title: A comparison of physiological and transcriptome responses to water deprivation and salt loading in the rat supraoptic nucleus

status: Public on Feb 05 2015

city: Bristol

first: DAVID

last: MURPHY

state: AVON

address: Whitson Street

department: Medicine and Dentistry

institute: University of Bristol

summary: Salt loading (SL) and water deprivation (WD) are experimental challenges that are often used to study the osmotic circuitry of the brain. Central to this circuit is the supraoptic nucleus (SON) of the hypothalamus, which is responsible for the biosynthesis of the hormones, vasopressin (AVP) and oxytocin (OXT), and their transport to terminals that reside in the posterior lobe of the pituitary. Upon osmotic challenge evoked by a change in blood volume or osmolality, the SON undergoes a function related plasticity that creates an environment that allows for an appropriate hormone response. Here, we have described the impact of SL and WD compared to euhydrated (EU) controls in terms of drinking and eating behaviour, body weight and recorded physiological data including circulating hormone data and plasma and urine osmolality. We have also used microarrays to profile the transcriptome of the SON following SL

overall_design: Microarrays were interrogated with RNA extracted from the supraoptic nucleus of either euhydrated (n=5) or 7-days salt loaded (2% w/v; n=5) rats. Each microarray represented an independent pool of 5 animals, and for each condition, 5 microarrays were performed.

first: Michael

last: Greenwood

first: Andre

last: Mecawi

first: See

middle: Z

last: Hoe

first: Mohd

last: Mustafa

first: Kory

last: Johnson

first: Ghada

last: Al-Mahmoud

first: Lucila

last: Elias

first: Julian

last: Paton

first: Jose

last: Antunes-Rodrigues

first: Harold

last: Gainer

first: David

last: Murphy

first: Charles

last: Hindmarch


title: A regulatory CD9+ B cell subset controls HDM-induced allergic airway inflammation

status: Public on Mar 01 2015

city: Nantes

first: Faouzi

last: Braza

address: 30 boulevard Jean Monnet

country: France

institute: Inserm

summary: Background: A specific subset of regulatory IL-10 producing B cells has been extensively studied in autoimmune and inflammatory pathologies. These cells are able to constrain exacerbated inflammation by inhibiting T cell mediated responses and maturation of antigen presenting cells. In allergic diseases, observations that increase of regulatory B cells is necessary for allergen tolerance suggest that development of allergic asthma would be associated with a defect in the regulatory B cells compartment. Objective: We sought to (i) characterize regulatory IL-10+ regulatory B cell subset in Balb/c mice by microarray and flow cytometry and (ii) investigate their regulatory capacity in vivo in a house dust mite model of allergic asthma. Results: We identified an IL-10 producing B cells subset able to control T cell proliferation in vitro in both control and asthmatic mice. This subset is decreased in allergic mice. IL-10+ Breg cells express high levels of CD9 and upregulate CD70 and CD73 after activation. Expression of CD9 allows identifying more than 50% of Bregs. Interestingly CD9+ B cells inhibit TH2-TH17 allergic airway inflammation in vivo after adoptive transfer in an IL-10 dependent manner. Conclusions: Herein, we demonstrate that induction of allergic asthma dampens the generation of Bregs contributing to exacerbated airway inflammation. We identified a distinct CD9+ Breg-cell population decreased in lung of HDM mice and able to control asthma and allergic airway inflammation by producing IL-10 after adoptive transfer. This study points B cells as an interesting therapeutic target in allergic asthma.

overall_design: IL-10+ B cells (n=3) and 3 IL-10- B cells (n=3) in control mice + IL-10+ B cells (n=3) and 3 IL-10- B cells (n=3) from asthmatic allergic (HDM) mice

first: F

first: J

last: Chesne

first: S

last: Dirou

first: G

last: Mahay

first: M

last: Durand

middle: A

last: Cheminant

first: A

last: Magnan

last: Brouard


title: Amino acid deprivation due to overexpression of UCP1 in skeletal muscle: signalling via FGF-21

status: Public on Feb 17 2015

city: Wageningen

first: Evert

middle: M.

last: van Schothorst

address: De Elst 1

country: Netherlands

institute: Wageningen University

summary: Recent studies on mouse and human skeletal muscle (SM) demonstrated the important link between mitochondrial function and the cellular metabolic adaptation. To identify key compensatory molecular mechanisms in response to chronic mitochondrial distress, we analyzed mice with ectopic SM respiratory uncoupling in uncoupling protein 1 transgenic (UCP1-TG) mice as model of muscle-specific compromised mitochondrial function. Here we describe a detailed metabolic reprogramming profile associated with mitochondrial perturbations in SM, triggering an increased protein turnover and amino acid metabolism with induced biosynthetic serine/1-carbon/glycine pathway and the longevity-promoting polyamine spermidine as well as the trans-sulfuration pathway. This is related to an induction of NADPH-generating pathways and glutathione metabolism as an adaptive mitohormetic response and defense against increased oxidative stress. Strikingly, consistent muscle retrograde signaling profiles were observed in acute stress states such as muscle cell starvation and lipid overload, muscle regeneration, and heart muscle inflammation, but not in response to exercise. We provide conclusive evidence for a key compensatory stress-signaling network that preserves cellular function, oxidative stress tolerance, and survival during conditions of increased SM mitochondrial distress, a metabolic reprogramming profile so far only demonstrated for cancer cells and heart muscle.-Ost, M., Keipert, S., van Schothorst, E. M., Donner, V., van der Stelt, I., Kipp, A. P., Petzke, K.-J., Jove, M., Pamplona, R., Portero-Otin, M., Keijer, J., and Klaus, S. Muscle mitohormesis promotes cellular survival via serine/glycine pathway flux.

overall_design: Control C57BL/6J wildtype male mice, aged 12 weeks, are compared to UCP1 transgene littermates fed purified low fat diet (BIOCLAIMS, Hoevenaars et al., Genes and Nutrition 2012) for 12 weeks . At the end, mice were sacrificed, gastrocnemius skeletal muscle was immediately dissected and snap frozen in liquid nitrogen. Total RNA was isolated, quantified and qualified, and subsequently used for global gene expression profiling using Agilent 8x60K microarrays. In total, 6 arrays of individual WT and 7 arrays of individual UCP1-TG samples were normalized, together with samples from the complete SUPERSERIES.

last: Ost

first: E

last: Keipert

first: I

last: van der Stelt

last: Klaus

last: Keijer


title: Expression data from wild-type control and Dnmt3a knockout osteoclast

status: Public on Feb 23 2015

city: Kyotanabe

first: Keizo

last: Nishikawa

state: Kyoto

address: 1-3, Tatara Miyakodani

department: Medical Life Systems

country: Japan

institute: Graduate School of Life and Medical Sciences

summary: Epigenetic regulation is a fundamental mechanism mediating various cellular processes. However, epigenetic mechanisms in osteoclastogenesis remain to be elucidated. We performed microarray analysis to investigate gene expression in osteoclasts derived from wild-type and Dnmt3aknockout mice.

overall_design: In vitro osteoclast culture were performed using wild-type control and Dnmt3a knockout bone marrow-derived monocyte/macrophage precursor cells.


title: Expression in parotid acinar cells during terminal differentiation

status: Public on Feb 03 2015

city: Louisville

first: Douglas

last: Darling

state: KY

address: 501 S. Preston St.

department: Oral Immunology and Infectious Diseases

country: USA

institute: University of Louisville

type:
Expression profiling by array
Other

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

platform_organism:
Mus musculus
Rattus norvegicus

overall_design: Refer to individual Series


title: Rapid increase of fibroblast growth factor 21 under protein malnutrition and its impact on growth and lipid metabolism

status: Public on Jan 15 2015

city: Kanagawa

first: Asako

last: Takenaka

address: Higashi-Mita 1-1-1, Tama-ku, Kawasaki

institute: Meiji University

summary:
Protein malnutrition promotes hepatic steatosis, decreases insulin-like growth factor (IGF)-I production, and retards growth. In order to identify new molecules involved in such changes, we conducted DNA microarray analysis for liver samples of rats fed isoenergetic low protein diet for 8 hours, and identified fibroblast growth factor 21 (Fgf21) as one of the most strongly up-regulated genes under conditions of acute protein malnutrition (P<0.05, FDR<0.001). In addition, amino acid deprivation from the culture media increased Fgf21 mRNA levels in rat liver-derived RL-34 cells (P<0.01). Thus, it was suggested that amino acid limitation directly increases Fgf21 expression.
FGF21 is a polypeptide hormone that regulates glucose and lipid metabolism. Using transgenic mice, FGF21 has also been shown to promote a growth hormone-resistant state and suppress IGF-I. Therefore, to further determine whether the up-regulation of Fgf21 under protein malnutrition causes hepatic steatosis and growth retardation following decrease in IGF-I, we fed isoenergetic low protein diet to Fgf21-knockout (KO) mice. Fgf21-KO did not rescue growth retardation and reduced plasma IGF-I concentration of mice fed the low-protein diet. Meanwhile, Fgf21-KO mice showed greater epididymal white adipose tissue weight as well as hepatic triglyceride and cholesterol levels under protein malnutrition (P<0.05). Taken together, we showed that protein deprivation directly increases Fgf21 expression. However, growth retardation and decreased IGF-I were not mediated by increased FGF21 expression under protein malnutrition. Furthermore, up-regulated FGF21 rather appears to have a protective effect against obesity and hepatic steatosis in protein malnourished animals.

overall_design: Livers of rats from 2 groups (control (15P) or low-protain (5P) diet fed groups), total of 6 samples (3 replicates for each group) were analyzed.

first: Yori

last: Ozaki

first: Kenji

last: Saito

first: Kyoko

last: Nakazawa

first: Morichika

last: Konishi

first: Nobuyuki

last: Itoh

first: Fumihiko

last: Hakuno

first: Shin-Ichiro

last: Takahashi

first: Hisanori

last: Kato


title: Expression data from mouse embryonic stem cells across a time course of Erk stimulation

status: Public on Jan 01 2015

city: Copenhagen

first: Josh

middle: M

last: Brickman

address: 3B Blegdamsvej

department: reNEW

country: Denmark

institute: Copenhagen University

summary:
Fgf signaling via Erk activation has been associated with both neural induction and the generation of a primed state for the differentiation of embryonic stem cells (ESCs) to all somatic lineages.  To dissect the role of Erk in both ESC self-renewal and lineage specification we explore the requirements for this pathway in various in vitro differentiation settings. A combination of pharmacological inhibition of Erk signaling and genetic loss of function experiments reveal a role for Erk signaling in suppressing endodermal differentiation, but not neural specification. Activation of Erk signaling in ESCs de-represses primitive endoderm (PrE) gene expression as a consequence of inhibiting the pluripotent/epiblast network. The early response to Erk activation correlates with functional PrE priming while sustained Erk activity results in PrE differentiation. Taken together, our results suggest that Erk signaling suppresses pluripotent gene expression to enable endodermal differentiation.
We use microarray analysis to determine the transcription response to Erk1/2 in mouse embryonic stem cells across a 24 hour window of time

overall_design: Mouse ESCs carrying a tamoxifen inducible constitutively active c-Raf fusion protein were stimulated for 6 time points (30minutes, 1 hour, 2 hours, 4 hours, 8 hours, and 24 hours) in the presence of 250nM PD173074. Uninduced (0h hours) and DMSO only treated cells served as controls.

first: William

middle: B

last: Hamilton


title: Toxicogenomics profiling of bone marrow from rats treated with topotecan in combination with oxaliplatin: a mechanistic strategy to inform combination toxicity.

