title: Gene expression of fly testes with meiotic arrest from different mutations

status: Public on Jul 13 2013

city: Ithaca

first: Jongmin

last: Kim

address: 930 Campus Road

department: Biomedical Sciences

institute: Cornell University

summary:
The role of different proteins, Always Early (Aly), Spermatocyte Arrest (Sa), Ubi-p63E (Magn) on the gene expression in spermatocyte differentation was assessed by microarray
ABSTRACT: The ubiquitin proteasome system (UPS) regulates many biological pathways by posttranslationally ubiquitinating proteins for degradation. Although maintaining a dynamic balance between free ubiquitin and ubiquitinated proteins is key to UPS function, the mechanisms that regulate ubiquitin homeostasis in different tissues through development are not clear. Here we show that loss of function of Drosophila magellan (magn), the polyubiquitin Ubi-p63E, results in specifically meiotic arrest sterility in males. Expression of ubiquitin from magn/Ubi-p63E contributes predominantly to maintaining the free ubiquitin pool in testes. Function of magn/Ubip63E is required cell autonomously for proper meiotic chromatin condensation, cell cycle progression and spermatid differentiation. magn/Ubi-p63E mutant germ cells develop normally to the spermatocyte stage but arrest at the G2/M transition of meiosis I with lack of protein expression of key meiotic cell cycle regulators Boule and Cyclin B. Loss of function of magn/Ubi-p63E did not strongly affect the spermatocyte transcription program regulated by the tTAF and tMAC genes. Knocking down proteasome function specifically in spermatocytes caused a different meiotic arrest phenotype, suggesting that the magn/Ubi-p63E phenotype may not result from general defects in protein degradation. Our results suggest a conserved role of polyubiquitin genes in male meiosis and a potential mechanism leading to meiosis I maturation arrest.

overall_design: RNA was obtained from whole testes of flies with following mutations: 1) aly[2]/aly[5p], 2) sa[1]/sa[2], 3) magn[12c]/magn[23b] or magn[12c]/magn[12c];pSC2,  4) red[1], e[1] (WT).  Each genotype had three biological replicates except magn which had four total biological replicates, two from magn[12c]/[23b] and two from [12c]/[12c]; pSC2

first: Chenggang

last: Lu

first: Xin

last: Chen

first: Margaret

middle: T

last: Fuller


title: Structural basis of a novel Interferon b signaling axis mediated via the ifnar1 receptor

city: Clayton

first: Sam

last: Forster

state: Victoria

address: 27 - 31 Wright Street

department: Monash Institute

country: Australia

institute: Monash University

summary: Type I interferons (IFNs) are a family of cytokines that play an important role in regulating immune responses to pathogens and tumors and are used therapeutically.  All IFNs are considered to signal via the heterodimeric IFNAR1-IFNAR2 complex, yet some subtypes such as IFN? can exhibit distinct functional properties, although the molecular basis of this is unclear.  Here we demonstrate IFN  uniquely and specifically ligates to IFNAR1 in an IFNAR2-independent manner and provide the structural basis of the IFNAR1-IFN  interaction. We show that the IFNAR1-IFN  complex transduces signals to modulate the expression of a set of genes independently of IFNAR2.  Moreover, we show the in vivo importance of the IFNAR1-IFN  signaling axis in a murine model of LPS-induced septic shock. Thus, we provide a molecular basis for understanding specific functions of IFN?.

overall_design: Interferon b induced gene expression in peritoneal exudate cells was measured 3hr post intra-peritoneal injection of 10,000IU/ml of interferon beta or saline into wildtype and Ifnar2-/- mice.  Three independant experiments were performed for each treatment in both genotypes using different mice for each sample.

first: Paul

last: Hertzog

first: Nicole

last: De Weerd

first: Jodee

last: Gould


title: Expression data from mouse optic nerve head after optic nerve crush

status: Public on Jul 15 2013

city: Boston

first: Tatjana

last: Jakobs

state: MA

address: 20 Staniford Street

department: Howe Laboratory of Ophthalmology

country: USA

institute: Massachusetts Eye and Ear Infirmary

summary: Reactive gliosis is a complex process that involves profound changes in gene expression. We used microarray to indentify differentially expressed genes and to investigate the molecular mechanisms of reactive gliosis in optic nerve head in response to optic nerve crush injury.

overall_design: C57Bl/6 female mice were 6-8 weeks old at the time of optic nerve crush surgery. The optic nerve in the left eye was crush 1 mm behind the globe for 10 seconds and the right eye served as contralateral control. The animals were allowed to recover for 1 day, 3 day, 1 week, 3 weeks and 3 months before the optic nerve heads were collected. The naive control mice did not receive any surgery in either eye. Due to the small tissue size of the mouse optic nerve head, two optic nerve heads were pooled together for each microarray chip. The left eyes and the right eyes of two mice were combined respectively to form one pair of experiment and control samples. There were five biological replicates (10 mice) for each condition.

first: Juan

last: Qu

middle: C


title: Mice cerbellum extracts: SCA7 KI mice vs. wild type mice

status: Public on Jul 24 2013

city: Paris

first: Morwena

last: Latouche

address: 47 Bd de l'Hôpital

country: France

institute: CRICM

summary:
Transcriptional profiling of mouse cerebellar extract comparing SCA7 KI mice with wild type mice. Female mice were killed by decapitation on post natal days 10 and 22 and 11 weeks.
Goal was to determine gene expression profiles differing between SCA7 KI mice and wild-type mice during post-natal developement of the cerebellum.

overall_design:
Gene expression profiling was performed using RNA extracted from the cerebellum of KI and WT mice at P10 (5 WT and 5 KI), P22 (5 WT and 4 KI) and 11 wks (5WT and 6 KI). After labeling, RNAs were hybridized on dual-label G4122F Agilent® chips; a mix of all P10 samples was used as common reference (green channel). Quality control included visual control of the reconstructed image of the chip, M/A plot, corner intensities, outliers, positive and negative intensities, normalization factors. Normalization and statistical analyses were carried out by using BRB-array Tools developed by Dr. Richard Simon and the BRB-ArrayTools development team (Biometrics Research Branch, http://linus.nci.nih.gov/BRB-ArrayTools.html). Genes with less than 50% present calls or with low variability along the arrays (less than 20% of values with at least 2-fold change in either direction from the gene’s median value) were excluded from further analysis. For the 1905 remaining probes an interaction between time and genotype was analyzed by regression analysis of the time course of expression. In brief, probes for which variation over time differed for the genotype class were fitted to the following model: log expression ~ time + time**2 + genotype + genotype*time + genotype*time**2. A univiariate p-value < 0.001 (random variance model) was set for significant probes (genotype*time + genotype*time**2)  and a False Discovery Rate (FDR) was calculated for each probe (Benjamini & Hochberg, 1995).
Differences in profiles were identified with a Self Organisation Tree Algorithm (MultiplExperiment Viewer (MeV), (Saeed et al, 2006). Expression values were averaged by group and then clustered according to their profile as a function of time.

first: Jean-Christophe

last: Corvol

first: Alice

last: Chort

first: Annie

last: Sittler

first: Giovanni

last: Stevanin

first: Alexis

last: Brice


title: Gene expression changes resulting from attenuation of Dicer activity

status: Public on Jul 17 2013

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: Despite smaller primary tumor burdens, Pten-/-Dicer-/+ mice develop seminal vesicle obstruction at high penetrance by 32 weeks, which is in sharp contrast to that observed in Pten-/- mice. This phenomenon implies that tumors in Pten-/-Dicer-/+ mice are more locally invasive. To corroborate this invasive phenotype, we examined global changes in gene expression using Agilent 44k whole genome expression microarrays. A total of 544 genes were statistically significantly altered by at least 1.4 fold in either Pten-/-Dicer-/+ or Pten-/-Dicer-/- mice, or both mice, as compared with Pten-/- mice. Approximately 22% genes were altered in the same trend in both Pten-/-Dicer-/+ and Pten-/-Dicer-/- mice, while 70% genes were only significantly affected in Pten-/-Dicer-/- mice. Very few genes were differentially regulated between Pten-/-Dicer-/+ and Pten-/-Dicer-/- mice or were only altered in Pten-/-Dicer-/+ mice. Data analysis identified that a list of genes associated with epithelial-mesenchymal transition, cell adhesion, migration, and extracellular matrix deposition are statistically significantly altered in favor of tumor metastasis in the Pten-/-Dicer-/+ mice. QRT-PCR confirmed the changes in expression of some genes including growth factors (Tgfb1 and Ctgf), transcription factors (Snail, Twist2, and Foxc1), protease (MMPs etc.), and extracellular matrix components (Collagens). This finding corroborates the phenotypic invasiveness of the tumors in Pten-/-Dicer-/+ mice at a molecular level.

overall_design:
Cancerous urogenital tissues from Pten-/- (Dicer WT), Pten-/-Dicer-/+ (Dicer HET), and Pten-/-Dicer-/- (Dicer KO) mice were profiled for gene expression, using Agilent microarrays.
multiple group comparison

first: Li

last: Xin

first: Joseph

last: Valdez


title: Expression data from Wild-type (WT) and Alb/AEG-1 mice which are transgenic mice with hepatocyte-specific overexpression of AEG-1 (Astrocyte elevated gene 1)

status: Public on Jul 01 2013

city: Richmond

first: Myrna

last: Serrano

state: VA

address: 1101 East Marshall St

institute: Virginia Commonwealth University

summary:
AEG-1 is overexpressed in human hepatocellular carcinoma (HCC) and positively regulates development and progression of HCC
A transgenic mouse with hepatocyte-specific expression of human AEG-1 was generated using mouse albumin promoter/enhancer in B6/CBA background.

overall_design: Hepatocytes were isolated from WT and Alb/AEG-1 mice for RNA extraction and Affymetrix microarray hybridization.

first: Devanand

last: Sarkar


title: Lactobacillus acidophilus and Helicobacter pylori stimulation of bone marrow derived macrophage

status: Public on Jul 02 2013

first: Sam

last: Forster

summary:
Helicobacter pylori causes chronic gastritis and avoids elimination by the immune system of the infected host. The commensal bacterium Lactobacillus acidophilus has been reported to exert beneficial effects as a supplement during H. pylori eradication therapy.
In the present study, we applied whole genome microarray analysis to compare the immune response induced in murine bone marrow derived macrophages (BMDM) stimulated with L. acidophilus, H. pylori, or with both bacteria in combination

overall_design: Microarray expression profiling was performed to analyze stimulation of bone marrow derived macrophages with Helicobacter pylori 251, Lactobacillus acidophilus NCFM or Lactobacillus acidophilus NCFM co-stimulated with Helicobacter pylori 251 were analyzed 5 hours after infection.

first: Gudrun

last: Weiss

first: Maria

last: Kaparakis-Liaskos


title: High-fat diet-mediated dysbiosis cooperates with oncogenic K-Ras activation to promote intestinal carcinogenesis independently of obesity.

