title: Phase 2 Study of Digitoxin for the Treatment of Airway Inflammation in Cystic Fibrosis

status: Public on Jan 09 2017

city: Baltimore

first: Seakwoo

last: Lee

state: Maryland

address: 600 N. Wolfe Street

institute: Johns Hopkins University, School of Medicine

summary:
Cystic Fibrosis lung disease progresses by a combination of accelerated airways inflammation and bacterial colonization and infection. Airways inflammation in CF is predominantly neutrophilic and complicates airway clearance therapies through cellular debris, excessive DNA, excessive and viscous mucous, and high concentrations of neutrophils,Il-8 and related cytokines liberated along the NFkB signaling pathway. We conducted a single site, randomized, double blind, placebo-controlled, proof-of-concept trial in which we evaluated the effects of 28 days of two dose levels (0.05 mg and 0.10 mg daily) of an older cardiac glycoside, digitoxin, as compared with placebo, on inflammatory markers in induced sputum obtained from 24 subjects with mild to moderate CF lung disease. Nasal epithelial cells from 23 subjects were analyzed for microarray analysis. CF patients 18 to 45 years old, any genotype combination, were eligible.
The primary objective was to measure the effects of digitoxin on IL-8 and neutrophil counts in induced sputum. Secondary objectives were to measure: 1) the pharmacokinetics of digitoxin in serum in stable CF patients, 2) safety indices, including ECG changes and sputum microbiology, in stable CF patients, 3) the effect of digitoxin on gene expression in nasal epithelial cells of stable CF patients and 4) quality of life scores using the CFQ-R©.  As expected, it took several weeks to achieve a detectable serum level of digitoxin in CF.  Digitoxin showed a trend towards reduction in sputum free neutrophil elastase and neutrophil counts, but was not associated with a reduction in sputum Il-8.  Digitoxin did not dampen sputum inflammation as measured by primary and secondary outcome measures over the 28 day study period.  However the patient groups receiving placebo and 50 micro gram digitoxin daily fell into similar patterns which were distinctly different from the patient group taking 100 micro gram digitoxin.  The mRNAs encoding chemokine/cytokine or cell surface receptors in immune cells were decreased in nasal epithelial cells at the higher dose, leading to pathway mediated reductions in Il-8, Il-6, lung epithelial inflammation, neutrophil recruitment and mucus hypersecretion.  It is possible that a longer treatment period would be necessary to detect a meaningful, dose- dependent change in sputum indices of inflammation in CF.  Importantly, there were no safety issues over the course of the study

overall_design: 46 total samples (pre- and post treatment of each 8 subjects for 50 micro gram, 100 micro gram digitoxin and 7 subjects for placebo) were analyzed using two way ANOVA model.

first: C

middle: C

last: Talbot Jr


title: Expression data for various immune cells

status: Public on Dec 31 2016

city: Suita

first: Takashi

last: Satoh

state: Osaka

address: 3-1 Yamada-oka

department: RIMD

country: Japan

institute: Osaka university

summary:
Segregated nucleus atypical monocyte (SatM) is novel monocyte cell type. Complehensive Gene expression pattern was examined not only in SatM but also its related cell type.
We used microarrays to investigate the character of Segregated nucleus atypical monocyte (SatM) and commeted progenitors

overall_design: Various cell types involved in innate immune systems were selected for RNA extraction and hybridization on Affymetrix microarrays.

first: Motooki

last: Ashihara

first: Yosuke

last: Minowa


title: Gene expression from mouse kras tumor-derived cell lines

city: Frederick

first: NA-YOUNG

last: SONG

state: MD

address: 1050 Boyles Street

country: USA

institute: NCI

summary:
Comparison of gene expression of KR Primary and KR 1 cell lines
KR Primary cells are established from lung tumors of Kras mice. This cell line was injected into B6 mice intratracheally and then KR 1 cell line was established.

overall_design: Cells were collected and total RNAs from cells were subjected to hybridization for Affymetrix microarray.

first: Yinling

last: Hu

first: Na-Young

last: Song


title: Transcriptome analysis of human HT1080 cells overexpressing full length or soluble nucleoplasmic fragment of NET29/TMEM120A, NET39/PPAPDC3 and NET47/TM7SF2

city: Edinburgh

first: Jose

middle: Ignacio

last: de las Heras

address: Max Born Crescent

department: Wellcome Trust Centre

country: United Kingdom

institute: University of Edinburgh

summary: The nuclear transmembrane proteins (NETs) NET29/TMEM120A, NET39/PPAPDC3 and NET47/TM7SF2 are able to reposition chromosomes towards/away from the nuclear envelope when overexpressed or knocked down in HT1080 cells. In this study we wanted to investigate the transcriptome changes after transfection of the full length NETs or a nucleoplasmic soluble fragment that does not localise to the nuclear envelope.

overall_design: Total RNA was isolated from HT1080 fibroblasts either untreated or expressing stably each NET-GFP fusion. In addition, total RNA was also extracted from HT1080 fibroblasts that were transiently transfected with either a NLS-GFP control or a soluble nucleoplasmic fragment for each NET, fused to GFP.

first: Nikolaj

last: Zuleger

middle: I

first: Eric

last: Schirmer


title: Hepatic gene expression data from cadmium-exposed mice

city: Shanghai

first: Qian

last: Ba

address: 320 Yueyang Rd

country: China

institute: Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences

summary:
Environmental cadmium, with a high average dietary intake, is a severe public health risk. However, the long-term health implications of environmental exposure to cadmium in different life stages remain unclear.
We used microarrays to explore the effects of early exposure to low-dose cadmium on hepatic gene expression.

overall_design: Female and male mice were continuously exposed by water or cadmium from the initial stage of life. At the later stage of life, the liver were collected for RNA extraction and hybridization on Affymetrix microarrays. We sought to find the effect of long-term cadmium exposure on hepatic gene expression and the gender difference.

first: Mian

last: Li

first: Hui

last: Wang


title: Gene expression from mouse lung tissues

summary: Comparison of gene expression of lung tissues between WT, IKKa floxed, Kras, and Kras;IKKa floxed mice

overall_design: Lung tissues were collected at 4 months post adeno-cre injection. Total RNAs from lung tissues were subjected to hybridization for Affymetrix microarray.


title: Expression data from mouse liver

status: Public on Dec 27 2016

city: Xuzhou

first: Shaohua

last: Fan

state: Jiangsu

address: No. 101, Shanghai Road

department: School of Life Science

institute: Jiangsu Normal University

summary:
LASS2 is expressed mostly in human liver. We explored roles of LASS2 in pathogenesis of hepatic steatosis. Hepatocyte-specific LASS2 knockout (LASS2-/-) mice were generated using Cre-LoxP system. LASS2-/- and wild-type (WT) mice were fed with chow or high-fat diet (HFD).
We performed global gene expression analysis for the mice livers in accordance with standard Affymetrix protocols to explore signaling pathways involved by LASS2 deficiency.

overall_design: The livers were obtained from four groups of mice for RNA extraction and hybridization on Affymetrix microarrays. The four groups of mice were as follows, WT chow: Wild-type mice fed by standard chow diet, LASS2-/- chow: LASS2-/- mice fed by standard chow diet, WT HFD: Wild-type mice fed by high-fat diet, LASS2-/- HFD: LASS2-/- mice fed by high-fat diet.


title: Ligase4 is essential for hematopoietic stem cell maintenance

city: Singapore

first: Henry

last: Yang

address: 28 Medical Drive

country: Singapore

institute: Cancer Science Institute of Singapore

summary: Hematopoietic stem cells (HSCs) maintain the blood system during steady state and in response to stress. As a result, the accumulation of DNA damage has been proposed as a principal factor that contributes to the functional decline in HSC renewal during aging and stress. However, how the HSCs are sustained in the face of increased DNA damage remains unknown. Here, we address this question by studying the role of non-homologous end joining (NHEJ) in HSC. Using a mouse model of a naturally occurring human hypomorphic Lig4 mutation, we show a definitive effect on the steady state of activated HSCs. This population is severely diminished in the Lig4 mutant mice from the loss of selfrenewing HSCs. Our data suggests that defective NHEJ resulting from this Lig4 mutation depletes only the cycling HSCs but not the dormant HSCs, demonstrating that Lig4 is required for maintaining HSC by preserving their cycling pool.

overall_design: Lig4mut/+ mice were intercrossed to generate Lig4mut and littermate wild-type control (WT - Lig4+/+) mice. HSC (CD150+CD48- KSL) were sorted from 6-8 week-old WT control and Lig4mut mice into Trizol. Samples were prepared for microarray analysis after RNA isolation using the Nugen kit (Ovation Pico WTA System V2). There are three biological replicates for each subtype (WT, Lig4mut).

first: Ji-hye

last: Park

first: Robert

middle: S

last: Welner

first: Daniel

middle: G

last: Tenen

first: Catherine

middle: T

last: Yan


title: Expression data from human iPSCs and iPSC-derived neurons

status: Public on Dec 30 2016

first: Hongkai

last: Ji

address: 615 North Wolfe Street, Rm E3638

department: Department of Biostatistics

institute: Johns Hopkins Bloomberg School of Public Health

summary:
In this dataset, we studied human dopaminergic neuron differenation from induced pluripotent stem cells (iPSCs). We included the gene expression data obtained from iPSCs and iPSC-derived dopaminergic neurons.
This dataset is used to predict chromatin accessibility in iPSCs and iPSC-derived neurons using BIRD (Big data Regression for predicting DNase I hypersensitivity).

overall_design: 2 samples of iPSCs and 2 samples of iPSC-derived neurons were analyzed.

first: Weiqiang

last: Zhou

first: Mingyao

last: Ying


title: Intermittent Hypoxia ageing

city: Kyoto

first: Akira

last: Hirasawa

state: Kyoto

address: 46-29 Yoshida Shimoadachi-cho, Sakyo-ku

department: Genomic Drug Discovery Science

institute: Kyoto University Graduate School of Pharmaceutical Sciences

summary: Expression data from mice exposed to intermittent hypoxia and mice reared for 12 months. We used microarrays to analyze the transcriptome of hippocampus from mice exposed to intermittent hypoxia or aged mice.

overall_design: RNA from mouse hippocampus was extracted and processed for hybridization on Affymetrix microarrays.

first: Sosuke

last: Yagishita

first: Keisuke

last: Yoshikawa

first: Takeo

last: Awaji


title: Expression data from microRNA-520f transfected PANC-1 pancreas carcinoma cells.