status: Public on Jan 21 2015

city: Bethesda

first: Myrtle

last: Davis Millin

state: MD

address: 31 Center Drive

institute: The National Cancer Institute

summary: Combinations of anticancer agents may have synergistic anti-tumor effects, but enhanced hematological toxicity often limit their clinical use. We examined whether “microarray profiles” could be used to compare early molecular responses following a single dose of agents administered individually with that of the agents administered in a combination.  Six patterns of co-expressed genes were detected at the 1-hour time point which indicate regulatory expression of genes dependent on the order of the administration. When topotecan is given first, several signal transduction transcription factors associated with cancer or inactivation of a tumor suppressor were co-regulating gene expression. These results suggest alterations in histone biology, chromatin remodeling, DNA repair, bone regeneration, and respiratory and oxidative phosphorylation are among the prominent pathways modulated in bone marrow from animals treated with an oxaliplatin/topotecan combination.

overall_design:
mRNA responses were compared within bone marrow of Sprague-Dawley rats after a single 30-minute treatment with topotecan at 4.7 mg/kg or oxaliplatin at 15 mg/kg alone to that of sequentially administered combination therapy or vehicle control
Please note that one of the 'Bone Marrow_Oxaliplatin _Vehicle 1' sample (1344-05H_4M 40) was considered an outlier and thus, was excluded from data analysis and GEO records.

last: Davis


title: Gene transcript alterations exhibited in luminal and basal epithelial compartments with impaired Ror2 signaling

status: Public on Jan 09 2015

city: Houston

first: Chad

last: Creighton

state: TX

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

summary: Microarray analyses revealed distinct gene expression alterations in the luminal and basal epithelial compartments in the absence of Ror2 with marked alterations observed in genes associated with actin filament-based processes and the actin cytoskeletal network.

overall_design: Given that Ror2 expression resides in both basal and luminal epithelial cells, we wanted to identify compartment-specific functions for Ror2 in coordinating development.   Accordingly, luminal and basal epithelial cell populations from shLUC and shRor2 outgrowths were isolated by FACS separation on the basis of CD24 and CD29 surface marker expression and gene expression analysis was subsequently performed using Agilent microarrays.

first: Kevin

last: Roarty

middle: J

first: Jeffrey

last: Rosen


title: Gene expression profiles of E8.5, E9.5 and E11.5 kidney precursors

status: Public on Jan 13 2015

city: Kumamoto

first: Atsuhiro

last: Taguchi

state: Kumamoto

department: IMEG

institute: Kumamoto Univ.

summary: Understanding processes how the early stage kidney precursor gives rise to metanephric mesenchyme, which is a committed progenitor cells of adult kidney is important for the regeneration of kidney in vitro. The combination of fluorescent activated cell sorting (FACS) plus microarray analysis offers a powerful, efficient and effective method for the creation of global gene expression profiles of the developing kidney precursors. Those gene expression data provides insights into not only the stage specific marker genes but also the signals working in each population, which should be informative for the directed differentiation of pluripotent stem cells in vitro.

overall_design: Osr1-GFP knock-in mice were used to isolate kidney precursor cells from embryos at E8.5, E9.5 and E11.5. At E9.5 and E11.5 embryos, to identify the differences between nephron progenitors and surrounding mesenchyme, nephron progenitor populations were further enriched by gating Osr1-GFP positive Integrin alpha8 positive Pdgfr alpha negative population and compared with Osr1-GFP positive cells other than that gate. RNA was isolated from cells and the gene expression profiles were determined by microarrays.

first: Ryuichi

last: Nishinakamura


title: Gene expression and complex network analyis of effects of anaethesia

status: Public on Jan 02 2015

city: Aberdeen

first: Damon

last: Lowes

state: Aberdeenshire

address: IMS, Foresterhill

department: Immunology, Infection and inflammation

country: United Kingdom

institute: University of Aberdeen

summary:
Most gene array studies use analysis of differential gene expression which gives no information on the interactions between genes
We used complex systems analyis of gene expression data to study brain gene expression in rats following a brief period of anaesthesia using isoflurane

overall_design: Male Sprague Dawley rats were studied (250-300g) following exposure for 15 minutes to either isoflurane in oxygen at a steady state concentration of 2% or oxygen alone. Anaimals were alowed to recover for 6 hours before brains were removed for RNA extraction and hybridization on Affymetrix microarrays to obtain expression profiles from which complex networks could be generated

first: Helen

last: Galley

first: Alexandro

last: Moura

first: Nigel

last: Webster


title: Comparison of microarray and RNA sequencing platforms for profiling microRNAs in formalin-fixed, paraffin-embedded human lung adenocarcinoma specimens

status: Public on Dec 31 2014

city: Buffalo

first: Santosh

middle: Kumar

last: Patnaik

state: NY

address: Elm and Carlton Streets

department: Thoracic Surgery

institute: Roswell Park Comprehensive Cancer Center

summary: MicroRNAs are useful biomarkers for various disease states, and their  preservation in formalin-fixed, paraffin-embedded (FFPE) tissue makes them particularly useful for clinicogenetic studies. Although global microRNA expression in FFPE samples is routinely measured with microarrays, the utility of RNA sequencing for such profiling has yet to be established. In this study, to appraise the suitability of RNA sequencing, microRNAs in RNA from pathologic stage I lung adenocarcinoma FFPE samples were quantified with 8x60K Agilent® SurePrint™ G3 Human miRNA 8x60k (release 16.0) microarray and Illumina® HiSeq™ 2000 sequencing platforms.

overall_design: Total RNA was extracted from eight tumor specimens and all eight were used in duplicate for microRNA quantification with the Agilent® SurePrint™ G3 Human miRNA 8x60k (release 16.0) microarray platform. Microarray experiments were conducted twice, once for each set of duplicates. All eight RNA samples, with two in duplicate, were also used for RNA sequencing on the Illumina® HiSeq™ 2000 sequencing platform.

middle: K

first: Daniel

last: Buitrago

first: Prasad

middle: S

last: Adusumilli


title: Large scale transcriptomic characterization of mice brain inflammation during Acute Lung Injury (brain)

city: MARSEILLE CEDEX 09

first: Aurelie

last: Bergon

address: parc scientifique de Luminy, case 928

institute: TAGC INSERM U1090

summary:
ARN sample of brain from mouse were obtened at 6 times points: 1h, 1h30, 3h, 4h, 18h, 24h, after injection of oleic acid or physiological serum
Brain total RNAs from mouse injected with acid oleic or physiological serum were profiled after hybridization with Agilent SurePrint G3 Mouse GE 8x60K Microarray to identify genes with differential expression

overall_design: Brain from 31 C57BL6 mice are divided into 6 groups . Each group included tree or two mices given physiological serum (Phi) and 3 mices given oleic acid (OA). Each group was identified according to the incubation time: 1h, 1h30, 3h, 4h, 18h and 24h.

first: Séverine

last: Garnier

first: Isabelle

last: Lesur

first: Elise

last: Yammine

first: Béatrice

last: Loriod

first: Laurence

last: Flori

first: Pascal

last: Rihet

first: Catherine

last: Nguyen


title: Large scale transcriptomic characterization of mice blood inflammation during Acute Lung Injury (PBMC)

summary:
ARN sample of PBMC from mouse were obtened at 6 times points: 1h, 1h30, 3h, 4h, 18H, 24h, after injection of oleic acid or physiological serum
PBMC total RNAs from mouse injected with acid oleic or physiological serum were profiled after hybridization with Agilent SurePrint G3 Mouse GE 8x60K Microarray to identify genes with differential expression

overall_design: Blood from 30 C57BL6 mice are divided into 6 groups . Each group included tree or two mices given physiological serum (Phi) and 3 mices given oleic acid (OA). Each group was identified according to the incubation time: 1h, 1h30, 3h, 4h, 18h and 24h.


title: Gene expression profiling in liver from control versus mutant Sox17 SHIVA fasted C57BL/6 mice

city: marseille

first: Thien-Phong

last: Vu Manh

address: 163 avenue de Luminy

institute: CIML

summary: The objective of this study was to test the impact of a mutation in the Sox17 gene (SHIVA mouse) on the ability of liver to mount a transcriptional response to 24 hours of fasting.

overall_design: Control female C57BL/6 versus SHIVA mice were fasted for 24 hours. Livers from 3 control and 4 SHIVA mice were harvested. RNA was purified for each individual mouse and reverse-transcribed.

first: Samuel

last: Rommelaere

first: Philippe

last: Naquet


title: Sox4 regulates proliferation, differentiation, and DNA methylation patterns in the intestinal epithelium

city: Chapel Hill

first: Charles

last: Perou

state: NC

address: 12-044 Lineberger Comprehensive Cancer Center CB# 7295

department: Professor of Genetics, and Pathology & Laboratory Medicine; Lineberger Comprehensive Cancer Center

institute: University of North Carolina at Chapel Hill

summary: Intestinal stem cells (ISCs) are responsible for maintaining the physiological function of the intestinal epithelium through the production of differentiated absorptive and secretory cellular lineages. In addition to producing specialized functional cells, ISCs must also drive constant proliferation in order to maintain the especially high rate of cellular turnover in the intestinal epithelium, which undergoes near total renewal every 5-7 days. Understanding the transcriptional mechanisms that control how ISCs and transit-amplifying progenitors (TAs) balance differentiation and proliferation in the intestine may provide valuable insight into common pathologies, such as inflammatory bowel disease and cancer. Here, we show that the Sry¬¬-box containing transcription factor, Sox4, is involved in the regulation of proliferation in the ISC/TA zone, the expression of ISC-associated genes, and the differentiation of enteroendocrine (EE) cells. Interestingly, we also observed a significant reduction in the expression of the methylcytosine dioxygenase, Tet1, in Sox4-deficient intestines. We find that Tet1, which initiates derepression of target genes via DNA demethylation, is specifically upregulated in ISC populations in wild-type animals. Additionally, Sox4-deficient intestines showed a significant reduction in levels of 5-hydroxymethylcytosine, the catalytic byproduct of TET protein activity, in the ISC/TA zone. Together, our data demonstrate that Sox4 regulates differentiation and proliferation in the intestinal epithelium, and suggests that it may influence these processes through induction of Tet1 and subsequent derepression of target genes through epigenetic mechanisms.

overall_design: reference x sample

first: Adam

middle: D

last: Gracz

first: Danny

middle: C

last: Trotier

first: James

middle: V

last: McCann

first: Chuck

last: Harrell

first: Scott

middle: T

last: Magness


title: Large scale transcriptomic characterization of mice blood inflammation during Acute Lung Injury

first: Aurelie

last: Bergon


title: Large scale transcriptomic characterization of mice lung inflammation during Acute Lung Injury (lung)

summary:
ARN sample of lung from mouse were obtened at 6 times points: 1h, 1h30, 3h, 4h, 18H, 24h, after injection of oleic acid or physiological serum
Lung total RNAs from mouse injected with acid oleic or physiological serum were profiled after hybridization with Agilent SurePrint G3 Mouse GE 8x60K Microarray to identify genes with differential expression

overall_design: Lung from 31 C57BL6 mice are divided into 6 groups . Each group included tree or two mices given physiological serum (Phi) and 3 mices given oleic acid (OA). Each group was identified according to the incubation time: 1h, 1h30, 3h, 4h, 18h and 24h.