city: München

first: Olivia

last: Prazeres da Costa

state: Bavaria

address: Trogerstr. 30

department: Medical Microbiology, Immunology and Hygiene

country: Germany

institute: Technische Universität München

summary: Several aspects of a Western lifestyle such as increased obesity and decreased physical activity are associated with increased risk for gastrointestinal cancers1. Although high-fat diet (HFD) induced low-grade inflammation has been closely linked to tumorigenesis2, however, the microbial shift that occurs due to diet and consequent alterations in host immunity have merely been considered to play a critical role during carcinogenesis. Here we show that HFD promotes tumor progression in the small intestine of genetically susceptible mice, however, independently of obesity and diet-induced chronic inflammation. HFD consumption cooperates with mutant K-Ras to mediate a shift in the composition of microbiota, which is associated with a decrease in Paneth cell antimicrobial host defense that compromises dendritic cell (DC) recruitment and MHCII presentation in the gut-associated lymphoid tissues (GALTs). DC recruitment in GALTs can be normalized and tumor progression attenuated completely when K-Ras mutant mice are supplemented with the short chain fatty acid butyrate, a bacterial fermentation end product, or partially when provided with probiotics. Importantly, Myd88-deficiency completely blocks tumor progression in K-ras mutants, however, rather by substantial changes in the microbiota than host-mediated signaling mechanisms. Strikingly, transfer of fecal samples from diseased donors into healthy adult K-ras mutants is sufficient to enhance tumor progression in the absence of HFD suggesting a pivotal role for distinct microbiota shifts in aggravating disease in the small intestine. Collectively, these data underscore the reciprocal interaction between host and environmental factors for the composition of intestinal microbiota that favors carcinogenesis and suggest tumor progression could potentially be “transmitted” in genetically predisposed individuals.

overall_design:
13 samples;
S103_396_GroupA_Arkan and S104_429_GroupA_Arkan represent the controls of the first group,
S105_394_GroupB_Arkan and S106_429_GroupB_Arkan represent ViRas (mutated) mice of the first group.
S982_groupA_ 1 and S983_groupA_2 represent the cotrols of the second group,
S984_groupB_3, S985_groupB_4 and S986_groupB_5 represent ViRas (mutant) mice of the second group,
S563_CO1979 represent the control of the third group,
S564_KO1_1231, S565_KO2_1984 and S566_KO3_2013 represent the ViRas (mutant) mice of the third group.
The first group are mice kept on HFD, second group kept on ND and third group kept on HFD plus treated with butyrate

first: Manon

middle: D

last: Schulz

first: Cigdem

last: Atay

first: Jessica

last: Heringer

first: Franziska

middle: K

last: Romrig

first: Begüm

last: Aydin

first: Sarah

last: Schwitalla

first: Paul

last: Ziegler

first: Wolfgang

last: Reindl

first: Buch

last: Thorsten

last: Polson

first: Carl

last: Alpert

first: Michael

last: Blaut

first: Lydia

last: Kriegl

first: Shawn

middle: W

first: Florian

middle: R

last: Greten

first: Thomas

last: Kirchner

first: Melek

last: Arkan


title: TIMP2 and TIMP3 have divergent roles in early renal tubulointerstitial injury

city: Edmonton

first: Zuocheng

last: Wang

address: 407 HMRC

country: Canada

institute: University of Alberta

summary: Tissue inhibitors of metalloproteinases (TIMP) are endogenous inhibitors of matrix metalloproteinases (MMP). While TIMP2 and TIMP3 inhibit MMPs, TIMP3 also inhibits activation of pro-MMP2 whereas TIMP2 promotes it. Here we assessed the differential role of TIMP2 and TIMP3 in renal injury using the unilateral ureteral obstruction model. Gene microarray assay showed that post-obstruction, the lack of TIMP3 had a greater impact on gene expression of intermediate, late injury- and repair-induced transcripts, kidney selective transcripts and solute carriers. Renal injury in TIMP3-/-, but not in TIMP2-/- mice increased expression of collagen type I/III, connective tissue growth factor, transforming growth factor-β and the downstream Smad2/3 pathway. Interestingly, ureteral obstruction markedly increased MMP2 activation in the kidneys of  TIMP3-/- mice which was completely blocked in the kidneys of TIMP2-/- mice. These changes are consistent with enhanced renal tubulointerstitial fibrosis in TIMP3-/- and its reduction in TIMP2-/- mice. The activity of tumor necrosis factor-α converting enzyme, caspase-3 and mitogen activated kinases were elevated in the kidneys of  TIMP3-/- but not TIMP2-/- mice, suggesting enhanced activation of apoptotic and pathological signaling pathways only in the obstructed kidney of  TIMP3-/- mice. Thus, TIMP2 and TIMP3 play differential and contrasting roles in renal injury, TIMP3 protects from damage whereas TIMP2 promotes injury through MMP2 activation.

overall_design: Kidneys from the wild type (WT), TIMP2-/- and TIMP3-/- mice undergoing sham or unilateral ureteral obstruction (UUO) procedures


title: Comparison of gene expression in wild type Drosophila testes with various meiotic arrest mutants

status: Public on Jun 27 2013

city: Cardiff

first: Helen

last: White-Cooper

address: Museum Avenue

department: Biosciences

country: United Kingdom

institute: Cardiff University

summary:
The expression of a very large number of genes changes as male germ cells pass through differentiation into spermatids and then sperm. Much of this transcriptional programme requires the activity of the meiotic arrest genes.
We extracted RNA from wild type testes, as well as aly mutants and Nxt1 mutants, and used microarrays to compare gene expression profiles.

overall_design: We dissected testes from 0-1 day old Drosophila males, taking care to remove accessory glands and ejaculatory ducts. The control sample expressed a tin-RNAi construct, and had normal testes. The aly mutant were homozygous for aly[5]. The Nxt1 mutants were Nxt1[z2-0488]/Nxt1[DG05102].


title: Gene regulated by ectopic expression of Sage in the entire Drosophila embryo

status: Public on Jun 06 2013

city: Baltimore

first: Deborah

middle: J

last: Andrew

state: MD

address: 725 N. Wolfe St., Hunterian G-1

department: Cell Biology

institute: Johns Hopkins University School of Medicine

summary: FoxA transcription factors play major roles in organ-specific gene expression. How FoxA proteins achieve specificity is unclear, given their broad expression patterns and requirements in multiple cell types. Here, we characterize Sage, a basic helix-loop-helix (bHLH) transcription factor expressed exclusively in the Drosophila salivary gland (SG). We identify Sage targets and show that not only are both Sage and the single Drosophila FoxA protein, Fork head (Fkh), required for expression of these genes, but coexpression of Sage and Fkh is sufficient to drive target gene expression in multiple other cell types. Sage and Fkh drive expression of the bZip transcription factor Senseless (Sens), which boosts expression of Sage/Fkh targets. Importantly, Sage, Fkh and Sens colocalize on salivary gland polytene chromosomes. Thus, Fkh drives cell-type specific gene expression as part of a tissue-specific transcription module that includes Sage and Sens, providing a new paradigm for how mammalian FoxA proteins acheive specificity.

overall_design: Three wild type (reference) samples were obtained from the Oregon R strain, age matched and treated the same as the three experimental samples isolated from Stages 11-16 embryos expressing UAS-Sage controlled by the tub-Gal4 driver.

first: Rebecca

middle: M

last: Fox


title: Environmental and simulation facility conditions can modulate a behavioral-driven altered gravity response of Drosophila imagoes transcriptome

status: Public on Jun 26 2013

city: Madrid

first: Raúl

last: Herranz

state: Madrid

address: Ramiro de Maeztu 9

department: Plant Cell Nucleolus, proliferation and microgravity

country: Spain

institute: Centro Investigaciones Biológicas

summary:
Genome-wide transcriptional profiling shows that reducing gravity levels in the International Space Station (ISS) causes important alterations in Drosophila gene expression. However, simulation experiments on ground, without space constraints, show weaker effects than space environment. A global and integrative analysis using the “gene expression dynamics inspector” (GEDI) self-organizing maps, reveals a subtle response of the transcriptome using different populations and microgravity and hypergravity simulation devices. These results suggest that, in addition to behavioural responses that can be detected also at the gene expression level, the transcriptome is finely tuned to normal gravity.
The alteration of this constant parameter on Earth can have effects on gene expression that depends both on the environmental conditions and the ground based facility used to compensate the gravity vector. Alternative and commons effects of mechanical facilities, like the Random Positioning Machine and a centrifuge, and strong magnetic field ones, like a cryogenically cooled superconductive magnet, are discussed.

overall_design:
We compare the effects over the gene expression profile of different gender/age Drosophila imagoes in 3-4 days-long experiments under altered gravity conditions into three GBF ("Ground Based Facilities" for micro/hyper- gravity simulation) using whole genome microarray platforms.

Descriptions of different GBFs ("treatments"):
LDC means "Large Diameter Centrifuge". Samples can be placed under three conditions: inside LDC (at certain g level), at the LDC rotational control and at external 1g control (outside the LDC).
RPM means "Random Positioning Machine". Samples can be placed under two conditions: inside RPM (at nearly 0g, Microgravity level) and at external 1g control (outside the RPM).
At the magnet, means INSIDE the Magnetic levitator (another GBF). Samples can be placed under four conditions: inside Magnet 0g* (at microgravity with magnetic field), inside Magnet at 1g* (internal control with magnetic field) or inside the magnet 2g* (at hypergravity with magnetic field) and at external 1g control (outside the magnet)

first: Raul


title: Gene expression data of Lsd1fl/fl and Lsd1fl/fl EpoRCre CD71_high / c-Kit_high pro-erythroblasts.

status: Public on Jun 25 2013

first: Marc

middle: A.

last: Kerenyi

state: Massachusetts

address: 1 Blackfan Street - Karp Research Building

department: Hematology / Oncology

institute: Boston Children's Hospital and Dana Farber Cancer Institute

summary: We discovered that mice lacking Lsd1 in the erythroid lineage die in utero of a lethal anemia around embryonic day E13.5. Lsd1 knockout embryos displayed an increase in CD71_high c-Kit_high pro-erythroblasts, followed by a drastic reduction of later maturation stages. To determine the genes altered by Lsd1-loss, CD71_high c-Kit_high pro-erythroblasts from Lsd1fl/fl and Lsd1fl/fl EpoRCre mice were FACS-purified to be analyzed by gene expression profiling.

overall_design: Primary CD71high c-Kithigh pro-erythroblasts were isolated by FACS-sorting from fetal livers of E13.5 Lsd1fl/fl and Lsd1fl/fl EpoRCre embryos. Total RNA from two biological replicates per genotype was extracted and used to hybridize to Affymetrix expression arrays using the Mouse Genome 430A array platform.

middle: A

first: Stuart

middle: H

last: Orkin


title: Shifted Metabolic Bias in Livers of Mice Lacking Hepatocytic Thioredoxin Reductase-1 Protects Against Acetaminophen Toxicity

status: Public on Jun 08 2013

city: Bozeman

first: Ed

last: Schmidt

state: MT

department: M&I Dept

institute: Montana State University

summary:
Genetic disruption of thioredoxin reductase 1 protects against acetaminophen (APAP) toxicity.
To determine the role of the thioredoxin system on xenobiotic metabolism we challeneged wildtype and txnrd1liver-null mice with acetaminophen.

overall_design:
Adult male wildtype and txnrd1 liver-null mice (C57BL6/J) were treated with either saline (PBS) or 100mg/kg APAP. Liver RNA was harvested eight hours after challenge and processed for microarray analysis.
Comparison of 2 treatment conditions in 2 genotypes, biological replicates in triplicate.

