced alterations in transcriptional regulation play a central role in establishing the persistent neuroplasticities that occur during drug addiction. Additionally, changes in gene expression associated with drug administration provide valuable insight into the molecular basis of drug abuse. The molecular mechanisms that underlie susceptibility to psychostimulant addiction remain unknown. Identifying the common gene transcriptional responses to psychostimulants can provide a mechanistic insight to elucidate the molecular nature of drug dependence.

overall_design:
Male Wistar rats (4 weeks old) were acclimatized for a week to their housing conditions prior to experiments. Thereafter, they were divided into two groups: (cohort 1) 4 groups of rats (n=12 rats per group) given saline only (i.p., "drug-naive" rats); and (cohort 2): 3 groups of rats given either methamphetamine, amphetamine or methylphenidate (5 mg/kg,i.p., â€œdrug-pretreated") for 7 days (2x daily) prior to behavioral assays. Conditioned place preference (CPP) tests were conducted a day after the final drug administration. Rats which showed CPP were evaluated for self-administration of the psychostimulants.
[Cohort 1] A day after the final self-administration test, brains of 2-3 rats from each subgroups (i.e. those which showed the most robust self-administration), as well as 5 rats from the control group were removed for microarray analysis. The striatum (rostral part of the caudate putamen and the nucleus accumbens [NAc]) and the prefrontal cortex were dissected and immediately frozen at -70Â°C. Total RNA was isolated and gene expression profiling was conducted on independent pools of total RNA from 2-5 animals per group.
[Cohort 2] A day after the final self-administration test, brains of 3 rats from each subgroups (i.e. those which showed the most robust self-administration), as well as 3 rats from the control group were removed for microarray analysis. The striatum (rostral part of the caudate putamen and the nucleus accumbens [NAc]) and the prefrontal cortex were dissected and immediately frozen at -70°C. Total RNA was isolated and gene expression profiling was conducted on independent pools of total RNA from three animals per group.

first: JaeHoon

last: Cheong


title: Lack of hepatic response of microRNA in mice following DB[a,h]A exposure


title: Expression data from rosiglitazone treated, rosiglitazone withdrawal and untreated control Zucker Diabetic Fatty rats.

status: Public on Jun 21 2013

city: Berkeley

first: Cyrus

middle: Farrokh

last: Khambatta

address: 309 Morgan Hall

department: Nutritional Sciences

institute: University of California at Berkeley

summary:
Insulin resistance and islet failure are the two etiological roots of type 2 diabetes mellitus, and understanding global islet gene expression may provide insight into the mechanisms that regulate islet function.
In this study we systematically investigated the gene expression profile and proliferative response of islets to insulin sensitization, insulin resistance, and islet failure.

overall_design: Five-week old male Zucker Diabetic Fatty rats (n=24) were randomized into one of three groups: four-week rosiglitazone treated, rosiglitazone withdrawal, or untreated controls.  Affymetrix GeneChip Rat Genome 230 2.0 gene arrays were performed on isolated islets to measure the gene expresion profile of islets at 9, 11, and 13 weeks of age.

first: Scott

last: Turner


title: DNA Methylation Restricts Lineage-Specific Functions of Transcription Factor Gata4 during Embryonic Stem Cell Differentiation

status: Public on Jun 24 2013

city: Kobe

first: Yuichi

last: Kumaki

address: 2-2-3 Minatojima-minamimachi, Chuo-ku

department: Center for Developmental Biology

institute: RIKEN

summary: DNA methylation changes dynamically during development and is essential for embryogenesis in mammals. However, how DNA methylation affects developmental gene expression and cell differentiation remains elusive. During embryogenesis, many key transcription factors are used repeatedly, triggering different outcomes depending on the cell type and developmental stage. Here, we report that DNA methylation modulates transcription-factor output in the context of cell differentiation. Using a drug-inducible Gata4 system and a mouse embryonic stem (ES) cell model of mesoderm differentiation, we examined the cellular response to Gata4 in ES and mesoderm cells. The activation of Gata4 in ES cells is known to drive their differentiation to endoderm. We show that the differentiation of wild-type ES cells into mesoderm blocks their Gata4-induced endoderm differentiation, while mesoderm cells derived from ES cells that are deficient in the DNA methyltransferases Dnmt3a and Dnmt3b can retain their response to Gata4, allowing lineage conversion from mesoderm cells to endoderm in part. Transcriptome analysis of the cells' response to Gata4 over time revealed groups of endoderm and mesoderm developmental genes whose expression was induced by Gata4 only when DNA methylation was lost, suggesting that DNA methylation restricts the ability of these genes to respond to Gata4, rather than controlling their transcription per se. Our data indicate that epigenetic regulation by DNA methylation functions as a heritable safeguard to prevent transcription factors from activating inappropriate downstream genes, thereby contributing to the restriction of the differentiation potential of somatic cells.

overall_design: To understand how mouse cells differentially respond to Gata4 in cell type- and DNA methylation-dependent manners and to examine what genes are differentially regulated, we analyzed temporal change of gene expression profile in response to Gata4 in ES or Flk1(+) mesoderm cells in WT and Dnmt3a-/-Dnmt3b-/- (DKO) background, in total 108 samples.

first: Masaaki

last: Oda

first: Chisa

last: Matsuoka

first: Masaki

last: Okano


title: gene expression profile of CBZ treated mice

status: Public on May 17 2013

city: Osaka

first: Tsukasa

last: Kawaguchi

address: 2-2 Yamada-oka, Suita

department: Gastroenterology and Hepatology

institute: Osaka University Graduate School of Medicine

summary: Carbamazepine (CBZ) is widely used in the treatment of neuropsychiatric disorders as an anticonvulsant. A recent report revealed that CBZ has an anti-fibrotic effect on the livers of α1-antitrypsin-deficient mice, raising the possibility of a hepatology-related therapeutic use for the drug.Given the fact that CBZ has complicated pharmacokinetic properties,  to comprehensively understand the its mechanism of action, we performed microarray analysis of the mouse liver tissues 2 hours after CBZ administration.