city: Nijmegen

first: Gerald

middle: W

last: Verhaegh

address: Geert Grooteplein Zuid 28

department: Urology

country: Netherlands

institute: Radboudumc

summary:
MicroRNA-520f regulates EMT, as it activates CDH1 (mRNA) and E-cadherin (protein) expression, and it suppresses tumor cell invasion. We have characterized miR-520f target genes through whole genome transcriptional profiling of miRNA transfected pancreas cancer cells (PANC-1).
In this dataset, we include the expression data obtained from A. non-transfected (Lipofectamine RNAiMAX reagent only), B. negative control miRNA  (mirVana #4464058), and C. miR-520f (mirVana #4464066) transfected PANC-1 cells (ATCC #CRL-1469). These data are used to obtain genes that are differentially expressed in response to miR-520f activity.

overall_design: In total 9 samples (each condition in triplicate) were analyzed. We generated the following pairwise comparisons using Partek Genomics Suite 6.6 and using ANOVA. A. non-transfected vs. C. miR520, and B. neg control vs. C. miR520. Genes that were significantly up or downregulated in the miR520-treated cells in comparison to both control groups were considered miR-520f target genes.

first: Jasmijn

last: van Kampen

first: Onno

last: van Hooij

first: Cornelius

middle: F

last: Jansen

first: Frank

middle: P

last: Smit

first: Paula

last: van Noort

first: Iman

last: Schultz

first: Roel

middle: Q

last: Schaapveld

first: Jack

middle: A

last: Schalken


title: Characterization of side population cells from spontaneously transformed mouse lung carcinoma cell lines

city: Hannover

first: Astrid

last: Rohrbeck

state: Niedersachsen

address: Carl-Neuberg-Straße 1

department: Department of Toxicology

country: Germany

institute: Medizinische Hochschule Hannover

summary: Background  The side population (SP) phenotype, a subset of cells that extrude the nucleic acid dye Hoechst 33342, has been reported to be enriched for stem cells in several human normal tissues, cancers and cell lines, and thus may be useful for the identification and isolation of cancer stem cells.    Methods  We demonstrated the presence of SP fractions in all analyzed tumor cell lines ranging between 7- 20% of cells. To identify gene expression patterns that contribute to SP phenotype, microarray analysis of SP and non-SP cells was performed. We additionally confirmed regulation of some genes by qRT-PCR.     Results  Surprisingly, only a subset of few genes in SP cells showed altered gene expression. A total of 11 genes in A2C12, 103 genes in cRAF_cMYC and 101 genes in beta5 SP cells were regulated. Most regulated genes are involved in transcription / transcriptional regulation and transport. In addition, we found no enrichment of previously described stem cell marker like CD24a, CD90 or CD133 and also the ABC transporter ABCG2 was only slightly increased in side population fraction of two cell lines. But despite the few differences between SP and non-SP cells, the beta5 tumor cells were highly tumorigenic due to their capacity to form an original murine tumor when injected in NOD/SCID mice.    Conclusion  These findings stand in contrast to other observations but indicate that there are further factors responsible for the SP phenotype and that SP cells alone are not suitable as a universal stem cell marker.

overall_design: To clarify differential gene expression profiles between SP and non-SP cells, microarray analysis was performed in three cell lines. All experiments were done in triplicate.

first: Jürgen

last: Borlak

first: Florian

last: Länger


title: HDAC inhibition, dopamine and long-term fear inhibition [amygdala data set]

status: Public on Dec 21 2016

city: Bolzano

first: Johannes

last: Rainer

address: Via A. Volta 21

department: Institute for Biomedicine

country: Italy

institute: Eurac Researc

summary:
Background: Extinction-based exposure therapy is used in treating anxiety- and trauma-related disorders, however there is the need to improve its limited efficacy in individuals with impaired fear extinction learning and to facilitate the inadequate protection against return-of-fear phenomena.
Methods: Spontaneous recovery and fear renewal tests, assessed persistence and context-independence of treatments rescuing deficient fear extinction in 129S1/SvImJ mice. To reveal neurobiological mechanisms supporting long-lasting extinction rescue, whole-genome expression profiling, qRT-PCR, immunohistochemistry and chromatin immunoprecipitation were used.
Results: Persistent and context-independent rescue of deficient fear extinction induced by dietary zinc-restriction was associated with enhanced expression of dopamine-related genes, such as genes encoding the dopamine- D1 (Drd1a) and -D2 (Drd2) receptor in the medial prefrontal cortex (mPFC) and amygdala. Moreover, enhanced histone acetylation was observed in the promoter of the extinction-regulated Drd2 gene in the mPFC, revealing a possibly involved gene regulatory mechanism. While enhancing histone acetylation, via administering the HDAC inhibitor MS275, does not induce successful fear reduction during extinction training, it promoted enduring and context-independent rescue of deficient fear extinction consolidation/retrieval once extinction learning was initiated. This was associated with enhanced neuronal histone acetylation in the mPFC and amygdala. Finally, as a proof of principle, mimicking enhanced dopaminergic signaling by L-dopa treatment rescued deficient fear extinction and co-administration of MS-275 rendered this effect enduring and context-independent.
Conclusion: Current data reveal that combining dopaminergic and epigenetic mechanisms is a promising strategy to improve exposure-based behavior therapy in extinction-impaired individuals by initiating the formation of an enduring and context-independent fear inhibitory memory.

overall_design: Amygdala cells from three zinc dieted mice versus three control mice taken after 2h of fear extinction

first: Nigel

last: Whittle

first: Verena

last: Maurer

first: Conor

last: Murphy

first: Daniel

last: Bindreither

first: Markus

last: Hauschild

first: Anja

last: Scharinger

first: Christina

last: Brehm

first: Taras

last: Valovka

first: Jörg

last: Strissnig

first: Nicolas

last: Singewald


title: HDAC inhibition, dopamine and long-term fear inhibition [mPFC data set]

overall_design: mPFC cells from three zinc dieted mice versus three control mice taken after 2h of fear extinction


title: HDAC inhibition, dopamine and long-term fear inhibition

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

overall_design: Refer to individual Series


title: Role of the endosomal TLR3, 7 and 9 receptors in anti-tumor immunity

status: Public on Dec 15 2016

city: Essen

first: Sven

last: Brandau

address: Hufelandstrasse 55

department: Otolaryngology

institute: University Hospital Essen

summary:
Analysis of gene expression on day four and day six after tumor inoculation.
We used microarrays to detail the global programme of gene expression underlying differences between wildtype and TLR knockout mice.

overall_design: Analysis of gene expression of tumor tissues obtained from wildtype and TLR-k.o. mice after injection with MOPC cells.

first: Johanna

last: Klein


title: Common differentiating agents facilitate transcriptional reprogramming by bromodomain inhibition

status: Public on Dec 25 2016

city: Cambridge

first: Barbara

middle: M

last: Bryant

state: MA

address: 215 First Street

institute: Constellation Pharmaceuticals

summary: Dimethyl sulfoxide (DMSO) and hexamethylene bisacetamide (HMBA) are biologically active molecules that have shown clinical efficacy in cancer and inflammation, though their therapeutic application has been limited, partly because their mechanism of action is unknown. We demonstrate that DMSO and HMBA facilitate rapid transcriptional reprogramming via competitive inhibition of bromodomain-containing proteins. These results identify novel therapeutic avenues and provide context to over 50 years of biomedical research with these agents.

overall_design: HL60 treated with differentiating agents

first: Robert

middle: J

last: Sims

first: Jennifer

last: Mertz

first: Patricia

last: Keller

first: Hari

last: Jayaram

first: Hon-Ren

last: Huang

first: Kerry

last: Spillane

first: Yong

last: Tang

first: Chris

last: Nasveschuk

first: Shihua

last: Yao

first: Florence

last: Poy

first: Alex

last: Taylor

first: Brian

middle: K

last: Albrecht

first: Richard

last: Cummings

first: Steve

last: Bellon


title: UTX controls lineage-specific epigenetic program of iNKT cells

status: Public on Dec 19 2016

city: Boston

first: Jialiang

address: 450 Brookline Avenue

institute: Dana-Farber Cancer Institute

summary: iNKT cells are innate-like lymphocytes that protect against infection, autoimmune disease, and cancer. However, little is known about epigenetic regulation of iNKT cell development. Here, we show that the H3K27me3 histone demethylase UTX is an essential cell-intrinsic factor that controls an iNKT lineage specific gene expression program and epigenetic landscape in a demethylase activity dependent manner. UTX deficient iNKT cells exhibit impaired expression of iNKT signature genes due to a decrease in activation-associated H3K4me3 and an increase in repressive H3K27me3 marks within the promoters that UTX occupies. Notably, we identified JunB as a novel regulator of iNKT development that partners with UTX to establish an iNKT lineage specific gene expression program. Moreover, we demonstrate that UTX-mediated regulation of super-enhancer accessibility is a key mechanism for iNKT lineage commitment. These findings uncover how UTX regulates iNKT cell development through multiple epigenetic mechanisms.

overall_design: Gene expression microarray profiles of wild type and UTX-KO iNKT cells were obtained after sorting iNKT cells into TRI reagent (Life Technologies) and RNA isolated using Rneasy plus kit (Qiagen)

first: Semir

last: Beyaz


title: Notch Activation Confers Enhanced Lymphoid Potential in Murine ESC/iPSC-derived HSC and Reconstitutes Adaptive Immunity In Vivo [Microarray expression]

first: Patrick

last: Cahan

address: 733 North Broadway, MRB 653

department: ICE and Biomedical Engineering

institute: Johns Hopkins University School of Medicine

summary: Hematopoietic stem cell (HSC) transplantation has the potential to cure blood disorders but is limited by donor availability. Hence innovative approaches to engineer HSC are critically needed. HoxB4 over-expression in mouse embryonic stem cell-derived HSC (ESC-HSC) confers long-term engraftment, yet lacks efficient lymphogenesis. Transcriptome comparison of ESC-HSC versus embryo-derived HSC showed that ESC-HSC are deficient in expression programs activated by Notch. Therefore, we aim to improve ESC-HSC by further providing Notch signals through Notch1 intra-cellular domain transgene activation or by ligand stimulation. Here, we report that Notch-enhanced ESC-HSC (nESC-HSC) confer clonal multipotentiality with robust lymphopoiesis that endows adaptive immunity. Notably, nESC-HSC further evolve to a hybrid cell-type co-expressing gene regulatory networks of hematopoietic stem/progenitor cells and differentiated lineages at single-cell level that accounts for multipotentiality. Our work reveals a proof-of-concept model of HSC engineering by assembling self-renewing factor and lineage-guiding pathway into one product-cell that functionally recapitulate HSC in vivo.