first: E

middle: E

first: S

middle: V

last: Iverson


title: The transcriptional response of mouse uterus to estrogen is genetically regulated

status: Public on Jun 11 2013

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

summary: The growth and development of the uterus in response to 17β-estradiol (E2) is genetically controlled, with marked variation observed depending on the mouse strain studied. Previous work from our laboratory using inbred mice that are high (C57BL6/J; B6) or low (C3H/HeJ; C3H) responders to E2 has led to the identification of quantitative trait loci (QTL) associated with phenotypic variation in uterine growth and eosinophil infiltration. The mechanisms underlying differential responsiveness to E2, and the genes involved, are unknown. Therefore, we used a microarray approach to show association of distinct E2-regulated transcriptional signatures with genetically controlled high and low responses to E2. Among the 6,664 E2-responsive uterine transcripts, several reside within our previously identified QTL, including the ERα-tethering factor Runx1, demonstrated to enhance E2-mediated transcript regulation. The level of RUNX1 in uterine epithelial cells was shown to be 3.5-fold greater in B6 compared to C3H. Analysis of cellular functions in sets of strain-dependent E2-responsive transcripts indicated C3H-selective enrichment of apoptosis, consistent with a 7-fold increase in the apoptosis indicator CASP3, and a 2.4-fold decrease in the apoptosis inhibitor Naip1 in C3H vs. B6 following treatment with E2. Our novel insights into the mechanisms underlying the genetic control of tissue sensitivity to estrogen have great potential to advance understanding of individualized effects in physiological and disease states.

overall_design: Eight-week-old female B6, C3H, and (B6 × C3H)F1 (B6C3) hybrid mice were purchased from The Jackson Laboratory (Bar Harbor, ME). Animals were ovariectomized at NIEHS, rested for 1 to 2 wk, and then subjected to treatment with either E2 (40.0 μg/kg BW injected i.p.) in 0.1 ml saline containing 0.25% ethanol, or ethanol/saline vehicle. Animals were euthanized and tissue collected at 2 or 24 h after injection. Uterine tissue from 3 animals per treatment group was collected, and snap-frozen in liquid nitrogen for subsequent RNA isolation. Frozen uterine tissue from three animals per treatment group was pulverized, then homogenized in Trizol (Invitrogen, Carlsbad, CA), and RNA was prepared according to the manufacturer's protocol. Isolated RNA was then further purified using the QIAGEN (Valencia, CA) RNeasy mini prep kit clean-up protocol. Gene expression analysis was conducted using Agilent Whole Mouse Genome 4x44 Multiplex format oligo arrays (014868; Agilent Technologies, Santa Clara, CA) following the Agilent 1-color microarray-based gene expression analysis protocol. Starting with 500 ng of total RNA, Cy3-labeled cRNA was produced according to the manufacturer's protocol. For each sample, 1.65 ug of Cy3-labeled cRNAs were fragmented and hybridized for 17 hours in a rotating hybridization oven. Slides were washed and then scanned with an Agilent Scanner.

first: Emma

last: Wall

first: Sylvia

last: Hewitt

first: Liwen

last: Liu

first: Roxana

last: del Rio

first: Laure

last: Case

first: Chin

middle: Y

last: Lin

first: Kenneth

middle: S

last: Korach

first: Cory

last: Teuscher


title: Environmental and facility conditions promote singular gravity responses of transcriptome during Drosophila metamorphosis

summary:
Genome-wide transcriptional profiling showed that reducing gravity levels in the International Space Station (ISS) causes important alterations in Drosophila gene expression intimately linked to imposed spaceflight-related environmental constrains during Drosophila metamorphosis. However, simulation experiments on ground testing space-related environmental constraints, show differential responses. Curiously, although particular genes are not common in the different experiments, the same GO groups including a large multigene family related with behavior, stress response and organogenesis are over represented in them. A global and integrative analysis using the gene expression dynamics inspector (GEDI) self-organizing maps, reveals different degrees in the responses of the transcriptome when using different environmental conditions or microgravity/hypergravity simulation devices
These results suggest that the transcriptome is finely tuned to normal gravity. In regular environmental conditions the alteration of this constant parameter on Earth can have mild effects on gene expression but when environmental conditions are far from optimal, the gene expression is much more intense and consistent effects.

overall_design:
We compare the effects over the gene expression profile of Drosophila melanogaster during metamorphosis (3-4 days-long experiments) to altered gravity conditions into three GBF ("Ground Based Facilities" for micro/hyper- gravity simulation) using whole genome microarray platforms. In addition we perform this series of experiments including or not two environmental constrains to the system, a cold step of three days at 12C (ΔT) and a containment of the samples in a chamber that limitate the amount of available oxygen (↓O2).

Descriptions of different GBFs ("treatments"):
LDC means "Large Diameter Centrifuge". Samples can be placed under three conditions: inside LDC (at certain g level), at the LDC rotational control and at external 1g control (outside the LDC).
RPM means "Random Positioning Machine". Samples can be placed under two conditions: inside RPM (at nearly 0g, Microgravity level) and at external 1g control (outside the RPM).
At the magnet, means INSIDE the Magnetic levitator (another GBF). Samples can be placed under four conditions: inside Magnet 0g* (at microgravity with magnetic field), inside Magnet at 1g* (internal control with magnetic field) or inside the magnet 2g* (at hypergravity with magnetic field) and at external 1g control (outside the magnet)


title: Dysregulation of Macrophage Activation Profiles by Engineered Nanoparticles

status: Public on Jun 01 2013

city: Corvallis

first: Susan

middle: C.

last: Tilton

state: OR

address: 1007 ALS Bldg

department: AG Envr & Molec Toxicology

institute: Oregon State University

summary:
To investigate how the phenotype of macrophages that have engulfed engineered nanoparticles (ENPs) differs from normal macrophages, we conducted Affymetrix microarray studies to identify the gene regulatory pathways affected by the ENPs.  To mimic potential occupational exposure scenarios, the experimental design involved pretreatment of mouse primary bone marrow macrophages with the ENPs (25 mg/ml) for 24 hr, followed by removal of residual ENPs and challenging the macrophages with the TLR4 ligand and surrogate bacterial stimulus, lipopolysachharide (LPS) for 4 hr.  The 4 hr challenge time was chosen based on preliminary studies which showed many of the proinflammatory gene expression responses peak between 2-6 hr after LPS treatment.
Transcriptional responses were measured by global microarray analysis of mouse primary bone marrow macrophage cells.

overall_design: Groups (N=3 replicates) of primary mouse bone marrow macrophages were pretreated with selected engineered nanoparticless (33 nm iron oxide(SPIO) or 50 nm amorphous silica) at concentrations of 25 mg/ml for 24 hours. After removing the nanoparticles, macrophages were challenged with fresh media containing 10ng/ml lipopolysaccharide (LPS).

first: Brian

last: Thrall


title: Environmental and simulation facility conditions can modulate gravity response of Drosophila transcriptome

first: Raúl

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

overall_design: Refer to individual Series


title: Transcriptional effects of CTGF inhibition and gemcitabine in the KPC mouse model of pancreatic ductal adenocarcinoma

status: Public on Jun 24 2013

city: San Francisco

first: Mark

middle: D.

last: Sternlicht

state: CA

address: 409 Illinois Street

department: Molecular Biology

institute: FibroGen, Inc.

summary: Pancreatic ductal adenocarcinoma (PDA) is characterized by abundant desmoplasia and poor tissue perfusion. These features are proposed to limit access of therapies to neoplastic cells and blunt treatment efficacy. Indeed, several agents that target the PDA microenvironment promote chemotherapy delivery and improve anti-neoplastic responses in murine models of PDA. Here, we employed the FG-3019 monoclonal antibody directed against the pleiotropic matricellular signaling molecule connective tissue growth factor (CTGF/CCN2). FG-3019 treatment increased PDA cell killing and led to a dramatic tumor response without altering gemcitabine delivery. Microarray expression profiling revealed the down-regulation by FG-3019 of several anti-apoptotic transcripts, including the master regulator Xiap, down-regulation of which has been shown to sensitize PDA to gemcitabine. Decreases in XIAP protein by FG-3019 in the presence and absence of gemcitabine were confirmed by immunoblot, while increases in XIAP protein were seen in PDA cell lines treated with recombinant CTGF. Therefore, alterations in survival cues following targeting of tumor microenvironmental factors may play an important role in treatment responses in animal models and, by extension, PDA patients.

overall_design: Total RNA was isolated from KPC mouse PDA tumors 9 days after initiation of treatment with IgG (n=7 biological replicates), FG-3019 (n=5), IgG + gemcitabine (n=6), or FG-3019 + gemcitabine (n=6) and hybridized to Affymetrix 430A 2.0 microarrays. CEL files were processed by GC-RMA and rescaled using median per-gene normalization in GeneSpring GX 7.3.1.

first: Albrecht

last: Neesse

first: Kristopher

last: Frese

first: David

last: Tuveson

first: Todd

last: Seeley


title: Effect of allergen sensitization on gene expression in dendritic cells from neonates of asthmatic vs control mothers

first: Alexey

last: Fedulov

address: 75 Francis St.

department: Brigham and Women's Hospital

institute: Harvard Medical School

summary: This study aims to demonstrate the link between epigenome-wide methylation aberrations at birth and genomic transcriptional changes upon allergen sensitization that occur in the neonatal dendritic cells (DC) due to maternal asthma. In an in vivo model reproducing human epidemiology findings, maternal but not paternal asthma predisposes the neonate to increased asthma risk, the effect is allergen-independent and is not genetic or environmental. Earlier we demonstrated that neonates of asthmatic mothers are born with a functional skew in splenic DCs that mediates the early-life asthma origin. These allergen-naive cells convey allergy responses to normal recipients, however minimal to no transcriptional or phenotypic changes were found to explain the functional pro-allergic alterations. In this study we profiled both allergen-naïve dendritic cells, and cells after allergen sensitization in vivo.    We found that while allergen-naive DCs from asthma-at-risk neonates have minimal transcriptional change compared to controls, upon allergen sensitization, multiple genes with pre-existing epigenetic alterations show significant transcriptional change.   .

overall_design: 24 samples from 2 batches, 3-4 replicates in each of 4 groups

first: Lyudmila

last: Mikhaylova

first: Lester

last: Kobzik


title: The Swi/Snf tumor suppressor complex establishes nucleosome occupancy at target promoters [expression]

status: Public on Jun 04 2013

first: Peter

last: Park

address: 10 Shattuck St

department: Center for Biomedical Informatics

summary: Precise nucleosome-positioning patterns at promoters are thought to be crucial for faithful transcriptional regulation. However, the mechanisms by which these patterns are established and dynamically maintained and subsequently contribute to transcriptional control are poorly understood. The Swi/Snf (Baf) chromatin remodeling complex is a master developmental regulator and tumor suppressor that is capable of mobilizing nucleosomes in biochemical assays. Yet, its role in establishing the nucleosome landscape in vivo is unclear. Here we have inactivated Snf5 and Brg1, core subunits of the mammalian Swi/Snf complex, to evaluate their effects on chromatin structure and transcription levels genome-wide. We find that inactivation of either subunit leads to disruptions of specific nucleosome patterning combined with a loss of overall nucleosome occupancy at a large number of promoters, regardless of their association with CpG islands. These rearrangements are accompanied by gene expression changes that promote cell proliferation. Collectively, these findings define a direct relationship between chromatin-remodeling complexes, chromatin structure, and transcriptional regulation.

