title: Densely Ionizing Radiation Effects on the Microenvironment Promote Aggressive Trp53 Null Mammary Carcinomas

status: Public on Oct 10 2014

city: new york

first: Mary Helen

last: Barcellos-Hoff

state: New York

address: 450 29th street

department: Radiation

country: USA

institute: New York University

summary:
Densely ionizing radiation is a major component of the space radiation environment and has potentially greater carcinogenic effect compared to sparsely ionizing radiation that is prevalent in the terrestrial environment. It is unknown to what extent the irradiated microenvironment contributes to the differential carcinogenic potential of densely ionizing radiation.  To address this gap, 10-week old BALB/c mice were irradiated with 100 cGy sparsely ionizing g-radiation or 10, 30, or 80 cGy of densely ionizing, 350 MeV/amu Si particles and transplanted 3 days later with syngeneic Trp53 null mammary fragments.  Tumor appearance was monitored for 600 days.  Tumors arising in Si-particle irradiated mice had a shorter median time to appearance, grew faster and were more likely to metastasize.  Most tumors arising in sham-irradiated mice were ER-positive, pseudo-glandular and contained both basal keratin 14 and luminal keratin 8/18 cells (designated K14/18), while most tumors arising in irradiated hosts were K8/18 positive (designated K18) and ER negative. Comparison of K18 vs K14/18 tumor expression profiles showed that genes increased in K18 tumors were associated with ERBB2 and KRAS while decreased genes overlapped with those down regulated in metastasis and by loss of E-cadherin.  Consistent with this, K18 tumors grew faster than K14/18 tumors and  more mice with K18 tumors developed lung metastases compared to mice with K14/18 tumors.  However, K18 tumors arising in Si-particle irradiated mice grew even faster and were more metastatic compared to control mice.  A K18 Si-irradiated host profile was enriched in genes involved in mammary stem cells, stroma, and Notch signaling.  Thus systemic responses to densely ionizing radiation enriches for a ER-negative, K18-positive tumor, whose biology is more aggressive compared to similar tumors arising in non-irradiated hosts.
Key Words: ionizing radiation; breast cancer; heavy ion radiation;initiation; promotion

overall_design:
3 different dose of Si were used.
Total RNA was extracted from mammary tumors derived from transplantations of non-irradiated p53null mammary fragments into irradiated hosts.  We analyzed a total of 45 Trp53-null tumors: 18 from sham-irradiated hosts, 9 from 10 cGy Si-irradiated hosts, 10 from 30 cGy Si-irradiated hosts, and 8 from irradiated hosts.

first: Irineu

last: Illa-Bochaca

first: Haoxu

last: Ouyang

first: Jonathan

last: Tang

first: Christopher

last: Sebastiano

first: Jian-Hua

last: Mao

first: Sylvain

last: Costes

first: Sandra

last: Demaria

first: Mary

middle: H


title: NAC45 and NAC86 direct sieve element differentiation that culminates in enucleation

status: Public on Oct 06 2014

city: Helsinki

first: Panu

last: Somervuo

address: Viikinkaari 4

country: Finland

institute: University of Helsinki

summary: Comparison of the expression profiles of nac45-2 nac86 mutant with col WT, and comparison of the expression profiles of NAC45 extopical induction with non-induction.

overall_design: Three-dye gene expression study with three biological replicates. Five-point time-series experiment and double-mutant vs wild-type comparison.

first: Kaori

last: Miyashima Furuta

first: Shri-Ram

last: Yadav

first: Satu

last: Lehesranta

first: Ilya

last: Belevich

first: Shunsuke

last: Miyashima

first: Anne

last: Vaten

first: Ove

last: Lindgren

first: Bert

last: De Rybel

first: Gert

last: Van Isterdael

first: Jung-ok

last: Heo

first: Raffael

last: Lichtenberger

first: Raquel

last: Rocha

first: Siripong

last: Thitamadee

first: Sari

last: Tähtiharju

first: Petri

last: Auvinen

first: Tom

last: Beeckman

first: Eija

last: Jokitalo

first: Ykä

last: Helariutta


title: Expression data from male and female Schlager hypertensive (BPH/2J) and normotensive (BPN/3J) kidneys

status: Public on Sep 28 2014

city: Penrith

first: Christine

middle: L

last: Chiu

state: New South Wales

address: Locked Bag 1797

department: School of Medicine

country: Australia

institute: Western Sydney University

summary:
Analysis of kidneys from 12 week BPH/2J hypertensive and age matched normotensive BPN/3J controls - males and females. The results provide insights into the genes that are involved in hypertension in both males and females, as well as highlight mechanisms that underlye sex differences in hypertension.
We show that female data can be used to refine candidate genes and pathways, as well as highlight potential mechanisms to explain the differences in prevalence and severity of disease between the sexes.

overall_design: Male and female kidneys from 12 week old hypertensive (BPH/2J) and normotensive (BPN/3J) mice were collected for RNA extraction and hybridization on Affymetrix microarrays. We used data obtained from male and female kidneys to identify common genes that are involved in the development of hypertension in males and females

first: Joanne

last: Lind


title: Contextual fear conditioning in the mouse hippocampus

status: Public on Oct 02 2014

city: Spokane

first: Lucia

last: Peixoto

state: WA

address: PO Box 1495

department: College of Medicine

institute: Washington State University, Spokane

summary: A fundamental question in neuroscience is how memories are stored and retrieved in the brain. Many neurological, psychiatric and neurodevelopmental disorders are associated with cognitive deficits. Therefore characterizing the biological basis of these processes is critical for understanding normal and abnormal brain function. It is known that long-term memory formation requires transcription and translation as well as epigenetic processes that control gene expression.  In this study we examined genome-wide gene expression changes during memory consolidation and after memory retrieval. We observe the largest changes in gene expression 30 minutes after memory acquisition and retrieval, and several novel genes were found to be affected by both. Interestingly, acquisition and retrieval of memory down-regulate different processes. Chromatin assembly is down-regulated after memory acquisition whereas RNA processing is down-regulated so after retrieval.  Histone variant H2AB levels are reduced following acquisition, while splicing factor Rbfox1 and NMDA receptor-dependent microRNA miR-219 are down-regulated following retrieval. We also show that miR-219 down-regulation after retrieval is accompanied by up-regulation of its target protein CAMKIIγ. Our study highlights for the first time the differential involvement of epigenetic mechanisms that control gene expression, such as histone variants and post-transcriptional RNA processing, during memory acquisition and retrieval.

overall_design: 72 total samples were analyzed, including animals trained in a contexual conditioning paradigm (FC) and controls. Tissue was collected at 30 minutes (FC30), 4 hours (FC4), 12 hours (FC12) and 24 hours after FC (FC24) as well as 30 minutes after testing for retrieval of the memory (RT30). Testing was performed at 24 hours after training over a 5-minute interval. Animals that were handled but not trained were dissected at the same time of day to control for variations due to circadian rhythms (CC30, CC4 andCC12). The protocol was repeated over the course of 2 weeks to obtain 9 animals (2 hippocampi) per group, so that 9 independent FC experiments were represented in each time point and all animals for each group were dissected at the exactly the same time of day.

first: Ted

last: Abel


title: Gene expression signature of fast and slow cycling intestinal crypt base columnar cell populations

status: Public on Sep 08 2014

city: Amsterdam

first: Richard

last: Volckmann

state: Noord-Holland

address: van der Boechorststraat 6a

department: Laboratory of Experimental Oncology and Radiobiology

country: Netherlands

institute: msterdam UMC and University of Amsterdam

summary: The identification of Lgr5 as an intestinal stem cell marker has made it possible to isolate and study primary stem cells from small intestine. Using the cell cycle specific expression og the mKi67 gene, we generated a novel Ki67-RFP knock-in allele which identifies dividing cells. Using Lgr5-GFP;Ki67-RFP mice, we isolated CBCs with distinct Wnt signaling levels and cell cycle features, and analyzed their global gene expression pattern using microarrays. We concluded that the cycling Lgr5hi stem cells exit the cell cycle in transition into the secretory lineage. Lgr5med Ki67low intermediate precursors reside in the zone of differentiation, resemble quiescent stem cells and generate the Dll1+ secretory precursors and the label retaining cells. Our findings support the cycling stem cell hypothesis and highlight the heterogeneity of early progenitors during lineage commitment.

overall_design: We used cell fractions of intestines from Lgr5-EGFP-ires-CreERT2 mice, expressing GFP under the control of the Lgr5 promoter, and Ki67-TagRFP mice where the RFP is fused to the C-terminus of the endogenous Ki67 gene. RNA was isolated from several FACS sorted cell populations of combinations expressing different levels of GFP and RFP: GFP high RFP high (Lgr5hi Ki67hi), GFP high RFP low (Lgr5hi Ki67low), GFP medium RFP high (Lgr5med Ki67high) and GFP medium RFP low (Lgr5med Ki67low).  Purified RNA was processed, hybridized, and scanned according to the manufacturer’s protocol and were hybridized on Affymetrix Mouse Gene ST 1.1 arrays).

first: Onur

last: Basak

first: Hans

last: Clevers


title: Tolerant and rejecting T cell microarray

status: Public on Sep 30 2014

city: Oxford

first: Duncan

last: Howie

state: Oxon

address: South Parks Road

department: Sir William Dunn School of Pathology

country: United Kingdom

institute: Oxford University

summary:
anti-CD4, CD8 and CD40L treated versus control murine CD4+ T cells from micegrafted with hESC derived xenografts.
Human embryonic stem cells (ESCs), by virtue of their capability to self-renew and differentiate into almost all body cell types, represent the first type of pluripotent stem cells (PSCs) to be used in clinical transplantation to humans in recent phase-I trials. As it is unlikely that any such cells or their progeny will survive in an allogeneic host, there is an urgent need to understand how to get long-term acceptance and functional differentiation with minimal immunosuppression. Here, we show that brief induction with combined monoclonal antibody-mediated coreceptor and costimulation blockade enables long-term survival and engraftment of murine ESCs, human ESCs, human induced PSCs, and human ESC-derived progenitor cells from all three embryonic germ layers. Tolerance induced to PSC-derived progenitors appears, remarkably, to extend to protection of their differentiated progenies, and sometimes even to different tissues derived from the same donor, suggesting linked-suppression as a likely operative mechanism. These results suggest that once tolerance has been established to PSC-derived progenitor cells, it can be extended to their differentiated progenies. Global gene expression profiling of graft infiltrating T-lymphocytes identifies gene sets that differ between rejecting and tolerant populations including gene upregulation in pathways associated with apoptosis, cell adhesion, transcription suppression and TGF synthesis; and gene downregulation in pathways associated with inflammation in recipients treated with combined coreceptor and costimulation blockade.

overall_design: Mice grafted with hESC derived tissues and untreated (control) or tolerised via injections of anti-CD4, anti CD8 and CD40L. CD3+ T cells isolated from the gratfs 30 days later.

first: Kathy

middle: O

last: Lui


title: Arabidopsis dark-induced senescence: wild type (Col-0) vs. pif quadruple (pif1pif3pif4pif5) mutant

status: Public on Aug 04 2014

city: Daejeon

first: Jinkil

last: Jeong

address: 291 Daehak-ro

department: Biological sciences

country: South Korea

institute: KAIST

summary: Transcriptional profiling of Arabidopsis dark-induced senescence comparing wild type (Col-0) with pif quadruple (pif1/3/4/5) mutant. After synchronized germination, the plants were grown under continuous white light for 7 days and transferred to darkness for 2 days to induce senescence. Goal was to determine the effect of PIFs on transcriptomic regulation during dark-induced senescence.