overall_design: The mice were orally administered 250 mg/kg of CBZ or DMSO and examined for the gene expression 2 hours later; 3 mice per group.

first: Takahiro

last: Kodama


title: FoxO1 Controls Effector to Memory Transition and Maintenance of Functional CD8 T-Cell Memory

status: Public on Jun 25 2013

first: Melba

middle: Marie

last: Tejera

address: 2015 Linden Drive

department: Pathobiological Sciences

summary: During a T cell response, naïve CD8 T cells differentiate into effector cells. Subsequently, a subset of effector cells termed memory precursor effector cells (MPECs) further differentiates into functionally mature memory CD8 T cells. The transcriptional network underlying this carefully scripted process is not well understood. Here, we report that the transcription factor FoxO1 plays an integral role in facilitating effector to memory transition and functional maturation of memory CD4 and CD8 T cells. We find that FoxO1 is not required for differentiation of effector cells, but in the absence of FoxO1, memory CD8 T cells displayed features of scenescence and progressive attrition in polyfunctionality, which in turn led to impared recall responses and poor protective immunity. These data suggest that FoxO1 is essential for active maintenance of functional CD8 T cell memory and protective immunity. Under competing conditions in bone marrow

overall_design: Single-cell suspensions from splenocytes of eight samples WT (control) and FoxO1-/- (experimental) LCMV-immune mice were prepared using standard procedures. CD8 T cells were then isoloated using Thy1.2 (CD90.2) (30-H12) microbeads (Miltenyi Biotec). Cells were then stained with anti-CD8, anti-CD44 and Db/NP396 MHC class I tetramer. Activated (CD8+CD44hi), naive (CD8+CD44lo), and  virus-specific  CD8 T cells were sorted using FACSAria II instrument (BD Biosciences). The purity of the cells was >95%. Total RNA was extracted from the sorted cells by Trizol Reagent. RNA samples were reverse transcribed and Cy3-labeled cDNAs were hyrbidized to Agilent whole Mouse Genome Oligo Microarrays. Fluorscence signals were detected using Agilent's Microarray Scanner system, data was analyzed using the Rosetta Resolver gene expression data analysis system and genes with a fold change < and p-values <0.01 were identified. Microarray data discussed in the paper is focused on virus-specific memory CD8 T cells from samples WT_Tet_2 vs KO_Tet_2.

first: Eui

last: Kim

first: Jeremy

middle: A

last: Sullivan

first: Erin

last: Plisch

first: M

last: Suresh


title: Gene expression in the liver, effect of maternal high-fat diet during or prior to pregnancy

status: Public on Jun 18 2013

city: Noda

first: Masakazu

last: Umezawa

address: 2641 Yamazaki

department: Department of Hygienic Chemistry, Faculty of Pharmaceutical Sciences

institute: Tokyo University of Science

summary: The present study aimed to examine the effect of high-fat diet prior to pregnancy on the liver of mouse offspring. Female C57BL/6J mice were fed a normal chow (15.2% fat by energy) (CTR and CTR-PP groups) or a high-fat chow (31.2% fat by energy) (HFD and HFD-PP groups) for 3−4 weeks and then mated with male C57BL/6J mice fed normal chow. Some mothers continued on the same diet until pups reached 21 days of age (CTR and HFD), and others were fed the different chows from gestational day 0 (CTR-PP and HFD-PP) to determine the effects of a high-fat diet during the pre-pregnancy period in HFD-PP/CTR and HFD/CTR-PP comparisons.

overall_design: RNA sample was taken from liver of 3-week-old mouse prenatally received high-fat diet prior to pregnancy, during pregnancy and lactation, or through prior to and during pregnancy and lactation, while control RNA was taken from control counterpart prenatally received normal diet alone. Comparisons among groups were made by one-color method with normalized data from Cy3 channels for data analysis.

first: Hiroshi

last: Hori

first: Shinya

last: Yanagita

first: Ken

last: Takeda


title: Cardiac gene expression (random section containing both ventricles) in C57BL/6 mice intratracheally instilled with Printex 90 carbon black nanoparticles (set 2)

status: Public on May 02 2013

first: Andrew

last: Williams

summary: C57BL/6 mice were exposed to vehicle or 0.162 mg carbon black nanoparticles by intratracheal installation and were sacrificed 1, 3 and 28 days post-exposure. Gene expression was investigated in two sets of mice treated according to the identical exposure protocol. MicroRNAs were investigated in the second set of mice.

overall_design: Individual total RNA (200 ng) from 6 mice per treatment group (control and 0.162mg) and Universal Mouse Reference total RNA (Stratagene, Mississauga, ON, Canada) was used to synthesize double-stranded cDNA.

first: Julie

last: Bourdon

first: Anne

last: Saber

first: Nicklas

last: Jacobsen

first: Sabina

last: Halappanavar

first: Hakan

last: Wallin

first: Carole

last: Yauk

first: Ulla

last: Vogel


title: Gabazine treatment of hippocampal organotypic cultures

status: Public on May 14 2013

city: Barcelona

first: giovanni

last: iacono

state: Spain

address: Baldiri Reixac, 4

department: single cell sequencing

institute: CNAG,Centro Nacional de Análisis Genómico

summary: The blockage of GABA-A ionotropic channels by means of gabazine is a widespread model of plasticity where the increased synaptic activity triggered by Gabazine leads to the up-regulation of a plethora of activity-dependent genes. Here, we sought to characterize the overall transcriptional response of GABA-A blocking of rat hippocampal organotypic cultures.