overall_design: Gene expression was measured in three cell types using multiple replicates for each sample.

first: Michael

last: Tolstorukov

first: Courtney

middle: G

last: Sansam

first: Ping

last: Lu

first: Edward

last: Koellhoffer

first: Katherine

last: Helming

first: Burak

last: Alver

first: Erik

last: Tillman

first: Julia

last: Evans

first: Boris

last: Wilson

first: Charles

last: Roberts


title: Expression data from MMTV-PPARd  mice, 1 week GW501516 treatment

status: Public on May 31 2013

city: Washington

first: Robert

middle: I

last: Glazer

state: DC

address: 3970 Reservoir Rd, NW

department: Oncology

institute: Georgetown University

summary: The role of murine peroxisome proliferator-activated receptor-delta (PPARd) in mammary tumorigenesis was assessed. Microarrays were used to analyse global gene expression to determine changes in MMTV-PPARd transgenic mice versus wild-type mice and the  effect of GW501516.

overall_design: RNA was isolated (RNeasy Mini Kit, Qiagen) from mammary gland tissue of  transgenic and wild-type mice maintained on normal rodent chow or 0.005% GW501516

first: Hongyan

last: Yuan


title: Identification of CD44 downstream target genes

first: NIEHS

last: Microarray Core

summary: CD44 expression has been shown to be enhanced in the liver and white adipose tissue (WAT) during obesity, suggesting a possible regulatory role for CD44 in metabolic syndrome. To study this hypothesis, we compared the gene expression profiles in liver and in WAT between WT and CD44 knockout (CD44KO) mice fed a high-fat diet (HFD) for 21 weeks. This analysis demonstrated that several genes associated with triglyceride synthesis and accumulation, including Mogat2, Cidea, Cidea, Apoa4, and Elovl7, were decreased in the livers of CD44KO mice compared to WT mice. Many genes encoding pro-inflammatory chemokines and chemokine receptors also were decreased in the livers of CD44KO mice. Analysis with WAT showed that genes associated with triglyceride accumulation, including Fasn, Elovl6 and Mogat2, were increased in WAT of CD44KO(HFD) mice compared to WT(HFD) mice. Moreover, many genes associated with inflammation, including cytokines (Cxcl14, Cxcl12, Il33, and Il2), cytokine receptors (Ccr1, Il6ra, Il10rb), trypases (Tpsb2, Tpsab1, Tpsg1), and cellular matrix proteins (Integrin α4 (Itga4), ItgaM, Itgb2), were decreased in WAT of CD44(HFD) compared to WT(HFD) mice. This study indicates that CD44 plays a critical role in regulating several aspects of metabolic syndrome.

overall_design: Liver and white adipose tissue (WAT) total RNAs were purified from 5 WT and 5 CD44 knockout mice fed with a high-fat diet for 21 weeks. Then, samples were applied on Agilent mouse genome chips.

first: Hong

last: Kang

first: Anton

last: Jetten


title: Gene expression profile of frazzled (fra) mutant Drosophila embryos

status: Public on May 21 2013

city: South Bend

first: Molly

middle: Duman

last: Scheel

state: IN

address: 1234 Notre Dame Ave.

institute: Indiana University School of Medicine

summary:
In order to analyze the global changes in gene expression resulting from loss of Fra signaling, we performed a microarray experiment comparing Drosophila embryos containing a loss of function fra[3] mutation to age matched wildtype
embryos.  RNA extracted from fra[3] mutant vs. wildtype embryos were hybridized to the Affymetrix GeneChip Drosophila Genome 2.0 .

overall_design: We selected Drosophila embryos at stage 13, which marks the onset of Fra expression in the embryonic CNS and the early stages of commissural axon guidance in the ventral nerve cord.  RNA was extracted from both fra[3] and wildtype embryos. Hybridization experiments were performed on Affymetrix Drosophila Genome 2.0 microarrays.

first: Joseph

last: Sarro

first: John

last: Tan

first: Erliang

last: Zeng

last: Duman-Scheel


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

status: Public on Feb 19 2014

city: Cantoblanco

first: Juan

middle: Carlos

last: Oliveros

address: Darwin 3

institute: CNB, CSIC

summary: T helper type 2 (Th2) responses are crucial for defense against infections by helminths and are responsible for the development of allergic reactions that can lead to severe clinical disorders, such as asthma or anaphylaxis, and ultimately to death. The induction of Th2 responses requires a specific activation process, triggered by specialized dendritic cells (DCs), by which naive CD4+ Th0 cells acquire the capacity to produce Th2 cytokines. However, the mechanistic basis of the functional specialization enabling DCs for the initiation of Th2 responses has remained elusive. Here we show that interleukin-4 (IL-4), a cytokine produced by basophils, mast cells and Th2-polarized CD4+ T helper cells, exerting a crucial function during anti-helminths and allergic Th2 responses, has a key role in the licensing/conditioning of DCs for the induction of Th2 responses, by bloking their potential to produce Th1-driving cytokines, such as IL-12, IL-18 and IL-23.

overall_design: Microarray analyses (duplicates) were for two types of comparisons:    1. moDCs stimulated with LPS from Escherichia coli versus C-moDCs non stimulated (control).    2. moDCs stimulated with LPS from Escherichia coli in presence of IL4 versus C-moDCs non stimulated (control).

first: Carlos

last: Ardavín

first: María

last: López-Bravo


title: Gene expression profile of Drosophila third instar larval wing imaginal discs overexpressing netrinA (netA) and frazzled (fra).

summary:
In order to analyze the global changes in gene expression resulting from induction of NetA-Fra signaling, we carried out a microarray experiment comparing Drosophila third instar wing imaginal discs in which Net+Fra had been overexpressed to age matched wild type wing imaginal discs.
RNA extracted from both +NetA-Fra overexpression and wildtype third instar imaginal discs were hybridized to the Affymetrix GeneChip Drosophila Genome 2.0 .

overall_design: Heat shock induced GFP-marked clones ectopically expressing NetA+Fra in larvae were generated.  Controls for this study included age matched wildtype third instar wing imaginal discs bearing GFP clones which were prepared in the same manner.  Total RNA was extracted from dissected +NetA-Fra vs. control third instar wing imaginal discs and hybridized to the Affymetrix GeneChip Drosophila Genome 2.0.


title: Impaired Transcriptional Response of the Murine Heart To Cigarette Smoke in the Setting of High Fat Diet and Obesity

status: Public on May 17 2013

first: Susan

last: Tilton

summary:
To identify biosignatures that describe these lifestyle susceptibility factors, we performed parallel exposures of regular weight (RW) C57BL/6 and diet-induced obese (DIO) C57BL/6 mice to cigarette smoke, either mainstream (MS) or sidestream (SS), mimicking both the smoker and environmental exposure through second-hand smoke, respectively.
Transcriptional responses were measured by global microarray analysis of heart tissue.

overall_design: Groups (N=6-8 biological replicates) of RW and DIO C57BL/6 mice (15-weeks old at start of exposures) were exposed to either filtered air (sham controls, SC), mainstream (MS) or sidestream (SS) cigarette smoke by nose-only inhalation exposure for 5 hr/day for a total of eight exposures over two weeks as follows: 5 consecutive days of exposure, followed by 2 days with no exposure, then three days of exposure, with necropsies occurring the day following the last exposure.

middle: C

first: Katrina

last: Waters


title: Expression data from mouse optic nerve head after elevation in intraocular pressure

first: Tatjana

last: Jakobs

address: 20 Staniford Street

institute: Massachusetts Eye and Ear Infirmary

summary:
Reactive astrocytes are typically studied in models that cause irreversible mechanical damage to axons, neuronal cell bodies, and glia.  We evaluated the response of astrocytes in the optic nerve head to a subtle injury induced by a brief, mild elevation of the intraocular pressure.  Astrocytes demonstrated reactive remodeling showing hypertrophy, process retraction and simplification of their shape.
We used microarray to indentify differentially expressed genes and to investigate the molecular mechanisms of astrogliosis in response to this subtle injury.

overall_design: Six- to eight-week old C57Bl/6 male mice were used in this experiment.  One eye underwent an elevation in intraocular pressure to 30 mmHg for 1 hour and then allowed to recover for 3 days.  The contralateral eye served as a control.  Due to the small tissue size of the mouse optic nerve head, two optic nerve heads were pooled together for each microarray chip.  We used 10 mice to generate five biological replicates for each condition.

first: Danial

last: Sun

last: Qu


title: Effects of overexpression of Sox2 on gene expression in adult mouse intestine

status: Public on May 11 2013

city: Bethesda

first: Andrey

last: Kuzmichev

state: Maryland

address: 35, Lincoln Drive

institute: NINDS/NIH

summary: In order to understand the molecular mechanisms of changes seen in the adult mouse intestine in response to Sox2 overexpression, gene expression was analyzed in the ileum upon 2-day Doxycycline (DOX) treatment of mice containing Dox-inducible Sox2 transgene. Repression of Cdx2 and of its intestinal targets was observed and confirmed by Western blotting and immunostaining. This effect of Sox2 was distinct from the effect of overexpression of Oct4.

overall_design: 6-8 week old TetON-Sox2, rtTA controls (no TetOP-Sox2 transgene), TetON-Oct4, and TetON-Sox2 X TetON-Oct4 mice (2 replicates) were treated for 2 days with 2 mg/ml DOX or were left untreated. Intestines (ileum part) were collected and total mRNA was extracted.

first: Ron

last: McKay


title: Cardiac gene expression (random section containing both ventricles) in C57BL/6 mice intratracheally instilled with Printex 90 carbon black nanoparticles (set 1)

status: Public on May 02 2013

city: Ottawa

first: Andrew

last: Williams

state: ON

address: 50 Columbine

institute: Health Canada

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

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

first: Julie

last: Bourdon

first: Anne

last: Saber

first: Nicklas

last: Jacobsen

first: Sabina

last: Halappanavar

first: Hakan

last: Wallin

first: Carole

last: Yauk

first: Ulla

last: Vogel


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

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


title: [E-MEXP-3786] IGF-I-induced chronic gliosis and retinal stress lead to neurodegeneration in an animal model of retinopathy

status: Public on Apr 30 2013

city: Bellaterra

first: Miquel

last: Garcia

state: -- Please Select (only U.S. / Can / Aus)

address: Campus UAB Edifici H

institute: UAB

summary:
Transcription profiling by array of mouse male retinas to investigate IGF-I-induced chronic gliosis and retinal stress
IGF-I exert multiple effects in different retinal cell populations in both physiological and pathological conditions. Transgenic mice overexpressing IGF-I in the retina showed impaired electroretinographic responses at 6-7 months of age that worsen with age. This retinal neuronal dysfunction was correlated with the loss of rod photoreceptors, bipolar, ganglion and amacrines cells. Neuronal alterations were preceded by the overexpression of  retinal stress markers, acute phase proteins and gliosis-related genes. IGF-I overexpression leads to chronic gliosis and microgliosis in TgIGF-I retinas, with mild oxidative stress, impaired recycling of glutamate and defective potassium buffering. These impaired supportive functions can contribute to neurodegeneration in TgIGF-I retinas, together with the increased production of pro-inflammatory cytokines, potential mediators of neuronal death.

overall_design: 3 transgenic  and 3 wild type biological replicates examined.