overall_design: Two-condition experiment, wild type vs. pif quadruple mutant. Biological replicates: 3 wild type replicates, 3 mutant replicates.

first: Giltsu

last: Choi


title: PPARγ controls alveolar macrophage identity [part1]

city: Zurich

first: Christoph

last: Schneider

address: Otto-Stern-Weg 7

department: Department of Biology, Institute of Molecular Health Sciences

country: Switzerland

institute: ETH Zurich

summary:
Tissue-resident macrophages comprise heterogeneous populations with unique functions and distinct gene expression signatures. While it has been established that they mostly originate from embryonic progenitors, the signals inducing a characteristic tissue-specific differentiation program remain unknown. Here we identify PPARγ as the crucial transcription factor determining perinatal alveolar macrophage (AM) development and identity. Development of the fetal monocyte derived AM precursor was largely abrogated in CD11c-Cre/Ppargfl/fl mice. To reveal the underlying changes in gene expression, we performed microarray analysis of sorted WT and KO AM and pre-AM from 3 different timepoints.
Part1: d2 and d11 sorts & array

overall_design: pre-AM FACS-sorted from lungs of d2 and mature AM from d11 PPARgfl/fl (WT) and CD11c-cre/PPARgfl/fl (KO) mice and subsequently processed for RNA extraction and hybridization on Affymetrix microarrays. 2 biological replicates per group, each composed of pooled cells from 2 individual mice

first: Samuel

middle: P

last: Nobs

first: Michael

last: Kurrer

first: Hubert

last: Rehrauer

last: Thiele

first: Manfred

last: Kopf


title: PPARγ controls alveolar macrophage identity

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

overall_design: Refer to individual Series


title: Comparison of the DNA methylation of bovine blastocysts and bovine sperm

status: Public on Sep 09 2014

city: Quebec

first: Eric

last: Fournier

state: Quebec

address: 2325 Rue de l'Universite

department: Departement des sciences animales

country: Canada

institute: Universite Laval

type: Methylation profiling by genome tiling array

summary: DNA from expanded bovine blastocysts and bovine sperm were extracted then subjected to methylation-sensitive enzymatic digestion and LM-PCR enrichment before being hybridized onto a microarray.

overall_design: Two-condition experiment, bovine blastocysts (pools of 10) vs bovine sperm. Four biological replicates of each tissue were hybridized to four two-color arrays in a dye-balanced design.

first: Habib

middle: A

last: Shojaei Saadi

first: Alan

middle: M

last: O'Doherty

first: Dominic

last: Gagné

first: Éric

first: Jason

middle: R

last: Grant

first: Marc-André

last: Sirard

first: Claude

last: Robert


title: PPARγ controls alveolar macrophage identity [part2]

summary:
Tissue-resident macrophages comprise heterogeneous populations with unique functions and distinct gene expression signatures. While it has been established that they mostly originate from embryonic progenitors, the signals inducing a characteristic tissue-specific differentiation program remain unknown. Here we identify PPARγ as the crucial transcription factor determining perinatal alveolar macrophage (AM) development and identity. Development of the fetal monocyte derived AM precursor was largely abrogated in CD11c-Cre/Ppargfl/fl mice. To reveal the underlying changes in gene expression, we performed microarray analysis of sorted WT and KO AM and pre-AM from 3 different timepoints.
Part2: adult sorts & array

overall_design: AM FACS-sorted from lungs of adult PPARgfl/fl (WT) and CD11c-cre/PPARgfl/fl (KO) mice and subsequently processed for RNA extraction and hybridization on Affymetrix microarrays. 2 biological replicates per group, each composed of pooled cells from 2 individual mice


title: Gene expression in whole lung and pulmonary macrophages reflects the dynamic pathology associated with airway surface dehydration

status: Public on Sep 11 2014

city: Chapel Hill

first: Hong

last: Dang

state: NC

address: 7027 Thurston-Bowles Bldg. CB#7248

department: CF Center

institute: UNC Chapel Hill

summary:
Scnn1b-Tg mice overexpress the beta subunit of the epithelial sodium channel (Scnn1b) in airway Club cells.  The general phenotype of these mice is described in three published manuscripts (Mall et al. 2004, Nature Medicine, 10(5):487-93;  Mall et al. 2008, Am J Respir Crit Care Med. 177(7):730-42; and Livraghi-Butrico et al. 2012, Physiol. Genomics 44(8):470-84. Briefly, overexpression of the Scnn1b transgene in airway Club cells leads to hyperabsorption of sodium from the airway surface liquid, dehydrated airway surface liquid and mucus, and reduced mucus clearance associated with accumulation of mucus plugs/plaques.  The data provided here represents mRNA expression data from disseccted whole trachea (distal and proximal ends cut 3-4 cartliage rings below the larynx and just above the bifurcation, respectively) from male WT and Scnn1b-Tg littermates (C57Bl/6NTac background) at 4 time points [postnatal days (PND) 0, 3, 10, and 42].  PND 0 trachea are histologically normal, a tracheal mucus plug/obstruction develops around PND 3, the plug is receding to more distal airways by PND 10, and the trachea is again histologically normal by PND 42.  The data from the WT mice provides a global look at mRNA changes across time, while the data from the Scnn1b-Tg line provides mRNA data that allows differential gene expression due to mucus obstruction to be queried.
The data presented for the purified is part of a larger body of work evaluating gene expression in whole lung, trachea, and purified macrophages.

overall_design: 30 total macrophage samples were analyzed;  three from each timepoint (postnatal day 0, 3, 10, and 42) for both wildtype and Scnn1b-transgenic mice grown in specific-pathogen-free facilities and from postnatal day 42 wildtype and Scnn1b-transgenic mice maintained in a germ-free facility.  In our manuscript, we were most interested in changes between WT and Scnn1b-Tg mice, however, the data can also be used to evaluate changes in gene expression across time (postnatal day 0, 3, 10, and 42).  This data can also be used to evaluate the differences in macrophage biology at postnatal day 42 when mice are grown in specific-pathogen-free versus germ-free environments.

first: Yogesh

last: Saini

first: Alessandra

last: Livraghi-Butrico

first: Wanda

middle: K

last: O'Neal

first: Richard

middle: C

last: Boucher


title: Wnt/beta-catenin-signaling in immortalized mouse adrenocortical cell line ATCL7

status: Public on Jul 11 2014

city: Ann Arbor

first: Rork

last: Kuick

state: MI

address: University of Michigan, SPH II, 1415 Washington Heights, Room M2533

institute: University of Michigan

summary: In order to investigate genes regulated by Wnt/Beta-catenin-signaling in immortalized mouse adrenocortical cells, we treated a pair of ATCL7 cell cultures, one with BIO, a small molecule mimicking Wnt/Beta-catenin-signaling, the other with a control treatment. We repeated this 3 additional times resulting in 4 pairs of samples. The Wnt/beta-catenin pathway is not basally active in ATCL7 cells, nor do these cells appear to contain any mutations in the Wnt/Beta-catenin pathway. ATCL7 cells were grown under standard conditions at 37°C in a humidified incubator containing 5% CO2. 250,000 ATCL7 cells per sample were treated with 0.5uM BIO (6-Bromoindirubin-3'-oxime) or 0.01% DMSO (v/v) for 24 hours, in DMEM:F12 growth media containing 100U/mL pencillin/streptomycin, 1X insulin-transferrin-selenium-X, 0.025% fetal bovine serum and 0.025% horse serum. Cells were harvested and RNA was extracted using an RNeasy Plus Mini Kit (Qiagen). Biotinylated cDNA were prepared according to the Ambion WT kit protocol from 250 ng total RNA (GeneAtlas™ WT Expression Kit User Manual P/N 702935 Rev. 3). We assayed the targets with Affymetrix Mouse Gene ST 1.1 strip arrays. We modeled the data using paired T-tests for each probe-set. We also supply a supplementary file holding the data and some statistical analysis, as well as probe-set annotation that we used at that time (users may wish to obtain new annotation though). We analyzed only 28944 probe-sets with category "main", "---", and "flmrna->unmapped" according to Affymetrix annotation.

overall_design: ATCL7 cells were grown under standard growth conditions at 37°C in a humidified incubator containing 5% CO2. 250,000 ATCL7 cells per sample were treated for 24 hours with 0.5uM BIO (6-Bromoindirubin-3'-oxime) or 0.01% DMSO (v/v) in growth media containing 100U/mL pencillin/streptomycin, 1X insulin-transferrin-selenium-X, 0.025% fetal bovine serum and 0.025% horse serum. Cells were harvested and RNA was extracted using an RNeasy Plus Mini Kit (Qiagen). Biotinylated cDNA were prepared according to the Ambion WT kit protocol from 250 ng total RNA (GeneAtlas™ WT Expression Kit User Manual P/N 702935 Rev. 3). We assayed the targets with Affymetrix Mouse Gene ST 1.1 strip arrays.

first: Elisabeth

last: Walczak

first: Gary

last: Hammer


title: Sf1+ mouse adrenocortical cells vs. Wnt-responsive mouse adrenocortical cells

summary: We sought to determine which gene transcripts are enriched in Wnt-responsive adrenocortical mouse cells compared to the entire adrenocortical mouse cell population in vivo. To this end, we employed transgenic reporter mice that label Wnt-responsive cells with GFP expression (TCF/Lef:H2B-GFP mice) or label all adrenocortical cells with GFP expression (Sf1:eGFP mice). GFP-positive adrenocortical cells were obtained from 6-week-old male TCF/Lef:H2B-GFP mice and Sf1:eGFP mice independently. 10 adrenals per genotype per sort were minced and digested by incubation in DMEM:F12 containing 0.1% collagenase/ 0.01% DNaseI solution for 1 h at 37°C. A single cell suspension was obtained following mechanical dispersion, filtration through a 40 micron nylon cell strainer, centrifugation at 1500rpm for 5 min followed by re-suspension in sterile 1X PBS containing 10% cosmic calf serum and 10μg/mL Propidium iodide. 10,000-50,000 viable GFP-positive cells were isolated via FACS using a BD FACSAria III cell sorter. RNA was extracted using an RNeasy Micro Kit (Qiagen) from 4 independent sorts per genotype. cDNA were prepared according to the NuGen WT-Pico V2 kit protocol from 5 ng total RNA (Ovation PicoSL WTA System V2 P/N 3312). Biotinylated single-stranded cDNA were prepared from 3ug of cDNA (Encore Biotin Module P/N 4200-12, 4200-60, 4200-A01). Targets were assayed on the Mouse Gene ST 1.1 strip arrays using the Affymetrix Gene Atlas system (software version 1.0.4.267). One TCF/Lef:H2B-GFP array was deemed low-quality and discarded. Two-sample T-tests were used to compare the two groups of samples. We also supply a supplementary file holding the data and some statistical analysis, as well as probe-set annotation that we used at that time (users may wish to obtain new annotation though). We analyzed only 28944 probe-sets with category "main", "---", and "flmrna->unmapped" according to Affymetrix annotation.

overall_design: GFP-positive adrenocortical cells were obtained from 6-week-old male TCF/Lef:H2B-GFP mice and Sf1:eGFP mice independently. 10 adrenals per genotype per sort were minced and digested by incubation in DMEM:F12 containing 0.1% collagenase/ 0.01% DNaseI solution for 1 h at 37°C. A single cell suspension was obtained following mechanical dispersion, filtration through a 40 micron nylon cell strainer, centrifugation at 1500rpm for 5 min followed by re-suspension in sterile 1X PBS containing 10% cosmic calf serum and 10μg/mL Propidium iodide. 10,000-50,000 viable GFP-positive cells were isolated via FACS using a BD FACSAria III cell sorter. RNA was extracted using an RNeasy Micro Kit (Qiagen) from 4 independent sorts per genoytpe. cDNA were prepared according to the NuGen WT-Pico V2 kit protocol from 5 ng total RNA (Ovation PicoSL WTA System V2 P/N 3312). Biotinylated single-stranded cDNA were prepared from 3ug of cDNA (Encore Biotin Module P/N 4200-12, 4200-60, 4200-A01). Targets were assayed on the Mouse Gene ST 1.1 strip arrays using the Affymetrix Gene Atlas system (software version 1.0.4.267).