overall_design: In each of the three biological replica, half of the organotypic hippocampal cultures derived from two rat littermates were treated with gabazine and compared to the untreated ones in order to determine the set of differentially expressed genes.

first: Giovanni

last: Iacono


title: Temporal induction of immunoregulatory processes coincides with age-dependent resistance to viral-induced type 1 diabetes [Rat]

status: Public on Jun 01 2013

city: Milwaukee

first: Martin

last: Hessner

address: 8701 Watertown Plank Road

institute: Medical College of Wisconsin

summary:
A need exists for biomarkers in T1D that can 1) sensitively and specifically detect disease-related immune activity prior to, and independent of, measurement of auto-antibodies towards islet cell antigens; 2) define immunopathological mechanisms; and 3) monitor changes in the inflammatory state associated with disease progression or response to therapeutic intervention.  In an effort to fill this gap, we have applied a novel bioassay to both human and BB rat T1D whereby the complex milieu of inflammatory mediators present in plasma can be indirectly detected through their ability to drive transcription in peripheral blood mononuclear cells (PBMCs) drawn from healthy, unrelated donors.  The resultant gene expressions are comprehensively measured with a microarray.  In our human studies, we find that plasma of recent-onset T1D patients induces expression of a pro-inflammatory signature consisting in part of many interleukin-1 (IL-1) regulated genes related to immunological activation and immunocyte chemotaxis compared to unrelated healthy controls.  This signature has been found to resolve in long-standing T1D subjects (>10 years post-onset), thus associating it with active autoimmunity.  Importantly, this signature has been detected in pre-onset samples of progressors to T1D years prior to onset and prior to development of auto-antibodies directed towards islet antigens.

In applying this approach to the BN rat, we observed that samples collected from both sub-strains at 60 days of age induced transcription of genes encoding cytokines, immune receptors, and signaling molecules consistent with a their shared susceptibility and immune activation.  The DRlyp/lyp signature was differentiated from that of the DR+/+ by more robust induction of many interleukin (IL)-1–regulated genes. Treatment of DRlyp/lyp rats with IL-1 receptor antagonist (IL-1RN) delayed onset and, in part, normalized the signature, suggesting that this approach may prove useful in monitoring the effect of therapeutic interventions in human T1D.  Consistent with the presence of TREG cells in DR+/+ rats, we observed induction of a signature possessing negative regulators of transcription and inflammation.

overall_design: Fresh PBMCs of healthy Brown Norway (BN) rats (~180 days old males, to avoid variation introduced by estrous or pubertal status) were isolated by density gradient centrifugation.  Transcription was induced by culturing PBMCs for 6 h at 37°C in 5% CO2 with 20% allogeneic BN (healthy-unrelated control), DRlyp/lyp, or DR+/+ plasma [PMID 18209091]. DRlyp/lyp and DR+/+ Plasma was pooled at various ages (30, 40, 50, 60 days old) to represent timepoints prior to onset in the DRlyp/lyp strain.

first: Yi-Guang

last: Chen

first: John

last: Mordes

first: Elizabeth

last: Blankenhorn

first: Himala

last: Kashmiri

first: Mary

last: Kaldunski

first: Shuang

last: Jia

first: Rhonda

last: Geoffrey

first: Xujing

last: Wang


title: Effect of Lactobacillus brevis 119-2 isolated from turnip “Tsuda kabu” on hepatic cholesterol level in cholesterol-administrated rat

status: Public on Apr 24 2013

city: Aomori

first: Yuji

last: Nakai

address: 2-1-1, Yanagawa

department: Institute of Regional Innovation

institute: Hirosaki University

summary: In previous in vitro study, we reported potential mechanism of cholesterol-lowering effect of Lactobacillus brevis119-2 (119-2) isolated from turnip “Tsuda kabu” is due to incorporation of cholesterol into 119-2 cell. In this study, we analyzed serum cholesterol and hepatic gene expression of Sprague-Dawley (SD) rat fed diet containing cholesterol with or without 119-2 for 2 weeks, to evaluate the cholesterol-lowering effect of 119-2 in vivo. Serum cholesterol of SD rat fed diet with 119-2 significantly decreased compared to SD rat fed diet without 119-2, and both viable and dead 119-2 indicated the effect. The result of hepatic gene analysis using DNA microarray suggested that potential mechanism of the cholesterol-lowering effect of 119-2 in vivo is inhibiting the activity of 3-hydroxy-3-methylglutaryl-CoA reductase by Insig (insulin induced gene) that is endoplasmic reticulum membrane protein, and catabolizing cholesterol to bile acid by Cyp7a1 (cytochrome P450 a1) that is the rate-limiting enzyme in the synthesis of bile acid from cholesterol. In addition, we concluded feeding 119-2 decreased serum low density lipoprotein (LDL) cholesterol by overexpression of Ldlr (LDL receptor gene). On the other hand, feeding Lactobacillus acidophilus ATCC43121 (ATCC) increased high density lipoprotein (HDL) cholesterol by over expression of Abca1 (ATP binding cassette sub-family A member 1 gene) and Angplt3 (Angiopoietin-like 3). These results suggested that 119-2 decrease the risk of atherosclerosis by serum cholesterol-lowering effect and improving effect of fatty liver and the LH (LDL cholesterol / HDL cholesterol) ratio.