first: Albert

last: Ribera


title: Drosophila CNS glial microarray

status: Public on Apr 24 2013

city: London

first: Joseph

middle: M.

last: Bateman

state: (Click to Select US State)

address: Guy's campus

institute: King's College London

summary:
Gliogenesis in the Drosophila CNS occurs during embryogenesis and also during the postembryonic larval stages. Several glial subtypes are generated in the postembryonic CNS through the proliferation of differentiated glial cells. The genes and molecular pathways that regulate glial proliferation in the postembryonic CNS are poorly understood. In this study we aimed to use gene expressing profiling of CNS tissue enriched in glia to identify genes expressed in glial cells in the postembryonic CNS.
We used microarrays to compare the gene expression profiles from the larval CNS of animals that had increased numbers of glial cells to identify genes that are expressed in glia.

overall_design: RNA was purified from the late third instar larval CNS from control larvae, or larvae expressing an activated form of the FGF receptor (Hlt[ACT]), or overexpressing the insulin receptor (InR) in glial cells using the glial specific driver repoGal4 to increase the number of glial cells and generate CNS tissue enriched in glia.

first: Amelie

last: Avet-Rochex


title: Cohesin and Polycomb proteins functionally interact to control transcription at silenced, restrained, and active genes [expression array data]

status: Public on Apr 25 2013

city: St Louis

first: Cheri

last: Schaaf

state: MO

address: 1100 South Grand Ave

department: Biochemistry & Molecular Biology

institute: Saint Louis University School of Medicine

summary: Cohesin is crucial for proper chromosome segregation, but also regulates gene transcription and organism development by poorly understood mechanisms. We find that in Drosophila, cohesin functionally interacts with Polycomb group (PcG) silencing proteins at both silenced and active genes. Cohesin unexpectedly facilitates binding of Polycomb Repressive Complex 1 (PRC1) to many active genes. In contrast, cohesin and PRC1 binding are mutually antagonistic at silenced genes. PRC1 depletion decreases phosphorylated RNA polymerase and mRNA at many active genes, but increases them at silenced genes. Cohesin also facilitates long-range interactions between Polycomb Response Elements in the invected-engrailed gene complex where it represses transcription. These multiple distinct cohesin-PcG interactions reveal a previously unrecognized role for PRC1 in facilitating productive gene transcription, and provide new insights into how cohesin and PRC1 control development.

overall_design: We extracted RNA from control and Ph RNAi-treated BG3 cells and measured changes in gene expression following Ph dose depletion by hybridization to Affymetrix arrays. We also extracted RNA from wild-type wing imaginal disc and measured control wing disc expression levels by hybridization to Affymetrix arrays.

first: Dale

last: Dorsett


title: Analysis of Drosophila salivary glands and Kc cells with depleted levels of linker histone H1 [Affymetrix Expression]

status: Public on Apr 22 2013

city: Bronx

first: Sandeep

middle: Nagaraj

last: Wontakal

state: NY

address: 1300 Morris Park Ave Chanin 402

institute: Albert Einstein College of Medicine

summary: Indicated cells were subjected to RNAi against linker histone H1, Nautilus (control), or GFP (control).  RNA was isolated and subjected to Affymetrix GeneChIP Drosophila Genome 2.0 arrays

overall_design: RNA was compared from cells treated with RNAi against control (Nautilus in the case of salivary glands or GFP in the case of Kc cells) and linker histone H1.  Kc cells were treated once with RNAi and RNA was collected 6 days later.

first: Arthur

last: Skoultchi


title: Critical Requirement of the DNA Methyltransferase, Dnmt1, for the Development and Function of Foxp3+ Regulatory T Cells

status: Public on Apr 21 2013

city: Philadelphia

first: Wayne

middle: W

last: Hancock

state: PA

address: 916B ARC, 3615 Civic Ctr Blvd

institute: CHOP/UPenn

summary: We investigated the role of DNMT1 in immune homeostasis by generating mice lacking DNMT1 in Foxp3+ T-regulatory (Treg) cells. These mice showed decreased peripheral Foxp3+ Tregs, complete loss of Foxp3+ Treg suppressive functions in vitro and in vivo, and died from autoimmunity by 3-4 weeks unless they received perinatal transfer of wild-type Tregs that prolonged their survival. Methylation of CpG-sites in the TSDR region of Foxp3 was unaffected by DNMT1 deletion, but microarray revealed more >500 proinflammatory and other genes were upregulated in DNMT1-/- Tregs. CD4-Cre-mediated DNMT1 deletion showed inability of conventional T cells to convert to Foxp3+ Treg under appropriate polarizing conditions. Hence, DNMT1 is absolutely necessary for maintenance of the gene program required for normal Treg development and function.

overall_design: RNA from three independent samples of magnetically separated CD4+CD25+ Treg of fl-DNMT1/Foxp3cre mice, compared to wild type (C57BL6) control

first: Liqing

last: Wang

first: Yujie

last: Liu

first: Rongxiang

last: Han

first: Tricia

middle: R

last: Bhatti

first: Ulf

last: Beier

first: Tatiana

last: Akimova


title: Cohesin and Polycomb proteins functionally interact to control transcription at silenced, restrained, and active genes

middle: A

type: Genome binding/occupancy profiling by genome tiling array

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

overall_design: Refer to individual Series


title: High expression genes in urethane-induced lung tumor

status: Public on Apr 16 2013

city: Sendai

first: Masayuki

last: Yamamoto

address: 2-1 Seiryo-machi, Aoba-ku

department: Medical Biochemistry

country: Japan

institute: Tohoku University Graduate School of Medicine

summary: We estimated differences of urethane-induced tumors between Nrf2+/+ and Nrf2-/- ICR mouse.  To identify Nrf2-regulated genes in tumors, we examined the mRNA expression profile both in tumor and non-tumor tissue of mouse 4 months after urethane administration.

overall_design: We performed microarray analyses using the comparable size of lung tumors (1.0 mm < tumor diameter < 1.5 mm) and intact non-tumor lung tissues derived either from Nrf2+/+ (n=8) or Nrf2–/–mice (n=8) at 16-weeks after urethane(1-g/kg body weight) treatment.

first: Hironori

last: Satoh

first: Takashi

last: Moriguchi


title: Transcriptome analysis of the injected mice overexpressing TFEB specifically in liver

status: Public on Apr 20 2013

city: Pozzuoli

first: Rossella

last: De Cegli

address: Via Campi Flegrei 34

country: Italy

institute: Tigem

summary: In order to identify the effects of TFEB overexpression on the liver transcriptome, we performed Affymetrix Gene-Chip hybridization experiments for the injected mice

overall_design: For the analysis on the injected mice overexpressing TFEB, total RNA was extracted from the liver of three mice; RNA extracted from the liver of not-injected mice was used as control.


title: Tumor suppressor p53 integrates host defense and cell fate during bacterial pneumonia

status: Public on Apr 19 2013

first: NIEHS

last: Microarray Core

address: 111 T.W. Alexander Drive

institute: NIEHS

summary: Gene expression analysis was conducted on lung RNA from C57BL/6J mice and compared to lung RNA from B6.129S2-Trp53tm1Ty/J mice (p53 NULL) to observe differences in baseline gene expression in mice with p53 deficiency.

overall_design: Lung RNA was isolated at baseline (saline airway exposure) in a total of 5 biological reps for both C57BL/6J (WT) and p53-deficient mice.

first: Jennifer

middle: H

last: Madenspacher

first: Pierre

last: Bushel

first: Jun

last: Lu

first: Kevin

last: Gerrish

first: B

last: Merrick

first: Michael

middle: B

last: Fessler


title: Transcriptome analysis of the injected Ppara-KO mice overexpressing TFEB specifically in liver

summary: Expression data from Ppara (peroxisome proliferator activated receptor alpha) KO mice injected with TFEB specifically in liver. In order to identify the effects of TFEB overexpression together with Ppara absence on the liver transcriptome, we performed Affymetrix Gene-Chip hybridization experiments for the injected mice

overall_design: For the analysis on the injected Ppara-KO mice overexpressing TFEB, total RNA was extracted from the liver of three mice; RNA extracted from the liver of not-injected mice was used as control.


title: Gene Expression in Postnatal Mouse Kidney Development

city: Stanford

first: Bo

last: Wu

state: Ca

address: 300 Pasteur Dr. Grant/S259

department: Urology

institute: Stanford University

summary:
INTRODUCTION AND OBJECTIVE: Obstruction and other processes that lead to renal damage can have different effects in adult versus developing kidneys.  These differences are important for understanding pathophysiology, but also could influence selection of biomarkers used for detection of renal damage that could be used to guide intervention.  In mice, significant renal development occurs postnatally, providing a model for understanding kidney development. To date, gene expression changes that occur mouse kidney growth and development postnatally have been poorly characterized.  We describe here a comprehensive gene expression of the developing mouse kidney based on microarray profiling.
METHODS: C57BL/6 mice were sacrificed and kidneys were harvested at embryonic day E19.5, and postnatal days P1, P3, P5, P7, P10, P14, P21, P28 and P35. RNA was extracted from kidneys and transcript profiling was performed using Agilent microarrays. Transcripts that undergo abrupt transitions in expression level over the time course were identified using StepMiner analysis (Sahoo, 2007). Ingenuity pathway analysis (IPA) was used to analyze the biological function and gene networks of gene expression data.
RESULTS: Transcript levels for 13645 probes (representing 12769 genes) were modulated significantly over the time course, with 6949 up-regulated and 6696 down-regulated. IPA was used to identify genetic pathways, networks and functions significantly altered over the time course. Interestingly, in days P10 to P14 gene functions significantly altered were up-regulated exclusively with the functions represented including lipid metabolism, small molecule biochemistry and molecular transport. Between days P5 to P7 down-regulated genes predominated with enriched functions including, gene expression, cell cycle, protein synthesis and embryonic development.  For P14 to P21 enriched functions included DNA replication, recombination and repair, cell cycle, tissue development, cellular assembly and organization, protein trafficking and cell morphology. In the late stages (P21 to P28) functional enrichment was seen for cell-to-cell signaling, tissue development, cellular movement.
CONCLUSIONS: This study provides the most comprehensive temporal survey of postnatal kidney development to date.  This data set provides a framework for interpreting nephropathies, such as those induced by congenital obstruction.

overall_design: time series design


title: Expression data from Drosophila S2* cells treated with the steroid hormone 20-hydroxy-ecdysone (20E)

status: Public on Apr 13 2013

city: Lausanne

first: Thomas

last: Flatt

address: UNIL Sorge, Biophore

department: Department of Ecology and Evolution

country: Switzerland

institute: University of Lausanne

summary:
Previously we and other teams have found that 20E modulates the induction and expression of antimicrobial peptides (AMPs) in immune-challenged Drosophila cell culture or whole animals.
To identify potential downstream targets of 20E involved in modulating the immune response we used Affymetrix gene chips (microarrays) to compare the transcriptomes of Drosophila S2* cells treated or not with 20E for 24 hours.

overall_design: Affymetrix Drosophila 2.0 Chips were probed in triplicate with RNA isolated from untreated S2* cells or cells treated with 1 microMolar 20E (Sigma) for 24 hours. cDNA products were hybridized at the Brown University Genomics Core Facility to Affymetrix GeneChip Drosophila_2.0 Genome Arrays (3 replicate chips per treatment).