first: Séverine

last: Garnier


title: Effect of Mucuna pruriens against Naja sputatrix envenomation

status: Public on Dec 22 2014

city: Kuala Lumpur

first: Shin Yee

last: Fung

address: Lembah Pantai

department: Department of Molecular Medicine

country: Malaysia

institute: University of Malaya

summary:
Mucuna pruriens  extract MPE pretreatment may have a direct protective effect on heart (other than immunological neutralization of the venom neurotoxin and phospholipase A2 by the anti-MPE antibodies) that renders the heart more resistant to the toxic action of the venom
The direct protective effect probably involves functional changes to the cardiac tissue that enable the heart to resist the reduction of contractility and rate induced by the cobra venom.To explore the possibility of the direct action of MPE pretreatment on heart and to understand the molecular events involved in the protection of MPE pretreatment against the lethal action of Naja sputatrix venom, gene expression studies were carried out using microarray analysis.

overall_design: Rats were divided into four groups (n=6): negative control (abbreviated as ‘negative’ group), MPE pretreated group (abbreviated as ‘MPE’ group), N. sputatrix venom-challenge group (abbreviated as ‘NS’ group) and N. sputatrix venom-challenge to MPE pretreated animals group (abbreviated as ‘MPE-NS’ group).  In the ‘MPE’ group, rats were injected with MPE at a dose of 21 mg/kg (i.p.), on day 0, 7 and 14, and sacrificed on day 21. In the ‘negative’ group (the untreated, control group), rats were injected with saline of the same volume and sacrificed also on day 21. Hearts were then harvested immediately.  In the N. sputatrix venom-challenge group (‘NS’ group), untreated rats were challenged with 1.5 LD50 (1.25 μg/g) of N. sputatrix venom whereas in the venom challenge to MPE pretreated animals group (the ‘MPE-NS’ group), MPE pretreated rats were challenged with 1.5 LD50 (1.25 μg/g) of N. sputatrix venom, both on day 21. For the ‘NS’ and ‘MPE-NS’ group, the rats were observed for 24 h after venom challenged and hearts were harvested as soon as death occurred or 24 h after the venom injection, whichever occurred first.

first: S

middle: Y


title: Identification of sexually dimorphically expressed genes in rat tissues

status: Public on Jan 05 2015

city: Macclesfield

first: Russell

last: Huby

state: Cheshire

address: Alderley Park

institute: AstraZeneca

summary: The sexually dimorphic expression of genes across 26 somatic rat tissues was using Affymetrix RAE-230 genechips. We considered probesets to be sexually dimorphically expressed (SDE) if they were measurably expressed above background in at least one sex, there was at least a two-fold difference in expression (dimorphism) between the sexes, and the differences were statistically significant after correcting for false discovery. 14.5% of expressed probesets were SDE in at least one tissue, with higher expression nearly twice as prevalent in males compared to females. Most were SDE  in a single tissue. Surprisingly, nearly half of the probesets that were (SDE) in multiple tissues were oppositely sex biased in different tissues, and most SDE probesets were also expressed without sex bias in other tissues. Two genes were widely SDE: Xist (female-only) and Eif2s3y (male-only). The frequency of SDE probesets varied widely between tissues, and was highest in the duodenum (6.2%), whilst less than 0.05% in over half of the surveyed tissues. The occurrence of SDE probesets was not strongly correlated between tissues. Within individual tissues, however, relational networks of SDE genes were identified. In the liver, networks relating to differential metabolism between the sexes were seen. The estrogen receptor was implicated in differential gene expression in the duodenum. To conclude, sexually dimorphic gene expression is common, but highly tissue-dependent. Sexually dimorphic gene expression may provide insights into mechanisms underlying phenotypic sex differences.

overall_design: 5 male and 5 female animals used. Data provided for all files that meet QC criteria

first: Philip

last: Glaves

first: Richard

last: Jackson


title: Network Analysis Reveals a Novel Role for the AP-1 Transcription Factor JUNB in Classical and Alternative Macrophage Activation

city: San Francisco

first: Charlie

last: Kim

state: CA

address: 1001 Potrero Ave

department: Medicine

institute: University of California, San Francisco

summary: Bone marrow-derived macrophages were generated from wild type and Junb knockout mice and tested for their responses to LPS treatment.

overall_design: Independent replicate wells from wild type and knockout bone marrow-derived macrophages were mock-treated or LPS-treated. RNA was isolated at 4 h post-treatment, amplified, and hybridized to Agilent Mouse 8x60k microarrays as a single color experiment.

first: Mary

middle: F

last: Fontana

first: Alyssa

last: Baccarella


title: Expression data from rat liver tissue during liver regeneration after partial hepatectomy.

status: Public on Dec 02 2014

city: Xinxiang

first: Cunshuan

last: Xu

address: No. 46, Construction East Road

country: China

institute: Henan Normal University

summary:
The liver has extraordinary powers of regeneration after partial hepatectomy (PH). Changes of gene expression play a key role in cell proliferation and differentiation during liver regeneration (LR). To understand the molecular mechanisms underlying LR, this study was designed to assess the changes of rat hepatic gene expression in a timely manner.
We used microarrays to further highlight the regulatory role of rat liver tissue in liver regeneration at gene transcription level.

overall_design: Rat liver regeneration after partial hepatectomy (PH) is a good model to study the regulation of cell proliferation. We gained regenerating liver at 9 time points (2, 6, 12,24, 30, 36, 72, 120, and 168h) after PH and measured gene expression profiles of rat liver tissue from 2h to 168h with rat Genome 230 2.0 gene chip. Each sample corresponding to one time point was hybridized onto one array. The experiment was repeated 3 times for each time point. In total, 10 time points were measured and 0h was used control group. After careful quality control analyses of each chip, Affymetrix GCOS 2.0 software was used to analyze the data. The relevance of gene expression profiles and biological processes was analyzed by bioinformatics and systems biology.

first: Gaiping

last: Wang

first: Yun

last: Zhou


title: Chromatin decondensation is sufficient to alter nuclear organization in embryonic stem cells

status: Public on Dec 01 2014

city: Edinburgh

first: Rob

last: Illingworth

state: Midlothian

address: Centre for Regenerative Medicine

department: Centre for regenerative Medicine

institute: The University of Edinburgh

summary: Determination of the specificity of activation by Ptn (TALE) fusion constructs transfected into mES cells by genome-wide expression analysis.

overall_design: Polyadenylated mRNA was prepared from mouse ES cells transfected with either eGFP, Ptn(TALE)VP64, Ptn(TALE)DEL or Ptn(TALE)Delta. 4 replicate hybridisations were prepared for each sample representing 2 biological and two technical replicates. RNA was extracted 48 post-transfection.

first: Pierre

last: Therizols

first: Robert

first: Celine

last: Courilleau

first: Shelagh

last: Boyle

first: Andrew

last: Wood

first: Wendy

last: Bickmore


title: Gene expression comparison of post-sepsis versus naïve mice-derived tumor associated macrophages

status: Public on Dec 25 2014

city: Ribeirão Preto

first: Jose

middle: Mauricio Segundo Correia

last: Mota

state: São Paulo

address: 3900 Bandeirantes Ave

department: Clinics

country: Brazil

institute: University of São Paulo

summary: To compare tumor associated macrophage (TAM) from naïve and sepsis surviving mice we have employed Agilent microarrays slides with almost 60,000 genes (39,430 mRNA and 16,251 long non coding RNAs). Other experiments we conducted demonstrated TAM accumulation was increased in post-sepsis subjects. For this reason, we asked if TAM from post-sepsis mice could also exhibit a different gene expression profile. Sepsis was induced by cecal and ligation puncture. Naïve mice were used as control group. All animals were treated with ertapenem (20 mg/kg, i.p., 6 hours after surgery, and then each 12 hours for 3 days). B16-F10 melanoma (30,000 cells) were injected subcutaneously at day 14 after sepsis induction. Fourteen days after tumor inoculation, animals were killed and tumors were harvested and digested (collagenase and DNAse). TAM was isolated by a Percoll gradient (70/30) followed by a 1-hour adhesion protocol, reaching a purity of ~75%. For comparative reasons, we assessed TAM from post-sepsis (n = 4), TAM from naïve mice (n = 4), bone marrow derived macrophage from naïve (n = 4) and from post-sepsis (n = 4), M1-polarized macrophage (n = 4) and M2-polarized macrophage (n = 4). We found only minor gene expression differences between TAM from naïve and from post-sepsis mice (61 genes were up-regulated and 98 genes were down-regulated, fold-change > 0.58  or < -0.58, and p < 0.01). We found genes related to leukocyte activation were down-regulated in TAM from post-sepsis mice (e.g. Ccr7, Cd86, H2-Ab1), as well as genes related to antigen processing and presentation of peptide or polysaccharide antigen via MHC class II (H2-DMb1, Cd74, H2-Eb1, H2-Ob). A gene related to M2 polarization was up-regulated (Marco). Also, we found a down-regulation of Nfkbid in post-sepsis-derived TAM. This led us to hypothesize TAM from post-sepsis mice exhibit a more M2-like phenotype, which may in part contribute to post-sepsis tumor expansion.

overall_design: Three independent experiments were conducted for TAM obtaining, each experiment using n = 4 for naïve and n = 4 for post-sepsis. We selected the 4 best within a group of 12 samples, following A260/280 and A260/230 ratios. For bone marrow derived macrophage from naïve and from post-sepsis, and for M1 and M2-polarized macrophage, we conducted two independent experiments using n = 3 per group. The best 4 samples in each group was selected to microarray processing and analysis.

first: Virginia

last: de-Deus-Wagatsuma

first: Caio

last: Leite

first: Lucas

middle: E

last: Souza

first: Paulo

last: Melo

first: Daniele

last: Nascimento

first: Jessica

last: Temporal

first: Florencio

last: Figueiredo

first: Houtan

last: Noushmehr

first: José Carlos

last: Alves-Filho

first: Fernando

middle: Q

last: Cunha

first: Eduardo

last: Rego


title: Epidermal RelA specifically restricts contact allergen-induced inflammation and apoptosis in skin

city: Cologne

first: Snehlata

last: Kumari

address: Kerpener Strasse 62

country: Germany

institute: University of Cologne

summary: Strong inhibition of NF-kB signaling in the epidermis results in spontaneous skin inflammation in mice and men. Since there is evidence for linkage between polymorphisms within the NF-kB signaling pathway and human inflammatory skin phenotypes, we asked whether partial functional inhibition of NF-kB signaling in epidermal keratinocytes can modulate clinically relevant skin inflammation. We therefore mutated rela specifically in the epidermis of mice (RelAE-MUT mice). These mice show no inflammatory phenotype. Induction of contact allergy, but not croton oil induced irritant dermatitis, resulted in stronger ear swelling and increased epidermal thickness in RelAE-MUT mice. Both contact allergen and croton oil treatment led to increase expression of calgranulins A and B (S100A8/ A9) in RelAE-MUT mice. Epidermal hyperproliferation in RelAE-MUT mice was non-cell autonomous since cultured primary epidermal keratinocytes from RelAE-MUT mice showed reduced proliferation compared to controls. These results demonstrate that epidermal RelA specifically regulates DTH-induced skin inflammation. In addition, we here describe an essential but non- specific function of RelA in the protection of epidermal keratinocytes from apoptosis. Our study identifies new functions of NF-kB signaling in the epidermis and corroborates a specific role of epidermal keratinocytes in the regulation of skin inflammation

overall_design: Mouse ear was treated with 2,4- Dinitro fluorobenzene and collected after 48 h of treatments. Two wild types and two mutant mice were used.