overall_design: Lactobacillus brevis119-2 (119-2) was isolated from turnip “Tsuda kabu” harvested in Matsue city, Shimane Prefecture, Japan, and was stored at Shimane Institute for industrial Technology. Male Jcl: SD rat (4 weeks of age) were obtained from CLEA Japan, Inc. (Tokyo, Japan). Rats were maintained under controlled environmental conditions (temperature 23 ± 3 ˚C, relative humidity 55% ± 25%, 12/12hr light - dark cycle) and given food and water ad libitum. All rats were acclimated 1 week prior to the experiment. Two groups of 11 rats each were treated respective group diets for 2weeks. Control group was fed high-cholesterol diet containing 10 g cholesterol/kg, 5 g cholic acid/kg, 985 g mouse & rat & rabbit diet (CRF-1) /kg obtained from Oriental yeast Co., Ltd (Tokyo, Japan). The other group was fed same highcholesterol diet with 10 g freeze-dried viable 119-2 /kg. This study and all procedures were approved by regulations and code of ethics in experimental animals Chitose Japan Food Research Laboratories.

first: Shinobu

last: Watanabe

first: Takuya

last: Katsube

first: Hideki

last: Hattori

first: Hiromasa

last: Sato

first: Tomoko

last: Ishijima

first: Keiko

last: Abe

first: Kenji

last: Sonomoto


title: Transcriptional profiling of dentate granule cells in 4 rat epilepsy models

status: Public on Jun 08 2013

city: Phoenix

first: Winnie

last: Liang

state: AZ

address: 445 N. Fifth Street

institute: Translational Genomics

summary: Global expression profiling of epileptogenesis has been confounded by variability across laboratories, epilepsy models, tissue sampled and experimental platforms, with the result that very few genes demonstrate consistent expression changes.  The present study minimizes these confounds by combining Affymetrix microarray datasets from seven laboratories, using three status epilepticus (SE) models of epilepsy in rats (pilocarpine, kainate, self-sustained SE or SSSE) and the rat kindling model. Total RNA was harvested from laser-captured dentate granule cells from 6 rats at three times during the early-to-mid latent phase that precedes epilepsy symptoms in the SE models (1, 3 and 10 days after SE), or 24 hr after the first stage 2, stage 4 and stage 5 seizure in the kindling model. Each epilepsy model was studied in two independent laboratories except SSSE. The initial goals of this study were to a) identify model-independent transcriptional changes in dentate granule cells that could point to novel intervention targets for epileptogenesis, b) characterize the basal transcriptional profile of dentate granule cells, and c) identify genes that have highly variable expression.

overall_design: Each experimental group consists of 6 rats (biological replicates) from one laboratory at a single time point, except for the SSSE group (6 at day 1 after SSSE, 5 controls and at day 3 after SSSE, 4 at day 10). Thus granule cells were harvested from 164 rats.

first: Ray

last: Dingledine

first: Douglas

last: Coulter

first: J

middle: V

last: Nadler

first: Wytse

last: Wadman

first: Claude

last: Wasterlain

first: James

middle: O

last: McNamara

first: Michael

last: Rogawski

first: Robert

last: Sloviter


title: Gene profiling of the early healing rat medial collateral ligament

status: Public on Jun 06 2013

last: Vanderby

address: 1111 Highland Ave

department: Orthopedics and Rehabilitation

institute: University of Wisconsin

summary: The objective of the study was to better understand the mechanism behind scar formation by identifying ECM factors and other unique genes differentially expressed during rat ligament healing via microarray. Rat medial collateral ligaments (MCL) were surgically transected or left intact. MCLs were collected at day 3 or 7 post-injury and used for microarray analysis. Results were compared to the normal intact ligaments.

overall_design: A total of 27 rats were used in the study. Animals were randomly placed in 1 of 3 groups (day 3, day 7, intact CX) with nine animals included with each time (9 rats/group). At the time of collection, MCLs from each time were placed into 3 pools (3 MCLs/pool), resulting in 3 reps per time, and usd for microarray analysis. A total of 9 gene chips were used for the experiment (3 chips/day).

first: Connie

last: Chamberlain


title: Comparison of Hob6-RFP positive and negative Flk-1+ cells (RFP reporter)

status: Public on Apr 16 2013

first: Hiroshi

last: Kataoka

state: Hyogo

department: Stem Cell Biology

institute: Riken Center for Developmental Biology

summary: ES derived Flk-1+ cells were separated by sorting into Hoxb6 positive and negative populations by RFP Hoxb6 reporter. Gene expression was compared between these two groups.

overall_design: Duplicate analysis of Hoxb6-RFP positive and negative Flk-1+ cells.


title: Comparison of Hob6-Venus positive and negative Flk-1+ cells (Venus reporter)

summary: ES derived Flk-1+ cells were separated by sorting into Hoxb6 positive and negative populations by Venus reporter. Gene expression was compared between these two groups.

overall_design: Duplicate analysis of Hoxb6-Venus positive and negative Flk-1+ cells.


title: Protective efficacy of orally administered, heat-killed Lactobacillus pentosus b240 against influenza A virus

status: Public on Mar 29 2013

city: Obihiro

first: Ryo

last: Takano

state: Hokkaido

address: Inada-cho

department: National Research Center for Protozoan Diseases

institute: Obihiro University of Agriculture and Veterinary Medicine

summary: Influenza A(H1N1)pdm virus caused the first human pandemic of the 21st century. Although various probiotic Lactobacillus species have been shown to have anti-microbial effects against pneumonia-inducing pathogens, the prophylactic efficacy and mechanisms behind their protection remain largely unknown. Here, we evaluated the prophylactic efficacy of heat-killed Lactobacillus pentosus b240 against lethal influenza A(H1N1)pdm virus infection in a mouse model. To further define the protective responses induced by b240, we performed virologic, histopathologic, and transcriptomic analyses on the mouse lungs. Although we did not observe an appreciable effect of b240 on virus growth, cytokine production, or histopathology, gene expressional analysis revealed that oral administration of b240 differentially regulates antiviral gene expression in mouse lungs. Our results unveil the possible mechanisms behind the protection mediated by b240 against influenza virus infection and provide new insights into probiotic therapy.