title: Genomic assessment of stress in the horse

status: Public on Jun 30 2014

city: Bordeaux

first: Aline

last: FOURY

address: 146 rue Léo Saignat

country: France

institute: INRAE

summary: Thanks to the sequencing of the equine genome in 2009, it is now possible to perform genomic analyses in the horse. Thus, we propose to assess chronic stress by a transcriptomic approach. Two groups of yearlings were maintained in impoverished (n=9) or enriched (n=10) social and sensory conditions. The transcriptomic analysis was performed in blood cells after 12 weeks of experimentation. Results were analyzed with the program TELiS in order to identify the biological pathways differentiating the 2 groups. The analysis showed an up-regulation of the factors CREB, ATF and GATA in impoverished conditions that could sign the distress of those animals since the same molecular pathway has been detected in socio-environmental adversity in humans. This transcriptomic analysis provides a biological signature of yearling welfare that completes the behavioral analyses and help to evaluate disease risk.

overall_design: Gene expression induced by environmental conditions in horse blood was measured after 12 weeks of experimentation. There were 9 samples for the impoverished conditions and 10 samples for the enriched conditions.

last: Foury

first: Léa

last: Lansade

first: Steve

middle: W

last: Cole

first: Bruno

last: Cardinaud

first: Claire

last: Neveux

first: Frédéric

last: Lévy

first: Marie-Pierre

last: Moisan


title: Stimulation of RA SFBs with IL1 or PDGF-D

status: Public on Aug 10 2014

city: Jena

first: Peter

last: Kupfer

address: Beutenbergstrasse 11a

country: Germany

institute: HKI Jena

summary: Synovial fibroblasts of 6 RA patients were treated with IL1 or PDGF-D. The aim of this study was to outline mechanism of the disease RA by a treatment with one of these cytokines.

overall_design: In total 6 patients were analyzed with 5 time points each (0h, 1h, 2h, 4h and 12h). The patients are biological replicates.

first: Raimund

last: Kinne

first: Reinhard

last: Guthke

first: Sebastian

last: Vlaic

first: Rene

last: Huber


title: Effect of Spot14 Loss on Gene Expression Profile of MMTV-PyMT Mouse Tumors

status: Public on Sep 01 2014

city: Oklahoma City

first: Elizabeth

last: Wellberg

state: Oklahoma

address: 975 NE 10th St, BRC 309

department: Pathology

institute: University of Oklahoma HSC

summary: The objective of this study was to determine the effect of Thyroid Hormone Responsive Protein Spot14 (Spot14) loss on the gene expression profiles of tumors from MMTV-Polyomavirus middle-T antigen (PyMT) mice.  MMTV-PyMT/S14-heterozygous mice were crossed with S14-heterozygous mice and 1 cm tumors from MMTV-PyMT control (wild-type S14) or MMTV-PyMT/S14-null offspring were profiled using Affymetrix gene arrays.  Tumor latency was not different between groups; however, tumors lacking S14 grew significantly slower than control tumors.  Loss of S14 also decreased the levels of de novo synthesized fatty acids in mammary tumors.  In additional studies, performed on MMTV-Neu mice, we found that S14 overexpression was associated with increased tumor cell proliferation and elevated levels of tumor fatty acids.  Gene expression profiling revealed that S14 loss and overexpression in mouse mammary tumors altered pathways associated with proliferation and metabolism.  This study provides important information about the role of S14 in mammary tumorigenesis and tumor metabolism.

overall_design: Microarray analysis was performed on 4 mammary tumors from MMTV-PyMT mice and 4 tumors from MMTV-PyMT/S14-null mice.

first: Steven

last: Anderson


title: Rational design of a ligand-based antagonist of jasmonate perception

status: Public on Jun 20 2014

city: Madrid

first: Gloria

middle: Garcia

last: Casado

state: Madrid

address: C/Darwin 3

department: Genomica

country: Spain

institute: CNB-CSIC

summary: The phytohormone (+)-7-iso-jasmonoyl-L-isoleucine (JA-Ile) is a major regulator of developmental and stress responses in plants. The perception of JA-Ile involves the formation of a ternary complex with the F-box protein COI1 and a member of the JAZ family of co-repressors, which leads to JAZ degradation. Coronatine (COR) is a bacterial phytotoxin that functionally mimics JA-Ile and interacts with the co-receptor COI1-JAZ complex with higher affinity than JA-Ile. Based on the crystal structure of the co-receptor, we designed ligand derivatives that spatially impede the interaction of the co-receptor proteins and, therefore, should act as competitive antagonists of COR or JA-Ile. One derivative, Coronatine O-methyloxime (COR-MO), shows a strong activity preventing COI-JAZ interaction and the subsequent JAZ degradation. COR-MO efficiently reverts the effects of JA-Ile or COR treatments on JA-mediated responses, such as anthocyanin accumulation, root-growth inhibition and gene expression in Arabidopsis plants. Moreover, it potentiates plant resistance preventing the effect of bacterially produced COR during Pseudomonas syringae infections in different plant species. In addition to the utility of COR-MO for Plant Biology research, our results underscore its biotechnological and agronomical potential for a safer and sustainable agriculture.

overall_design: Two-condition experiment, Col-0 vs Col-0 plants treated 2h with Coronatine 0-methyloxime (COR-MO) and  Col-0 plants treated 2h with Coronatine vs Col-0 plants treated 2h with Coronatine plus COR-MO. Biological replicates: 4 control and  4  treated replicates

first: I

last: Monte

first: M

last: Hamberg

first: A

last: Chini

first: S

last: Gimenez-Ibañez

first: G

last: García-Casado

last: Porzel

first: F

last: Pazos

last: Boter

first: R

last: Solano


title: Gene Expression profiles of colon from Hif-1α+/+, Hif-1αLSL/LSL

status: Public on May 14 2014

first: XIANG

last: XUE

state: Michigan

address: 1301 E. Catherine Street

institute: Umich

summary:
To investigate the detailed molecular mechanisms for the regulatory role of HIF-1α in colon, microarray gene expression analysis was performed on colon RNA isolated from 6- to 8-week-old  Hif-1α+/+, Hif-1αLSL/LSL mice.
Background & Aims: The progression and growth of solid tumors leads to a state where tumors outgrow their capacity for efficient oxygenation and nutrient uptake and an increase in tumor hypoxia. Tumor hypoxic response is mediated by hypoxia-inducible factor (HIF)-1a and HIF-2a. These transcription factors regulate a battery of genes that are critical for tumor oxygenation, tumor metabolism, and cell proliferation and survival. Therefore, inhibitors of HIF have been sought for as anti-neoplastic agents in several different kinds of cancers. Interestingly, in ischemic and inflammatory diseases of the intestine, activation of HIF-1a is beneficial, and can reduce intestinal inflammation. The efficacy of pharmacological agents that chronically activate HIF-1a are decreased due to the tumorigenic potential of HIF.  However, recent advance in understanding HIF signaling have identified mechanisms, which could allow for isoform specific activators. Activation of HIF-2a increases colon carcinogenesis and progression in mouse models. However, the role of chronic HIF-1a activation is unclear in the progression in colon cancer. The present data demonstrates that activation of HIF-1a in epithelial cells does not increase colon carcinogens or progression in two mouse models of colon cancer, and provides the proof of principle that HIF-1a activation maybe safe as therapies for inflammatory bowel disease.

overall_design: Global gene expression profiling in colon RNAs isolated from 6- to 8-week-old Hif-1α+/+ (n=5, Shah 019) and Hif-1αLSL/LSL (n=5, Shah 020).

first: Xiang

last: Xue

first: Yatrik

last: Shah


title: KAP1(TRIM28/TIF1beta) represses differentiation-inducible genes in embryonic stem cells through cooperative binding with PRC1(Ring1b/Rnf2) and derepresses pluripotency-associated genes

status: Public on May 09 2014

first: Tom

middle: Klaus

last: Kerppola

address: 1150 West Medical Center Drive

department: Biological Chemistry

summary:
This SuperSeries is composed of the SubSeries listed below.
GSE56626
GSE56628


title: KAP1(TRIM28/TIF1beta) represses differentiation-inducible genes in  embryonic stem cells through cooperative binding with PRC1(Ring1b/Rnf2) and derepresses pluripotency-associated genes (expression)

summary: Embryonic stem (ES) cells express pluripotency-associated genes and repress differentiation-inducible genes.  The activities of these genes are coordinately reversed during differentiation.  The changes in the transcriptome upon conditional KAP1 knockout in ES cells overlapped with the changes during embryoid body formation.  KAP1 repressed differentiation-inducible genes and derepressed pluripotency-associated genes in ES cells.  KAP1 formed complexes with polycomb repressive complexes 1 (PRC1) through an interaction that was mediated by the KAP1 coiled-coil region.  KAP1 and PRC1 bound cooperatively at the promoters of differentiation-inducible genes and repressed their transcription.  In contrast, KAP1 bound the transcribed and flanking sequences of pluripotency-associated genes, did not enhance PRC1 binding, and derepressed their transcription.  KAP1 had opposite effects on differentiation-inducible and pluripotency-associated gene transcription both in ES cells and in differentiating embryoid bodies.  The region of KAP1 that mediated the interaction with PRC1 was required for KAP1 enhancement of PRC1 binding and for KAP1 repression of transcription at differentiation-inducible promoters. This region of KAP1 was not required for KAP1 suppression of PRC1 binding or for KAP1 derepression of transcription at pluripotency-associated promoters.  The opposite effects of KAP1 on transcription of differentiation-inducible versus pluripotency-associated genes contributed to the reciprocal changes in their transcription during differentiation.

overall_design: Analysis of the transcript levels in mouse embryonic stem cells before and after conditional KAP fl/fl knockout

first: Bo

last: Cheng

first: Xiaojun

last: Ren

first: Johnson

last: Craig


title: Expression data from differentiated 3T3-L1 pre-adipocytes.

status: Public on Apr 04 2014

city: Guelph

first: David

last: Mutch

state: Ontario

address: 50 Stone Road East

department: Human Health & Nutritional Sciences

institute: University of Guelph

summary:
Stearoyl-CoA desaturase (SCD) is the rate-limiting enzyme catalyzing the conversion of saturated fatty acids palmitate and stearate to monounsaturated fatty acids palmitoleate and oleate. During adipocyte differentiation, SCD expression increases concomitantly with several transcription factors and lipogenic genes.
We used microarrays to examine gene expression in differentiated pre-adipocytes treated with and without an SCD inhibitor.

overall_design: On day 7 of adipocyte differentiation, total RNA was extracted from adipocytes. Two conditions were selected for comparison: total RNA extracted from adipocytes treated with DMSO (control) and or a SCD inhibitor.

first: Flavia

last: Badoud


title: PPAR-alpha dependent regulation of vanin-1 mediates hepatic lipid metabolism.