overall_design: The gene expression of murine hematopoietic stem cells and HSC-like cells derived from differntiation of embryonic stem cells were profiled by microarrays.

first: Yi-Fen

last: Lu

first: George

last: Daley


title: Integrated functional genomics and craniofacial morphogenesis within the FaceBase Consortium: TGFBR2 mutant

status: Public on Jan 13 2017

city: Los Angeles

first: Michael

last: Kesling

address: 2250 Alcazar Street

institute: University of Southern California

summary: Congenital malformations in facial bones significantly impact the overall representation of the face. Establishing correlations between gene expression and morphogenesis of craniofacial structures may lead to new discoveries of molecular mechanisms of craniofacial development. Thus in the present investigation, we will generate gene expression profiles of facial bones at embryo stage 14.5 to establish their roles in regulating craniofacial development.

overall_design: To perform global gene expression profiling analysis of mandible and maxilla development and integrate these datasets with cell lineage and quantitative 3D dynamic imaging analyses. In collaboration with the ontology group within the FaceBase consortium, we will define anatomical landmarks and morphometric parameters of the developing mandible. Wnt1cre;Tgfbr2fl/+ mice were mated with Tgfbr2fl/fl mice and pregnant females were sacrificed at embryonic day 14.5 (E14.5), with observance of a vaginal plug denoting E0. Mutant embryos were identified by the presence of cleft palate and calvarial defect. The mandible and maxilla were dissected away from these mutant embryos and control litter mates, then each mandible and maxilla was divided into its distal and proximal ends.

first: Yang

last: Chai

first: Carolina

last: Parada

first: Alexandre

last: Grimaldi

first: Thach

middle: V

last: Ho

first: Jill

last: Harunaga

first: Bridget

last: Samuels

first: Vasu

last: Punj


title: Ipsilateral and contralateral retinal ganglion cells express distinct genes during decussation at the optic chiasm

status: Public on Dec 05 2016

city: New York

first: Qing

last: Wang

state: NY

department: Pathology and Cell Biology

institute: Columbia University

summary: The retinal projection neurons, retinal ganglion cells (RGCs), can be categorized into distinct morphological and functional subtypes and by the laterality of their projections. Here, we used a new method for purifying the sparse population of ipsilaterally projecting RGCs in mouse retina from their contralaterally-projecting counterparts during embryonic development through rapid retrograde labeling followed by fluorescence-activated cell sorting (FACS). Through microarray analysis, we have uncovered the distinct molecular signatures that define and distinguish ipsilateral and contralateral RGCs during the critical period of axonal outgrowth and decussation, with over three hundred genes differentially experienced within these two cell populations. Amongst the genes upregulated in ipsilateral RGCs are many that are known to be expresed in progenitors cells and mark “immaturity," including Math5 (Atoh7), Sox2, and cyclin D2. Many of these differentially regulated genes were subsequently validated via in vivo expression analysis. Thus, the molecular signatures of ipsilateral and contralateral RGCs and the mechanisms that regulate their differentiation are more diverse than previously expected.

overall_design: Embryonic day (E16) mouse RGCs were labeled with tetramethylrhodamine-conjugated dextran from the optic tract ex vivo. Ipsilateral and contralateral retinas from 2 litters of embryos were dissected 2 hours following dye application and subsequently dissociated using papain. Rhodamine-positive RGCs were isolated using fluorescence-activated cell sorting (FACS) for microarray studies.

first: Carol

last: Mason


title: Beta-catenin-regulated genes in pancreatic cancer cells

status: Public on Dec 01 2016

city: Worcester

first: Brian

last: Lewis

address: 364 Plantation Street, LRB 521

department: Molecular, Cell and Cancer Biology

institute: University of Massachusetts Medical School

summary:
Activation of the canonical Wnt signaling pathway is commonly observed in pancreatic cancer. We therefore sought to identify a gene expression profile associated with the activation of this pathway in pancreatic cancer cells.
We used microarrays to identify differentially expressed genes upon expression of an activated form of beta-catenin or its negative regulator ICAT (beta-catenin-interacting protein 1).

overall_design: Pancreatic cancer cells stably transfected to express beta-catenin or ICAT were grown in DMEM tissue culture medium containing 10% FBS. Cells were grown in monolayer culture prior to RNA extraction and hybridization on Affymetrix microarrays. Three independent samples of each genotype were analyzed.


title: Gene expression data from the tumor cell supernatant-induced MDSCs

status: Public on Dec 13 2016

city: Tianjin

first: Jiaxuan

last: Xin

address: weijin Road 94

department: Department of Immunology

institute: Nankai University

summary:
Myeloid derived suppressor cells (MDSCs) markedly expand and participate in the suppression of immune responses in inflammation and tumor microenvironment. It was confirmed that MDSCs could be generated in vitro from bone marrow cells (BMCs) after 4 days GM-CSF only or GM-CSF plus IL-6 treatment.
To identify the regulation of MDSCs in tumor microenvironment, we analyzed the gene expression from tumor cell ID8 supernant-induced MDSCs compared to BMCs.

overall_design: BMCs were obtained from the femurs of C57BL/6 mice and cultured in RPMI-1640 medium supplemented with 5% FBS. To prepare the tumor cell supernatant-induced CD11b+Gr1+ MDSCs in vitro, 5×10^4 1D8 tumor cells (upper chamber) were co-cultured with 2×10^6 BMCs (lower chamber) in a 24-transwell plate for 4 days. Then, total RNA was extracted by using Trizol reagent to perform microarray to analyze the differentially gene expression in ID8 supernatant-induced MDSCs or BMCs.

first: Zhiqian

last: Zhang

first: Rongcun

last: Yang


title: Expression data from uterus of SD rat during pre-implantation period.

status: Public on Nov 30 2016

city: lucknow

first: anila

last: dwivedi

state: Uttar Pradesh

address: jankipuram ext. sitapur road

department: Endocrinology division

country: India

institute: CSIR CDRI

summary:
Contraceptive action of Ormeloxifene(Orm), a non-steroidal anti-implantation agent, is well established, however, the molecular targets and pathways regulated by Orm are still not known . The present study was aimed at identifying the genes and pathways modulated by the Orm treatment in rats during uterine receptivity
We used microarrays to detail the global programme of gene expression underlying molecular targets and pathways identified under the influence of Ormeloxifene .

overall_design: SD rat uterus of day 5 pregnancy were selected for RNA extraction and hybridization on Affymetrix microarrays. In one group rats were fed with Ormeloxifene (contraceptive dose) on day 1 of pregnancy and rats of second group were given vehicle alone,i.e. Orm treated (T) and control (C).

first: Anila

last: Dwivedi

first: Vijay

last: Sirohi

first: S

last: Rath


title: Smo and Ets-2 signaling in fibroblasts effects gene expression

status: Public on Nov 22 2016

city: Columbus

first: Jason

middle: R

last: Pitarresi

state: Ohio

address: 460 W. 12th Ave

institute: Ohio State University Medical Center

summary: These experiments aim determine the effects of Smo and Ets-2 signaling on fibroblast gene expression.

overall_design: To achieve this, we used a genetic model in which Smo or Ets-2 was conditionally deleted in stromal fibroblasts in a Kras-driven mouse model ofpancreatic cancer. We isolated fibroblasts from pancreata mice with either wild type, Smo null, or Ets-2 null fibroblasts.

first: Michael

last: Ostrowski


title: Expression data of in vitro generated regulatory T cells overexpressing E47

status: Public on Dec 06 2016

city: Freiburg

first: Kristina

last: Schachtrup

address: Breisacher Str. 117

department: Center for Chronic Immunodeficiency

institute: University Medical Center Freiburg

summary:
E47 represses Foxp3 transcription, albeit indirectly through the activation of unknown negative regulatory of Foxp3 transcription.
To identify target genes of E47 in regulatory T cells, we compared gene expression profiles of Treg cells overexpressing E47 compared to control-vector transduced cells.

overall_design: Regulatory T cells were generated in vitro by stimulating MACS-purified CD4+CD25- T cells from the lymph nodes of C57BL/6 mice with anti-CD3/anti-CD28 in the presence of IL-2 and TGF-beta overnight. The next day cells were retrovirally transduced with either pMIT-bHLH-ER or pMIT-E47-ER. Cells were further cultured under the same conditions for 24 hr and subsequently transduced cells were FACS sorted as CD4+Thy1.1+. Finally, cells were cultured for 6 hr with anti-CD3/anti-CD28 in the presence of IL-2 and Tamoxifen for mRNA preparation. Three independent experiments with one set (control bHLH and E47) of RNA samples were analysed.

first: Katharina

last: Rauch

last: Sigvardsson


title: Expression data from Oct4+ cell fraction in SFEBq cultured mouse embryonic stem cells

status: Public on Nov 17 2016

city: Bunkyo-ku

first: Fumiko

last: Toyoshima

state: Tokyo

address: 1-5-45 Yushima

department: Medical Research Laboratory

institute: Institute of Science Tokyo

summary:
To further characterize residual undifferentiated cells after neural induction of embryonic stem cells, we performed DNA microarray analysis to identify genes expressed predominantly in residual undifferentiated cells expressing Oct4.
We used microarrays to detail the global programme of gene expression underlying cellularization and identified distinct classes of up-regulated genes in residual undifferentiated cells after neural induction of mouse embryonic stem cells by SFEBq.

overall_design: Oct4-Venus knock-in mouse embryonic stem cells (ESCs) were cultured in SFEBq to induce neural differentiation. Oct4-Venus+ cell fraction of undifferentiated ESC (ESC), Oct4-Venus+/Pecam1- cell fraction of ESCs cultured in SFEBq for 3 days (epiblast stem cell (EpiSC)-like cell), and Oct4-Venus+ cell fraction of ESCs cultured in SFEBq for 7 days were selected for RNA extraction and hybridization on Affymetrix microarrays.