first: Benjamin

last: Herzberg

first: Ruth

last: Pofahl

first: Thomas

last: Krieg

first: Ingo

last: Haase


title: 3 Week IV Study of RGMC Ab in Female Sprague Dawley Rats

status: Public on Nov 14 2014

city: North Chicago

first: Rita

last: Ciurlionis

state: IL

address: 1 North Waukegan Road

institute: Abbvie

summary: High levels of hepcidin, the main regulator of systemic iron metabolism leads to various diseases. Targeting hepcidin and lowering its concentration is a possible form of intervention in order to treat these diseases. High turnover rate of hepcidin is a major drawback of therapies directly targeting this peptide. We developed two monoclonal antibodies (mAbs) ABT-207 and h5F9-AM8 which inhibit hemojuvelin also known as repulsive guidance molecule c (RGMc) and downregulate hepcidin. After a single application of these antibodies hepcidin expression in liver and its concentration in serum were reduced. Serum iron increased for several weeks. The RGMc antibodies show a pronounced dose response relationship in rats with h5F9-AM8 having an IC50 (UIBC) of ~80 fold higher than ABT-207. When hepcidin levels were downregulated iron deposition in the liver was visible histologically one week post application. The anitbody-mediated iron deposition was not associated with any toxicologically relevant effect at the doses and timepoints evaluate. Iron depositions seen after 14 weekly treatments with ABT-207 were partially reversible in rats and in cynomolgus monkeys. Due to their long-lasting effects and excellent safety profile, both RGMc-blocking antibodies ABT-207 and h5F9-AM8 are favorable clinical candidates for diseases characterized by high serum hepcidin levels like anemia of chronic disease.

overall_design:
Female Sprague-Dawley rats [Crl:CD®(SD)IGS BR], weighing ~200 g at study initiation were obtained from Charles River Laboratories, Inc.  Rats were housed singly in ventilated, stainless steel, wire-bottom hanging cages, fed non-certified Rodent Chow and water ad libitum and acclimated for at least 5 days after arrival.  Rats were randomly assigned to various treatment groups (5 rats/group) and were dosed once weekly by IV injection via tail vein with vehicle (30mM Histidine, 8% w/v Sucrose, pH6.0, + 0.02% Tween 80) or with 0.02, 0.2, or 20 mg/kg of RGMc antibody for a total of 4 doses.  All rats were sacrificed under isoflurane anesthesia 24 hours after final dose. Liver and spleen waere flash frozen in liquid nitrogen and stored at 80°C until processing for gene expression profiling on the Affymetrix platform.
total of 12 samples, 3 biological replicates (rats) from each of 4 treatments groups 1. vehicle control (30mM Histidine, 8% w/v Sucrose, pH6.0, + 0.02% Tween 80) 2. 0.02 mg/kg RGMC Ab 3. 0.2 mg/kg RGMC Ab 4.  20 mg/kg RGMC Ab; rats were dosed by IV injection via  tail vein once weekly for 4 total doses, dose volume 2mL/kg/week

first: Liguori

last: Michael

first: Ciurlionis

last: Rita


title: The NFKB inducing kinase (NIK) modulates hematopoiesis during stress

status: Public on Nov 29 2014

city: MAdrid

first: Gustavo

last: Melen

state: Madrid

address: Avda. Menendez Pelayo 65

country: Spain

institute: FIB Hospital NIño Jesus

summary: The genetic programs that maintain hematopoiesis during steady state in physiologic conditions are different from those activated during stress. Here we show that hematopoietic stem cells (HSCs) with deficiencies in components of the alternative NFkB pathway (the NFkB inducing kinase, NIK, and the downstream molecule NFkB2) had a defect in response to stressors such as supraphysiological doses of cytokines, chemotherapy and hematopoietic transplantation. NIK-deficient mice had peripheral blood and bone marrow leukocyte numbers within normal ranges (except for the already reported defects in B-cell maturation), however, HSCs showed significantly slower expansion capacity in in vitro cultures compared to wild type HSCs. This was due to a delayed cell cycle and increased apoptosis. In vivo experiments showed that NIK-deficient HSCs did not recover at the same pace as controls when challenged with myeloablative chemotherapy. Finally, NIK-deficient HSCs showed a significantly decreased competitive repopulation capacity in vivo. Using HSCs from mice deficient in one of two downstream targets of NIK, i.e., either NFkB2 or c-Rel, only NFkB2 deficiency recapitulated the defects detected with NIK-deficient HSCs. Our results underscore the role of NIK and the alternative NFkB pathway for the recovery of normal levels of hematopoiesis after stress.

overall_design: To explore the consequences of the defective NIKaly/aly protein in alternative NFKB signalling in HSCs, we investigated the gene expression profile of highly purified fresh LSK cells isolated from NIKWT and NIKaly/aly mice. We performed microarray analysis using total RNA from sorted LSK population using Agilent Whole Mouse Genome Oligo Microarrays.

first: Africa

last: Gonzalez-Murillo


title: Trichloroethylene-induced mRNA expression changes in B6C3F1 mouse liver

city: SuZhou

first: Tao

last: Chen

state: JiangSu

address: 199 Ren-Ai-rd

institute: Soochow University

summary: To examine changes, if any, in the expression of mRNAs in the liver tissue of mice, we have employed whole genome microarray expression profiling as a discovery platform to identify genes responsive to Trichloroethylene (TCE) treatment.  In our results, the expression levels of 431 mRNAs were changed after TCE exposure, of which 291 were up-regulated and 140 were down-regulated. Using qPCR, we validated six of the mRNA expression changed genes, viz., Jun, Cdkn1a, Rad51b, Uhrf1, Svil and Ihh.

overall_design: Six B6C3F1 male mice were oral administrated with either corn oil or TCE (dissolved in corn oil, 1000mg/kg b.w per day) for 5 days.  The expression changes of mRNAs in TCE exposured mouse liver were screened by whole genome microarray expression profiling and were validated by qPCR.


title: Expression profiling of brain structures of dependent and non-dependent rats self-administering alcohol and naive controls

status: Public on Nov 13 2014

city: New York

first: William

last: Shin

address: 1130 St Nicholas Ave

department: Systems Biology

institute: Columbia University

summary: Rats were trained to orally self-administer alcohol in a concurrent, two-lever, free-choice contingency using a modification of the sweet solution fading procedure (O'Dell et al., 2004; Roberts et al., 2000; Vendruscolo et al., 2012). Following acquisition of self-administration, rats were allowed to self-administer unsweetened alcohol (10%) for 4 weeks and were then assigned to two groups matched by levels of responding: one group (dependent group) was exposed to chronic, intermittent ethanol vapors for 4 weeks to induce dependence; the other group (nondependent group) was not exposed to ethanol vapor. After a month of vapor exposure, rats were again tested during acute withdrawal (6-8 hours after removal from the vapor chambers) until stable levels of alcohol intake were achieved. As expected, alcohol vapor-exposed rats self-administered significantly greater amounts of alcohol than control rats not exposed to alcohol vapor during acute withdrawal. Rats were sacrificed during protracted abstinence (3 weeks after the end of alcohol vapor exposure) along with age-matched alcohol naive rats.

overall_design: 96 gene expression profiles (GEP) were obtained from 8 brain regions believed to be relevant in alcohol’s reinforcing properties using the Affymetrix RN230.2 platform. Specifically, the following brain regions were microdissected and analyzed from nondependent and dependent alcohol self-administering rats as well as age-matched alcohol naive rats: (a) medial prefrontal cortex (MPF), (b) shell and (c) core NAc sub-regions, (d) central nucleus (CeA) and (e) basolateral nucleus of the amygdala (BLA), (f) dorsolateral and (g) ventral bed nucleus of the stria terminalis (BNST), and (h) ventral tegmental area (VTA).

first: Vez

last: Repunte-Canonigo

first: Leandro

last: Vendruscolo

first: Celine

last: Lefebvre

first: Lena

last: van der Stap

first: Tomoya

last: Kawamura

first: Joel

last: Schlosburg

first: Andrea

last: Califano

first: George

last: Koob

first: Pietro

middle: P

last: Sanna


title: Deconstruction of DNA methylation patterns during myogenesis reveals Myf5 super-enhancer hypomethylation in the establishment of the muscle lineage

status: Public on Nov 10 2014

city: Badalona

first: Miguel

middle: A

last: Peinado

state: Barcelona

address: Ctra. de Can Ruti, camí de les escoles, s/n

institute: IGTP

summary: Cellular differentiation involves widespread epigenetic reprogramming, including modulation of DNA methylation patterns. We have investigated DNA genome-wide methylation dynamics in embryonic stem cells, primary myoblasts, terminal differentiated myotubes and mature myofibers. About 1000 differentially methylated regions (DMRs) have been indentified during muscle-lineage determination and terminal differentiation. As a whole, muscle lineage commitment was characterized by a major gain of DNA methylation, while muscle differentiation was accompanied by loss of DNA methylation in CpG-poor regions. Notably, hypomethylated regions in muscle cells were neighboured by enhancer-type chromatin, suggesting the involvement of DNA methylation in the regulation of cell-type specific enhancers. Indeed, one of the hypomethylations detected in muscle cells affected the super-enhancer of the master transcription factor Myf5. Super-enhancers have been defined as large clusters of transcriptional enhancers driving cell-identity and gene expression, but how these lineage-specific super-enhancers are specifically activated or repressed in different tissues is not well understood. We demonstrated that the binding of the transcription factor USF1 to Myf5 locus occurs upon DNA demethylation of the super-enhancer region in myogenic committed cells. Taken all together, we have characterized the unique DNA methylation signatures of muscle-committed cells and highlighted the importance of DNA methylation mediated regulation of cell identity super-enhancers.

overall_design: We have investigated DNA genome-wide methylation dynamics in embryonic stem cells, primary myoblasts, terminal differentiated myotubes and mature myofibers by AIMS-seq techniques and coupled to microarray expression data by SurePrint G3 Mouse 8x60K from Agilent Technologies. Samples were in triplicates, except for  ESCs (quadruplicates).

first: Elvira

last: Carrió

first: Mònica

last: Suelves


title: T-cell intracellular antigen (TIA) proteins deficiency in murine embryonic fibroblasts alters cell cycle progression and induces autophagy

status: Public on Nov 05 2014

city: Cantoblanco

first: Juan

middle: Carlos

last: Oliveros

address: Darwin 3

institute: CNB, CSIC

summary:
Background: Mice lacking either T-cell intracellular antigen 1 (TIA1) or TIA1-related/like protein (TIAR/TIAL1) show high rates of embryonic lethality, suggesting a relevant role for these proteins during embryonic development. However, intrinsic molecular and cellular consequences of either TIA1 or TIAR deficiency remain poorly defined.

Results: By using genome-wide expression profiling approach, we demonstrate that either TIA1 or TIAR inactivation broadly alter normal development-associated signaling pathways in murine embryonic fibroblasts (MEF). Indeed, these analyses highlighted alterations of cytokine-cytokine and ECM-receptor interactions and Wnt, MAPK, TGF-beta dependent signaling pathways. Consistent with these results, TIA1 and TIAR knockout (KO) MEF show reduced rates of cell proliferation, cell cycle progression delay and increased cell size. Furthermore, TIA-proteins deficiency also caused metabolic deficiencies, increased ROS levels and DNA damage, promoting a gentle rise of cell death. Concomitantly, high rates of autophagy were detected in both TIA1 and TIAR KO MEF with induction of the formation of autophagosomes, as evidenced by the up-regulation of the LC3B protein, and autolysosomes, measured by colocalization of LC3B and LAMP1, as a survival mechanism attempt.