status: Public on Apr 24 2014

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

institute: Wageningen University

summary: Peroxisome proliferator-activated receptor alpha (PPARα) is a key regulator of hepatic fat oxidation that serves as an energy source during starvation. Vanin-1 has been described as a putative PPARα target gene in liver, but its function in hepatic lipid metabolism is unknown. We investigated the regulation of vanin-1, and total vanin activity, by PPARα in mice and humans. Furthermore, the function of vanin-1 in the development of hepatic steatosis in response to starvation was examined in Vnn1 deficient mice, and in rats treated with an inhibitor of vanin activity. Liver microarray analyses reveals that Vnn1 is the most prominently regulated gene after modulation of PPARα activity. In addition, activation of mouse PPARα regulates hepatic- and plasma vanin activity. In humans, consistent with regulation by PPARα, plasma vanin activity increases in all subjects after prolonged fasting, as well as after treatment with the PPARα agonist fenofibrate. In mice, absence of vanin-1 exacerbates the fasting-induced increase in hepatic triglyceride levels. Similarly, inhibition of vanin activity in rats induces accumulation of hepatic triglycerides upon fasting. Microarray analysis reveal that the absence of vanin-1 associates with gene sets involved in liver steatosis, and reduces pathways involved in oxidative stress and inflammation. We show that hepatic vanin-1 is under extremely sensitive regulation by PPARα and that plasma vanin activity could serve as a readout of changes in PPARα activity in human subjects. In addition, our data propose a role for vanin-1 in regulation of hepatic TG levels during fasting.

overall_design: Livers of wild type and vanin-1 knockout mice that were fed or fasted for 24h were subjected to gene expression analysis

first: Jann

last: Van Diepen

middle: J

first: Rinke

last: Stienstra


title: Antidiabetic Rosiglitazone Remodels the Adipocyte Transcriptome by Redistributing Transcription to PPARg-Driven Enhancers [Affymetrix]

status: Public on May 02 2014

city: Cincinnati

first: Hee-Woong

last: Lim

state: Ohio

address: 3333 Burnet Ave. MLC 7024

department: Division of Biomedical Informatics

institute: Cincinnati Children's Hospital Medical Center

summary: Rosiglitazone (rosi) is a powerful insulin sensitizer, but serious toxicities have curtailed its widespread clinical use. Rosi functions as a high-affinity ligand for PPARg, the adipocyte-predominant nuclear receptor (NR). The classic model, involving binding of ligand to the NR on DNA, explains positive regulation of gene expression, but ligand-dependent repression is not well understood. We have now addressed this issue by studying the direct effects of rosiglitazone on gene transcription, using global run-on sequencing (GRO-seq). Rosi-induced changes in gene body transcription were pronounced after 10 minutes and correlated with steady-state mRNA levels as well as with transcription at nearby enhancers (eRNAs). Upregulated eRNAs occurred almost exclusively at PPARg binding sites, to which rosi treatment recruited the coactivator MED1. By contrast, transcriptional repression by rosi involved a loss of MED1 from eRNA sites devoid of PPARg and enriched for other TFs including AP-1 factors and C/EBPs. Thus, rosi activates and represses transcription by fundamentally different mechanisms that could inform the future development of antidiabetic drugs.

overall_design: Mature 3T3-L1 were treated with rosi or DMSO. Steady-state mRNA levels were monitored at various time points after the treatment between 0 minutes and 48 hours using Affymetrix Mouse Gene 1.1 ST Array.

first: Sonia

middle: E

last: Step

first: Jill

last: Marinis

first: Andreas

last: Prokesch

last: Steger

first: Seo-Hee

last: You

first: Kyoung-Jae

last: Won

first: Mitchell

last: Lazar


title: Effect of Spot14 Overexpression on Gene Expression Profile of MMTV-Neu Mouse Tumors

status: Public on Mar 01 2014

first: Elizabeth

last: Wellberg

summary: The objective of this study was to determine the effect of Thyroid Hormone Responsive Protein Spot14 (Spot14) overexpression on the gene expression profiles of tumors from MMTV-Neu mice.  Hemizygous MMTV-Neu and MMTV-Spot14 mice were bred and 1 cm tumors from Neu control or Neu/Spot14 bitransgenic offspring were profiled using Affymetrix gene arrays.  Tumors from Neu/Spot14 mice emerged significantly earlier than controls, but expressed many genes associated with lactogenic differentiation and were not highly metastatic.  These results from the mouse model are consistent with observations from primary human breast tumors, which indicate that high Spot14 gene expression was directly correlated with a luminal subtype and a positive ER status.  Overexpression of Spot14 in cultured mammary epithelial cells stimulated proliferation but not differentiation.  Together, these data suggest that, in vivo, Spot14 is expressed in well-differentiated cells, and promotes the expansion of this population in the context of oncogenic signaling pathway activation.

overall_design: Microarray analysis was performed on 13 mammary tumors from MMTV-Neu mice and 9 tumors from MMTV-Neu/MMTV-Spot14 mice.

first: Steven

last: Anderson


title: Quantitative proteomics analysis of signalosome dynamics in primary T cells identifies the surface receptor CD6 as a Lat adaptor-independent TCR signaling hub

status: Public on Mar 02 2014

city: Turku

first: Kartiek

last: Kanduri

address: Tykistokatu 6

institute: Turku Centre for Biotechnology

summary: The aim of the dataset was to study on a genome-wide level the impact of Lat deficiency on gene expression in resting and activated CD4+ T cells

overall_design: Lat+ and Lat− CD4+ T cells were isolated from lymph nodes and spleen of Latfl-dtr Tmat-Cre mice using a Dynabeads untouched mouse CD4 cells kit (Life Technology) and further purified by cell sorting. Lat+ CD4+ T cells were defined as: CD5+, hDTR+, CD8−, TCRγδ−, CD25−, CD69−, CD62L+, lineage (CD11c, CD11b, CD19, CD45R, CD161)− and Lat− CD4+ Tcells were defined as: CD5+, hDTR−, CD8−, TCRγδ−, CD25−, CD69−, CD62L+, lineage (CD11c, CD11b, CD19, CD45R, CD161)−. Sorted Lat+ or Lat−  CD4+ T cells were then kept in vitro for 4 hours without stimulation or activated for 4 hours using anti-CD3 antibody and anti-CD28 antibody. Cell samples corresponding to three biological replicates were analyzed and gene expression profiles were obtained from total RNA.

first: Romain

last: Roncagalli

first: Simon

last: Hauri

first: Fréderic

last: Fiore

first: Yinming

last: Liang

first: Zhi

last: Chen

first: Amandine

last: Sansoni

first: Rachel

last: Joly

first: Aurelie

last: Malzac

first: Harri

last: Lähdesmäki

first: Riitta

last: Lahesmaa

first: Sho

last: Yamasaki

first: Takashi

last: Saito

first: Marie

last: Malissen

first: Ruedi

last: Aebersold

first: Matthias

last: Gstaiger

first: Bernard


title: Follicular B (FoB) cells purified from miR-17-92 transgenic mice, stimulated with LPS/IL-4 for 13.5 or 25.5 hours

status: Public on Apr 01 2014

city: La Jolla

first: Steven

last: Head

state: CA

address: 10550 N Torrey Pines Rd

institute: The Scripps Research Institute

summary: We have generated a miR-17-92 transgenic allele (termed miR-17-92 Tg) whose expression can be turned on conditionally by Cre recombinase (Xiao et al, Nature Immunology, 9:405-14, 2008). The mice were crossed to CD19-Cre mice to turn on the transgene expression specifically in B cells.

overall_design:
Follicular B(FoB) cells were purified from CD19-Cre;miR-17~92 Tg/Tg mice (TG1, TG2, TG3) and miR-17~92 Tg/Tg mice (WT1, WT2, WT3) by MACS depletion of cells positive for CD5, CD43, and CD93 (also known as AA4.1). The purified B cells were stimulated with LPS/IL-4 for 13.5hr or 25.5hr.
The purity of follicular B cells was examined by flow cytometry and was greater than 95% for all samples. Total RNA was extracted using RNeasy kit (QIAGEN).

first: Changchun

last: Xiao

first: Hyun

middle: Y

last: Jin


title: Arabidopsis thaliana:seedlings treated by cis-cinnamic acid derivatives versus control seedlings

status: Public on Dec 28 2013

city: Fuchu

first: Naoya

last: Wasano

state: Tokyo

address: Saiwai-cho 3-5-8

country: Japan

institute: Tokyo University of Agriculture & Technology

summary: Transcriptional profiling of Arabidopsis thaliana seedlings treated with cis-cinnamic acid derivatives constructed by Nishikawa et al. (2013) Phytochemistry (http://dx.doi.org/10.1016/j.phytochem.2013.08.013), evaluating the candidate of herbicide chemicals by observing early response of gene expressions in Arabidopsis seedlings.

overall_design: Two-condition experiment, cis-CA analogue-treated seedlings vs. control seedlings. Biological replicates:2 control replicates, 2.


title: Effect of the repression of NLP function on nitrate-inducible gene expression in Arabidopsis thaliana

status: Public on Jan 07 2014

city: Bunkoy-ku

first: Shuichi

last: Yanagisawa

address: Yayoi 1-1-1

department: Biotechnology Research Center

institute: The University of Tokyo

summary: Plants take up nitrate in soils and utilize it both for nitrogen assimilation and as a signaling molecule. Thus, an essential role of nitrate in plants is triggering changes in gene expression patterns, including immediate induction of the expression of genes involved in nitrate transport and assimilation as well as several transcription factor genes and genes related with carbon metabolism and cytokinin biosynthesis and response. Recently we identified NIN-like proteins (NLPs) as transcription factors governing nitrate-inducible gene expression in Arabidopsis. Because of their similar DNA-binding property, nine NLP proteins may play redundant roles in controlling nitrate-regulated gene expression in Arabidopsis. The physiological roles of NLPs were therefore assessed by generating transgenic Arabidopsis plants expressing NLP6 fused to the transcriptional repression domain of SUPERMAN (SUPRD), which has an ability to convert transcriptional activators into transcriptional repressors. Our transcriptome analysis revealed that levels of nitrate-inducible expression of nitrate transporter genes (NRT1.1 and NRT2.1), nitrate reduction enzyme genes (NIA1, NIA2 and NIR1), the genes associated with ammonium assimilation (GLT1 for glutamine-2-oxoglutarate aminotransferase and ASN2 for asparagine synthetase), LBD37-39 transcription factor genes and genes encoding homologs of rice nitrate-inducible NIGT1 transcriptional repressor, were reduced in the NLP6-SUPRD lines. Furthermore, levels of nitrate-inducible expression of the genes associated with the oxidative pentose phosphate pathway (G6PD2 and G6PD3 for glucose-6-phosphate dehydrogenases, and 6-phosphogluconate dehydrogenase genes), cytokinin biosynthesis (IPT3) and signal transduction (A-type ARR genes), a gene encoding a Ser/Thr protein kinase associated with a calcineurin B–like calcium sensor (CIPK3) were also found to be largely decreased by reductions in NLP activity. Because induction folds by nitrate and reduction folds by decreases in the NLP activity were well proportional, the NLP activity appeared to be responsible for most of nitrate responsiveness of the genes whose expression occurs immediately after nitrate treatment.

overall_design: Overall design: Gene expression in 3.5-day-old seedlings treated with or without 10 mM potassium nitrate was compared between the transgenic lines expressing a chimeric repressor form of NLP6 (NLP6-SUPRD) and the parental control line.

first: Mineko

last: Konishi


title: Response of subgroup Ib 3xbhlh mutant and wild type at - Fe to +/- salicylic acid

status: Public on Dec 01 2013

city: Saarbrücken

first: Petra

last: Bauer

address: Campus A2.4

institute: Saarland University

summary: Subgroup Ib BHLH genes are induced by Fe deficiency. BHLH038 and BHLH039 were shown to be connected with salicylic acid. The triple knockout  3xbhlh  (bhlh039-1 bhlh100-1 bhlh101-1) shows a stronger leaf chlorosis at - Fe than the wild type. The responses of this triple mutant were studied at - Fe in comparison to the wild type in the presence and absence of salicylic acid (SA).