first: Megumi

last: Ikeda


title: miRNA profiles in formalin-fixed and paraffin embedded (FFPE) breast cancer tissues

city: Duesseldorf

first: Silke

last: Schultz

address: Merowingerplatz 1A

department: Department of Obstetrics and Gynaecology

institute: University Hospital Duesseldorf

summary: We describe a miRNA profiling analysis of matched ductal carcinoma in situ and invasive duct carcinoma components of FFPE breast carcinomas with the purpose to identify potential prognostic markers

overall_design: miRNA extracted from 16 matched DCIS/IDC and 24 pure DCIS preparations was profiled using Illumina miRNA BeadChip platform

first: Hans

last: Neubauer

first: Karl

last: Sotlar

last: Bonin

first: Tanja

last: Fehm

first: Diethelm

last: Wallwiener


title: TGF-beta, COUP-TFII, and Gli1/Zic transcription factor dynamics revealed in Retinoic acid induced Neural Tube Defect

first: Brendan

middle: H

last: Grubbs

state: CA

address: 4661 W. Sunset Blvd.

department: Obstetrics and Gynecology

summary: The morphologic changes of neuroepithelial cells, and their interactions with surrounding cells, are fundamental to primary neurulation and are a function of several timed signaling gradients. Retinoic acid administration at fetal day E10 induces neural tube defects in 84.2% of rat pups. Negative selection using A2B5 and E-NCAM has been validated for isolation of neuroepithelial cells for culture. Here we report the isolation and analysis of the fundamental actors in primary neurulation by flow cytometry with CD147 positive selection followed by whole transcriptome analysis of this purified population via microarray enhanced with the ERCC RNA internal controls. Comparison of the gene expression in Retinoic acid exposed versus wild-type isolates shows excellent correspondence to known neural tube defect genes. Analysis of transcription factor binding sites in regulatory regions of differentially expressed genes, implicates a binding site “cross-roads” where improper signaling through a multitude of pathways could potentially elicit neural tube defects.

overall_design: Six samples total, three replicates each, of pooled biological replicates. ERCC ExFold mix 1 added to CTR ERCC ExFold mix 2 added to RA.

first: Matthew

middle: E

last: Thornton


title: Microarray analysis of gene expression in HDAC9-knockdown macrophages.

status: Public on Nov 06 2016

city: shang hai

first: Qian

last: Zhang

address: xiangyin road 800

institute: Second military medical university

summary: To investigate the role of HDAC9 in innate immnue, we measured the gene expression profile in HDAC9-knockdown macrophages in the absence of innate stimuli by gene-chip in order to find wherther HDAC9 knockdown affect the innate immune factor. We found knockdown of HDAC9 barely affected transcription of innate immnue signaling transducers. HDAC9, as a class IIa HDAC, shuttle between the nucleus and cytoplasm. Here we showed that high expression of cytoplasmic HDAC9, maybe play a Post-translational regulation role in macrophages.

overall_design: Peritoneal macrophages transfected with control siRNA, as control group, or transfected with HDAC9 siRNA,as experimental group, and 48 hr later extracted total RNA

first: Cao

middle: X

last: Tao

first: li

last: Xia


title: ALS-causing mutations differentially affect PGC-1alpha expression and function in the brain vs. peripheral tissues

status: Public on Nov 10 2016

city: Ulm

first: Hanna

last: Bayer

address: Helmholtzstrasse 8/1

institute: Ulm University

summary:
Amyotrophic later sclerosis is a motor neuron disease accompanied by metabolic changes. PGC (PPAR gamma coactivator)-1alpha is a master regulator of mitochondrial biogenesis and function and of critical importance for all metabolically active tissues. PGC-1alpha is a genetic modifier of ALS.
We used microarray analysis to identify PGC-1alpha target genes in the brain.

overall_design: Total mRNA from striata of three homozygous B6.129-Ppargc1atm1Brsp/J and three wild type littermates were used for the analysis.

first: Karlheinz

last: Holzmann

first: Anke

last: Witting


title: Expression data from mouse aortas

city: Beijing

first: Xiao

last: Yang

address: 20 Dongdajie

institute: Beijing Institute of Biotechnology

summary:
Aortic aneurysm is a life-threatening cardiovascular disorder due to the predisposition for dissection and rupture. Genetic studies have proved the involvement of the transforming growth factor-β (TGF-β) pathway in aortic aneurysm. Smad4 is the central mediator of canonical TGF-β signaling. However, the exact role of Smad4 confined to the smooth muscle cells (SMCs) in the pathogenesis of aortic aneurysm is largely unknown. Furthermore, whether TGF-β signaling disruption in SMCs could directly trigger aortic wall inflammation remains poorly investigated. Recently, we revealed a pivotal role of smooth muscle Smad4 signaling in maintaining aortic wall homeostasis and protecting against the development of aortic aneurysm and dissection. To evaluate the underlying mechanism by which Smad4 regulate VSMC functions and affects aneurysm formation and development, Smooth muscle specific Smad4 Knockout mice and the control littermate were sacrificed at 6 weeks old, and their aortic ateries were collected.We combined 3-5 vessels for one sample, and 2 samples for each phenotype. Subsequently, a total of 400ng RNA was used following Affymetrix instruction and 2 ug of cRNA were hybridized for 16 hr at 45°. GeneChips were scanned using the Scanner 7G and the data was analyzed with Expression Console using Affymetrix default analysis settings and global scaling as normalization method. RMA analysis was employed to evaluate the gene expression.
We used microarrays to detect the global gene expression in the aortic arteries of smooth muscle cell specific Smad4 knockout mice (Smad4-KO)compared with wild type littermates (WT) at 6 weeks old and identified distinct classes of altered genes.

overall_design: The aortas of smooth muscle cell specific Smad4 knockout mice (Smad4-KO) and wild type littermates (WT) were collected at 6 weeks old. We combine 3-5 vessels in one tube and for a single Affymetrix microarray. Total RNA was extracted and a total of 400ng RNA was used following Affymetrix instruction. 2 biological samples for each genotype.

first: Peng

first: Jicheng

last: Chen

first: Siyuan

last: Hou

first: Yu

last: Lan


title: Chronic Binge Alcohol Administration Dysregulates Expression of Hippocampal Genes Involved in Immune Function, Neurotransmission and Neurogenesis in Simian Immunodeficiency Virus-Infected Macaques

status: Public on Dec 12 2016

city: New Orleans

first: Patricia

middle: E.

last: Molina

state: LA

address: 1901 Perdido Street

department: Physiology

institute: LSU Health Sciences Center

summary: HIV-associated neurocognitive disorder is prevalent despite wide-spread use of effective anti-retroviral therapy (ART). Alcohol use disorders (AUDs) exacerbate neurocognitive dysfunction in HIV+ patients. Previously we have shown that chronic binge alcohol administration (CBA, 13 – 14 g EtOH/kg/wk) starting 3 months prior to simian immunodeficiency virus (SIV) infection in rhesus macaques unmasks behavioral deficits. The underlying mechanisms of neurocognitive alterations due to alcohol and SIV are not known. The aim of this study was to explore the alterations in hippocampal gene expression of CBA administered, SIV-infected (CBA/SIV+; N=2) macaques and isocaloric sucrose administered, SIV-infected (SUC/SIV+; N=2) macaques in contrast to uninfected (SIV-; N=2) macaques. Transcriptomes of hippocampal samples dissected from brains obtained at necropsy (16 months post-SIV inoculation) were analyzed using Illumina Custom algorithm to determine differentially expressed genes (p-value filter of ≤ 0.05; either ≥ 1.3 fold change or ≤ 0.76 fold change) between SUC/SIV+ and SIV-, CBA/SIV+ and SIV-, and CBA/SIV+ and SUC/SIV+.  We used Gene Codis to determine enrichment of specific Gene Ontology Biological Processes from both the SUC/SIV+ and CBA/SIV+ gene lists. Gene Codis analysis revealed over-representation of genes involved in neurodevelopment, neurotransmission, interferon-signaling, and antigen presentation in the CBA/SIV+ group. Further analysis of differentially expressed genes between SIV- and CBA/SIV+ showed predominantly up-regulation of immune function genes and down-regulation of nervous system development and synaptic transmission genes in CBA/SIV+ animals. These findings  provide insight into the potential mechanisms by which CBA may enhance neurobehavioral deficits.

overall_design: Rhesus macaques from three experimental groups; SIV- (N=2), sucrose SIV infected (SUC/SIV+; N=2), and CBA SIV infected (CBA/SIV+; N=2) were used in the study. Animals were 4-6 years of age at the beginning of the study. Following three months of CBA administration, animals were inoculated intravenously with 10,000 times the ID50 of SIVmac251, which was provided by Preston Marx (TNPRC). Alcohol or sucrose administration continued throughout the study. Sixteen months post-SIV inoculation animals were euthanized. Hippocampal RNA from necropsy time point was used in the study.

first: John

last: Maxi

first: Jovanny

last: Zabaleta

first: Gregory

last: Bagby

first: Steve

last: Nelson

first: Peter

last: Winsauer


title: Thy-1 Expression Enriches for Self-Renewing Murine MRUs [FVB]

city: Palo Alto

first: Neethan

middle: Amit

last: Lobo

address: 265 Campus Drive

department: Institute for Stem Cell and Regenerative Medicine

institute: Stanford University

summary: Enriched cell populations from murine mammary epithelium were isolated by FACS and subjected to Affymetrix Mouse 430 2.0 microarray analysis.

overall_design: 10 Affymetrix array hybridizations were performed on RNA samples that were extracted from sorted mammary epithelial cell populations. Cell populations include Thy-1+CD24medCD49fhigh stem cells, Thy-1-CD24medCD49fhigh progenitor cells, CD24medCD49fmed myoepithelial cells, CD24highCD49fmed luminal progenitor cells and CD24medCD49f-/low differentiated luminal cells.

first: Maider

last: Zabala

first: Dalong

last: Qian

first: Michael

last: Clarke


title: Functional roles of Acetylated Histone Marks at Mouse Meiotic Recombination Hotspots (expression)

status: Public on Nov 04 2016

city: Tampa

middle: Lamoine

last: Cleveland

state: FL

address: 12902 USF Magnolia Drive

institute: H. Lee Moffitt Cancer Center

summary: Meiotic recombination is initiated by the Spo11 endonuclease, which directs DNA double strand breaks at discrete regions in the genome coined hotspots. Here we report the profiles and dynamics of histone modifications at the cores of mouse recombination hotspots in early meiotic prophase. To define the spectrum of possible regulators of histone methylation and acetylation at all stages of meiosis I, expression analyses of histone acetylases/deacetylases (HATs/HDACs) and and HMTs/HDMTs genes when comparing those expressed in spermatogonia, pre-leptotene and leptotene/zygotene versus pachytene meiotic stages.