overall_design: Six-week-old female BALB/c mice were used in the study. Oral administration of b240 was initiated in mice at six weeks of age. Mice were orally administered heat-killed Lactobacillus pentosus b240 every day at a dose of 10 mg/mouse in 200 μl of buffered saline for 5 weeks. The control group received saline. To investigate the effects of oral administration of b240 on host immune responses to CA04 virus infection, 9 mice per group were infected with 10 MLD50 of CA04 virus on day 21 post-b240 administration. Three mice per group were euthanized on days 1, 3, and 6 post-infection and their lungs were collected. To investigate the immune responses induced by oral administration of b240 in the lungs of uninfected mice, 15 mice per group were mock-infected with PBS on day 21 post-b240 administration. Three mice per group were euthanized on days 14, 21, 22, 24, and 27 post-b240 administration (-7, 0, 1, 3, and 6 days post-mock infection) and their lungs were collected. These lung tissues were subjected to microarray analysis (three biological replicates per each group).

first: Maki

last: Kiso


title: Hob6 positive and negative cells

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

overall_design: Refer to individual Series


title: Generation of oligodendroglial cells by direct lineage conversion

status: Public on Apr 07 2013

city: Stanford

first: Samuele

last: Marro

state: California

address: 256 Campus Drive

institute: Stanford University

summary: We report the generation of induced oligodendrocyte precursor cells (iOPCs) by direct lineage conversion. Forced expression of the three transcription factors Sox10, Olig2 and Zfp536 was sufficient to convert mouse and rat fibroblasts into iOPCs with morphologies and gene expression signatures that resemble OPCs.

overall_design: We compared the global gene expression pattern of iOPCs, fibroblasts, primary OPCs from the neonatal rat brain, and their differentiated progeny. We purified iOPCs by O4 immunopanning three weeks after infection and extracted total RNA. Acutely isolated rat cortical OPCs were either used directly for RNA extraction or expanded in mitogen-containing media for 24h before switching into differentiation medium, lacking PDGF/NT-3 and containing T3. Cells were harvested for microarray analysis 3 and 6 days after induction of differentiation.

last: Yang

first: Marius

last: Wernig


title: Gene expression patterns following unilateral traumatic brain injury reveals a local pro-inflammatory and remote anti-inflammatory response

status: Public on Apr 12 2013

city: Atlanta

first: Benem-Orom

middle: Andrew

last: Davids

state: ga

address: 720 Westview Drive SW

department: Neurobiology

institute: Morehouse School of Medicine

summary: Abstract   Background  Traumatic brain injury (TBI) results in irreversible damage at the site of impact and initiates cellular and molecular processes that lead to secondary neural injury in the surrounding tissue. We used microarray analysis to determine which genes, pathways and networks were significantly altered using a rat model of TBI. Adult rats received a unilateral controlled cortical impact (CCI) and were sacrificed 24h post-injury. The ipsilateral hemi-brain tissue at the site of the injury, the corresponding contralateral hemi-brain tissue, and naïve (control) brain tissue were used for microarray analysis. Ingenuity Pathway Analysis (IPA) software was used to identify molecular pathways and networks that were associated with the altered gene expression in brain tissues following TBI.  Results  Inspection of the top fifteen biological functions in IPA associated with TBI in the ipsilateral tissues revealed that all had an inflammatory component. IPA analysis also indicated that inflammatory genes were altered on the contralateral side, but many of the genes were inversely expressed compared to the ipsilateral side. The contralateral gene expression pattern suggests a remote anti-inflammatory molecular response. We created a network of the inversely expressed common (i.e., same gene changed on both sides of the brain) inflammatory response (IR) genes and those IR genes included in pathways and networks identified by IPA that changed on only one side. We ranked the genes by the number of direct connections each had in the network, creating a gene interaction hierarchy (GIH). Two well characterized signaling pathways, toll-like receptor/NF-kappaB signaling and JAK/STAT signaling, were prominent in our GIH.  Conclusions   Bioinformatic analysis of microarray data following TBI identified key molecular pathways and networks associated with neural injury following TBI. The GIH created here provides a starting point for investigating therapeutic targets in a ranked order that is somewhat different than what has been presented previously. In addition to being a vehicle for identifying potential targets for post-TBI therapeutic strategies, our findings can also provide a context for evaluating the potential of therapeutic agents currently in development.

overall_design: The ipsilateral hemi-brain tissue at the site of the injury, the corresponding contralateral hemi-brain tissue, and naïve (control) brain tissue (n=3 for each) were used for RNA isolation. The TBI injured animals were Todd 1, 2 Todd, and Todd 3, each yielding an ispilateral and contralateral sample. The naïve animals were Xu 13 control, Xu 2 control, and Xu 6 control.

first: T

middle: E

last: White

first: G

middle: D

last: Ford

first: M

middle: C

last: Surles-Zeigler

first: A

middle: S

last: Gates

last: LaPlaca

first: B


title: Minor compensatory changes in SAGE Mdr1a (P-gp), Bcrp, and Mrp2 knockout rats do not detract from their utility in the study of transporter-mediated pharmacokinetics.