first: Florentina

last: Rus

first: Kamna

last: Aggarwal

first: Mei

last: Tong

first: Kendi

last: Okuda

first: Anni

last: Kleino

first: Elisabeth

last: Yates

first: Marc

last: Tatar

first: Neal

last: Silverman


title: E.coli Infected Bladder Samples (PBS, WT and all mutants)

status: Public on May 14 2013

first: Douglas Scott

last: Merrell

state: MD

address: 4301 Jones Bridge Road

department: Dept. of Microbiology and Immunology

institute: Uniformed Services University

summary:
Study of host response in mice to uropathogenic E. coli (UPEC) infection and the contribution of deletion of the Cnf and HlyA1 toxins to the host response. Mice were infected with UPEC in the bladder for 24 hrs and RNA was isolated from whole bladder to analyze on Agilent whole mouse 2-channel arrays against normal untreated mouse bladder RNA. Biological replicates were analyzed for each condition.
Infection: genotype of E. coli CP9 (UPEC) strain

first: Douglas


title: Expression data from a Charcot-Marie-Tooth 1B neuropathy mouse model

status: Public on May 01 2013

city: Milano

first: Maurizio

last: D'Antonio

address: via Olgettina 58

department: DIBIT

institute: San Raffaele Scientific Institute

summary: We have generated mouse models of real CMT1B mutations in the gene encoding for myelin protein zero (P0). One of these mutants, P0S63del is retained in the ER where it elicits an unfolded protein response (UPR). Genetic ablation of the UPR factor CHOP restores the motor capacity in S63del mice. We used microarray to decipher the molecular mechanism undelying the P0S63del neuropathy and the rescue in S63del/Chop null nerves.

overall_design: Sciatic nerves were dissected from WT, S63del, Chop null and S63del/Chop null mice at three different time points: (i) postnatal day 5 (P5) when myelination has just started and only the primary effects of the presence of the mutant protein should be detected; (ii) P28, around the peak of myelination, when all the downstream targets of CHOP should be activated; and (iii) 4 months, to check for secondary effects of the disease and because this was the time-point when the motor and morphological rescue due to the ablation of CHOP were clearly detectable.

first: Lawrence

last: Wrabetz


title: Distinct roles for Toll and autophagy pathways in double-stranded RNA toxicity in a Drosophila model of expanded repeat neurodegenerative diseases

status: Public on Apr 05 2013

city: Brisbane

first: Gareth

last: Price

state: Queensland

address: Carmody Road

institute: Queensland Facility for Advanced Bioinformatics

summary: Dominantly inherited expanded repeat neurodegenerative diseases are typically caused by the expansion of existing variable copy number tandem repeat sequences in otherwise unrelated genes. Repeats located in translated regions encode polyglutamine that is thought to be the toxic agent, however in several instances the expanded repeat is in an untranslated region, necessitating multiple pathogenic pathways or an alternative common toxic agent. As numerous clinical features are shared by several of these diseases, and expanded repeat RNA is a common intermediary, RNA has been proposed as a common pathogenic agent. Various forms of repeat RNA are toxic in animal models, by multiple distinct pathways. In Drosophila, repeat-containing double-stranded RNA (rCAG.rCUG~100) toxicity is dependent on Dicer processing evident with the presence of single-stranded rCAG7, which have been detected in affected HD brains. Microarray analysis of Drosophila rCAG.rCUG~100 repeat RNA toxicity revealed perturbation of several pathways including innate immunity. Recent reports of elevated circulating cytokines prior to clinical onset, and age-dependent increased inflammatory signaling and microglia activation in the brain, suggest that immune activation precedes neuronal toxicity. Since the Toll pathway is activated by certain forms of RNA, we assessed the role of this pathway in RNA toxicity. We find that rCAG.rCUG~100 activates Toll signaling and that RNA toxicity is dependent on this pathway. The sensitivity of RNA toxicity to autophagy further implicates innate immune activation. Expression of rCAG.rCUG~100 was therefore directed in glial cells and found to be sufficient to cause neuronal dysfunction. Non-autonomous toxicity due to expanded repeat-containing double-stranded RNA mediated activation of innate immunity is therefore proposed as a candidate pathway for this group of human genetic diseases.

overall_design: The heads from newly eclosed male Drosophila were used for RNA extraction and profiling on Affymetrix Drosophile Genome 2.0 microarrays. Nine samples were analysed, representing control and experimental lines. Two independent lines of rCAG.rCUG~100 double-stranded RNA were analysed in triplicate. These were compared to 4xUAS control analysed in triplicate. All transgenes were expressed using the elavII-GAL4 pan-neuronal driver. Candidates were selected from the pool of transcripts which showed a 'present' call in all samples. T-tests were performed on raw values to determine samples that showed a significant difference with a P-value < 0.05.

first: Saumya

middle: E

last: Samaraweera

first: Deon

middle: J

last: Venter

first: Robert

last: Richards


title: Expression in Drosophila Insensitive mutant

status: Public on Apr 04 2013

city: New York

first: Jakub

middle: Orzechowski

last: Westholm

address: 1275 York Avenue, Box 252

department: Developmental Biology

institute: Memorial Sloan-Kettering Cancer Center

summary: Affymetrix arrays measuring gene expression in 3 Drosophila Insensitive mutant embryos and 3  Drosophila wt mutant embryos

overall_design: 6 samples, 3 replicates of Insensitive mutants and 3 replicates of wt

first: Westholm

last: Jakub

first: Qi

last: Dai

first: Eric

last: Lai


title: Transcriptome analysis of liver samples from PPARa KO and control mice injected with HDAd-TFEB

first: Rossella

last: De Cegli


title: Regulation of gene expression by RORgamma in Th17 cells

status: Public on Apr 17 2013

city: RTP

first: NIEHS

last: Microarray Core

summary: We observed significant growth inhibition of melanoma tumor in RORγ-/- mice, suggesting an important role for the T helper 17 cell (TH17) pathway in tumor immunity. Though RORgamma t (RORγt) plays a critical role in the development of IL-17-secreting Th17 cells, the role of other genes remained an open question. To explore the expression of unknown genes with anti-tumor properties, gene expression analysis was performed.

overall_design: Sorted naïve TH cells (CD4+CD25-CD62Lhigh) from RORc+/+ and RORc-/-mice were differentiated under TH17 polarizing conditions. After 4 days, cells were harvested, RNA was isolated and gene expression analysis was performed.

first: Hong

middle: S

last: Kang

first: Rahul

last: Purwar

first: Thomas

last: Kupper

first: Anton

middle: M

last: Jetten


title: Expression data from wild-type mice starved as compared to wild-type control mice

summary:
In order to identify the effects of starvation on the liver transcriptome, we performed Affymetrix Gene-Chip hybridization experiments for the starved mice
Transcriptome analysis of the starved mice

overall_design: For the analysis on the starved mice,total RNA was extracted from the liver of two mice; RNA extracted from the liver of two wt mice was used as control.


title: HP1a, Su(var)3-9, SETDB1 and POF stimulate or repress gene expression depending on genomic position, gene length and expression pattern in Drosophila melanogaster

city: Umea

first: Jan

last: Larsson

address: Umea University

country: Sweden

institute: Umea University

summary: Heterochromatin protein 1a (HP1a) is a chromatin associated protein that has been well studied in many model organisms, such as Drosophila, where it is a determining factor for classical heterochromatin. HP1a is associated with the two histone methyltransferases SETDB1 and Su(var)3-9, which mediate H3K9 methylation marks and participate in the establishment and spreading of HP1a enriched chromatin. While HP1a is generally regarded as a factor that represses gene transcription, several reports have linked HP1a binding to active genes, and in some cases, it has been shown to stimulate transcriptional activity. To clarify the function of HP1a in transcription regulation and its association with Su(var)3-9, SETDB1 and the chromosome 4 specific protein POF, we conducted genome-wide expression studies and combined the results with available binding data in Drosophila melanogaster. The results suggested that HP1a has a repressing function on chromosome 4, where it preferentially targets non-ubiquitously expressed genes (NUEGs), and a stimulating function in pericentromeric regions. Further, we showed that the effects of SETDB1 and Su(var)3-9 are similar to HP1a, and on chromosome 4, Su(var)3-9, SETDB1 and HP1a target the same genes. In contrast, transposons are repressed by HP1a and Su(var)3-9 but are un-affected by SETDB1 and POF. In addition, we found that the binding level and expression effects of HP1a are affected by gene length. Our results indicate that genes have adapted to be properly expressed in their local chromatin environment.

overall_design: We prepared total RNA from 1st instar larvae trans-heterozygous for HP1a04/HP1a05, trans-heterozygous Su(var)3-9evo/Su(var)3-906, homozygous Setdb110.1/ Setdb110.1 mutants and trans-heterozygous HP1a04 PofD119/HP1a05 PofD119 double mutants three biological replicates, as well as from six biological replicates of wildtype control 1st instar larvae.

first: Lina

last: Lundberg

first: Per

last: Stenberg


title: Single Feature Polymorphism (SFP) Data from Drosophila Genomic DNA

status: Public on Mar 15 2013

city: La Jolla

first: zhi

last: zhang

address: 10901 North Torrey Pines Rd.

department: Development and Ageing

institute: Sanford-Burnham Medical Research Institute

summary:
Natural populations of the fruit fly, Drosophila melanogaster, segregate genetic variation that leads to cardiac disease phenotypes. Drosophila is well-known as a model for studying the mechanisms by which human disease genes cause pathology, including heart disease, but it is less well appreciated that they may also model the genetic architecture of disease, since flies presumably also have diseases that have a genetic basis. It is reasoned that most of these aberrant inbred line effects would be due to capture of rare variants of large effect as homozygotes, allowing the variants to be mapped rapidly using contemporary genomic approaches.
In order to map the genetic variants in flies, we used single feature polymorphism (SFP) analysis to contrast the genome-wide genotype frequencies between pools of flies with aberrant and normal heart phenotype.  SFP analysis is an indirect method for genome-wide genotyping that utilizes differential hybridization of genomic DNA to probes on a DNA chip that was initially designed for gene expression profiling, but can be used for species where genotyping chips are not available.

overall_design: DNA was prepared from three independent pools of 15 flies for each of the two types, as well as from the two parental lines.  The samples were sheared and labeled with biotin, then hybridized to Affymetrix Drosophila expression microarray chips. Mismatch hybridization, namely a significant difference in the hybridization intensity between the parental lines, was detected from all perfect match (PM) probes, located in over 9,000 probes with an estimated False Discovery Rate of 11%.

first: Zhi

last: Zhang

first: Rolf

last: Bodmer

first: Greg

last: Gibson


title: Overexpression of spliced XBP1 in cultured Adipocytes

city: Boston

first: Margaret

last: Gregor

state: MA

address: 665 Huntington Ave

department: Genetics and Complex Diseases

institute: Harvard School of Public Health

summary: We overexpressed the spliced form of transcription factor XBP1 in mature F442A adipocytes by adenoviral infection.  Control virus expressed GFP alone.

overall_design: mouse sXBP1 overexpressed in mouse F442A adipocytes compared to control (GFP alone). Four replicates of each treatment were analyzed.