Conclusions: Taken together, these observations support that TIA proteins orchestrate a transcriptome programme to activate specific developmental decisions. This program is likely to contribute to mouse physiology starting at early stages of the embryonic development. TIA1/TIAR might function as cell sensors to maintain homeostasis and promote adaptation/survival responses to developmental stress.

overall_design: Two independent replicates were performed for each experimental condition and hybridized to Agilent SurePrint G3 Mouse 8x60 microarrays.

first: Carmen

last: Sánchez-Jiménez

first: José

middle: M

last: Izquierdo


title: Gene expression alteration in chondrocyte by A-CEBP overexpression.

status: Public on Nov 01 2014

city: TOKYO

first: Taku

last: Saito

address: 7-3-1 Hongo, Bunkyo-ku

department: Orthopaedic Surgery, Faculty of Medicine

institute: The University of Tokyo

summary: To investigate loss-of-function of the C/EBP family members, we used A-CEBP which exerts a dominant-negative effect against all CEBPs. DOX-inducible overexpression of A-CEBP into mouse chondrocyte cell line ATDC5 increased expressions of early differentiation markers, decreased those of late differentiation markers. In addition, A-CEBP altered many genes related with skeletal development, cartilage, cell cycle, inflammation and apoptosis.

overall_design: We established stable ATDC5 cells which express GFP or A-CEBP by DOX induction. We started differentiation of these cells by ITS supplement immediately after DOX induction, harvested mRNA after 3 weeks, and performed microarray analysis.

first: Tomotake

last: Okuma


title: Expression profile of BCR-ABL1-transformed, Cdk4 R24C, Cdk6 R31C cell lines

status: Public on Nov 04 2014

city: Madrid

first: Marcos

last: Malumbres

address: Melchor Fernandez Almagro 3

department: Molecular Oncology

institute: Centro Nacional de Investigaciones Oncológicas (CNIO)

summary: Cdk4 and Cdk6 are two related kinases that bind D-type cyclins and regulate cell cycle progression. Due to their relevance in cancer, Cdk4/6 inhibitors are currently in advanced clinical trials in multiple tumor types. Cdk4/6 are inhibited by INK4 proteins that exert tumor suppressing functions. To test the significance of this inhibitory mechanism we have generated knock-in mice that express a Cdk6 mutant (Cdk6 R31C) insensitive to INK4-mediated inhibition. Cdk6R/R mice display altered development of the hematopoietic system without resulting in enhanced tumor susceptibility, either in the presence or absence of p53. The presence of the Cdk6 R31C allele results in defective potential of hematopoietic progenitors in adoptive transfer assays or after induced damage. These defects are rescued after complete insensitivity to INK4 inhibitors in Cdk4R/R; Cdk6R/R double mutant mice, and INK4-resistant mice display increased susceptibility to hematopoietic and endocrine tumors. In BCR-ABL-transformed hematopoietic cells, the presence of the Cdk6 R31C allele results in increased binding of p16INK4a to wild-type Cdk4, whereas the double mutant is fully insensitive to INK4 inhibitors resulting in accelerated disease onset. Our observations reveal that Cdk4 and Cdk6 cooperate in tumor development and suggest a role for Cdk6 in buffering INK4 protein levels thus contributing to the development of hematopoietic tumors. The presence of the Cdk4 R24C and Cdk6 R31C alleles results in relevant changes in the expression profiles of cancer cells including deregulation of apoptosis and other processes.

overall_design:
p185BCR-ABL1 was used to transform wild-type or double knock-in Cdk4 R24C; Cdk6 R31C fetal livers. Cell lines were isolated as spontaneous immortal and transformed clones after transduction of fetal liver with a p185 BCR-ABL1-transgene. RNA was isolated from asynchronous cultures.
Two-condition experiment, Cdk4R-Cdk6R cells versus wild-type cells. Biological replicates: 3 control replicates, 3 transfected replicates.

first: Malumbres

last: Marcos

first: Sexl

last: Veronika


title: Systems analysis of transcriptional data provides insights into muscle's biological response to botulinum toxin-A (BoNT-A)

city: La Jolla

first: Kavitha

last: Mukund

state: California

address: 9500 Gilman Drive #0412

institute: University of California, San Diego

summary: Introduction:The purpose of this study is to provide athe first global transcriptomic profiling and systems analysis of BoNT-A treated muscle over a one year period. Microarray analysis was performed on rat TA muscle from 4 groups (n=4/group) at 1,4, 12 and 52 weeks after BoNT-A injection and saline injected rats at 12 weeks as control. Fold changes were computed at each time point with respect to control. Results: Dramatic transcriptional adaptation occurs at 1 week with a paradoxical increase in expression of slow and immature isoforms; increased expression of genes in competing pathways of repair and atrophy; impaired mitochondrial biogenesis and increased metal ion imbalance. ECM adaptations occurred at 4weeks to the basal lamina and fibrillar ECM. The muscle transcriptome returned to the unperturbed state 12 weeks post-injection. Conclusion: Transcriptional adaptations resemble denervated muscle albeit some differences. Overall gene expression, across time, correlates with the generally accepted BoNT-A time course.

overall_design: Samples of Tibialis anterior (TA) muscle from 4 groups (n=4/group) of rats sacrificed at 1, 4, 12, and 52 weeks after BoNT-A injection, subject to affymetrix microarray analysis. In addition, contralateral TA from saline injected rats extracted at 12 weeks after saline injection was used as control tissue for the microarray analysis.

first: Margie

last: Mathewson

first: Viviane

last: Minamoto

first: Samuel

middle: R

last: Ward

first: Shankar

last: Subramaniam

first: Richard

middle: L

last: Lieber


title: The PDZ-binding motif of SARS-CoV envelope protein is a determinant of viral pathogenesis

status: Public on Oct 31 2014

summary: A recombinant SARS-CoV lacking the envelope (E) protein is attenuated in vivo. Here we report that E protein PDZ-binding motif (PBM), a domain involved in protein-protein interactions, is a major virulence determinant in vivo. Elimination of SARS-CoV E protein PBM by using reverse genetics led to attenuated viruses (SARS-CoV-mutPBM) and to a reduction in the deleterious exacerbate immune response triggered during infection with the parental virus (SARS-CoV-wt). Cellular protein syntenin bound E protein PBM during SARS-CoV infection. Syntenin activates p38 MAPK leading to overexpression of inflammatory cytokines, and we have shown that active p38 MAPK was reduced in lungs of mice infected with SARS-CoVs lacking E protein PBM (SARS-CoV-mutPBM) as compared with the parental virus (SARS-CoV-wt), leading to a decreased expression of inflammatory cytokines and to viral attenuation. Therefore, E protein PBM is a virulence factor that activates pathogenic immune response most likely by using syntenin as a mediator of p38 MAPK induced inflammation.

overall_design: Three biological replicates were independently hybridized (one channel per slide) for each sample type (SARS-CoV-wt, SARS-CoV-mutPBM, Mock). Slides were Sure Print G3 Agilent 8x60K Mouse (G4852A-028005)

last: Jiménez-Guardeño

last: Nieto-Torres

first: Marta

last: DeDiego

last: Regla-Nava

first: Raul

last: Fernández-Delgado

first: Carlos

last: Castaño-Rodríguez

first: Luis

last: Enjuanes


title: Gene expression profiles of mouse embryonic stem cells (mESCs) after genetic depletion of Id1 and knock-down of Zrf1

city: Barcelona

first: Enrique

last: Blanco

address: Dr. Aiguader 88

department: Gene Regulation, Stem Cells and Cancer

institute: Center for Genomic Regulation (CRG)

summary: Id proteins are dominant negative regulators within the HLH family of proteins. In embryonic stem cells (ESCs), Id1 and Id3 maintain the pluripotent state by preventing neural differentiation. The Id1-interacting protein Zrf1 plays a crucial role as a chromatin-bound factor in specification of the neural fate from ESCs. Here, we show that Id1 blocks Zrf1 recruitment to chromatin, thus preventing the activation of neural genes during ESC differentiation. Moreover, genetic deletion of Id1 in ESCs caused misexpression of more than 6000 genes. Interestingly, the expression of almost half of those genes was restored upon further depletion of Zrf1. We therefore identified Zrf1 as a transcriptional regulator downstream of Id1 in ESCs.

overall_design: In Id1KO mESCs, Zrf1 expression was depleted by using shRNAs. Four replicates corresponding to four independent biological samples per group were collected.

first: Luigi

last: Aloia

first: Arantxa

last: Gutierrez

first: Luciano

last: Di Croce


title: The transcription repressors Bach2 and Bach1 promote B cell development by repressing the myeloid program

status: Public on Oct 26 2014

city: Sendai

first: ari

last: itoh

state: Miyagi

address: 2-1 Seiryo-machi, Aobaku

institute: Tohoku univ.

summary: Mature lymphoid cells express the transcriptional repressor Bach2, which imposes regulation on humoral and cellular immunity. Here we found critical roles for Bach2 in the development of cells of the B lineage, commencing from the common lymphoid progenitor (CLP) stage, with Bach1 as an auxiliary. Overexpression of Bach2 in pre-pro-B cells deficient in the transcription factor EBF1 and single-cell analysis of CLPs revealed that Bach2 and Bach1 repressed the expression of genes important for myeloid cells (‘myeloid genes’). Bach2 and Bach1 bound to presumptive regulatory regions of the myeloid genes. Bach2hi CLPs showed resistance to myeloid differentiation even when cultured under myeloid conditions. Our results suggest that Bach2 functions with Bach1 and EBF1 to promote B cell development by repressing myeloid genes in CLPs.

overall_design: WT and Bach1 and Bach2 double deficient (DD) CLPs. Multipotent progenitors (MPPs) infected with control-GFP and Bach2-GFP and cultured several condition. Follicular B cells (Fo B) stimulated with IgM. Three expreriments was performed in this paper.

first: Ari

last: Itoh-Nakadai

first: Yuichi

last: Miura

first: Kazuhiko

last: Igarashi


title: DNA Methylation Across Monozygotic Twin Pairs and Their Parents

status: Public on Sep 30 2014

city: London

first: Christina

last: Castellani

state: Ontario

address: Biological and Geological Sciences Building

department: Biology

country: Canada

institute: The University of Western Ontario

type: Methylation profiling by genome tiling array

summary: Two families with monozygotic twins discordant for schizophrenia

overall_design: NimbleGen Human DNA Methylation 3x720k CpG Island Plus RefSeq Promoter Microarray

first: Shiva

last: Singh


title: Expression data from rat adult and pups heart and hippocampal tissue.

status: Public on Oct 14 2014

city: Philadelphia

first: Junhyong

last: Kim

state: PA

address: 433 S University Avenue

institute: University of Pennsylvania

summary: To assess in order to assess potential disparities in gene expression due to developmental differences we performed a comparison between hippocampus and heart tissues from rat and mouse pup (one week old) and adult (10 week old) animals.

overall_design: Using heart and hippocampal tissue from mouse  (C57BL/6) and rat (Sprague Dawley) we investigate via microarrays, gene expression divergence at the tissue level between a Brain and a Non-brain tissue. We also investigated any developement difference in gene expression between pups and adult animals. For the pups samples we used 3 biological replicates and for the adult samples we used 2 biological replicates with 2 technical replicates for each.

first: Chantal

last: Francis

first: Shreedhar

last: Natarajan

first: Miler

last: Lee

first: Mugdha

last: Khaladkar

first: Peter

last: Buckley

first: Jai-Yoon

last: Sul

first: James

last: Eberwine


title: Secreted Frizzled-Related Protein 5 is Downregulated in Obesity and Promotes β-Cell Proliferation

status: Public on Oct 10 2014

city: Genève

first: Jordi

last: Altirriba

address: Rue Michel-Servet 1

department: Dpts de Médecine Interne et de Physiologie cellulaire et Métabolisme

country: Switzerland

institute: Centre Médical Universitaire de Genève

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

overall_design: Refer to individual Series

first: Sandra

last: Rebuffat

first: Joana

last: Oliveira

first: Nuria

last: Palau

first: Ainhoa

last: Garcia

first: Yaiza

last: Esteban

first: Belen

last: Nadal

first: Ramon

last: Gomis


title: Expression data from Soma dissected from single-cell rat Hippocampal neurons

summary: To assess neuronal expression divergence between mice and rats, we used the Affymetrix array platform to assay the transcriptomes of micro-dissected individual soma and pool of dendrites of hippocampal neurons in dispersed primary cell cultures from  rat and  mouse.