overall_design: Wild type and 3xbhlh seedlings (bhlh039-1 bhlh100-1 bhlh101-1) were grown at – Fe and treated for six hours with or without 100 µM SA. Three biological replicates were generated.

first: Felix

last: Maurer


title: Sel1L is Indispensable for Mammalian ERAD, ER Homeostasis and Survival

status: Public on Dec 04 2013

first: Guido

last: Hooiveld

summary: Sel1L is an adaptor protein for the E3 ligase Hrd1 involved in endoplasmic reticulum-associated degradation (ERAD). Its physiological importance in mammalian ERAD, however, remains to be established. Here, using the inducible Sel1L knockout mouse and cell models, we provide the first in vivo evidence that Sel1L is indispensable for Hrd1 stability, ER homeostasis and survival. Acute loss of Sel1L leads to premature death in adult mice within 3 weeks with profound pancreatic atrophy. Contrary to current belief, our data show that mammalian Sel1L is required for Hrd1 stability and ERAD function both in vitro and in vivo. Sel1L deficiency disturbs ER homeostasis, activates ER stress, attenuates translation and promotes cell death. Serendipitously, using biochemical approach coupled with mass spectrometry, we found that Sel1L deficiency causes the aggregation of both small and large ribosomal subunits. Thus, Sel1L is an indispensable component of mammalian ERAD and ER homeostasis, which is essential for protein translation, pancreatic function, cellular and organismal survival.

overall_design: Pancreas tissue of wild type and inducible Sel1L knockout mice were subjected to gene expression analysis.

first: Shengyi

last: Sun

first: Guojun

last: Shi

first: Xuemei

last: Han

first: Adam

middle: B

last: Francisco

first: Yewei

last: Ji

first: Nuno

last: Mendonça

first: Xiaojing

last: Liu

first: Jason

last: Locasale

first: Kenneth

last: Simpson

first: Gerald

last: Duhamel

first: Sander

last: Kersten

first: John

last: Yates III

first: Qiaoming

last: Long

first: Ling

last: Qi


title: Natural variation of transcriptional networks in Arabidopsis thaliana in response to salt stress

status: Public on Jan 01 2014

city: Wuhan

first: Zhulong

last: Chan

state: Hubei Province

address: No. 1, Shizishan St, Nanhu

department: College of Horticulture and Forestry Sciences

country: China

institute: Huazhong Agricultural University

summary: Arabidopsis ecotypes of Sha and Ler showed differences in tolerance to salinity stress. A previous study indicated that a premature stop codon resulting in a truncated Response to ABA and Salt 1 (RAS1) protein in Sha contributes to the increased salt tolerance relative to Ler ecotype. Sha exhibited higher germination rates and longer roots on MS plate, presumably due to the decreased ABA sensitivity in Sha. More Sha plants also survived in soil after salt treatment with relatively lower electrolyte leakage when compared to Ler. Transcriptome analysis revealed that expression levels of many genes were changed between Sha and Ler ecotypes and by salt treatments. About 500 transcripts were commonly changed by at least one salinity effect and one ecotype effect, and 171 of them were co-regulated by all four comparisons. Transcripts involved in redox, secondary metabolism, auxin metabolism, photosynthesis, cell wall, and protein synthesis were mainly down-regulated by salinity effects, while transposable element genes, microRNA and antisense sequences, histone superfamily genes, and biotic stress related genes were significantly changed by Sha ecotype effects and only slightly by salinity. Several metabolic pathways such as stress, TCA, hormone/lipid/secondary metabolism, redox, development, and GO terms involved in stress, oxidation, and defense response were enriched by both salinity and ecotype effects. Ninety-five highly inducible genes were identified as candidates of RAS1 target genes and the functions involved hormone metabolism, biotic stress, RNA, DNA synthesis, protein metabolism, cell, and microRNA metabolism. All these results indicated that the Sha ecotype was possibly preconditioned to abiotic stress relative to Ler through regulation of signaling pathways and stress responsive gene expression.  These comparative transcriptomic and analytical results also confirm the complexity of ABA responses and salt stress tolerance mechanisms, and they suggest additional targets for improving tolerance.

overall_design: Ten days old seedlings of two Arabidopsis ecotypes, Sha and Ler, were treated with 100 mM NaCl on MS plate. Plant materials were collected for RNA extraction at 4th days after treatments.


title: The effect of anti-CSF1R treatment on liver gene expression

status: Public on Jan 31 2014

city: Roslin

first: Kristin

last: Sauter

address: Easter Bush, Midlothian

institute: Roslin Institute/The University of Edinburgh

summary: The expression was designed to determine whether prolonged depletion of Kupffer cells has any effect on liver-specific gene expression.

overall_design: 2 treated samples and 3 control samples

first: David

last: Hume


title: Jnk1 in murine hepatic stellate cells is a crucial mediator of liver fibrogenesis

status: Public on Nov 27 2013

first: Guido

last: Hooiveld

summary: Hepatic fibrosis is a wound-healing response to chronic liver injury, which may result in cirrhosis and liver failure. The c-Jun N-terminal kinase-1 (JNK1) gene has been shown to be involved in liver fibrosis. Here, we aimed to investigate the molecular mechanism and identify the cell-type involved in mediating the JNK1-dependent effect on liver fibrogenesis Wild-type (WT), JNK1−/− and JNK1Δhepa (hepatocyte-specific deletion of JNK1) mice were subjected to bile duct ligation (BDL). Additionally, we performed bone marrow transplantations (BMT), isolated primary hepatic stellate cells (HSCs) and studied their activation in vitro. Serum markers of liver damage (liver transaminases, alkaline phosphatase and bilirubin) and liver histology revealed reduced injury in JNK1−/− compared to WT and JNK1Δhepa mice. Hepatocyte cell death and proliferation was reduced in JNK1−/− compared to WT and JNK1Δhepa. Parameters of liver fibrosis such as Sirius Red staining as well as Collagen IA1 and αSMA expression were down-regulated in JNK1−/− compared to WT and JNK1Δhepa livers, 4 weeks after BDL. To delineate the essential cell-type, we performed BMT of WT and JNK1-/- into JNK1-/- and WT mice, respectively. BMT experiments excluded bone marrow derived cells from having a major impact on the JNK1-dependent effect on fibrogenesis. Hence, we investigated primary HSCs from JNK1−/− livers showing reduced transdifferentiation compared with WT and JNK1Δhepa-derived HSCs. We conclude that JNK1 in HSCs plays a crucial role in hepatic fibrogenesis and thus represents a promising target for cell-directed treatment options for liver fibrosis.

overall_design: Control (JNK1f/f), JNK1 null (JNK1-/-) and hepatocyte-specific JNK1 null (JNK1Δhepa) mice were subjected to control, acute and chronic injury, i.e. sham or bile-duct ligation for 48h or 28 days resp., whereafter gene expression profiles were determined.

first: Gang

last: Zhao

first: Maximilian

last: Hatting

first: Yulia

last: Nevzorova

first: Mark

middle: V

last: Boekschoten

first: Oliver

last: Drvarov

first: Tania

last: Roskams

first: Michael

last: Müller

first: Francisco

last: Cubero

first: Christian

last: Trautwein


title: Gut-derived short-chain fatty acids are vividly assimilated into host carbohydrates and lipids

status: Public on Oct 21 2013

summary: Acetate, propionate and butyrate are the main short-chain fatty acids (SCFAs) that arise from the fermentation of fibers by the colonic microbiota. While many studies focus on the regulatory role of SCFAs, their quantitative role as a catabolic or anabolic substrate for the host has received relatively little attention. To investigate this aspect, we infused conscious mice with physiological quantities of stable isotopes [1-13C]acetate, [2-13C]propionate or [2,4-13C2]butyrate directly into the cecum, which is the natural production site in mice, and analyzed their interconversion by the microbiota as well as their metabolism by the host. Cecal interconversion - pointing to microbial cross-feeding - was high between acetate and butyrate, low between butyrate and propionate and almost absent between acetate and propionate. As much as 62% of infused propionate was used in whole-body glucose production, in line with its role as gluconeogenic substrate. Conversely, glucose synthesis from propionate accounted for 69% of total glucose production. The synthesis of palmitate and cholesterol in the liver was high from cecal acetate (2.8% and 0.7%, respectively) and butyrate (2.7% and 0.9%, respectively) as substrates, but low or absent from propionate (0.6% and 0.0%, respectively). Label incorporation due to chain elongation of stearate was approximately 8-fold higher than de novo synthesis of stearate. Microarray data suggested that SCFAs exert only a mild regulatory effect on the expression of genes involved in hepatic metabolic pathways during the 6h infusion period. Altogether, gut-derived acetate, propionate and butyrate play important roles as substrates for glucose, cholesterol and lipid metabolism.

overall_design: Mice were infused in cecum with stably-labelled isotopes of the three main short chain fatty acids or control solution.  After 6 hrs, livers were removed and pooled RNA samples were subjected to gene expression profiling.

first: Gijs

last: den Besten

first: Katja

last: Lange

first: Dirk-Jan

last: Reijngoud


title: Response of mammary tissue to high-LET HZE particle (Silicon ions) radiation or low-LET gamma-rays

status: Public on Nov 30 2013

city: Berkeley

first: Jonathan

last: Tang

address: 1 Cyclotron Road, MS-977

department: Cancer and DNA Damage Response

institute: Lawrence Berkeley National Laboratory

summary: Transcriptional profiling of mammary tissue irradiated at 10 weeks of age with either 100 cGy sparsely ionizing gamma-rays, or 10 cGy or 30 cGy densely ionizing radiation (350 MeV/amu Si). Mammary tissue was collected 1 weeks, 4 weeks, and 12 weeks post-irradiation.

overall_design: Four radiation treatment groups: sham, 100 cGy sparsely ionizing gamma-rays, 10 cGy or 30 cGy densely ionizing radiation (350 MeV/amu Si).  Three time points post-irradiation (1, 4, and 12 weeks).  Three or four replicates per time point.

first: Ignacio

last: Fernandez-Garcia

first: Sangeetha

last: Vijayakumar

first: Haydeliz

last: Martinez-Ruis

first: Irineu

last: Bochaca

last: Nguyen

first: Jian-Hua

last: Mao

first: Sylvain

last: Costes

first: Mary

middle: H

last: Barcellos-Hoff


title: Maternal Western-style high fat diet induces sex-specific physiological and molecular changes in two-week-old mouse offspring

first: Guido

last: Hooiveld

summary: Maternal diet is associated with the development of metabolism-related and other non-communicable diseases in offspring. Underlying mechanisms, functional profiles, and molecular markers are only starting to be revealed. Here, we explored the physiological and molecular impact of maternal Western-style diet on the liver of male and female offspring. C57BL/6 dams were exposed to either a low fat/low cholesterol diet (LFD) or a Western-style high fat/high cholesterol diet (WSD) for six weeks before mating, as well as during gestation and lactation. Dams and offspring were sacrificed at postnatal day 14, and body, liver, and blood parameters were assessed. The impact of maternal WSD on the pups' liver gene expression was characterised by whole-transcriptome microarray analysis. Exclusively male offspring had significantly higher body weight upon maternal WSD. In offspring of both sexes of WSD dams, liver and blood parameters, as well as hepatic gene expression profiles were changed. In total, 686 and 604 genes were differentially expressed in liver (p≤0.01) of males and females, respectively. Only 10% of these significantly changed genes overlapped in both sexes. In males, in particular alterations of gene expression with respect to developmental functions and processes were observed, such as Wnt/beta-catenin signalling. In females, mainly genes important for lipid metabolism, including cholesterol synthesis, were changed. We conclude that maternal WSD affects physiological parameters and induces substantial changes in the molecular profile of the liver in two-week-old pups. Remarkably, the observed biological responses of the offspring reveal pronounced sex-specificity.