middle: F

first: Gokhan

last: Hotamisligil


title: Gene regulation by the lysine demethylase KDM4A in Drosophila

status: Public on Apr 01 2013

city: Stockholm

first: Mattias

last: Mannervik

address: Arrheniuslaboratories E3

department: Molecular Biosciences, the Wenner-Gren Institute

institute: Stockholm University

summary:
Lysine methylation of histones is associated with both transcriptionally active chromatin and with silent chromatin, depending on what residue is modified. Histone methyltransferases and demethylases ensure that histone methylations are dynamic and can vary depending on cell cycle- or developmental stage. KDM4A demethylates H3K36me3, a modification enriched in the 3’end of active genes. The genomic targets and the role of KDM4 proteins in development remain largely unknown.
To investigate the link between dKDM4A and transcription, and to unravel molecular targets on a genome-wide scale, we used microarrays to decipher gene expression changes in dKDM4A mutant 1st instar larvae and identified classes of up-regulated and down-regulated genes.

overall_design: Three replicates of 200 dKDM4A KG04636 / ∆dKDM4A and dKDM4A precise KG06436 / dKDM4A precise NP0618 Drosophila 1st instar larvae for RNA extraction and hybridization on Affymetrix microarrays.

first: Filip

last: Crona

first: Olle

last: Dahlberg


title: Transcription factors MYOCD, SRF, Mesp1 and SMARCD3 significantly enhance the cardio-inducing effect of GATA4, TBX5, and MEF2C during direct cellular reprogramming

status: Public on Mar 31 2013

city: Durham

first: Nicolas

last: Christoforou

state: North Carolina

address: 136 Hudson Hall

department: Biomedical Engineering

institute: Duke University

summary: Transient over-expression of defined combinations of master regulator genes can effectively induce cellular reprogramming: the acquisition of an alternative predicted phenotype from a differentiated cell lineage. This can be of particular importance in cardiac regenerative medicine wherein the heart lacks the capacity to heal itself, but simultaneously contains a large pool of fibroblasts. In this study we determined the cardio-inducing capacity of ten transcription factors to actuate cellular reprogramming of mouse embryonic fibroblasts into cardiomyocyte-like cells. Over-expression of transcription factors MYOCD and SRF alone or in conjunction with Mesp1 and SMARCD3 significantly enhanced the basal but necessary cardio-inducing effect of the previously reported GATA4, TBX5, and MEF2C. In particular, combinations of five or seven transcription factors significantly enhanced the activation of cardiac reporter vectors, and induced an upregulation of cardiac-specific genes. Global gene expression analysis also demonstrated a significantly greater cardio-inducing effect when the transcription factors MYOCD and SRF were used. Detection of cross-striated cells was highly dependent on the cell culture conditions and was enhanced by the addition of valproic acid and JAK inhibitor. Although we detected Ca2+ transient oscillations in the reprogrammed cells, we did not detect significant changes in resting membrane potential or spontaneously contracting cells. This study further elucidates the cardio-inducing effect of the transcriptional networks involved in cardiac cellular reprogramming, contributing to the ongoing rational design of a robust protocol required for cardiac regenerative therapies.

overall_design: Mouse embryonic fibroblasts were transduced lentiviruses allowing the inducible overexpression of three unique sets of transcription factors and negative control. A total of four experimental groups which included three biological replicates in each.

first: Malathi

last: Chellappan

first: Andrew

last: Adler

first: Robert

middle: D

last: Kirkton

first: Tianyi

last: Wu

first: Russell

last: Addis

first: Nenad

last: Bursac

first: Kam

last: Leong


title: Histamine H3 Receptor Integrates Peripheral Inflammatory Signals in the Neurogenic Control of Immune Responses and Autoimmune Disease Susceptibility

status: Public on Mar 06 2013

city: 89 Beaumont ave

first: Dimitry

last: Krementsov

state: VT

address: 312C Rowell bldg, 106 Carrigan drive

department: BHSC

institute: University of Vermont

summary: Histamine H3 receptor (Hrh3/H3R) is primarily expressed by neurons in the central nervous system (CNS) where it functions as a presynaptic inhibitory autoreceptor and heteroreceptor. Previously, we identified an H3R-mediated central component in susceptibility to experimental allergic encephalomyelitis (EAE), the principal autoimmune model of multiple sclerosis (MS), related to neurogenic control of blood brain barrier permeability and peripheral T cell effector responses. Furthermore, we identified Hrh3 as a positional candidate for the EAE susceptibility locus Eae8. Here, we characterize Hrh3 polymorphisms between EAE-susceptible and resistant SJL and B10.S mice, respectively, and show that Hrh3 isoform expression in the CNS is differentially regulated by acute peripheral inflammatory stimuli in an allele-specific fashion. Next, we show that Hrh3 is not expressed in any subpopulations of the immune compartment, and that secondary lymphoid tissue is anatomically poised to be regulated by central H3R signaling. Accordingly, using transcriptome analysis, we show that, inflammatory stimuli elicit unique transcriptional profiles in the lymph nodes of H3RKO mice compared to WT mice, which is indicative of negative regulation of peripheral immune responses by central H3R signaling. These results further support a functional link between the neurogenic control of T cell responses and susceptibility to CNS autoimmune disease coincident with acute and/or chronic peripheral inflammation. Pharmacological targeting of H3R may therefore be useful in preventing the development and formation of new lesions in MS, thereby limiting disease progression.

overall_design: 8 pooled samples from at least 3 mice per pool

first: D

middle: N

first: E

last: Wall

first: R

last: Martin

first: M

last: Subramanian

last: Noubade

last: Del Rio

first: G

last: Mawe

first: J

middle: P

last: Bond

last: Poynter

last: Blankenhorn

first: C

last: Teuscher


title: Gene expression profiles of the small intestine and Peyer's patches from mice that were orally infected with Toxoplasma

status: Public on Mar 20 2013

city: Cambridge

first: Kirk

last: Jensen

address: 77 Massachusetts Ave. Bldg 68-270

institute: MIT

summary:
The Toxoplasma type I ROP16 kinase directly activates the host STAT3 and STAT6 transcription factors and when transgenically expressed in the orally virulent type II strain, promotes host resistance to oral challenge.
The transcriptional profile of type II and II+ROP16I infected Peyer's patches and intestines from orally infected mice on day 5 was determined to elucidate host signaling pathways and molecular gene targets that correlate with protective immunity in the gut of orally challenged animals

overall_design: C57BL/6 female mice were orally gavaged with 1000 tissue cysts of the type II or II+ROP16I strain.  On Day 5 of infection the Peyer's patches and intestines were analyzed for parasite burden by bioluminescence imaging. Individual Peyer's patches and intestinal sections, corresponding to the middle third of the intestine (~jejunum), that had equivalent parasite burden were snap frozen in liquid nitrogen. The samples were crushed using a sterile 16 G needle in tubes on dry ice.  In the case of the intestine, the sample was resuspended in TRizol, extruded through a needle using a syringe and RNA was isolated according to manufacturer's protocol; for the Peyer's patch, the sample was suspended in cell lysis buffer and RNA isolated using the RNeasey kit (Invitrogen) according to the manufacter's protocol.

first: Jeroen

last: Saeij


title: E.coli Infected Bladder Samples (PBS, WT and 2 mutants)

status: Public on Feb 06 2013

city: Bethesda

first: Douglas Scott

last: Merrell

summary:
Study of host response in mice to uropathogenic E. coli (UPEC) infection and the contribution of deletion of the Cnf and HlyA1 toxins to the host response. Mice were infected with UPEC in the bladder for 24 hrs and RNA was isolated from whole bladder to analyze on Agilent whole mouse 2-channel arrays against normal untreated mouse bladder RNA. Biological replicates were analyzed for each condition.
Infection: genotype of E. coli CP9 strain

first: Douglas


title: Long non-coding RNAs regulate adipogenesis (Affymetrix)

status: Public on Feb 15 2013

first: Cole

last: Trapnell

address: 7 Divinity Ave

department: Stem Cell and Regenerative Biology

institute: Harvard University

summary:
Adipogenesis involves the regulation of hundreds of genes by several well-studied proteins, but the role of long, noncoding RNAs in this process has not been defined.  We track the regulation of hundreds of lncRNAs during adipocyte differentiation, and find several that are essential for this process.
We profiled knockdown of lncRNAs that are upregulated during mouse adipocyte development

overall_design: We compared adipocytes differentiated in vitro after knockdown of 10 lncRNAs against control adipocytes and pre-adipocytes using Affymetrix expression microarrays.  When cultured primary-preadipytes reached 70-80% confluence, we transfected siRNAs against each lincRNA. 24 hours after transfection, cells were recovered in full culture media and grown to confluence for differentiation.  Total RNA was collected from control pre-adipocytes (D0) prior to differentation. Four days after recovery, total RNA was collected from each knockdown, a scramble control, and an untransfected control  (D4).

first: Lei

last: Sun

first: Loyal

last: Goff

first: Ryan

last: Alexander

first: Alice

last: Lo

first: Manolis

last: Kellis

first: Harvey

last: Lodish

first: John

middle: L

last: Rinn


title: Exploring new pathways involved during experimental renal fibrogenesis in the Unilateral Ureteral Obstruction

status: Public on Feb 10 2013

city: VILLEJUIF

first: christophe

last: desterke

address: 14-16 avenue Paul Vaillant Couturier

department: UFR medecine institute Andre Lwoff

institute: university Paris Sud11

summary: Chronic kidney disease (CKD) is a burden for Public Health and concerns millions of individuals worldwide. Independently of the cause, CKD is secondary to the replacement of functional renal tissue by extra-cellular matrix proteins (i.e fibrosis) that progressively impairs kidney function. The pathophysiological pathways that control the development of renal fibrosis are common to most of the nephropathies involving native kidneys or kidney grafts. Unfortunately, very few treatments are available to stop renal fibrosis and most of the therapeutic strategies are often barely able to slow down the progression of fibrogenesis in native kidneys. Therefore, it is mandatory to discover new therapeutic pathways to stop renal fibrosis. Our objective is to study new pathways involved in renal fibrosis. We thus decided to use the model of Unilateral Ureteral renal Obstruction in mice, a fast and reproducible  experimental model of  renal fibrosis.

overall_design: We studied renal fibrosis using experimental model of ureteral unilateral obstruction in mice, which was performed by complete ligation of the left ureter. The control lateral right kidney served as internal control.

first: Lola

last: Lecru

first: Christophe

last: Desterke

first: Amélia

last: Vernochet

first: Antoine

last: Dürrbach

first: Hélène

last: François


title: Expression profiling of palatal shelves in Tbx1 mutant mice

status: Public on Apr 02 2013

city: London

first: Matthew

last: Arno

state: LONDON

address: 150 Stamford Street

department: Genomics Centre

institute: King's College London

summary: To assess the influence of Tbx1 on gene expression profile within the developing palate we performed a microarray screen using RNA isolated from dissected secondary palate shelves of E13.5 wild type, Tbx1+/- and Tbx1-/- mice. Significant differences were identified between genotypes, with a total of 67 genes demonstrating at least a 2-fold change (p<0.05) in expression. These were clustered into 5 groups, including those downregulated in mutant compared to wild type and heterozygote (n=36); those progressively downregulated from wild type to mutant (n=12); those upregulated in heterozygote and downregulated in mutant compared to wild type (n=2); those progressively upregulated from wild type to mutant (n=12) and those downregulated in heterozygote and upregulated in mutant compared to wild type (n=5). High-throughput real time quantitative RT-PCR confirmed a total of 18 genes significantly changed between wild type and mutant and 24 between heterozygote and mutant. Amongst these, 15 were present in both groups and all except 1 were downregulated in the mutant. There were no significant differences in gene expression between wild type and heterozygous palatal shelves.