overall_design: Using microdissected soma and dendrites from primary cultures of hippocampal neurons of two mouse strains (C57BL/6 and Balb/c) and one rat strain (Sprague-Dawley), we investigate via microarrays, subcellular localization of mRNAs in neurons


title: Transcription in wounded rat vocal folds and vocal fold fibroblasts

status: Public on Oct 09 2014

city: Madison

first: Nathan

last: Welham

state: WI

address: K4/723 CSC, 600 Highland Avenue

institute: University of Wisconsin School of Medicine and Public Health

summary: We used microarrays to characterize transcriptome profiles of rat vocal fold tissue following surgical injury (vs. naive tissue); rat vocal fold fibroblasts harvested from scar tissue at the 60 d time point (vs. naive fibroblasts);  rat vocal fold scar fibroblasts treated with siRNA against the collagen chaperone protein rat gp46 (vs. scramble siRNA).

overall_design: Adult Fischer 344 rat vocal fold tissue was harvested at 3, 14, and 60 days following surgical injury (control = age-matched naive tissue); rat vocal fold scar fibroblasts were obtained via explant culture of tissue obtained 60 days following surgical injury and harvested at 80% confluence during passage 1 (control = age-matched naive rat vocal fold fibroblasts); rat vocal fold scar fibroblasts were treated for 1 h with 50 nM liposome-delivered siRNA against rat gp46 when 80% confluent at passage 1, cultured for an additional 24 h in fresh media, then harvested (control = rat vocal fold scar fibroblasts treated with 50 nM liposome-delivered scramble siRNA).


title: wnt1-induced mammary tumor from Rarb KO mice vs. those from Rarb wt (control)

status: Public on Oct 23 2014

city: Montréal

first: Xingxing

last: LIU

state: QC

address: 1160 Pine Ave

department: Biochemistry, GCC

institute: McGill University

summary: Previously we have demonstrated that inactivation of retinoic acid receptor beta (Rarb) in the mouse results in a protective effect against ErbB2-induced mammary gland tumorigenesis although Rarb has been reported as a tumor suppressor before. In the current study, we further confirmed that ablation of Rarb has a very similar impact on Wnt1-induced mammary gland tumorigenesis as those on ErbB2-induced mammary gland tumorigenesis. Nevertheless, the mechanisms by which Rarb confers its effects on tumor progression is quite different although both involving in tumor microenvironment (TME) remodeling. In the Wnt1 tumors, ectopic wnt1 produced by malignant luminal cells activates nearby stromal cells by a paracrine manner. In return, the stromal cells secreted IGF1 to regulate the growth of tumor cells. There is a need of Rarb expression in this interaction. Deletion of Rarb inhibits both wnt1/β-catenin signaling and IGF1/Akt axis in the myoepithelial tumor cells which results in the suppression of epithelial-mesenchymal transition (EMT) in these tumors. Since wnt1 tumors resemble basal-like breast cancer with a poor clinical prognosis in which EMT is one of the most important way for tumor cells to survive against standard treatment and to go to metastasis, we propose that (1) the stromal gene expression signature of Rarb ablation in wnt1 tumors could have some clinical value in predicting the breast cancer outcome; and (2) Rarb antagonist might be a potential therapeutic strategy in EMT-driven aggressive cancers such as basal-like breast cancer.

overall_design: Laser capture microdissection (LCM) was performed to separate the mammary tumor samples into epithelial cell compartment and stromal cell compartment. Transcriptional profiling of the two compartments were investigated by microarray analysis.

last: Liu

first: Vincent

last: Giguere


title: Lymphoid progenitor gene expression in Notch1 activated Gfi1-deleted cells

status: Public on Oct 01 2014

city: Cincinnati

first: H. Leighton

last: Grimes

state: OH

address: 3333 Burnet Ave. MLC 7038

department: Immunobiology

institute: Cincinnati Childrens Hospital Medical Center

summary: Growth factor independent 1 (Gfi1) is a transcriptional repressor originally identified as a common integration site in Moloney-murine-leukemia-virus-induced T-cell leukemia. Gfi1-/- mice display increased apoptosis of developing thymocytes and T lymphopenia; however, there are contradictory reports of the absolute number of Gfi1-/- early T lineage progenitors. We used floxed alleles of Gfi1 crossed to various T-cell-specific Cre transgenes to map the requirements for Gfi1 during lymphoid priming and development.  We show that Gfi1 is necessary for the proper formation and function of both lymphoid-primed multipotent progenitors and early T lineage progenitors.  These defects correlate with a global inability of Gfi1-/- progenitors to enforce the activation of lymphoid genes including IL7R, Rag1, Flt3 and Notch1.  Forced expression of intracellular Notch1 fails to rescue the Gfi1-/- defective lymphoid gene signature or Gfi1-/- T cell development.  Instead, activation of Notch1 in Gfi1-/- cells results in a potent synthetic lethal phenotype that is most dramatic in immature thymocytes, but absent in mature peripheral T cells where developmental transcriptional programs are silent.  Moreover, we find that the requirement for Gfi1-transcriptional integration of Notch-driven lymphoid transcriptional programs is cell autonomous. Our data indicate that Gfi1 is required at multiple independent stages of lymphoid development.  In hematopoietic progenitors Gfi1 is necessary to integrate Notch1 signaling, mediate lymphoid priming, the formation of early T lineage progenitors and subsequent T lineage commitment.

overall_design: Lineage negative cells were purified by magnetic beads from RosaCreERT2 Gfi1 ex4-5 floxed mice and an activated Notch1 signal was introduced using a GFP+ retroviral vector.  GFP+ progenitors were FACS-sorted and cultured in semi-solid media for one week to allow sufficient time to to instruct lymphoid differentiation, then replated in 1uM 4-OHT or EtOH control.  After an additional 7 days, CFU were disrupted and RNA was isolated for global gene expression using microarrays.

first: H

last: Phelan


title: Genotoxic, epigenetic, and transcriptomic effects of tamoxifen in mouse liver

status: Public on Oct 11 2014

city: Jefferson

first: Volodymyr

last: Tryndyak

address: 3900 NCTR Rd

department: Division of Biochemical Toxicology

institute: US-FDA National Center for Toxicological Research

summary: Tamoxifen is a non-steroidal anti-estrogenic drug widely used for the treatment and prevention of breast cancer in women; however, there is evidence that tamoxifen is hepatocarcinogenic in rats, but not in mice. Additionally, it has been reported that tamoxifen may cause non-alcoholic fatty liver disease (NAFLD) in humans and experimental animals. The goals of the present study were to (i) investigate the mechanisms of the resistance of mice to tamoxifen-induced hepatocarcinogenesis, and (ii) clarify effects of tamoxifen on NAFLD-associated liver injury. Feeding female WSB/EiJ mice a 420 p.p.m. tamoxifen-containing diet for 12 weeks resulted in an accumulation of tamoxifen-DNA adducts, (E)-α-(deoxyguanosin-N2-yl)-tamoxifen (dG-TAM) and (E)-α-(deoxyguanosin-N2-yl)-N-desmethyltamoxifen (dG-DesMeTAM), in the livers. The levels of hepatic dG-TAM and dG-DesMeTAM DNA adducts in tamoxifen-treated mice were 578 and 340 adducts/108 nucleotides, respectively, while the extent of global DNA and repetitive elements methylation and histone modifications did not differ from the values in control mice. Additionally, there was no biochemical or histopathological evidence of NAFLD-associated liver injury in mice treated with tamoxifen. A transcriptomic analysis of differentially expressed genes demonstrated that tamoxifen caused predominantly down-regulation of hepatic lipid metabolism genes accompanied by a distinct over-expression of the lipocalin 13 (Lcn13) and peroxisome proliferator receptor gamma (Pparγ), which may prevent the development of NAFLD. The results of the present study demonstrate that the resistance of mice to tamoxifen-induced liver carcinogenesis may be associated with its ability to induce genotoxic alterations only without affecting the cellular epigenome and an inability of tamoxifen to induce the development of NAFLD.

overall_design: Female and male WSB/EiJ mice were fed diet containing 420 p.p.m. tamoxifen for 12 weeks, and then tamoxifen-DNA adduct formation and gene expression profiles in the livers from four control and four tamoxifen-treated mice were investigated.

first: Aline

last: de Conti

first: Mona

middle: I

last: Churchwell

first: Tao

last: Han

last: Fuscoe

first: John

last: Latendresse

first: Levan

last: Muskhelishvili

first: Frederick

last: Beland

first: Igor

last: Pogribny


title: Overlapping DNA methylation dynamics in mouse intestinal cell differentiation and early stages of malignant progression

status: Public on Sep 11 2014

first: Miguel

last: Peinado

summary: Mouse models of intestinal crypt cell differentiation and tumorigenesis have been used to characterize the molecular mechanisms underlying both processes. DNA methylation is a key epigenetic mark and plays an important role in cell identity and differentiation programs and cancer.  To get insights into the dynamics of cell differentiation and malignant transformation we have compared the DNA methylation profiles along the mouse small intestine crypt and early stages of carcinogenesis. Genome-scale analysis of DNA methylation together with microarray gene expression have been applied to compare intestinal crypt stem cells (EphB2positive), differentiated cells (EphB2negative), ApcMin/+ adenomas and the corresponding non-tumor adjacent tissue, together with small and large intestine samples and the colon cancer cell line CT26.   Compared with late stages, small intestine crypt differentiation and early stages of carcinogenesis display few and relatively small changes in DNA methylation. Hypermethylated loci are largely shared by the two processes and affect the proximities of promoter and enhancer regions, with enrichment in genes regulated by PRC2 and associated with the intestinal stem cell signature. The hypermethylation is progressive, with minute levels in differentiated cells, as compared with intestinal stem cells, and reaching full methylation in advanced stages. Hypomethylation shows different signatures in differentiation and cancer and is already present in the non-tumor tissue adjacent to the adenomas in ApcMin/+mice, but at lower levels than advanced cancers. Taking into account the parallelisms between human and mouse intestinal carcinogenesis, this study provides a reference framework to interpret the alterations found in human cancer.

overall_design: We have analyzed ApcMin/+ adenomas and the corresponding non-tumor adjacent tissue, together with small and large intestine samples and the colon cancer cell line CT26. Samples were in triplicates, except for  tissue adjacent to adenoma (in duplicates).

first: Marta

last: Forn


title: Heterogeneous stock rats that differ in glucose tolerance

status: Public on Sep 18 2014

city: Milwaukee

first: Leah

last: Solberg Woods

address: 8701 Watertown Plank Road

department: Pediatrics

institute: Medical College of Wisconsin

type:
Expression profiling by array
SNP genotyping by SNP array


title: Cerebellar oxidative DNA damage and altered DNA methylation in the BTBR T+tf/J mouse model of autism and similarities with human post mortem cerebellum.