overall_design: Wild-type meiotic samples design is described in GSE21447. To collect Spo11-/- meiotic samples, 10 to 16 weeks old male Spo11-/- testes were used for sorting multiple meiotic fractions.  Spermatogonia, pre-Leptotene and Leptotene/Zygotene sorted meiotic fractions were collected twice from total 4 and 3 Spo11-/- mice testes respectively .  These combined samples were used for subsequent RNA purification, labeling and hybridization to Affymetrix arrays.

first: Philippe

last: Bois

first: Mohammad

last: Fallahi

first: Irina

last: Getun

middle: L


title: Expression data for 211  primary tumors from patients with colorectal cancer

status: Public on Nov 28 2016

city: Parkville

first: Oliver

last: Sieber

state: VIC

address: 1G Royal Parade

country: Australia

institute: Walter and Eliza Hall Insitute of Medical Reseach

summary: Samples were taken from surgically resected tumor specimens from patients with colorectal cancer. The expression profiles were determined using the Affymetrix GeneChip Human Exon 1.0 ST Array version 2. Gene mutation status was determined using Sanger sequencing.

overall_design: 211 colorectal cancers samples were analyzed for both microarray expression (Plus2.0 platform) and mutation status of several genes.


title: Thy-1 Expression Enriches for Self-Renewing Murine MRUs

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

overall_design: Refer to individual Series


title: Antagonism of B cell enhancer networks by STAT5 drives leukemia and poor patient survival

city: Minneapolis

first: Lynn

last: Heltemes Harris

state: MN

address: 2101 6th St. SE

institute: University of Minnesota

summary: The transcription factor STAT5 plays a critical role in B cell acute lymphoblastic leukemia (B-ALL).  How STAT5 mediates this effect is unclear.  Here we demonstrate that STAT5 activation cooperates with defects in the pre-BCR signaling components encoded by Blnk, Btk, Prkcb, Nfkb1, and Ikzf1 to initiate B-ALL.  STAT5 antagonizes NF-κB and IKAROS by opposing regulation of shared target genes.  STAT5 binding was enriched at super-enhancers, which were associated with an opposing network of transcription factors, including PAX5, EBF1, PU.1, IRF4, and IKAROS.  Patients with high ratios of active STAT5 to NF-κB or IKAROS have more aggressive disease.  Our studies illustrate that an imbalance of two opposing transcriptional programs drive B-ALL, and suggest that restoring the balance of these pathways may inhibit B-ALL.

overall_design: Gene expression profiling was performed on cells isolated from lymph nodes of Stat5b-CA, Stat5b-CA x Blnk+/-, Stat5b-CA x Xid-/-, Stat5b-CA x Pkrcb-/-, Stat5b-CA x Ebf1+/- and Stat5b-CA x Rag2-/- leukemic mice and pre B cells sorted from bone marrow of C57BL/6 wild type mice, Xid Mice, and Stat5b-CA non-leukemic mice. 40 Samples.

first: Casey

last: Katerndahl

last: Heltemes-Harris

first: Mark

last: Willette

first: Christine

last: Henzler

first: Seth

last: Fritze

first: Rendong

last: Yang

first: Hilde

last: Schjerven

first: Kevin

last: Silverstein

first: Laura

middle: B

last: Ramsey

first: Greg

last: Hubbard

first: Andrew

last: Wells

first: Roland

last: Kuiper

first: Blanca

last: Scheijen

first: Frank

middle: N

last: van Leeuwen

first: Markus

last: Müschen

first: Steven

last: Kornblau

last: Farrar


title: Distal axotomy enhances retrograde presynaptic excitability onto injured pyramidal neurons via trans-synaptic signaling

status: Public on Nov 02 2016

city: Chapel Hill

first: Anne

middle: Marion

last: Taylor

state: North Carolina

address: 152 MacNider, CB 7575

department: Biomedical Engineering

institute: UNC-Chapel Hill

summary: Injury of descending motor tracts remodels cortical circuitry and leads to enhanced neuronal excitability, thus influencing recovery following injury. The neuron-specific contributions remain unclear due to the complex cellular composition and connectivity of the CNS. We developed a microfluidics-based in vitro model system to examine intrinsic synaptic remodeling following axon damage. We found that distal axotomy of cultured rat pyramidal neurons caused dendritic spine loss at synapses onto the injured neurons followed by a persistent retrograde enhancement in presynaptic excitability over days. These in vitro results mirrored hyper-activity of directly injured corticospinal neurons in hindlimb motor cortex layer Vb following spinal cord contusion. In vitro axotomy-induced hyper-excitability coincided with elimination of inhibitory presynaptic terminals, including those formed onto dendritic spines. We identified netrin-1 as downregulated following axotomy and exogenous netrin-1 applied 2 days after injury normalized spine density, presynaptic excitability, and the fraction of inhibitory inputs onto injured neurons. These findings demonstrate a novel model system for studying the response of pyramidal circuitry to axotomy and provide new insights of neuron-specific mechanisms that contribute to synaptic remodeling.

overall_design: We analyzed axon injury induced transcriptional changes in triplicate using the Affymetrix Rat Gene 2.0 ST Array platform.

first: Tharkika

last: Nagendran

first: Rylan

middle: S

last: Larsen

first: Rebecca

last: Bigler

first: Shawn

last: Frost

first: Benjamin

middle: D

last: Philpot

first: Randolph

last: Nudo


title: DNA methylome analysis of pediatric acute lymphoblastic leukemia cells reveals stochastic de novo DNA methylation in CpG islands.

status: Public on Oct 31 2016

city: Uppsala

first: Jessica

last: Nordlund

address: Box 1432, BMC

department: Department of Medical Sciences

country: Sweden

institute: Uppsala University

type: Expression profiling by high throughput sequencing

type: Methylation profiling by high throughput sequencing

summary: We used whole genome bisulfite sequencing (WGBS) to determine the DNA methylation levels at single base-pair resolution of four patients with different subtypes of pediatric ALL together with RNA-sequencing to increase our understanding of the leukemic transformation in ALL.

overall_design:
The ALL genomes of four patients (Patients P1-P4) were sequenced in bone marrow samples collected at diagnosis, to an average 20-30-fold sequence depth per base. Patient 1 has the recurrent B-cell precursor ALL (BCP-ALL) translocation t(12;21)ETV6-RUNX1, Patient 2 has BCP-ALL with two non-recurrent translocations, Patient 3 has BCP-ALL with a normal karyotype, and Patient 4 has T-cell immunophenotype ALL (T-ALL). The four ALL genomes were compared to pools of B-cells (n=7) and T-cells (n=17) from healthy blood donors and a CD34+ reference (GSM791828). We also interrogated potential effects of epigenetics on gene expression using RNA-sequencing data from three of the ALL samples (P1, P2, and P4) and B- and T-cells. 450k BeadArray data GSM1203860, GSM1203904, GSM1204111 and GSM1203962 corresponding to P1-4 was used for validation.
----------------------------------------
Submitter declares reads will be made available through dbGaP/EGA

first: Per

last: Wahlberg

first: Anders

last: Lundmark

first: Stephan

last: Busche

first: Amanda

last: Raine

first: Karolina

last: Tandre

first: Lars

last: Rönnblom

first: Daniel

last: Sinnett

first: Erik

last: Forestier

first: Tomi

last: Pastinen

first: Gudmar

last: Lönnerholm

first: Ann-Christine

last: Syvänen


title: Gene expression analysis of early haematopoietic progenitors

city: Stevenage

first: Nikolai

middle: Nikolaevich

last: Belyaev

address: Gunnels Wood Road

department: Refractory Respiratory Inflammation

institute: GlaxoSmithKline

summary: The common myelo-erythroid progenitor (CMP) was subdivided based on expression of CD27. To understand the relationship between the various CD27 fractions of the CMP and downstream progenitors (granulocyte-monocyte progenitor, GMP, and megakaryocyte-erythroid progenitor, MEP), genome-wide transcriptional analysis was used.

overall_design: FACS purified CMP CD27+, CMP CD27-, GMP and MEP progenitors from C57BL/6 adult 4-6 weeks old mice were hybridised to Affymetrix Mouse Genome 430_2 GeneChip

first: Alexandre

last: Potocnik


title: Expression profiling of cell growth on different layers

status: Public on Oct 24 2016

city: St. Lucia

first: Othmar

last: Korn

state: Queensland

address: University of Queensland

institute: Australian Institute for Bioengineering and Nanotechnology

summary: Human embryonic stem cells (hESCs) and induced pluripotent stem cells (hiPSCs) hold great promise for applications in drug discovery and regenerative medicine. While tremendous ongoing efforts are focused on establishing more optimal cellular microenvironments for hESCs/hiPSCs to facilitate their differentiation into the specific phenotypical functions of interests, it is still challenging to systematically determine the optimal environment and the circumstances supporting each environment, due to a lack of control over the microenvironmental factors in a three-dimensional (3D) space. In this study, we developed a 3D cellular microenvironment plate (3D-CEP), which consisted of a polydimethylsiloxane (PDMS) microfluidic device combined with a thermo-responsive poly(N-isopropylacrylamide)-β-poly(ethylene glycol) (PNIPAAm-β-PEG) hydrogel (HG), as a platform for hESC/hiPSC culture and analysis. The HG/3D-CEP system enables tuning of both chemical and physical environmental cues as well as in situ monitoring of cells. H9-derived hESCs cultured in the HG/3D-CEP system maintained pluripotent marker expression for octamer-binding transcription factor 4 (OCT4), (sex determining region Y)-box 2 (SOX2), NANOG, stage-specific embryonic antigen 4 (SSEA4), and TRA-1-60, but did not express the differentiation marker SSEA1 under self-renewing conditions. Small variations between different test environments and their influence on the development of biological networks could be further examined using global gene expression techniques. We envision that this HG/3D-CEP system will serve as a versatile platform for developing targeted functional cell lines derived from hESCs/hiPSCs and facilitate advances in more precise drug screening and regenerative medicine

overall_design: H9-derived hESCs cultured in the HG/3D-CEP system – high mebil gel, low mebil gel, matrigel, sphere culture, controls, 3 replicates per condition.