overall_design: C57BL/6 dams were exposed to either a low fat/low cholesterol diet (LFD) or a Western-style high fat/high cholesterol diet (WSD) as six weeks pre-treatment before mating, as well as during gestation and lactation. Offspring were sacrificed at postnatal week two, livers were removed and RNA samples were subjected to gene expression profiling.

first: Mona

last: Mischke

first: Mark

last: Boekschoten

first: Torsten

last: Plösch

first: Wilma

last: Steegenga


title: Transcriptome sequencing and microarray design for functional genomics in the extremophile Arabidopsis relative Thellungiella salsuginea

status: Public on Nov 19 2013

city: Potsdam

first: Ellen

last: Zuther

address: Am Muehlenberg 1

department: Transcript Profiling

institute: MPI of Molecular Plant Physiology

summary: Arabidopsis thaliana is not particularly stress tolerant and may lack protective mechanisms required to survive extreme environmental conditions. Thellungiella salsuginea has therefore attracted increasing interest as an alternative plant model species that possesses high tolerance of various abiotic stresses. While the T. salsuginea genome has recently been sequenced, its annotation is still far from complete and, due to the low number of ESTs available, evidence for actual transcriptional activity is lacking for most genes. ESTs were generated from a non-normalized and a normalized library synthesized from RNA pooled from plant samples from different developmental stages and grown under abiotic stress conditions. The ESTs of Thellungiella was sequenced by 454  pyrosequencing method. More than 1 million sequence reads were assembled into 42,810 unigenes, approximately 50% of which could be functionally annotated. From this sequence information, we constructed a 44k Agilent oligonucleotide microarray. A comparison of same-species and cross-species hybridization results showed the superior performance of the newly designed array for Thellungiella samples. In addition, the array was validated in a cold acclimation experiment that used the appropriately adapted MapMan software for analysis and visualization.

sample_organism:
Arabidopsis thaliana
Eutrema salsugineum

overall_design: To examine the quality of the Thellungiella array and to assess whether hybridization results from a dedicated array are superior to cross-species hybridization using the Arabidopsis array from the same manufacturer, we performed reciprocal array hybridizations. In this experiment, RNA from the Yukon accession of Thellungiella and RNA from the Col-0 accession of Arabidopsis were both hybridized on the Agilent Thellungiella and Arabidopsis expression arrays. For both species, RNA was extracted from acclimated and non-acclimated plants from three independent biological replicates.

first: Yang

last: Lee

first: Federico

last: Giorgi

first: Marc

last: Lohse

first: Björn

last: Usadel

first: Sven

last: Klages

first: Richard

last: Reinhardt

first: Dirk

last: Hincha


title: Expression profiling of Troy positive gastric cells

status: Public on Oct 23 2013

city: Dresden

first: Daniel

middle: E.

last: Stange

address: Fetscherstr. 74

institute: University Clinic Dresden

summary: Proliferation of the self-renewing epithelium of the gastric corpus occurs almost exclusively in the isthmus of the glands, from where cells migrate bi-directionally towards pit and base. The isthmus is therefore generally viewed as the stem cell zone. We find that the stem cell marker Troy is expressed at the gland base by a small subpopulation of chief cells. By lineage tracing using a Troy-eGFP-ires-CreERT2 allele, single marked cells are shown to generate entirely labeled gastric units over periods of months. This phenomenon accelerates upon tissue damage. Troy+ chief cells can be cultured to generate long-lived gastric organoids. Troy marks a specific, 'plastic' subset of differentiated chief cells capable of replenishing entire gastric units, essentially serving as a quiescent ‘reserve’ stem cell.

overall_design:
An EGFP-ires-CreERT2 cassette was introduced into the transcriptional start side of Tnfrsf19 (Troy), resulting in the expression of EGFP and CreERT2 under the control of endogenous Troy-regulatory sequences. Troy is expressed in basally located chief and parietal cells. Using FACS, Troy positive chief and parietal cells can be isolated separately. Expression profiling was performed on these two cell types: three arrays of sorted chief cells, two arrays of sorted parietal cells. As a reference, two arrays of separately isolated whole gastric corpus glands were added.
In addition, single sorted Troy positive chief cells can be placed in culture, forming 3D cultures called organoids. Three arrays were generated from different organoid cultures, one time in normal medium containing the factors EGF, Gastrin, FGF10, Noggin, Wnt3a and Rspondin (EGFNWR medium) and one time in medium containing only EGF and Rspondin (ER medium).

first: Hans

last: Clevers


title: Transcriptome analysis of Paracoccus denitrificans during Cu-limitation

status: Public on Nov 18 2013

city: Norwich

first: Matthew

middle: John

last: Sullivan

state: Norfolk

address: Earlham Road

department: School of Biological Sciences

institute: University of East Anglia

summary: Transcriptional profiling of Paracoccus denitrificans PD1222 wild type grown to mid-exponential phase in minimal media with either 13 uM (Cu-H) or 0.5 uM (Cu-L) Cu regimes. The goal was to define the effects of Cu-limitation on denitrification genes

overall_design:
Two growth conditions, three biological replicates of each condition. Each sample hybridised in a two-channel hybridization against Paracoccus denitrificans genomic DNA as the comparator/reference, which also acted as a control for spot quality.
Cu-concentration 13 uM (Cu-H) versus 0.5 uM Cu (Cu-L) in anaerobic growth conditions.

first: Gary

last: Rowley

first: David

last: Richardson


title: Pleiotropic Effects of the Trichloroethylene-Associated P81S VHL Mutation on  Metabolism, Apoptosis and ATM-Mediated DNA Damage Response

status: Public on Sep 01 2013

city: Raleigh

first: Michelle

last: DeSimone

address: 112 Derieux Place

department: Genetics

institute: NCSU

summary:
Gene expression data from VHL teratomas comparing genes differentially expressed based on apoptotic response to tumor microenvironment.

Abstract
BACKGROUND:
The risk relevance of the P81S von Hippel-Lindau (VHL) gene hotspot mutation identified in clear cell renal cell carcinoma from individuals exposed occupationally to trichloroethylene (TCE) is not known. VHL mutations in hereditary VHL syndrome strongly correlate with phenotypic associations, but specific sporadic mutations in VHL that uniquely alter its protein function may provide a selective growth advantage for somatic cells harboring these mutations.
METHODS:
VHL deficient (Vhl -/- ) mouse embryonic stem cells were generated that stably express wild-type, P81S, or R167Q human VHL protein. Under hypoxic conditions, cell lines were examined for hypoxia-inducible transcription factor family (HIF) stabilization and E3-ubiquitin ligase complex interactions. In vivo, teratomas were examined for tumor size, proliferation, apoptosis, and immunohistochemistry and subjected to gene expression analysis. Wild-type, R167Q, and P81S VHL-expressing teratomas were also exposed to 5 Gy ionizing radiation to quantify apoptotic response. Proliferation and apoptosis and teratoma growth were analyzed by either Student t test or analysis of variance with Bonferroni correction. All statistical tests were two-sided.
RESULTS:
The P81S VHL mutation produces deregulation of HIF factors in cell culture but exhibits a growth advantage in the tumor microenvironment, in part because of suppression of apoptosis (P81S mean = 0.9%, 95% confidence interval = 0.6 to 1.2%; WT mean = 7.6%; 95% confidence interval = 6.4 to 8.8%; P < .001) coupled with sustained proliferation. Transcriptional analysis of P81S teratomas revealed the induction of metabolic pathways, antiapoptotic genes, and global suppression of key DNA damage response genes not observed in VHL wild-type or R167Q mutants. In vivo irradiation exposure showed that P81S mutant is resistant to ionizing radiation-induced apoptosis.
CONCLUSIONS:
The TCE-associated P81S VHL mutation can initiate a unique adaptive response required for selective tumor growth through pleiotropic effects on metabolic diversification, apoptosis suppression, and alteration of the DNA damage response.

overall_design: Three genotypes of VHL teratomas were examined: Three replicate wildtype VHL, Three replicate R167Q VHL, and Four replicate P81S VHL (representing two replicates of two different P81S clones)

first: W

last: Rathmell

last: Threadgill


title: Transcriptome signature of white adipose tissue, liver, and skeletal muscle in 24 hours fasted mice (C57Bl/6J)

status: Public on Nov 04 2013

city: Graz

first: Andreas

last: Prokesch

state: Styria

address: Harrachgasse 21/7

department: Institute of Cell Biology, Histology, and Embryology

country: Austria

institute: Medical University Graz

summary: Fasting is the process of metabolic adaption to food deprivation that is taking place in most organisms, e.g. during the daily resting phase in mammals. Furthermore, in biomedical research fasting is used in most metabolic studies to synchronize nutritional states of study subjects. Because there is a lack of standardization for this procedure, we need a deeper understanding of the dynamics and the molecular players in fasting. In this study we investigated the transcriptome signature of white adipose tissue, liver, and skeletal muscle in 24 hours fasted mice (and chow fat controls) using Affymetrix whole-genome microarrays.

overall_design: Food was withdrawn from the fasting group at the beginning of the light phase (9 a.m.) when mice are in their inactive phase. Mice were sacrificed 24 hours later by cervical dislocation. Chow-fed controls had ad libitium access to food during this time. Edidymal white adipose tissue, liver, and skeletal muscle were dissected out, shock frozen in liquid nitrogen and stored at -80°C.

first: Michael

last: Schupp

first: Fang

last: Chen

first: Erika

last: Briggs

first: Shilpa

last: Rao

first: Juliane

middle: G

last: Bogner-Strauss

first: Mitch

last: Lazar

first: Don

last: Baldwin

first: Ariane

last: Pessentheiner

first: Helmut

last: Pelzmann


title: Caspase-1 deficiency reduces intestinal and hepatic triglyceride-rich lipoprotein secretion

status: Public on Sep 15 2013

first: Guido

last: Hooiveld

summary:
Background and Aims: Inflammasome-mediated caspase-1 activity regulates the maturation and release of the pro-inflammatory cytokines interleukin (IL)-1ß and IL-18. Recently, we showed that caspase-1 deficiency strongly reduces high fat diet-induced adiposity although the mechanism is still unclear. We now aimed to elucidate the mechanism by which caspase-1 deficiency reduces modulates resistance to high fat diet-feeding fat accumulation in adipose tissue by focusing on the role of caspase-1 in the regulation of triglyceride (TG)-rich lipoprotein metabolism. Methods: Caspase-1 deficient and wild-type mice (both C57Bl/6 background) were used to determine postprandial TG kinetics, intestinal TG absorption, VLDL-TG production as well as TG clearance, all of which strongly contribute to the supply of TG for storage in adipose tissue. Micro-array and qPCR analysis were used to unravel intestinal and hepatic metabolic pathways involved. Results: Caspase-1 deficiency reduced the postprandial response to an oral lipid load, while tissue specific clearance of TG-rich lipoproteins was not changed. Indeed, an oral olive oil gavage containing [3H]TG revealed that caspase-1 deficiency significantly decreased intestinal chylomicron-TG production and reduced the uptake of [3H]TG-derived FA by liver, muscle, and adipose tissue. Similarly, caspase-1 deficiency reduced the hepatic VLDL-TG production without reducing VLDL-apoB production, despite an elevated hepatic TG content. Pathway analysis revealed that caspase-1 deficiency reduces intestinal and hepatic expression of genes involved in lipogenesis. Conclusions: Absence of caspase-1 reduces assembly and secretion of TG-rich lipoproteins, thereby reducing the availability of TG-derived FA for uptake by peripheral organs including adipose tissue. We anticipate that caspase-1 represents a novel link between innate immunity and lipid metabolism.