summary: The molecular pathogenesis of autism is complex and involves numerous genomic, epigenomic, proteomic, metabolic, and physiological alterations.  Elucidating and understanding the molecular processes underlying the pathogenesis of autism is critical for effective clinical management and prevention of this disorder.  The goal of this study is to investigate key molecular alterations postulated to play a role in autism and their role in the pathophysiology of autism.  In this study we demonstrate that DNA isolated from the cerebellum of BTBR T+tf/J mice, a relevant mouse model of autism, and from human post-mortem cerebellum of individuals with autism, are both characterized by an increased levels of 8-oxo-7-hydrodeoxyguanosine (8-oxodG), 5-methylcytosine (5mC), and 5-hydroxymethylcytosine (5hmC).  The increase in 8-oxodG and 5mC content was associated with a markedly reduced expression of the 8-oxoguanine DNA-glycosylase 1 (Ogg1) and increased expression of de novo DNA methyltransferases 3a and 3b (Dnmt3a and Dnmt3b).  Interestingly, a rise in the level of 5hmC occurred without changes in the expression of ten-eleven translocation expression 1 (Tet1) and Tet2 genes, but significantly correlated with the presence of 8-oxodG in DNA.  This finding and similar elevation in 8-oxodG in cerebellum of individuals with autism and in the BTBR T+tf/J mouse model warrant future large-scale studies to specifically address the role of genetic alterations in OGG1 in pathogenesis of autism.

overall_design: Gene expression profiles in the cerebellum of 8 weeks old  BTBR T+tf/J mice that exhibit an autism-like behavioral phenotype and control C57BL/6J mice were examined using high-throughput Agilent whole genome 8x60K mouse microarrays.

first: Svitlana

last: Shpyleva

first: Samuil

last: Ivanovsky

first: Jill

middle: S

last: James


title: Quercetin decreases high-fat diet induced bodyweight gain and accumulation of hepatic and circulating lipids in mice.

city: Wageningen

first: Evert

middle: M.

last: van Schothorst

address: De Elst 1

institute: Wageningen University

summary: Dietary flavonoids are supposed to be protective against cardiovascular diseases (CVD). Elevated circulating lipid levels and hepatic lipid accumulation are known risk factors for CVD. We investigated the effects and underlying molecular mechanisms of the flavonoid quercetin on hepatic lipid metabolism in mice with diet induced body weight gain and hepatic lipid accumulation. Adult male mice received a high-fat diet without or with supplementation of 0.33% (w/w) quercetin for 12 weeks. Body weight gain was 29% lower in quercetin-fed mice (p<0.01), while the energy intake was not significantly different. Quercetin supplementation reduced hepatic lipid accumulation with 71% (p<0.05). 1H nuclear magnetic resonance serum lipid profiling revealed that the supplementation lowered serum lipids (p<0.0001). Global gene expression profiling of liver showed that key target genes of the transcription factor Constitutive androstane receptor (Car; official symbol Nr1i3) were regulated, in particular Cytochrome P450 2b (Cyp2b) genes. Quercetin can decrease high-fat diet induced body weight gain, hepatic lipid accumulation and serum lipid levels, which might be explained by the regulation of Cytochrome P450 genes under transcriptional control of CAR, an effect which is likely dependent on dietary background.

overall_design: Liver samples were obtained from 24 C57BL/6J male adult mice. All mice started with a three week adaptation phase, in which they were fed a normal-fat diet.  During the intervention of 12 weeks, the mice received a high-fat diet without (HF) or with supplementation of 0.33% (w/w) quercetin (HF-Q). Based on visual inspection, three arrays lacked homogenous hybridization and were therefore excluded.

first: Elise

last: Hoek-van den Hil

first: Jaap

last: Keijer


title: Secreted Frizzled-Related Protein 5 is Downregulated in Obesity and Promotes β-Cell Proliferation [10 days]

first: Jordi

last: Altirriba

summary: Obesity is associated with an increase in β-cell mass in response to the rising demand for insulin. β-cell plasticity is essential to maintaining glucose homeostasis, however, the cellular and molecular mechanisms by which β-cell mass is regulated remain poorly understood. Recently, we described the existence of a crosstalk between the peripancreatic adipose tissue and β-cells as a novel mechanism that participates in the regulation of β-cell plasticity. Here, we identify the secreted frizzled-related protein (Sfrp) 5 as down-regulated in the pancreatic islets of obese rats as well as in the pancreatic islets of human obese patients. Our results demonstrate that the silencing of Sfrp5 induces an increase in β-cell proliferation, which we correlate with the activation of Wnt signaling and of the MAPK and PI3 kinase pathways. Together, these findings expand our understanding of the mechanisms underlying β-cell proliferation under conditions of obesity. Furthermore, this study opens new insights into the specific targeting of Sfrp5 as a novel therapeutic strategy for balancing β-cell mass.

overall_design: Adult male Wistar rats (Charles River Laboratories, Wilmington, MA), 7 wk old (weighing 225–250 g), were caged individually in a 12-h light, 12-h dark cycle in a temperature- and humidity-controlled environment. Animals were divided into two dietary sets for 10 days. One group was fed with standard chow diet (supplying 8% of calories as fat; type AO4 from Panlab, Barcelona, Spain). The second group was fed with a cafeteria diet (66% of calories as fat), as previously described (Endocrinology 2012;153:177-87). Pancreatic islets were isolated through collagenase perfusion of the pancreas, Histopaque gradient and hand-picking under microscopic guidance. Ten micrograms of total RNA from islets were converted into cRNA, biotinylated, fragmented, and hybridized to GeneChip Rat Genome 230 2.0 (Affymetrix, Santa Clara, CA). Ten microarrays were hybridized, five with independent samples coming from rats fed with standard chow (lean group) and five with independent samples coming from rats fed with the cafeteria diet (obese group).

first: Sandra

last: Rebuffat

first: Joana

last: Oliveira

first: Nuria

last: Palau

first: Ainhoa

last: Garcia

first: Yaiza

last: Esteban

first: Belen

last: Nadal

first: Ramon

last: Gomis


title: Secreted Frizzled-Related Protein 5 is Downregulated in Obesity and Promotes β-Cell Proliferation [30 days]

overall_design: Adult male Wistar rats (Charles River Laboratories, Wilmington, MA), 7 wk old (weighing 225–250 g), were caged individually in a 12-h light, 12-h dark cycle in a temperature- and humidity-controlled environment. Animals were divided into two dietary sets for 30 days. One group was fed with standard chow diet (supplying 8% of calories as fat; type AO4 from Panlab, Barcelona, Spain). The second group was fed with a cafeteria diet (66% of calories as fat), as previously described (Endocrinology 2012;153:177-87). Pancreatic islets were isolated through collagenase perfusion of the pancreas, Histopaque gradient and hand-picking under microscopic guidance. Ten micrograms of total RNA from islets were converted into cRNA, biotinylated, fragmented, and hybridized to GeneChip Rat Genome 230 2.0 (Affymetrix, Santa Clara, CA). Ten microarrays were hybridized, five with independent samples coming from rats fed with standard chow (lean group) and five with independent samples coming from rats fed with the cafeteria diet (obese group).


title: Expression data from rat dissected dendrites

first: Junhyong

last: Kim

summary: Using microdissected dendrites from primary cultures of hippocampal neurons of two mouse strains (C57BL/6 and Balb/c) and one rat strain (Sprague-Dawley), we investigate via microarrays, subcellular localization of mRNAs in dendrites of neurons to assay the evolutionary differences in subcellular dendritic transcripts localization.

overall_design: To assess neuronal dendrite expression divergence between mice and rats, we used the Affymetrix array platform to assay the transcriptomes of micro-dissected individual dendrites of hippocampal neurons in dispersed primary cell cultures from Sprague-Dawley rat (9 biological replicates), C57BL/6 mouse  (14 biological replicates), and Balb/c mouse (5 biological replicates)

first: Chantal

last: Francis

first: Shreedhar

last: Natarajan

first: Miler

last: Lee

first: Mugdha

last: Khaladkar

first: Peter

last: Buckley

first: Jai-Yoon

last: Sul

first: James

last: Eberwine


title: Analysis of conditional loss of Geminin in neural tube and paraxial tissues at E10.5 by laser capture microdissection

city: Saint Louis

first: Kristen

last: Kroll

state: MO

address: 320 McDonnell Sciences/660 S. Euclid Ave.

department: Developmental Biology

institute: Washington University School of Medicine

summary: To better understand the role of Geminin during germ layer specification, we bred floxed Geminin mice to Mox2-Cre mice. Mutants (fl/fl; cre/o) had spinal neural tube defects with complete penetrance.  We obtained neural tube and paraxial tissue by laser capture microdissection and analyzed total RNA by microarray.

overall_design: Spinal neural tube and paraxial tissue were obtained separately by laser capture microdissection from wild-type and mutant E10.5 embryos. There were 2 replicates of each sample.

first: Ethan

last: Patterson

first: Laura

last: Dieden


title: Gene expression profiles in the heart tissues of heart-specific Bmal1 knockout mice

status: Public on Sep 27 2014

city: Wakayama

first: Akira

last: Kohsaka

address: 811-1, Kimiidera

department: Physiology

institute: Wakayama Medical University

summary: Mice without cardiac Bmal1 function develop severe progressive heart failure with age.  To examine the mechanism underlying the failing heart phenotype observed in heart-specific Bmal1 knockout mice, microarray analyses were performed.  The analyses revealed that broad classes of genes regulating cellular energy metabolism were upregulated or downregulated in the heart tissues of heart-specific Bmal1 knockout mice compared with those of control animals.

overall_design: Heart total RNA extracted from six animals per genotype (control and heart-specific Bmal1 knockout) was pooled and then used for a microarray analysis.


title: Gene expression analysis in the lungs of Fra-2 Transgenic mice

status: Public on Sep 26 2014

city: Giessen

first: Jochen

last: Wilhelm

state: Hessen

address: Aulweg 132

department: Institute for Lung Health

institute: Justus-Liebig University Giessen

summary: The aim of this experiment is to identify novel gene candidates being regulated in Fra-2 overexpressing mice. Fra-2 over-expressing mice (Fra-2 TG) develop vascular remodeling and pulmonary fibrosis. Fra-2, as a trascription factor, is responsible for downstream target genes expression. Comparison of the mRNA expressed from WT  and Fra-2 TG  animals will help to identify Fra-2 target genes. The microarray analysis will be performed in mRNA isolated from  lung homogenate. The lungs of the mice were extensively perfused. The right part was snap-froen and transfered to (-80°C). The total RNA was isolated and quantified.

overall_design: Comparison of transgenes vs. wild-types. Hybridization of samples from 4 wild-type and 4 transgene animals = 8 single-color hybridizations

first: Willhelm

last: Jochen

first: Biasin

last: Valentina


title: Gene expression of the intermediate and outer interzone of murine embryos at 15.5 days of gestation

status: Public on Sep 22 2014

city: Vienna

first: Florien

last: Jenner

address: Veterinärplatz 1

department: Equine Surgery

country: Austria

institute: University of Veterinary Medicine Vienna

summary: Nascent embryonic joints, interzones, contain a distinct cohort of progenitor cells responsible for the formation of the majority of articular tissues. However, to date the interzone has largely been studied using in situ analysis for candidate genes in the context of the embryo rather than using an unbiased genome wide expression analysis on isolated interzone cells, leaving significant controversy regarding the exact role of the intermediate and outer interzone layers in joint formation. Therefore, in this study, using laser capture microdissection (three biological replicates), we selectively harvested the intermediate and outer interzones of mouse embryos at gestational age 15.5 days, just prior to cavitation, when the differences between the layers should be most profound. Microarray analysis (Agilent Whole Mouse Genome Oligo Microarrays) was performed and the differential gene expression between the intermediate interzone cells and outer interzone cells was examined by performing a 2-sided paired student t-test and pathway analysis. 197 genes were differentially expressed (≥ 2-fold) between the intermediate interzone and the outer interzone with a p-value ≤ 0.01. Of these, 91 genes showed higher expression levels in the intermediate interzone and 106 were expressed higher in the outer interzone. Pathway analysis of differentially expressed genes suggests an important role for inflammatory processes in the interzone layers, especially in the intermediate interzone, and hence in joint and articular cartilage development. The high representation of genes relevant to chondrocyte hypertrophy and endochondral ossification in the outer interzone suggests that it undergoes endochondral ossification.