overall_design: Secondary palatal shelf pairs were carefully microdissected from E13.5 Tbx1+/+; Tbx1+/- and Tbx1-/- embryos (3 embryos per genotype as biological replicates). RNA was extracted from each pooled shelf pair generating nine RNA samples in total, each one analysed using a single microarray.

first: Martyn

middle: T

last: Cobourne


title: Gene expression Data from Toxoplasma gondii-Infected Murine Bone Marrow-Derived STAT6 and STAT3 Deficient Macrophages

first: Kirk

last: Jensen

summary:
The Toxoplasma type I ROP16 kinase directly activates the host STAT3 and STAT6 transcription factors and regulates the expression of many host genes. However, many of genes lack known STAT3/6 transcription factor binding sites in their promoter regions.
We wanted to understand what fraction of  host genes that are modulated by ROP16 were dependent on the STAT3 and STAT6 signaling pathways.

overall_design: Bone marrow-derived macrophages (BMMs) from mLys-Mcre Stat3fl/fl mice were infected with type II (Pru A7), type II +ROP16 I, type II Δgra15, or type II Δgra15 + ROP16I and gene expression was analyzed 18 hrs after infection. This data set was generated side by side with infections performed in B6 BMDMs, the gene expression results for that experiment were previoiusly submitted under the GEO accession number GSE29404. In addition, gene expression of wild type B6 and Stat6-/- BMDMs were infected with the II+ROP16I strain.

first: Ken

last: Hu

first: Jeroen

last: Saeij


title: Development of gene expression signatures in testis for plin1-null mice

status: Public on Mar 26 2013

city: Beijing

first: min

last: chen

address: No.2, Yuan Ming Yuan West Road

country: China

institute: China Agricultural University

summary: We have employed whole genome microarray expression profiling as a discovery platform to identify the effect of plin1 on gene expression during testis development. Testis of day 21, day 40, and day 60 in plin1-null mice and wild type mice were analyzed. Expression of a list genes (including cyp51, prm1, tnp2) from this signature was quantified in the same RNA samples by real-time PCR, confirming the influence of plin1 on testis development.

overall_design: plin1 knockout alteration gene expression in mice testis was measured at different development phases: day 21 meiosis phase, day 40 puberty phase, and day 60 mature phase. There independent experiments were performed at each time (d21, d40, d60).

first: Min

last: Chen

first: Qing

middle: Y

last: Meng

first: Ning

last: Li


title: HIF- and non-HIF-Regulated Hypoxic Responses Require the Estrogen-Related Receptor in Drosophila

status: Public on Feb 05 2013

city: Richmond

first: Keith

last: Baker

state: VA

address: 1220 E. Broad St.

institute: VCU School of Medicine

summary: Low-oxygen tolerance is supported by an adaptive response that includes a coordinate shift in metabolism and the activation of a transcriptional program that is driven by the hypoxia-inducible factor (HIF) pathway. The precise contribution of HIF-1 in the adaptive response, however, has not been determined. Here we investigate how HIF-1 influences hypoxic adaptation throughout Drosophila development. We find that hypoxic-induced transcriptional changes are comprised of HIF-dependent and HIF-independent pathways that are distinct and separable. We show that normoxic set-points of carbohydrate metabolites are significantly altered in dHIF mutants and that these animals are unable to mobilize glycogen in hypoxia. Furthermore, we find that the estrogen-related receptor (dERR), which is a global regulator of aerobic glycolysis in larvae, is required for a competent hypoxic response.  dERR binds to dHIF and participates in the HIF-dependent transcriptional program in hypoxia. In addition, dERR acts in the absence of dHIF in hypoxia and a significant portion of HIF-independent transcriptional responses can be attributed to dERR actions, including upregulation of glycolytic transcripts. These results indicate that competent hypoxic responses arise from complex interactions between HIF-dependent and -independent mechanisms, and that dERR plays a central role in both of these programs.

overall_design: Fly eggs were collected onto egg caps with yeast paste . The caps were replaced after overnight incubation periods and kept at 25ºC, until mid-L2. At mid-L2, larvae were transferred to a fresh egg cap with blue yeast paste (0.3% bromophenol blue), and allowed to develop until achieving the partial clear gut L3 stage (-10 to -4 hrs prior to metamorphic onset). Appropriately staged animals were moved to fresh agar plates and allowed to age an additional 6 hours at 25ºC (normoxic treatment). Alternatively, animals were placed in an airtight Modular Incubator Chamber for 6 hours at 25ºC after a gas mixture containing 4% oxygen balanced with nitrogen was flashed into the chamber (hypoxic treatment).  Mutant larvae were sorted for the absence of GFP expression using dissecting stereoscope with fluorescence at mid-L2. Microarray analyses were performed on at least three biological replicates of w1118, dHIF mutants, or dERR mutants at the partial clear gut third instar larval stage and were treated for 6 hours in normoxia or 4% O2. For each biological replicate, at least 10 larvae were collected and washed with 1×PBS. Larvae were placed in TRIzol (Invitrogen, Carlsbad, CA) and homogenized using VWR disposable pellet mixer. Total RNA was isolated using a TRIzol/RQ1 DNase (Promega, Madison, WI) hybrid extraction protocol. Template labelings were performed using the GeneChip 3' IVT Express Kit according to the manufacturer’s  specifications (Affymetrix, Santa Clara, CA). Hybridizations to Affymetrix GeneChip Drosophila Genome 2.0 arrays were performed using the manufacturers recommendations. Every chip was scanned at a high resolution by the Affymetrix GeneChip® Scanner 3000 according to the GeneChip Expression Analysis Technical Manual procedures (Affymetrix, Santa Clara, CA).

first: Yan

first: Luciana

last: Gentile

first: Catherin

middle: I

last: Dumur


title: Expression analyses in Drosophila ovaries

city: Iowa City

first: Alexey

last: Soshnev

state: Iowa

address: 3159C MERF 375 Newton Rd

department: Biochemistry

institute: University of Iowa

summary: Suppressor of Hairy-wing [Su(Hw)] is a multi-zinc finger DNA binding factor required for gypsy insulator function and female germline development in Drosophila. The enhancer-blocking and barrier functions of the gypsy retrotransposon involve Su(Hw) binding to twelve clustered Su(Hw) binding sites (SBSs) and recruitment of the Centrosomal Protein of 190 kD (CP190) and Modifier of mdg4 67.2 kD isoform (Mod67.2) insulator proteins. In contrast, the Su(Hw) germline function involves binding to non-clustered genomic SBSs and does not require CP190 or Mod67.2. Here, we use genome-wide expression analyses in the ovary to identify the first Su(Hw) regulated target genes.

overall_design: Ovaries for RNA isolation were dissected from 4-6 hour old virgin females of wild type (Canton S and BL15598) and su(Hw) null sterile mutants (su(Hw)A2663/v and su(Hw)Pb/2)  Drosophila melanogaster. At this stage of development, ovaries only contain egg chamber stages 1-8. Loss of Su(Hw) causes apoptosis at stage 9. Thus, the experimental design compares transcriptional changes in the ovary prior to induction nof apoptosis in su(Hw) mutants.

first: Ryan

last: Baxley

first: Pamela

middle: K

last: Geyer


title: The BEN domain is a novel sequence-specific DNA binding domain conserved in neural transcriptional repressors

first: Jakub

last: Westholm

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Expression data from D. melanogaster pupal wings

status: Public on Feb 01 2013

city: Marseille

first: Benjamin

last: Prudhomme

address: Parc scientifique de Luminy case 907

institute: IBDM-CNRS

summary: The goal of this gene expression profiling experiment was to identify the entire set of transcription factors expressed during late pupal wing development (~80h APF) when pigmentation genes are expressed

overall_design: We used Affymetrix microarrays to profile the expression of the transcription factors in late pupal wings of Oregon R flies. The staging of the flies was made by eye, based on the extent of wing pigmentation. RNA was extracted from batches of 40 flies and three biological replicates were analyzed.

last: Prud'homme


title: Reconstruction of the dynamic regulatory network that controls Th17 cell differentiation by systematic perturbation in primary cells (Affymetrix timecourse IL23 KO)

status: Public on Mar 07 2013

city: Berkeley

first: Nir

last: Yosef

state: CA

address: Berkeley

department: EECS

institute: UC Berkeley

summary: Despite their enormous importance, the molecular circuits that control the differentiation of Th17 cells remain largely unknown. Recent studies have reconstructed regulatory networks in mammalian cells, but have focused on short-term responses and relied on perturbation approaches that cannot be applied to primary T cells. Here, we develop a systematic strategy – combining transcriptional profiling at high temporal resolution, novel computational algorithms, and innovative nanowire-based tools for performing gene perturbations in primary T cells – to derive and experimentally validate a temporal model of the dynamic regulatory network that controls Th17 differentiation. The network is arranged into two self-reinforcing and mutually antagonistic modules that either suppress or promote Th17 differentiation. The two modules contain 12 novel regulators with no previous implication in Th17 differentiation, which may be essential to maintain the appropriate balance of Th17 and other CD4+ T cell subsets. Overall, our study identifies and validates 39 regulatory factors that are embedded within a comprehensive temporal network and identifies novel drug targets and organizational principles for the differentiation of Th17 cells.

overall_design: Time course microarray data for Th17 differentiation, comparing IL23r-/- to WT

first: Aviv

last: Regev


title: Targeted disruption of BMAL1 in the peripheral reproductive axis results in infertility in female mice.

city: Madison

first: Brian

last: Johnson

state: WI

address: 1400 University Ave

department: Oncology

institute: UW-Madison

summary: The product of the Bmal1 locus is an essential component of the circadian clock that plays important roles in various aspects of reproductive biology, and its disruption results in infertility. In an effort to identify the identity of the tissue specific clock that is responsible for this infertility, we used the steroidogenic factor-1 (Sf1) promoter to drive Cre-mediated recombination and genetically delete Bmal1 within cells of the reproductive axis. We show that Bmal1 within the reproductive axis of females is essential for normal fertility through its role in maintaining implantation, but is not required for normal estrous cycling. At the root of this biology appears to be a defect in the regulation of ovarian steroidogenic acute regulator (StAR) and its role in maintaining progesterone synthesis. This conclusion is based upon three observations.  First, that deletion of Bmal1 within the reproductive axis leads to lower levels of StAR mRNA, and lower progesterone levels.  Second, that progesterone supplementation of these conditional mutants rescues implantation. Third, transplantation of wild type ovaries into Bmal1 reproductive axis mutants results in 100% fertility.  Our study suggests that ovarian Bmal1 is an essential peripheral clock governing implantation and fertility in female mice.

overall_design: Ten week old female Bmal1fxfx mice positive or negative for Cre-recombinase driven by the sf-1 promoter, housed in 12 hour light:12 dark, ad lib feeding and drinking conditions were sacrificed at ZT12  on 3.5dpc (3.5 days post copulation). For each array analysis, a pool of 3 RNA samples from 3 individual Bmal1fx/fxCresf-1 ovaries labeled with cy3 were co-hybridized with a pool of 3 RNA samples from Bmal1fx/fx ovaries labeled with cy5, according to Agilent protocols.

last: Liu

first: Chris

middle: A

last: Bradfield