status: Public on Apr 08 2013

city: Indianapolis

first: Keith

middle: M

last: Goldstein

address: Lilly Corporate Center

department: Investigative Toxicology

institute: Eli Lilly & Co.

summary: Mdr1a-, Bcrp-, and Mrp2-knockout rats are a more practical species for ADME studies than murine models and previously demonstrated expected alterations in pharmacokinetics of various probe substrates.  At present, gene expression and pathology changes were systematically studied in small intestine, liver, kidney, and brain tissue from male SAGE Mdr1a-, Bcrp-, and Mrp2-knockout rats versus wild-type Sprague Dawley controls.  Gene expression data supported the relevant knockout genotype.  As expected, Mrp2-knockout rats were hyperbilirubinemic and exhibited upregulation of hepatic Mrp3.  Overall, few alterations were observed within 137 ADME-relevant genes.  The two most consequential changes were upregulation of intestinal carboxylesterase in Mdr1a-knockouts and catechol-O-methyltransferase in all tissues of Bcrp-knockout rats.  Previously reported upregulation of hepatic Mdr1b P-glycoprotein in proprietary Wistar Mdr1a-knockout rats was not observed in the SAGE counterpart investigated herein.  Relative liver and kidney weights were 22-53% higher in all three knockouts, with microscopic increases in hepatocyte size in Mdr1a- and Mrp2-knockout rats, and glomerular size in Bcrp- and Mrp2-knockouts.  Increased relative weight of clearing organs is quantitatively consistent with reported increases in clearance of drugs that are not substrates of the knocked-out transporter.   Overall, SAGE knockout rats demonstrated modest compensatory changes, which do not preclude their general application to study transporter-mediated pharmacokinetics.   However until future studies elucidate the magnitude of functional change, caution is warranted in rare instances of extensive metabolism by catechol-O-methyltransferase in Bcrp-knockouts and intestinal carboxylesterase in Mdr1a-knockout rats, specifically for molecules with free catechol groups and esters subject to gut wall hydrolysis.

overall_design: 3 groups of knockout animals compared to wild-type male Sprague Dawley control rats. 4 animals per group. Assayed the following tissues: brain, duodenum, ileum, jejunum, kidney (cortex-anterior pole), kidney (medulla), liver. Hybridized to Affymetrix Rat Genome 230 v2 [Rat230_2] arrays.

first: Maciej

middle: J

last: Zamek-Gliszczynski

first: April

last: Paulman

first: Thomas

middle: K

last: Baker

first: Timothy

middle: P

last: Ryan


title: Gene expression analyses of hematopoietic stem cell (HSC) subsets in wildtype or CD41-KO mice

status: Public on Apr 11 2013

first: Christos

last: Gekas

address: Carrer del Doctor Aiguader 88, Lab277

institute: Centre for Genomic Regulation (CRG)

summary: The hematopoietic stem cell (HSC) compartment is heterogeneous, yet our understanding of the identities of different HSC subtypes is limited. Here we show that platelet integrin CD41 (αIIb), currently thought to only transiently mark fetal HSCs, is expressed on an adult HSC subtype that accumulates with age. CD41+ HSCs were largely quiescent and exhibited myeloerythroid and megakaryocyte gene priming, governed by Gata1, whereas CD41- HSCs were more proliferative and exhibited lymphoid gene priming. When isolated without the use of blocking antibodies, CD41+ HSCs possessed long-term repopulation capacity upon serial transplantations and showed a marked myeloid-bias compared to CD41-HSCs, which yielded a more lymphoid-biased progeny. CD41-knockout mice displayed multilineage hematopoietic defects coupled with decreased quiescence and survival of HSCs, suggesting that CD41 is functionally relevant for HSC maintenance and hematopoietic homeostasis. Transplantation experiments indicated that CD41-KO associated defects are long-term transplantable and HSC-derived, and in part mediated through the loss of platelet mass leading to decreases in HSC exposure to important platelet released cytokines, such as TGFβ1. In summary, our data provide a novel marker to identify a myeloid-biased HSC subtype that becomes prevalent with age, and highlights the dogma of HSC regulation by their progeny.

overall_design: For microarray analysis, 1000 HSCs were FACS sorted from pools of 4-5 mice directly into lysis buffer, RNA extracted and whole transcript amplification was performed as previously described (Gonzalez-Roca E, Garcia-Albeniz X, Rodriguez-Mulero S, Gomis RR, Kornacker K, Auer H. Accurate expression profiling of very small cell populations. PLoS One. 2010;5:e14418.)

last: Graf


title: Genes affected by Satb1 deficiency in HSC, LMPP and CLP

status: Public on Mar 20 2013

city: Suita

first: Takafumi

last: Yokota

state: Osaka

address: 2-2 Yamadaoka

department: Hematology & Oncology

institute: Osaka University

summary: To understand  gene expression signatures between wild-type and Satb1-deficient cells

overall_design: To examine genes regulated by Satb1 expression, sets of microarrays were conducted with Lin- c-kitHi Sca-1+ Flt3- HSC-enriched cells, Lin- c-kitHi Sca-1+ Flt3+LMPP-enriched cells, and Lin- c-kitLo Sca-1Lo IL7Rα+ CLP-enriched cells derived from E18.5 FL of Satb1-null mice or their WT littermates.