overall_design: 2 study groups (intermediate and outer interzone) with three biological replicates (1 biological replicate = 1 embryo)

first: Arne

last: Ijpma

first: Mairead

last: Cleary

first: Daphne

last: Heijsman

first: Roberto

last: Narcisi

last: van der Spek

first: Andreas

last: Kremer

first: Rene

last: van Weeren

first: Pieter

last: Brama

first: Gerjo

last: van Osch


title: Gene expression profiles in heterogeneous stock rats that differ in glucose tolerance

first: Leah

middle: C

last: Solberg Woods

summary: Using heterogeneous stock (HS) rats, we have identified a region on rat chromosome 1 that maps multiple diabetic traits.  We sought to use global expression analysis to determine if genes within this region are differentially expressed between HS rats with normal glucose tolerance and those with glucose intolerance

overall_design: HS rats were euthanized at 17 weeks of age and liver was immediately frozen in liquid nitrogen.  RNA was extracted from liver of 23 HS rats with glucose intolerance and 23 HS rats with normal glucose.  The Affymetrix 230_2 array was used to probe transcript abundance levels.

first: Shirng-Wern

last: Tsaih

first: Katie

last: Holl

first: Shuang

last: Jia

first: Mary

last: Kaldunski

first: Michael

last: Tschannen

first: Jaime

last: Wendt Andrae

first: Shun-Hua

last: Li

first: Alexander

middle: J

last: Stoddard

first: John

last: Parrington

first: Margarida

last: Ruas

first: James

last: Meigs

first: Raymond

middle: G

last: Hoffmann

first: Pippa

last: Simpson

first: Howard

last: Jacob

first: Martin

last: Hessner


title: Expression profiles of globular bushy cells (GBCs) during maturation

status: Public on Jun 24 2014

city: Heidelberg

first: Christoph

last: Koerber

address: Im Neuenheimer Feld 307

department: Institute of Anatomy and Cell Biology

institute: University of Heidelberg

summary:
Calyx of Held giant presynaptic terminals in the medial nucleus of the trapezoid body of the auditory brainstem form axosomatic synapses that have advanced to one of the best-studied synaptic system of the mammalian brain. As the auditory system matures and adjusts to high fidelity synaptic transmission, the calyx undergoes extensive structural and functional changes: it is formed around postnatal day 3 (P3), achieves immature function until hearing onset around P10 and can be considered mature from P21 onwards. This setting provides the unique opportunity to examine the repertoire of genes driving synaptic structure and function.
We  performed cell type-specific gene expression profiling of  globular bushy cells (GBCs), the neurons giving rise to the calyx of Held, at different maturational stages (P3, P8 and P21).

overall_design: We identified GBCs by stereotaxic injection of fluorescently labelled retrograde tracer Cholera toxin B into the contralateral MNTB of anesthetized rats. Animals were sacrificed 24h after injection, the brain was taken out and flash frozen. 12µm thick brainstem cryosections were prepared and 200 fluorescently labelled GBCs per animal were excised from the VCN using laser microdissection. Cells were collected from 6 animals at P3 (synapse formation), 9 animals at P8 (juvenile synapse) and 5 animals at P21 (mature synapse). RNA was isolated from the collected cells and linearly amplified in order to perform cell-type specific expression profiling.

first: Anna

last: Dondzillo

first: Gisela

last: Eisenhardt

first: Oliver

last: Wafzig

first: Thomas

last: Kuner

last: Körber


title: CDH1 knockout in mice

status: Public on Jul 01 2014

city: Munich

first: Stefan

last: Krebs

address: Feodor-Lynen-Str. 25

department: Gene Center

institute: Ludwig-Maximilian University

summary: Employing Cre/loxP technology, a mouse model of liver specific Cdh1 (E-cadherin) depletion was created (fl/fl | +/wt). Previously, the mice had already been compared to littermates with normal Ecadherin levels (fl/fl | wt/wt), using a broad range of laboratory methods (Serum parameters, long-term weight analysis, histology, western blot, etc.). To analyze the effect of Cdh1 (E-Cadherin) depletion on the liver homeostasis on the RNA-level over the course of 3 time-points, liver tissue was aquired from mice groups aged 1 week, 3 weeks and 6 weeks.

overall_design: Mice with liver-specific Cdh1 depletion were compared to wildtype-like littermates. 1 week: n=2+2; 3 weeks: n=3+3; 6 weeks: n=3+3. Samples (mice) were not paired.

first: Marlon

last: Schneider

first: Felix

last: Hiltwein

first: Jessica

last: Grill

first: Helmut

last: Blum

first: Andrea

last: Klanner

last: Bauersachs

first: Christiane

last: Bruns

last: Longerich

first: David

last: Horst

first: Lydia

last: Brandl

first: Enrico

last: de Toni

first: Andreas

last: Herbst

first: Frank

middle: T

last: Kolligs


title: Reprogramming by Sall4, Nanog, Esrrb and Lin28 produces high quality iPSCs with a molecular signature of developmental potency that resembles ESCs.

status: Public on Sep 08 2014

city: Cambridge

first: Yossi

last: Buganim

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute

summary: To reveal a gene expression signature associated with developmental competence, we selected the following groups of iPSC lines for microarray analysis. i) “Poor quality” iPSCs: This group included the three OSKM-iPSC lines Nanog-GFP OSKM#2, Oct4-GFP OSKM#2 and KH2 OSKM27, that either did not produce fully developed pups or produced very low number of pups;  ii) “Good quality” iPSCs: This group included BC_2 OSKM28 and Nanog-GFP SNEL#3, both of which gave rise to live, normal pups that survived only few hours; iii) “High quality” iPSCs consisting of Nanog-GFP SNEL#2 and Oct4-GFP SNEL#1, both of which generated live pups that survived postnatally (representative pups from each iPSC group are shown in Figure S5). iv) As controls we used Nanog-GFP, Oct4-GFP and KH229 ESCs.

overall_design: Poor, good and high quality iPSC lines together with 3 embryonic stem cell lines were subjected to agilent microarray

first: Yosef

first: Styliani

last: Markoulaki

first: Batool

last: Akhtar-Zaidi

first: Yupeng

last: He

first: Prathapan

last: Thiru


title: Murine Abdominal Aortic Aneurysm, PPE Model - In Vivo Modulation of miRNA-24 (Day 7)

status: Public on Aug 31 2014

city: Stanford

first: Joshua

last: Spin

state: CA

address: 300 Pasteur Drive

institute: Stanford University

summary:
Transcriptional profiling of infrarenal aortic tissue from Male 10-week-old C57BL/6J mice after AAA-induction with porcine pancreatic elastase, compared with sham-operated saline-injected mice. One day after AAA-induction, the mice were injected intraperitoneally with either lentiviral packaged miR-24 antagomir (anti-miR-24) or miR-24 mimic (pre-miR-24), or a scrambled microRNA control (scr-miR). Aortic samples were obtained 7 days after operation.
The goal was to examine gene expression in developing AAA in this model, and to compare the effects of scr-miR, anti-miR-24 and pre-miR-24.

overall_design: Four condition experiment, one infrarenal aorta per array. Sham vs. scr-miR-PPE vs. anti-miR-24-PPE vs. pre-miR-24-PPE, all harvested at Day 7 post-operatively. After QC, the final analysis group (uploaded here) consisted of 18 arrays: Sham-Saline-treated (4 arrays), scr-miR-PPE-treated (5 arrays); pre-miR-24-PPE-treated (3 arrays); and anti-miR-24-PPE-treated (6 arrays).


title: Neutrophils promote M2 polarization of macrophages during Nippostrongylus brasiliensis infection

status: Public on Aug 30 2014

city: San Francisco

first: Charlie

last: Kim

address: 1001 Potrero Ave

department: Medicine

institute: University of California, San Francisco

summary: Microarray profiling of amplified total RNA isolated from neutrophils sorted from naïve, Nippostrongylus brasiliensis (Nb)-infected, or lipopolysaccharide (LPS)-treated mice.

overall_design: 2-3 independent replicates collected from each treatment/infection group. RNA isolated and amplified from FACS-sorted neutrophils. Hybridized as a one color experiment.

first: Fei

last: Chen

first: William

last: Gause

first: Eunice

first: Charles


title: Murine Abdominal Aortic Aneurysm, PPE Model: Transcriptional Profiling of Sham vs. AAA at Day 7

summary:
Transcriptional profiling of infrarenal aortic tissue from Male 10-week-old C57BL/6J mice after AAA-induction with porcine pancreatic elastase, compared with sham-operated mice. Includes samples obtained 7 days after aneurysm induction.
Goal was to examine gene expression in developing AAA in this model, and compare with miRNA profiling performed using the same tissue.

overall_design: Two condition experiment, one infrarenal aorta per array. Sham vs. PPE at Day 7 post-operatively. Total 10 arrays: 5 sham D7, 5 PPE D7.


title: Expression data from rats esophagi

status: Public on Aug 16 2014

city: columbus

first: Ni

last: Shi

address: 400w 12th ave

department: comprehensive cancer center

institute: ohio state university

summary: This microarray study was performed to investigate the molecular events in esophageal SCC carcinogenesis in NMBA induced rat esophageal SCC models.

overall_design: Rats were housed 3 per cage under standard conditions: 20 ± 2ºC, 50±10% relative humidity, and 12 hours light/dark cycles. After two weeks of acclimation to the animal facility, the rats were administered s.c. injections of 0.2 ml of either NMBA (0.3 mg/kg body weight) or a 1:4 mixture of dimethyl sulfoxide (DMSO):H2O (the solvent for NMBA) 3 times per week for 5 weeks.

first: Tong


title: Transcriptional profiling of murine porcine-pancreatic elastase-induced abdominal aortic aneurysm at day 7, with parallel miRNA profiling and miR-24 in vivo modulation.

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

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

overall_design: Refer to individual Series


title: Foxo3 Regulated Genes in G1E-ER-GATA-1 Cells

status: Public on Aug 09 2014

first: Andrew

last: DeVilbiss

address: 1111 Highland Ave, WIMR 4028

department: Cell and Regenerative Biology

institute: UW-Madison

summary: The ensemble of Foxo3-regulated genes in the erythroid G1E-ER-GATA-1 cell line was determined by knocking down Foxo3 using siRNA, and measuring genome wide transcription by microarray analysis

overall_design: G1E-ER-GATA-1 cells were treated with  control or Foxo3-specific siRNA by nucleofection at t = 0 h and t = 24 h. At t = 24 h, cells were treated with ß-estradiol to activate ER-GATA-1. RNA was harvested at t = 48 h and processed for microarray analysis.

first: Yoon

last: Kang

first: Skye

last: McIver

middle: W

first: Emery

middle: H

last: Bresnick


title: Exosc8-Regulated Genes in Fetal Liver-Derived Erythroid Progenitor Cells

summary: Exosc8 and Exosc9 are components of the exosome that establish a barricade to erythroid maturation. Here, we knocked down Exosc8 in fetal liver-derived erythroid progenitor cells to determine the cohort of Exosc8-regulated genes in erythroid cells.

overall_design: Freshly isolated fetal liver progenitor cells were infected with retrovirus expressing shRNA targeting either luciferase or Exosc8. Total RNA was isolated from these cells after 3 days ex-vivo culture, during which the cells underwent erythroid maturation.