first: K

last: Kamei

first: Y

last: Koyama

last: Tokunaga

last: Mashimo

first: M

last: Yoshioka

first: C

last: Fockenberg

last: Nakashima

first: R

last: Mosbergen

first: O

last: Wells

last: Chen


title: MiROvaR, a microRNA-based predictor of early relapse for ovarian cancer patients [validation set; OC133]

city: Milan

first: Loris

last: De Cecco

address: via Venezian 1

institute: IRCSS Istituto Nazionale Tumori

summary: Despite a pathological complete response, risk-of-relapse remains a challenge for most of epithelial ovarian cancer (EOC) patients and an ad-hoc predictor can be a valuable clinical tool. We developed a 35 miRNAs-based predictor of Risk of Ovarian Cancer Relapse (MiROvaR) using a training set of patients from MITO-2 (Multicentre Italian Trials in Ovarian Cancer-2; Pignata S et al. J Clin Oncol. 2011 Sep 20). MiROvaR performance was confirmed in two independent validation cohorts.

overall_design: Fresh frozen samples were collected from a series of 133 consecutive ovarian cancer patients  who underwent primary surgery at  CRO, National Cancer Institute (Aviano, Italy) and were profiled on Illumina platform at INT-Milan. Ethical Statement: All of the patients  whose biological samples were included in the study, gave their signed consent to donate the tissues remaining after the diagnostic procedures for research purposes. The study was approved by the Independent Ethics Committee of the Fondazione IRCCS Istituto Nazionale dei Tumori di Milano (INT-MI) where the miRNA profile was performed.   Clinical codes:  Age (years)  Histology: according to International Federation of Gynecological and Obstetrics guidelines ( 1: Serous; 2: Mucinous; 3: Endometrioid; 4: Undifferentiated; 5: Clear cell; 6: Mixed or other; NA:  Missing information)  Stage: according to International Federation of Gynecological and Obstetrics guidelines  Grading: according to WHO (BL: border line; G1: well differentiated; G2: moderately differentiated; G3: poorly differentiated; undiff: undifferentiated; NA: missing information)  Debulking: NED: not evident disease; mRD: minimal residual disease (<1cm) ; GRD: gross residual disease (>1cm); NO: not operated; NA: missing information  Time to relapse (TTR, months) code: 0=no relapse; 1=relapse  Overall survival (OS, months) code: 0=alive; 1=dead


title: MiROvaR, a microRNA-based predictor of early relapse for ovarian cancer patients


title: Combined blockade of MET and EGFR abolishes liver regeneration

status: Public on Oct 27 2016

city: Pittsburgh

first: George

last: Michalopoulos

state: Pennsylvania

address: 411 SBST, 200 Lothrop Street

institute: University of Pittsburgh

summary:
Receptor tyrosine kinases MET and EGFR are critically involved in initiation of liver regeneration. Other cytokines and signaling molecules also help in the early part of the process.  Regeneration employs effective redundancy schemes to compensate for missing signals. Elimination of any single signaling pathway only delays but does not abolish the process. Our present study, however, shows that combined systemic elimination of MET and EGFR signaling abolishes liver regeneration, prevents restoration of liver mass and leads to liver decompensation. Our results demonstrate that liver function is dependent on synchronous availability of signaling from these two pathways. The study shows that MET and EGFR separately control many non-overlapping signaling endpoints, allowing for compensation when only one of the signals is blocked. The combined elimination of the signals however was not tolerated. The results provide critical new information on interactive MET and EGFR signaling and the contribution of their combined absence to regeneration arrest and liver decompensation.
We used microarrays to detail the global programme of gene expression in METKO-canertinib mouse liver  following a partial hepatectomy

overall_design: Systemic inhibition MET-EGFR signaling pathway in mice liver regeneration in mice was carried out by using a tamoxifen inducible system EGFR was inhibited by using Canertinib added to diet. Partial hepatectomy was carried out and liver tissue harvested at defined time points and gene arrays carried out.

first: Shirish

last: Paranjpe


title: The human amniotic fluid stem cell secretome counteracts doxorubicin-induced cardiotoxicity

status: Public on Oct 30 2016

city: Genova

first: Ulrich

last: Pfeffer

address: L. Benzi 10

institute: IRCCS AOU San Martino - IST

summary: The anthracycline, doxorubicin (Dox), is widely used in oncology, but it may it may cause a cardiomyopathy which has dismal prognosis and cannot be effectively prevented. The secretome of multipotent human amniotic fluid-derived stem cells (hAFS) has previously been demonstrated to reduce ischemic cardiac damage. Here, it is shown that the hAFS conditioned medium (hAFS-CM) antagonizes senescence and apoptosis of cardiomyocytes and cardiac progenitor cells, two major features of Dox cardiotoxicity. Mechanistic studies with primary mouse neonatal cardiomyocytes reveal that hAFS-CM inhibition of Dox-elicited senescence and apoptosis is paralleled by decreased DNA damage and is associated with nuclear translocation of NF-kB and upregulation of a set of genes controlled by NF-kB, namely Il6 and Cxcl1, which promote cardiomyocyte survival, and Cyp1b1 and Abcb1, which encode for proteins involved in Dox metabolism and efflux, respectively. The PI3K/Akt signaling cascade, upstream of NF-kB, is potently activated by the hAFS-CM and pre-treatment with a PI3K inhibitor abrogates NF-kB accumulation into the nucleus, modulation of its target genes, and prevention of Dox-initiated senescence and apoptosis in response to the hAFS-CM. This work may lay the ground for the development of a stem cell-based paracrine therapy of chemotherapy-related cardiotoxicity.

overall_design: one chip for each sample, one control (Doxorubicin treated mouse neonatal cardiomyocytes) one treated sample (human amniotic fluid stem cell secretome + Doxorubicin treated mouse neonatal cardiomyocytes)

first: Sveva

last: Bollini

first: Pietro

last: Ameri


title: Role of Gq/11 and G12/13 signalling in Type II alveolar epithelial cells

status: Public on Oct 25 2016

city: Nottingham

first: Alison

middle: Elizabeth

last: John

state: NOTTS

address: Clinical Sciences Bulding, City Hospital Campus

department: Respiratory Medicine

institute: University of Nottingham

summary: We have used microarrays to identify individual genes and pathways regulated by  Gq/11 or G12/13 signalling in type II alveolar epithelial cells isolated from the lungs of knockout mice.

overall_design: Type II alveolar epithelial cells were isolated from the lungs of mice either singly deficient in Gna11 or Gna12 or double deficient in Gnaq/Gna11 or Gna12/Gna13 genes. Cells were cultured for 7 days and RNA processed from the untreated epithelial cells to compare gene expression patterns in cells from single and double knockout animals.

first: Gino

last: Miele


title: Thy-1 Expression Enriches for Self-Renewing Murine MRUs [BL6]

first: Neethan

last: Lobo

overall_design: 14 Affymetrix array hybridizations were performed on RNA samples that were extracted from sorted mammary epithelial cell populations. Cell populations include Thy-1+CD24medCD49fhigh stem cells, Thy-1-CD24medCD49fhigh progenitor cells, CD24medCD49fmed myoepithelial cells, CD24highCD49fmed luminal progenitor cells and CD24medCD49f-/low differentiated luminal cells.

middle: A

first: Maider

last: Zabala

first: Dalong

last: Qian

first: Michael

middle: F

last: Clarke


title: Expression data from BNL CL.2 liver cells when cultured with iron, RAW 264.7 macrophages or both

status: Public on Oct 22 2016

city: Barcelona

first: Marco

last: Constante

address: C/ Dr. Aiguader, 88

country: Spain

institute: CRG

summary: We found that co-culturing BNL CL.2 liver cells with RAW 264.7 macrophages increased IRP binding in the first. To further investigate this modulation we investigated the gene expression profile in BNL CL.2 cells cultured alone, with iron, with RAW 264.7 macrophages or in the presence of both iron and macrophages. This novel reconstituted liver cell-macrophage communication pathway with the present gene expression data provides a platform for addressing how macrophages participate in the iron homeostasis of liver cells and, ultimately, in systemic iron homeostasis.

overall_design: We used microarrays to determine the gene expression modulation in BNL CL.2 cells in response to 24h culture with 100 micromolar ferric ammonium citrate (FAC), co-culture with RAW 264.7 macrophages or both

first: Mark

last: Isalan


title: Liver expression data from four mouse strains treated with vehicle or PF-04287881 for seven days

status: Public on Oct 21 2016

first: Merrie

last: Mosedale

address: 301 Pharmacy Lane, Kerr Hall CB#7569

department: Division of Pharmacotherapy and Experimental Therapeutics

institute: UNC Eshelman School of Pharmacy

summary: PF-04287881 induced varying degrees of liver necrosis and phospholipidosis in a 34-inbred strain Mouse Diversity Panel (MDP) study. Four strains with differing susceptibilities to these phenotypes (MA/MyJ, NZW/LacJ, SM/J, WSB/EiJ) were selected for analysis of gene expression changes in the liver. The objective of this study was to identify gene expression changes that drive PF-04287881-induced liver injury.

overall_design: Thirty-one total samples were analyzed: N=4 per treatment and strain, except PF-04287881-treated WSB/EiJ (N=3) where one animal died before the completion of the study due to gavage error. Two strains exhibited findings of PF-04287881-induced Kupffer cell vacuolation and were coded as phospholipidosis responders (MA/MyJ and NZW/LacJ). One strain exhibited findings of single cell necrosis and was coded as a necrosis responder (NZW/LacJ).

first: Karissa

last: Adkins


title: Data of gene expressions induced by the interaction between Kupffer cells and cancer cells dependently on Dectin-2

status: Public on Oct 18 2016

city: Meguro-ku

first: Yoshitaka

last: Kimura

address: T block (56th Bldg.), Komaba 4-6-1

department: Institute of Industrial Science

institute: The University of Tokyo

summary:
Metastasis to distal organ is a fatal cause of cancer death and liver is one of the most common site of metastasis leading to bad prognosis. Although it has been known that innate immune cells play critical roles in the regulation of liver metastasis, how they control the tumor development is still largely unclear. We found that Dectin-2 (Clec4n), a C-type lectin receptor (CLR), suppresses liver metastasis and such Dectin-2-mediated anti-tumor rejection requires Kupffer cells, liver-residing macrophages, which express Dectin-2 dominantly in liver.
We used microarray to examine comprehensive gene expressions induced by Dectin-2 when anti-tumoral Kupffer cells interact with cancer cells

overall_design: Kupffer cells isolated from naïve wild-type or Dectin-2 KO mice were co-cultured with SL4, mouse colon carcinoma cell line. Subsequently, total RNA was extracted from whole cells and analyzed by microarray. As controls, wild-ype and Dectin-2-deficient Kupffer cells were separately cultured from SL4 cells and each total RNA was mixed.