Keywords: Expression profiling by array

overall_design: Wild-type (WT) and Casp1-null mice were maintained at lab chow. Animals, aged between 14 and 16 weeks (n=3 per genotype), were killed and liver and intestinal segments were removed. Livers were isolated from mice that were fasted over night, whereas intesines were removed from mice 2 hrs after they received an oral lipid load.Total RNA was isolated and subjected to gene expression profiling.

first: Janna

middle: A

last: van Diepen

first: Rinke

last: Stienstra

first: Ko

last: Willems van Dijk

first: Patrick

last: Rensen


title: Exon level gene expression profile of the prefrontal cortex region of Df(16)A+/- mice, a mouse model of 22q11.2 microdeletion syndrome

city: New York

first: Bin

last: XU

state: NY

address: 1051 Riverside Drive

institute: columbia university

summary: Df16(A)+/- mice line is a model of human 22q11 microdeletion syndrome. We conducted an unbiased evaluation of the transcriptional difference in the prefrontal cortex between mutant and wild type animals at exon level. These mice were generated by chromosomal engineering and carry a microdeltion of ~1.3Mb in the mouse locus syntenic to the human 22q11.1 The reasoning behind this expression profiling is that consistent alterations in transcriptional programs reflect either downstream (immediate or remote) effects of the deficiency or reactive (compensatory) changes, and can thus point to affected biological processes and molecular functions. Df(16)A+/- mice line is a model of human 22q11 microdeletion syndrome.

overall_design: Adult mutant mice and their wild type littermate were selected. Prefrontal cortex tissues were dissected, total RNA were extracted, processed and hybridized on Affymetrix microarrays. We sought to obtain difference of expression profiles between mutant and wild mice at exon level.

last: Xu

first: Joseph

last: Gogos

first: Maria

last: Karayiorgou


title: Hypothalamic gene expression of appetite regulators in a cancer-cachectic mouse model [Dataset 2]

status: Public on Nov 14 2013

summary: Appetite is frequently affected in cancer patients, leading to anorexia and consequently insufficient food intake. In this study, we report on hypothalamic gene expression profile of a cancer cachectic mouse model with increased food intake. In this model, mice bearing C26 colon adenocarcinoma have an increased food intake subsequently to the loss of body weight. We hypothesize that in this model, appetite regulating systems in the hypothalamus, which apparently fail in anorexia, are still able to adapt adequately to changes in energy balance. Therefore studying the changes that occur on appetite regulators in the hypothalamus might reveal targets for treatment of cancer-induced eating disorders. By applying transcriptomics, many appetite regulating systems in the hypothalamus could be taken into account, providing an overview of changes that occur in the hypothalamus during tumour growth. We show that hypothalamic expression of orexigenic neuropeptides NPY and AgRP was higher, whereas expression of anorexigenic genes CCK and POMC were lower in TB compared to controls. In addition, serotonin and dopamine signalling pathways were found to be significantly altered in TB mice. Serotonin levels in brain showed to be lower in TB mice compared to control mice, while dopamine levels did not change. Moreover, serotonin levels inversely correlated with food intake. Transcriptomic analysis of the hypothalamus of cachectic TB mice with an increased food intake showed changes in NPY, AgRP and serotonin signalling. Serotonin levels in the brain showed to correlate with changes in food intake. Targeting these systems seems a promising strategy to avoid the development of cancer-induced eating disorders.

overall_design: C26-colon adenocarcinoma cells were subcutaneously inoculated in CDF1 mice. After 20 days, hypothalami were dissected and subjected to gene expression profiling. The total dataset consists of 2 parts; dataset 1, a pilot stuy in which mice were injected with increasing number of tumour cells and pooled samples were arrayed; and dataset 2, the main study in which mice were injected with 1 million tumour cells and samples were individually arrayed.

first: Jvalini

middle: T

last: Dwarkasing

first: Francina

last: Dijk

first: Mark

last: Boekschoten

first: Joyce

last: Faber

first: Josep

middle: M

last: Argilès

first: Alessandro

last: Lavianio

first: Michael

last: Müller

first: Renger

middle: F

last: Witkamp

first: Klaske

last: van Norren


title: Krüppel-like factor 3 KO and rescue expression data in murine embyronic fibroblasts

status: Public on Oct 17 2013

city: Sydney

first: Jon

last: Burdach

state: NSW

address: UNSW

department: BABS

institute: University of New South Wales

summary:
Krüppel-like factor 3 (KLF3) is a transcriptional repressor that has roles in adipogenesis, B-cell maturation and erythropoiesis (for review see Pearson et al., 2012).
We profiled gene expression in murine embryonic fibroblasts (MEFs) where Klf3 had been knocked-out and where the same cell had been rescued with Klf3 using microarrays.

overall_design: Klf3 KO murine embryonic fibroblast cell lines were produced from Klf3 KO mice.  These cells were rescued with epitope tagged Klf3 (Klf3-V5) using retroviral delivery (murine stem cell virus). Stable clones were selected uner puromycin seletion and total RNA was taken for array

first: Alister

middle: P

last: Funnell

first: Crisbel

last: Artuz

first: Mak

middle: K

last: Sin

first: Lit

last: Tan

first: Richard

middle: C

last: Pearson

first: Merlin

last: Crossley


title: Agilent data from Arabidopsis thaliana enriched guard cell tissue of ost1-2,slac 1-5, gl1-1 and landsberg erecta

status: Public on Nov 20 2013

city: Wuerzburg

first: Susanne

middle: Elma

last: Kneitz

address: Biozentrum, Am Hubland

department: Physiologigcal Chemistry

institute: University of Wuerzburg

summary: To identify genes of the guard cell transcriptome of Arabidopsis thaliana enriched guard cell samples of ost1-2 and slac1-5 mutants were compared to their wildtype.

overall_design: Total samples analysed are 11: biological independent replicates of: enriched guard cells (slac1-5) vs. enriched guard cells (gl1-1); enriched guard cells (ost1-2) vs. guard cells (ler);

first: Hubert

last: Bauer

first: Peter

last: Ache

first: Khaled

last: Al-Rasheid

first: Sophia

last: Sonnewald

first: Uwe

first: Alistair

last: Hetherington

first: Rainer

last: Hedrich


title: Comparison of arf2, gnc gnl and arf2 gnc gnl transcriptomes

status: Public on Jul 15 2013

city: Freising-Weihenstephan

first: Claus

last: Schwechheimer

address: WZW - Lehrstuhl Systembiologie der Pflanzen, Am Hochanger 4

institute: Claus Schwechheimer

summary: We have used Agilent whole genome arrays (v4) to compare the gene expression changes between 10-day-old Arabidopsis wild type seedlings and arf2-8 (Ellis et al., 2005), gnc gnl (Richter et al., 2011) and arf2 gnc gnl mutants (all Col ecotype).

overall_design: Three independent biological samples were prepared for each genotype.

first: Carina

last: Behringer

first: René

last: Richter


title: Differential Gene Regulation during murine in vivo heart ischemia comparing wildtype and Per2 deficient mice

status: Public on Aug 21 2013

city: Denver

first: Tobias

last: Eckle

state: CO

address: 12700 E 19th Avenue

department: Anesthesiology

institute: UC Denver

summary: Disruption of peripheral circadian rhyme pathways dominantly leads to metabolic disorders. Studies on circadian rhythm proteins in the heart indicated a role for Clock or Per2 in cardiac metabolism. In fact, Per2-/- mice have larger infarct sizes with a deficient lactate production during myocardial ischemia. To test the hypothesis that cardiac Per2 represents an important regulator of cardiac metabolism during myocardial ischemia, we performed lactate measurements during reperfusion in Per1-/-, Per2-/- or wildtype mice followed by gene array studies using various ischemia-reperfusion protocols comparing wildtype and Per2-/- mice. Lactate measurements in whole blood confirmed a dominant role of Per2 for lactate production during myocardial ischemia. Surprisingly, high-throughput gene array analysis  of eight different conditions on one 24-microarray plate revealed dominantly lipid metabolism as differentially regulated pathway in wildtype mice when compared to Per2-/-. In all treatment groups, the enzyme enoyl-CoA hydratase, which is essential in fatty acid beta-oxidation, was regulated in wildtype animals only. Studies using nuclear magnet resonance imaging (NMRI) confirmed altered fatty acid populations with higher mono-unsaturated fatty acid levels in hearts from Per2-/- mice. Unexpectedly, studies on gene regulation during reperfusion revealed solely pro inflammatory genes as differentially regulated 'Per2-genes'. Subsequent studies on inflammatory markers showed increasing IL6 or TNFa levels during reperfusion in Per2-/- mice. In summary, these studies reveal a novel role of cardiac Per2 for fatty acid metabolism or inflammation during myocardial ischemia and reperfusion.

overall_design: We pursued studies on Per2 dependent gene expression during myocardial ischemia or reperfusion to understand its impact on cardiac metabolism. We designed different ischemia and reperfusion protocols and performed a high-throughput expression profiling of 24 samples at a time using an industry-standard whole mouse gene array (Affymetrix, Mouse Gene 2.1 ST 24-Array). To understand differential gene regulation during different conditions we performed 1) 30 minutes of ischemia without reperfusion, 2) ischemic preconditioning (IP, 4 x 5 minutes ischemia and reperfusion), as known cardioprotective mechanism, and 3) 30 minutes of ischemia followed by 60 minutes of reperfusion. Based on three arrays per condition the total number of arrays was 24, which we analyzed at the same time on a multi plate array to avoid inter-array variations. Quality analysis using Partek Genomics Suite 6.6 revealed high confidence in the quality of the microarray data and all samples met 'Quality Assurance/Quality Control' (QA/QC) criteria.

first: Bifeng

last: Gao

first: Todd

last: Woessner

first: An

last: Doan


title: Transcriptional and translational effect of the lack of translation initiation factor eIF(iso)4E

status: Public on Jul 26 2013

city: MEXICO CITY

first: TZVETANKA

middle: DIMITROVA

last: DINKOVA

state: DISTRITO FEDERAL

address: CIRCUITO EXTERIOR, CIUDAD UNIVERSITARIA DELEGACION COYOACAN

department: BIOCHEMESTRY

country: Mexico

institute: UNIVERSIDAD NACIONAL AUTONOMA DE MEXICO, FACULTAD DE QUIMICA

type:
Expression profiling by array
Other

summary: One of the most regulated steps of translation initiation is the recruitment of an mRNA by the translation machinery. In eukaryotes, this step is mediated by the 5´end cap-binding factor eIF4E bound to the bridge protein eIF4G and forming the eIF4F complex. In plants, different isoforms of eIF4E and eIF4G form the antigenically distinct eIF4F and eIF(iso)4F complexes proposed to mediate selective translation. Using a microarray analysis of polyribosome- and non-polyribosome-purified mRNAs from 15 day-old Arabidopsis thaliana wild type [WT] and eIF(iso)4E knockout mutant [AteIF(iso)4E-1] seedlings we found 79 transcripts shifted from polyribosomes toward non-polyribosomes, and 47 mRNAs with the opposite behavior in the mutant. The translationally decreased mRNAs were overrepresented in root-preferentially expressed genes and proteins from the endomembrane system, including several transporters such as the phosphate transporter PHOSPHATE1 (PHO1), Sucrose transporter 3 (SUC3), the ABC transporter-like with ATPase activity (MRP11) and five electron transporters, as well as signal transduction-, protein modification- and transcription-related proteins.