first: Yusuke

last: Satoh


title: Influence of short-time feeding of rats with an iron-deficient diet on their hepatic gene expression profiles

status: Public on Mar 21 2013

city: Kanagawa

first: Asuka

last: Kamei

address: LiSE 4F C-4, 3-25-13 Tonomachi, Kawasaki-ku, Kawasaki-shi

department: Project for development of food functionality assessment methods

institute: Kanagawa Academy of Science and technology

summary: Iron deficiency-induced anemia is generally a representative nutritional problem in most populations. We reported that the anemia due to dietary iron deficiency causes a variety of changes in nutrient metabolism, even leading to apoptosis as a result of associated endoplasmic reticulum (ER) stress in the rat liver. On the other hand, it appears that non-anemic iron-deficiency causes no serious problem because no appreciable down-regulation of hemoglobin synthesis occurs. Biochemically, iron is essential for activation of cytochrome-related enzymes and its deficiency should yield some physiological problems. We performed a comprehensive transcriptome analysis to define the effects of non-anemic iron deficiency on hepatic gene expression.  Four-week-old rats were fed a low-iron diet (ca. 3 ppm iron) for 2 days. These rats were compared with those fed a control diet (48 ppm iron) by pair feeding. On day 3, the rats were sacrificed under anesthesia, and their livers were dissected for DNA microarray analysis. Rats in the iron-deficient diet group, showed that their serum ferritin and iron levels decreased with an increase in the serum total iron binding capacity (TIBC) level, while the hemoglobin level was not changed. In the DNA microarray study, we identified 91 up-regulated and 186 down-regulated probe sets that characterized the iron-deficient diet group. In the up-regulated probe sets, genes involved in glucose and lipid metabolic processes were significantly enriched, whereas genes related to organic acid metabolic process, cellular ketone metabolic process, lipid metabolic process, oxidation reduction, response to drug, response to extracellular stimulus and gas transport were significantly enriched in the down-regulated probe sets. These results suggest that even the non-anemic iron-deficiency exerts various influences on nutrient metabolisms in the liver.

overall_design: Three-week-old male rats (Sprague Dawley) were purchased from Charles River Japan (Kanagawa, Japan) and housed in a room maintained at 24 ± 1°C and 40 ± 5% humidity with a 12-h light/dark cycle (light 08:00–20:00; dark 20:00–08:00). Rats were given a normal diet (Research Diets, Inc., New Brunswick, NJ, USA) as control and water for 24 h ad libitum. The composition of the control diet, 48 ppm iron, was based on the AIN-93G diet; Avicel was used in place of cellulose which may contain a trace amount of iron. On day 3, diet was removed at 18:00 and the feeding was conducted between 09:00 and 17:00 for another 4 days to synchronize the feeding behaviors. On day 8, rats were divided into two groups with similar average body weights. Rats in the one group (n = 5) were given ad libitum an iron-deficient diet, ca. 3 ppm iron, that was prepared by removal of iron (ferric citrate) from the control diet, and those in the other group (n = 5) were fed the control diet by pair feeding. On day 1 and day 3 of feeding with the experiment diet, the hemoglobin level of each rat was measured for the blood samples collected from the tail vein. On day 3, each rat was sacrificed under anesthesia after 1.5 h feeding, prior to excising the liver which was soon immersed in RNAlater.

first: Yuki

last: Watanabe

first: Kaori

last: Kondo

first: Shinji

last: Okada

first: Fumika

last: Shinozaki

first: Tomoko

last: Ishijima

first: Yuji

last: Nakai

first: Takashi

first: Soichi

last: Arai

first: Keiko

last: Abe


title: Expression data from cultured rat right ventricular papillary muscles

status: Public on Mar 19 2013

city: Charlottesville

first: Charles

last: Haggart

state: VA

address: 415 Lane Road

department: Biomedical Engineering

institute: University of Virginia

summary:
Several different mechanical signals have been proposed to control the extent and pattern of myocardial growth and remodeling, though this has largely been studied using in vitro model systems that are not representative of intact myocardium or in vivo models in which isolating the effects of individual candidate stimuli is exceedigly difficult. We used a unique tissue culture system that allows the simultaneous control of multiple mechanical inputs and other potentially confounding stimuli (e.g., hormonal).
Following a 12 hour culture period under prescribed mechanics, we used microarrays to identify genes that are up- or down-regulated in response to different amounts of mean stretch and cyclic shortening.

overall_design: Muscles were dissected (one from each of 12 different male LBN-F1 rats) and cultured for 12 hours in a pseudo-sterile muscle culture system under one of four mechanical input schemes (i.e., three biological replicates per mechanical input group). We prescribed low or high values of both time averaged stretch and cyclic shortening. Specifically, we targeted 4% or 16% mean stretch (from slack length) and 4% of 16% cylic shortening (% of slack length) over the 12 hour culture period to give the following four groups: high mean stretch x high shortening (group A); high mean stretch x low shortening (group B); low mean stretch x low shortening (group C); low mean stretch x high shortening (group D). This 2 x 2 factorial design allowed us to identify individual genes and/or molecular pathways that might be regulated by one or both of these mechanical inputs indpendent from other candidate mechanical or hormonal stimuli.

middle: R

first: Elizabeth

middle: G

last: Ames

first: Jeffrey

middle: W

last: Holmes


title: The 3’UTR of FMR1 mRNA is a target of miR101, miR129-5p and miR-221: implications for the molecular pathology of FXTAS at the synapse.

status: Public on Mar 07 2013

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

institute: IPMC/CNRS

summary: While FMR1 is silenced in Fragile X syndrome (FXS), its expression is elevated (2-8 fold) in premutated individuals. These people may develop the Fragile X-associated Tremor Ataxia Syndrome (FXTAS), a late onset neurodegenerative disorder characterized by ataxia and parkinsonism. In addition, people carrying the premutation can be affected by a set of neurological and behavioural disorders during young age. Problems of memory have been detected in these patients as well in the mice model for FXTAS. To date little is known concerning the metabolism of FMR1 mRNA, notwithstanding the importance of the finely tuned regulation of the expression of this gene. In the present study we identified three microRNAs that specifically target the 3’UTR of FMR1 and can modulate its expression throughout the brain and, in particular, at the synaptic level. The expression level of miR-221 is reduced in brain and synaptosomal preparations of young FXTAS mice suggesting a general deregulation of transcripts located at the synapse of these mice. By transcriptome analysis we show here a robust deregulation of the expression levels of genes involved in learning, memory and autistic behavior, Parkinson disease and neurodegeneration. Interestingly, many of those deregulated mRNAs are target of the same miRNAs that modulate the expression of FMR1 at the synapse.