first: Hideyuki

last: Yanai

first: Tadatsugu

last: Taniguchi


title: Association of dysfunctional synapse defective 1 (SYDE1) with restricted fetal growth – SYDE1 regulates placental cell migration and invasion

city: TauYau

first: Yun-Shien

last: Lee

state: Taiwan

address: TauYau

department: Dept. Biotechnology

country: Taiwan

institute: Ming Chuan Univ

summary: In this study, we identify SYDE1 as a novel GCM1 target gene. We demonstrate that SYDE1 promotes placental cell migration and invasion and that the GCM1-SYDE1 axis is crucial for placental development. Importantly, retarded placental and fetal growth with defective spongiotrophoblast layer, compromised vasculogenesis, and abnormal maternal-trophoblast interface are noted in the Syde1 homozygous knockout (KO) placenta. Along this line, decreased SYDE1 expression is observed in human IUGR placentas. We further demonstrated that components of the renin-angiotensin system (RAS) and Syde2 are differentially expressed in Syde1-KO placenta, which might contribute to normal neonatal delivery in Syde1-KO mothers

overall_design: E14.5 wild-type and Syde1-knockout placentas were collected for RNA extraction and hybridization on Affymetrix microarrays. The differentially expressed genes between wild-type and Syde1-knockout were selected and validated with quantitative real-time PCR and immunoblotting.

first: Hsiao-Fan

last: Lo

first: Ching-Yen

last: Tsai

first: Chie-Pein

last: Chen

first: Liang-Jie

last: Wang

first: Chia-Yu

first: Chung-Tiang

last: Liang

first: Mei-Leng

last: Cheong

first: Hungwen


title: Mammary transcriptome of rats treated with low-dose environmental chemicals at critical developmental windows

status: Public on Oct 19 2016

city: New York

first: Kalpana

last: Gopalakrishnan

address: 1428 Madison Avenue, Atran Building 03-02

institute: Icahn School of Medicine at Mount Sinai

summary: Exposure to common environmental chemicals, including those found in personal care products has been linked to mammary cancer at high doses in animal models. Their effects at low doses at levels comparable to human exposure, especially during critical windows of development remain poorly understood. Using a Sprague-Dawley rat model, we investigated the effects of of three environmental chemicals – diethyl phthalate (DEP), methyl paraben (MPB) and triclosan (TCS) – on the transcriptome of normal developing mammary glands at low doses mimicking human exposure. Rats were exposed during three windows of early development – perinatal (gestation day (GD) 1 - 20 or postnatal day (PND) 1 - 20), prepubertal (PND 21 - 41) and pubertal (PND 42 - 62), as well as chronic exposure from birth to end of lactation (PND 1 - 146). Mammary gland whole-transcriptomes were profiled by Affymetrix rat gene 2.0 st arrays.

overall_design: Female Sprague-Dawley rats were treated by oral gavage with low doses of diethyl phthalate (DEP), methyl paraben (MPB) or triclosan (TCS). These low doses were previously determined to produce urinary biomarker concentrations comparable to those reported for the US population (Teitelbaum SL et al, 2016). Control animals received the vehicle, olive oil (OIL). Exposure consisted of three short term windows – perinatal (gestation day (GD) 1 - 20 or postnatal day (PND) 1 - 20), prepubertal (PND 21 - 41) and pubertal (PND 42 - 62), as well as chronic exposure from birth to end of lactation (PND 1 - 146). There were 3-5 animals in each experimental group.

first: Susan

last: Teitelbaum

first: Luca

last: Lambertini

first: James

last: Wetmur

first: Fabiana

last: Manservisi

first: Laura

last: Falcioni

first: Simona

last: Panzacchi

first: Fiorella

last: Belpoggi

first: Jia


title: ADAM9 Up-regulates N-Cadherin via MiR-218 Suppression in Lung Adenocarcinoma Cells

status: Public on Oct 11 2016

city: Taipei

first: Liang-Chuan

last: Lai

address: 1 Jen-Ai Road, Sec 1

institute: National Taiwan University

summary:
Identification of miRNAs that differentially expressed in brain metastatic cells and were predicted to target CDH2.
To investigate which miRNAs could regulate CDH2 expression in brain-metastatic lung cancer cells, we examined the miRNA expression profiles in brain-metastatic lung cancer cells and their parental cells using Illumina miRNA microarray. By comparing the endogenous expression of all miRNAs, 146 miRNAs were selected by 2-fold changes in brain-metastatic lung cancer cells. Furthermore, we used several algorithms in miRSystem to predict which miRNA whose target gene was CDH2. There were 44 miRNAs that were predicted to target CDH2. In total, we identified nine miRNAs whose target gene was CDH2 and whose expression was significantly different between the highly metastatic cells and their parental cells (Fig. 2A). Among these miRNAs, four miRNAs were found to be down-regulated and five miRNAs were up-regulated in brain-metastatic lung cancer cells (Fig. 2B).

overall_design: Total RNA obtained from human lung cancer cells (F4) compared to brain metastasis lung cancer cells (BM).

first: Yuh-Ping

last: Sher


title: Expression data from three layers in the growth plate

status: Public on Oct 05 2016

city: Boston

first: Shigeki

last: Nishimori

address: 50 Blossom Street, Thier 1101

department: Medicine

institute: Massachusetts General Hospital

summary: The developing vertebrate growth plates in long bones have three morphologically distinct layers of chondrocytes: Round Cell layer, Flat Cell layer, and Hypertrophic Cell layer. Round chondrocytes differentiate into flat chondrocytes, and then flat chondrocytes differentiate into hypertrophic chondrocytes. To investigate the genetic programs underlying the chondrocyte differentiation, we obtained total RNA from the microdissected cryosections from each layer and then performed microarray analysis.

overall_design: We euthanized 3 litters at birth to obtain biological triplicate data. Using cryosections of unfixed fresh frozen hind limbs, we manually dissected each layer on the glass slide under a dissecting microscope. We collected each piece of the sections in lysis buffer and stored at -80°C prior to RNA extraction. To prepare one sample, we dissected 18 to 20 tibiae from the same litter.

first: Henry

middle: M

last: Kronenberg


title: Activity-dependent transcriptional profiling of basolateral amygdala neurons in response to valence-specific stimuli

status: Public on Oct 16 2016

city: Cambridge

first: Joshua

last: Kim

address: 43 Vassar

institute: MIT

summary: Activity-dependent transcriptional profiling was performed in the basolateral amygdala in order to identify unique genetic markers for functionally distinct neuronal populations

overall_design: RNA was pools from from 2 mice per sample, 3 mice per group. RNA from mice that underwent shock and female were compared

first: Michele

last: Pignatelli

first: Sangyu

last: Xu

first: Shigeyoshi

last: Itohara

first: Susumu

last: Tonegawa


title: Cell type-specific chromatin states differentially prime squamous cell carcinoma tumor-initiating cells for epithelial to mesenchymal transition [expression 1]

status: Public on Oct 15 2016

city: Brussels

first: Cédric

last: Blanpain

address: Route de Lennik 808

country: Belgium

institute: ULB

summary: Epithelial to mesenchymal transition (EMT) in cancer cells has been associated with metastasis, stemness and resistance to therapy. The reason why some tumors undergo EMT and other not might reflect intrinsic properties of their cell of origin, although this possibility is largely unexplored. By targeting the same oncogenic mutations to discrete skin compartments, we show cell type-specific chromatin and transcriptional states differentially prime tumors to EMT.  Squamous cell carcinomas (SCCs) derived from intrafollicular epidermis (IFE) are generally well-differentiated, while hair follicle (HF) stem cell-derived SCCs frequently exhibit EMT, efficiently form secondary tumors, and possess increased metastatic potential.  Transcriptional and epigenomic profiling revealed IFE and HF tumor-initiating cells possess distinct chromatin landscapes and gene regulatory networks associated with tumorigenesis and EMT that correlate with accessibility of key epithelial and EMT transcription factor binding sites.  These findings highlight the importance of chromatin states and transcriptional priming in dictating tumor phenotypes and EMT.

overall_design: KrasG12D and YFP expression combined with deletion of p53 were induced in Hair Follicle Stem cells (SCs) and their progeny using Lgr5CREER/KRasG12D/p53fl/fl/Rosa-YFP mice, and in the Intra Follicular Epidermis and the infundibulum using K14CREER/KRasG12D/p53fl/fl/Rosa-YFP mice by intraperitoneal tamoxifen injection. Cells were harvested and compared prior oncogenic hits and in fully grown tumours.

first: M

last: Latil

first: D

last: Nassar

first: B

last: Beck

first: S

last: Boumhadi

first: A

last: Brisebarre

first: C


title: Increased gene expression in the peridontium of unopposed molars in rats

status: Public on Nov 01 2016

city: Geneva 14

first: PIerre

last: Burkhard

address: 4 rue Gabrielle-Perret-Gentil

department: Department of Clinical Neurosciences

country: Switzerland

institute: HUG

summary:
The crowns of the right maxillary molars were removed  in 28 days old male Wistar rats (experimental).   Gene expression patterns were examined in the periodontal ligaments (PDLs) of the ipsilateral and contralateral mandibular molars, three and fifteen days later. Rats whith no dental interventions served as controls.
We used microarrays to detail gene expression underlying post-emergent tooth eruption and identified distinct classes of up-regulated genes during this process.

overall_design: The first mandibular molars were extracted and the periodontal ligament tissue was scraped with a scalpel from each root of the molar and RNA extraction and Transcriptome profiling was performed using Affymetrix.

first: Domna

last: Dorotheou


title: TZD-induced beige fat activation

status: Public on Oct 03 2016

city: ann arbor

first: Jun

last: Wu

state: MI

address: 210 washtenaw ave.

institute: University of Michigan

summary: Beige fat cells dissipate energy through mitochondrial uncoupling protein UCP1 defending against obesity and can be activated by thermogenic stimuli in white adipose tissue.  Here, we provide candidate molecules involved in beige fat activation induced the TZD, rosiglitazone.

overall_design: Microarray analysis of the differentiated inguinal fat cells in the absence or presence of 1 uM rosiglitazone for 4 d. These samples were profiled using Affymetrix mouse 430 2.0 arrays, 6 samples in total

first: Heejin

last: Jun


title: Genome-wide analysis of gene expression by IFN-beta in U6A cells expressing WT or T387A STAT2

status: Public on Sep 20 2016

city: cleveland

first: Yuxin

last: Wang

state: OH

address: 9500 Euclid avenue

department: Cancer Biology

institute: cleveland clinic foundation

summary: We used an Illumina Gene Expression Array to understand in more detail how T387 phosphorylation affects ISG induction. mRNA preparations from U6A cells expressing wild-type or T387A STAT2, treated with IFN-β for 0, 4, 8, or 24 h, were analyzed.