overall_design: For transcriptional analysis used total RNA of AteIF(iso)4E-1 seedlings of 15 days old to known the changes on transcripts leves by the eIF(iso)4E absence, using as control Wt seedlings. The experiments were performed in duplicate, and swap analysis were done. For translational analysis, used non-polysomal and polysomal RNA of AteIF(iso)4E-1 seedlings of 15 days old in order to known the transcripts that are modified in their translational levels by the eIF(iso)4E absence, using as control non polysomal and polysomal RNA of Wt seddlings.

first: Ana

last: Martínez-Silva

first: Tzvetanka

middle: D

last: Dinkova


title: Comparison of osmotic stress related gene expression in Col-0, sid2-1 single, wrky54wrky70 double and wrky54wrky70sid2-1 triple mutants.

status: Public on Aug 31 2013

city: Helsinki

first: Jing

last: Li

address: Viikinkaari 5D

department: Department of Bioscience

institute: University of Helsinki

summary: To explore the possible cause for the enhanced tolerance to osmotic stress exhibited by wrky54wrky70 double mutant, we have used Agilent Arabidopsis (V4) Gene Expression Microarray to characterize the effect of these mutations under the osmotic stress treatment. In addition to wild type and wrky54wrky70 double mutant, sid2-1 single and wrky54wrky70sid2-1 triple mutant were also included in the microarray experiment. When comparing to untreated control samples, 58 genes were identified as representatives to show the different expression level among different mutants under the 15% PEG6000 treatment for one day. Expression of six genes (RAB18, LTI78, KIN1,NCED3,P5CS1 and PRODH) from this gene list were quantified by qRT-PCR, confirming the suppressed induction in wrky54wrky70 double mutant under the osmotic stress.

overall_design: Osmotic stress induced gene expression in Col-WT, sid2-1 single, wrky54wrky70 double and wrky54wrky70sid2-1 triple mutants was measured after exposure to 15% PEG6000 treatment for one day. For each array, three labeled aRNA sample were hybridized and three biological replicates for each sample with dye swaps were made.

first: Sebastien

last: Besseau

first: Petri

last: Törönen

first: Nina

last: Sipari

first: Hannes

last: Kollist

first: Liisa

last: Holm

first: Tapio

middle: E

last: Palva


title: Effect of overexpression of Arabidopsis Dof5.8 from the MP promoter.

status: Public on Jun 11 2013

city: Bunkoy-ku

first: Shuichi

last: Yanagisawa

address: Yayoi 1-1-1

institute: The University of Tokyo

summary: Vascular formation in the leaves of higher plants begins with the selection of cells poised to become preprocambial cells, some of which eventually develop into procambial cells. The initiation of this process is accompanied by auxin-responsive and MONOPTEROS (MP) transcription factor-mediated modulations in gene expression. Here, we show that MP directly activates the expression of Dof5.8, which encodes a transcriptional repressor. Consistently, mutations within Dof5.8 enhanced the phenotype of a weak allele of mp, resulting in abnormal root and cotyledon development. However, although mp mutants showed reduced vascular patterns in cotyledons, the mp dof5.8 double mutants displayed both reduced and more complex vascular patterns in individual cotyledons. Thus, Dof5.8 appears to be associated with both positive and negative regulatory mechanisms for vascular network formation in leaves. Furthermore, both over-expression of Dof5.8 and expression of a Dof5.8 construct engineered to possess enhanced repressor activity in preprocambial cells prevented the formation of procambium for secondary and higher order veins, suggesting a predominantly negative regulatory role for Dof5.8. These results imply that proper vascular patterns in leaves are formed through the modulation of both positive and negative regulation by Dof5.8. MP may direct this fine-tuning mechanism by mediating the expression of Dof5.8.

overall_design: Gene expression in 4-day-old shoots was compared between the Dof5.8-overexpressing lines and control lines.

first: Mineko

last: Konishi


title: Does Phosphatidylserine (PS) affect gene expression in FD mice?

status: Public on Apr 02 2013

city: Rehovoth

first: David

last: Zeevi

address: WIS

department: Computer Science

country: Israel

institute: Weizmann Institute of Science

summary: Genes associated with transcription regulation and development processes were up-regulated in the cerebrum of PS-treated mice.

overall_design: at 4 months of age 6 FD mice were gavaged with either 200mg/kg PS (3 mice) or medium-chain triglycerides (MCT, 3 mice) every other day for a period of 3 months

first: Ron

last: Bochner


title: Agilent data from Arabidopsis thaliana enriched guard cell tissue and leafs.

status: Public on Jun 04 2013

first: Susanne

last: Kneitz

address: Am Hubland, Biocenter

department: Physiological Chemistry I

summary: To identify genes of the guard cell transkriptome of Arabidopsis thaliana enriched guard cell samples were compared with total leaf tissue. Genes of the abscisic acid and humidity response of Arabidopsis thaliana guard cells were identified by treatment with ABA-Spray and low humidity. Ost1-2 and slac1-3 mutants were compared to their wildtype.

overall_design: total samples analysed are 35: 4 biolocigal independent replicates of: total leaf (COL-0) vs. enriched guard cells (COL-0); ABA-sprayed enriched guard cells (gl1-1) vs. control-sprayed enriched guard cells (gl1-1); enriched guard cells (slac1-3) vs. enriched guard cells (gl1-1);guard cells (ost1-2) vs. guard cells (ler);low humidity(20%rh) treated  enriched guard cells (COL-0) vs. high humidity(80%) treated enriched guard cells (COL0)

first: Hubert

last: Bauer

first: Peter

last: Ache

first: Silke

last: Lautner

first: Jörg

last: Fromm

first: Wolfram

last: Hartung

first: Khaled

last: Al-Rasheid

first: Sophia

last: Sonnewald

first: Uwe

first: Nicole

last: Lachmann

first: Ralf-Rainer

last: Mendel

first: Florian

last: Bittner

first: Alistair

last: Hetherington

first: Rainer

last: Hedrich


title: Multiple tissue expression data from inbreds and F1 of CAST, PWK, and WSB

status: Public on May 01 2013

city: chapel hill

first: Yunjung

last: Kim

state: North Carolina

address: 120 Mason farm road

institute: UNC at Chapel Hill

summary:
We create catalogues of genes showing significant strain, parent-of-origin, dominance, sex effect in inbreds and reciprocal F1 hybrids of three wild-derived strains (CAST, PWK, WSB) across 4 different tissues (brain, kidney, liver, and lung)
We used microarrays to validate the Brain results of RNAseq from inbred and F1 of 3 by 3 diallel.

overall_design: Brain, liver, kidney and lung RNA from the same mice used for RNAseq were hybridized to Affymetrix Mouse Gene 1.1 ST 96-Array Plate arrays using a GeneTitan instrument from Affymetrix.

first: Kim

last: Yunjung


title: Short chain fatty acids induce ANGPTL4 via PPARγ

status: Public on Mar 11 2013

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

institute: Wageningen University

summary: Angiopoietin-like protein 4 (ANGPTL4, also referred to as Fiaf) has been proposed as circulating mediator between the gut microbiota and fat storage in adipose tissue. Very little is known about mechanisms of regulation of ANGPTL4 in the colon. Here we show that transcription and subsequent secretion of ANGPTL4 in human T84 and HT-29 colonocytes is highly induced by physiological concentrations of products of bacterial fermentation, the short chain fatty acids (SCFA). Induction of ANGPTL4 by SCFA cannot be mimicked by the histone deacetylase inhibitor Trichostatin A. SCFA induce ANGPTL4 by activating the nuclear receptor PPARγ, as shown by use of PPARγ antagonist, PPARγ knock-down, and transactivation assay, which shows activation of PPARγ but not PPARα and PPARδ. At concentrations required for PPARγ activation and ANGPTL4 induction in colonocytes, SCFA do not stimulate PPARγ in mouse 3T3-L1 and human SGBS adipocytes, suggesting that SCFA act as selective PPARγ modulators (SPPARM), which is supported by coactivator peptide recruitment assay and structural modelling. Consistent with the notion that fermentation leads to PPAR activation in vivo, feeding mice a diet rich in inulin was associated with induction of PPAR target genes and pathways in the colon, as shown by microarray and subsequent gene set enrichment analysis. It can be concluded that 1) SCFA potently stimulate ANGPTL4 synthesis in human colonocytes; 2) SCFA transactivate and bind to PPARγ by serving as selective PPAR modulators. Our data point to activation of PPARγ as a novel mechanism of gene regulation by SCFA in the colon.

overall_design: Mice received a control diet, or a diet supplemented with 10% inulin for 10 days. After an overnight fast colon was removed, epithelial cells were scraped off, and subjected to gene expression profiling.

first: Katja

last: Lange

first: Michael

last: Müller

middle: J


title: Arabidopsis thaliana:goniothalamin-treated seedlings versus control seedlings

status: Public on Mar 27 2013

city: Fuchu

first: Naoya

last: Wasano

address: Saiwai-cho 3-5-8

institute: Tokyo University of Agriculture & Technology

summary: Transcriptional profiling of Arabidopsis thaliana seedlings treated with goniothalamin, highlighting to the physiological function of phytochemicals by observing early response of gene expressions in Arabidopsis seedlings.

overall_design: Two-condition experiment, goniothalamin-treated seedlings vs. control seedlings. Biological replicates:2 control replicates, 2 goniothalamin-treated.


title: Arabidopsis thaliana: trans-2-hexenal-treated seedlings versus control seedlings

status: Public on Mar 01 2013

summary: Transcriptional profiling of Arabidopsis thaliana seedlings treated with trans-2-hexenal, highlighting to the physiological function of plant volatile chemicals by observing early response of gene expressions in Arabidopsis seedlings.

overall_design: Two-condition experiment, trans-2-hexenal-treated seedlings vs. control seedlings. Biological replicates:2 control replicates, 2 trans-2-hexenal-treated.


title: Arabidopsis thaliana roots: inoculated roots with a bacterium Antarctic (Pseudomonas sp, Dac-bac TI-8) vs untreated  roots (control)

status: Public on Mar 28 2013

city: Cordoba

first: German

middle: Alexis

last: Gonzalez

state: Cordoba

address: Av. Armada Argentina 3555

department: School of Engineering

country: Argentina

institute: Catholic University of Cordoba

summary: Transcriptional profiling of Arabidopsis thaliana roots comparing  inoculated roots with a bacterial strain Antarctic (Pseudomonas sp, Da-bac TI-8) vs untreated  roots (control)

overall_design: Two-condition experiment, inoculated roots vs. untreated roots (control). Biological replicates: 4 inoculated roots replicates vs. 4 untreated roots replicates (control)

first: Graciela

last: Berríos

first: Carolina

last: Bizama

first: Gustavo

last: Cabrera

first: Elmer

last: Fernández

first: Germán

last: González

first: Cristobal

last: Fresno

first: Manuel

last: Gidekel

first: Ana

last: Gutiérrez


title: Arabidopsis thaliana:cyanamid-treated seedlings versus control seedlings

summary: Transcriptional profiling of Arabidopsis thaliana seedlings treated with cyanamid, highlighting to the physiological function of phytochemicals by observing early response of gene expressions in Arabidopsis seedlings

overall_design: Two-condition experiment, cyanamid-treated seedlings vs. control seedlings. Biological replicates:2 control replicates, 2 cyanamid treated.