overall_design: Knock-In versus Wild Type, 3 replicates.

first: B

last: Bardoni

first: P

last: Barbry

last: Mari

first: K


title: RUNX1 reshapes the epigenetic landscape at the onset of hematopoiesis

status: Public on Feb 11 2013

city: Birmingham

first: Salam

middle: Adli

last: Assi

address: IBR

department: Institute for Cancer and Genomic Sciences

country: United Kingdom

institute: University of Birmingham

summary: Cell fate decisions during hematopoiesis are governed by lineage-specific transcription factors, such as RUNX1, SCL/TAL1, FLI1 and C/EBP family members. In order to gain insight about how these transcription factors regulate the activation of hematopoietic genes during embryonic development, we measured the genome-wide dynamics of transcription factor assembly on their target genes during the RUNX1-dependent transition from hemogenic endothelium to hematopoietic progenitors. Using a RUNX1-/- embryonic stem cell differentiation model expressing an inducible RUNX1 gene, we show that in the absence of RUNX1, SCL/TAL1, FLI1 and C/EBP-beta prime hematopoietic genes and that this early priming is required for correct temporal expression of the myeloid master regulator PU.1 and its downstream targets. After induction, RUNX1 binds to numerous new sites, initiating a local increase of histone acetylation and rapid global alterations in the binding patterns of SCL/TAL1 and FLI1. The acquisition of hematopoietic fate controlled by RUNX1 therefore does not represent the establishment of a new regulatory layer on top of a pre-existing hemogenic endothelium program but instead entails global reorganization of lineage-specific transcription factor assemblies.

overall_design: Microarray expression data obtained from differentiating murine hematopoietic cells, 3 independent biological replicates (measured twice) from iRUNX1 culture -/+DOX induction

first: Monika

last: Lichtinger

first: Richard

last: Ingram

first: Rebecca

last: Hannah

first: Dorothee

last: Müller

first: Deborah

last: Clarke

first: Michael

last: Lie-A-Ling

first: Laura

last: Noailles

first: MS

last: Vijayabaskar

first: Mengchu

last: Wu

first: Daniel

last: Tenen

first: David

last: Westhead

first: Valerie

last: Kouskoff

first: Georges

last: Lacaud

first: Berthold

last: Göttgens

first: Constanze

last: Bonifer


title: Genes expressed in age-induced mitochondrial DNA deletion mutation containing / Electron Transport abnormal cells

status: Public on Mar 01 2013

city: Edmonton

first: Allen

last: Herbst

state: AB

address: 114C BARB

institute: University of Alberta

summary: Muscle tissue was longitudinally characterized histologically for electron transport function by staining 1mm of quadriceps muscle at 70 micron intervals for the activities of two complexes in the mitochondrial electron transport chain, Cytochrome C Oxidase and Succinate Dehydrogenase. Unstained serial cryosections were prepared for Laser Capture Microdissection. Target cells from the serial sections were isolated and pooled for RNA extraction, amplification and hybridization on Affymetrix microarrays. We selected homogeneous populations of muscle fibers for expression profiling based upon  the presence/absence of electron transport dysfunction caused by the somatic accumulation of mitochondrial DNA deletion mutations.

overall_design: The design of this experiment is limited by the source tissue which is individually identified cells harboring intracellular clonal expansions of mitochondrial DNA deletion mutations. These unique and rare cells were identified in rat Vastus lateralis tissue in an aged 36-month old F344xBN F1 hybrid rat by exhaustive serial sectioning and subsequent histological characterization. Unstained serial sections where isolated by LCM and the purified RNA was amplified by 2 rounds of RNA based transcription prior to fragmentation and hybridization on rat genome affymetrix chips. Two populations of cells were analyzed,  Electron transport deficient and  normal control cells from the same animal.

first: Judd

last: Aiken


title: Identification of genes involved in cell differentiation of rat oral epithelial cell line ROE2

status: Public on Feb 22 2013

city: Toyama

first: Yoshiaki

last: Tabuchi

state: Toyama

address: 2630 Sugitani

department: Life Science Research Center

institute: University of Toyama

summary: The use of in vitro cell culture systems has been of central importance for research of physiology, pharmacology, and toxicology, and functions at the cellular and molecular levels. We have developed an immortalized oral epithelial cell line ROE2 from fetal transgenic rats harboring temperature-sensitive simian virus 40 large T-antigen. Here, to identify genes involved in ROE2 cell differentiation, global-scale gene expression analysis was carried out using a GeneChip® system.

overall_design: ROE2 cells, an immortalized oral epithelial cell line from transgenic rats harboring temperature-sensitive simian virus 40 large T-antigen, were cultured for 0, 3, 6 and 9 days at 37˚C. Total RNA samples were prepared from the cells, and quality of the RNA was analyzed using a Bioanalyzer 2100. Gene expression was monitored by an Affymetrix GeneChip® system with a Rat Genome 230 2.0 array. Sample preparation for array hybridization was carried out as described in the manufacturer's instructions.

first: Ayako

last: Kariya

first: Shigehito

last: Wada