overall_design: Total RNA obtained from U6A cells expressing wild-type or T387A STAT2, treated with IFN-β for 0, 4, 8, or 24 h


title: Transcriptome analysis of liver and kidneys of rats chronically fed a NK603 Roundup-tolerant genetically modified maize [liver]

status: Public on Oct 01 2016

city: London

first: Matthew

last: Arno

state: LONDON

address: 150 Stamford Street

department: Genomics Centre

institute: King's College London

summary:
There is an ongoing debate on the potential toxicity of genetically modified food. The ability of rodent feeding trials to assess the potential toxicity of these products is highly debated since a 2-year study in rats fed NK603 Roundup-tolerant genetically modified maize, treated or not with Roundup during the cultivation, resulted in anatomorphological and blood/urine biochemical changes indicative of liver and kidney structure and functional pathology.
We used microarrays to detail the alterations in gene expression profiles associated with the consumption of a Roundup-tolerant genetically modified maize (NK603) sprayed or unsprayed with a Roundup herbicide from these same animals.

overall_design: Female rats were fed a diet containing 33% of a Roundup-tolerant genetically modified maize (NK603) sprayed or unsprayed with a Roundup herbicide (n=9). Control female rats were fed a diet containing 33% of the isogenic line of the same maize (n=10). Samples of liver were taken for gene expression analysis

middle: J

first: Robin

last: Mesnage


title: Expression data from thalamic dLGN nucleus in control and Sema6A knock-out mice at P0

status: Public on Sep 21 2016

city: San Juan de Alicante

first: Guillermina

last: López-Bendito

state: Alicante

address: Av. Ramón y Cajal, s/n

department: Developmental Neurobiology

institute: Instituto de Neurociencias de Alicante CSIC & UMH

summary:
Misguided visual thalamic axons leads to changes in gene expression in visual thalamic neurons.
We used microarrays to determine the global programme of gene expression due to altered connectivity.

overall_design: Mouse thalamic tissue from identified dLGN nuclei was selected at postnatal stage P0 for RNA extraction and hybridization on Affymetrix microarrays. We used two conditions: heterozygous (controls)  and homozygous knock-out of Sema6A (Sema6A-/-) mice. Each sample is composed by pooling the thalamic nuclei tissue from pups of the same condition from different litters.

last: Lópz-Bendito

first: Verónica

last: Moreno-Juan

first: Cecilia

last: Mezzera


title: Transcriptome analysis of liver and kidneys of rats chronically fed a NK603 Roundup-tolerant genetically modified maize

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

overall_design: Refer to individual Series


title: Transcriptome analysis of liver and kidneys of rats chronically fed a NK603 Roundup-tolerant genetically modified maize [kidney]

overall_design: Female rats were fed a diet containing 33% of a Roundup-tolerant genetically modified maize (NK603) sprayed or unsprayed with a Roundup herbicide (n=9). Control female rats were fed a diet containing 33% of the isogenic line of the same maize (n=10). Samples of kidney were taken for gene expression analysis


title: Effect of maple syrup extract high on the liver of mice fed a high-fat diet [I]

status: Public on Sep 12 2016

city: Kanagawa

first: Asuka

last: Kamei

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

department: Project for development of food functionality assessment methods

institute: Kanagawa Academy of Science and technology

summary: The effects of the administration of maple syrup extract (MSXH) on hepatic gene expression were investigated in mice fed high-fat diet.

overall_design: Male C57BL/6J mice aged 3 weeks were purchased from Charles River Japan (Kanagawa, Japan) and housed in a room maintained at 21 ± 1°C and 50 ± 10% relative humidity with a 12-h light/dark cycle (light 08:00–20:00; dark 20:00–08:00). Mice were preliminary fed a low-fat diet (LFD) which contained fat at 10 kcal% for acclimation.  After a week of acclimation, mice were divided four groups (n=10 each) and fed for 4 weeks on diet which contained fat at 45 kcal% as high-fat diet (HFD), 45 kcal% plus 0.02% MSXH (002MSXH), 45 kcal% plus 0.05% MSXH (005MSXH), and LFD .  Mice were given a diet and water for 24 h ad libitum. On day 30th after 16 h fasted, animals were euthanized under anesthesia to excise the livers and to collect the blood.

first: Yuki

last: Watanabe

first: Fumika

last: Shinozaki

first: Akihito

last: Yasuoka

first: Kousuke

last: Shimada

first: Tomoko

last: Ishijima

first: Tsudoi

last: Toyoda

first: Soichi

last: Arai

first: Takashi

last: Kondo

first: Keiko

last: Abe


title: Effect of maple syrup extract high on the liver of mice fed a high-fat diet [III]


title: Effect of maple syrup extract high on the liver of mice fed a high-fat diet [II]


title: Gene expression of murine IgG2-memory B cells from spleen and bone marrow

city: Berlin

first: Pawel

last: Durek

address: Charitéplatz 1

institute: Deutsches Rheuma-Forschungszentrum

summary: We compared gene expression profiles of murine IgG2b+ memory B cells isolated from spleen and bone marrow of C57BL/6J mice and mice obtained at a pet shop.

overall_design: 6x10E04-1.5xE05 IgG2b+ memory B cells from spleens and bone marrow of WT C57BL/6 J Crl mice or mice obtained at a pet shop in Berlin, Germany were isolated using a FACSAria II sorter following magnetic enrichment of CD19+ cells. A single cell suspension of spleen or bone marrow cells was prepared, CD19+ cells isolated by MACS technology (Miltenyi Biotec) and then FACSorted for IgG2b+IgM-IgD-CD19+CD38+CD138-CD11c-GL7-PI- small lymphocytes.   Total RNA was extracted using the RNA MiniPrep kit (Zymo Research). The integrity of isolated RNA was assessed for each sample using an Agilent 2100 Bioanalyzer (Agilent, Waldbronn, Germany) and amount was checked with a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE). Double-stranded complementary RNA was synthesized from 1 µg total RNA using Message AmpII Biotin (Ambion, USA). Fifteen micrograms of fragmented cRNA of each sample were hybridized to MG 430_2 GeneChips (Affymetrix). Hybridization was performed in a Hybridization Oven 640, and chips were washed and stained in the Fluidics Station 400 (both Affymetrix). Finally, the arrays were scanned with a GeneChip Scanner 3000 using the GCOS software, version 1.4, both Affymetrix. All relevant GCOS data of quality checked microarrays were analyzed with High Performance Chip Data Analysis (HPCDA, unpublished), using the BioRetis database (www.bioretis-analysis.de), as described and validated previously.

first: René

last: Riedel

first: Victor

last: Greiff

first: Daniel

last: Schulz

first: Ulrike

last: Menzel

first: Stefan

last: Kröger

first: Ulrik

last: Stervbo

first: Claudia

last: Haftmann

first: Kathrin

last: Lehmann

first: Patrick

last: Maschmeyer

first: Mairi

last: McGrath

first: Sandra

last: Naundorf

first: Stefanie

last: Schmidt

first: Özen

last: Sercan-Alp

first: Sibel

last: Durlanik

first: Melanie

last: Weber

first: Kerstin

last: Westendorf

first: Jakob

last: Zimmermann

first: Mir-Farzin

last: Mashreghi

first: Sai

middle: T

last: Reddy

first: Hyun-Dong

last: Chang

first: Andreas

last: Radbruch


title: N-arachidonoyl dopamine or vehicle control treated NRAS-G12D transformed Ba/F3 cells expression data

status: Public on Sep 08 2016

city: Shanghai

first: Min

last: Wu

address: Scientific and technology plaza, Ruijin Road II

institute: Shanghai Institute of hematology

summary:
RAS oncogenic mutations are common in human cancers, but RAS proteins have been difficult to target. We sought to identify pharmacological agents to block the RAS oncogenic signaling by a distinct mechanism. Since the biological activity of RAS proteins rely upon lipid modifications and RAS regulates lipid metabolisms in cancer cells, we screened a bioactive lipid library using a RAS specific cell viability assay. We report the discovery of a new class of inhibitors for RAS transformation. Compounds in the class represented by endocannabinoid N-arachidonoyl dopamine (NADA) can induce cell oncosis, independent of its ability to engage cannabinoid receptors. Further analyses show that NADA is more active in inhibiting the NRAS transformation and signaling than that of KRAS4B. Mechanistically, NADA blocks the plasma membrane translocation of NRAS, but not that of KRAS4B. In addition, NADA inhibits the plasma membrane translocation and neoplastic transformation of oncogenic KRAS4A. Interestingly, NADA also redistributes the cytoplasmic NRAS to the Golgi apparatus in a palmitoylation-dependent manner. The results indicate that NADA inhibits NRAS and KRAS4A plasma membrane translocation by targeting a novel molecular process. The new findings would help to develop novel targeted therapies for a broad range of human cancers.
To confirm the oncogenic RAS pathway interference of NADA, we performed microarray assay to detail the gene expression pattern change in order to figure out the RAS pathway affection and further indicate the underlying mechnism of the compound function.

overall_design: In the microarray assay, two groups were included, which are NRAS-G12D transformed Ba/F3 (Ba/F3-N ) cells treated with vehicle or 1 μM NADA for 12 hours, respectively. Each group contains three replicates. In each sample, 1×107 cells were harvested and for RNA extraction. After quality control, the samples were subjected to the Affymetrix Mouse Genome 430 2.0 Array according to the manufacturer’s instructions.

first: Wu

last: Min


title: Effect of maple syrup extract high on the liver of mice fed a high-fat diet.

first: Asuka

last: Kamei


title: De novo generation of somatic stem cells from differentiated cells [mammary]

status: Public on Sep 10 2016

city: Padova

first: Silvio

last: Bicciato

address: via U. Bassi 59/b

department: Molecular Medicine

institute: University of Padova

summary: To investigate the role of YAP/TAZ as factors able to convert differentiated cells into stem cells of the same tissue, we compared the expression profiles of mammary organoids (yOrg) obtained by doxycycline-inducible expression of YAP in luminal differentiated mammary cells with original luminal differentiated mammary cells (Lum) and organoids from native mammary stem cells (Org).

overall_design: We collected RNA from Org, yOrg and Lum. Samples were then processed for total RNA extraction and hybridization on Affymetrix microarrays. Three biological replicas (A, B, C) were used for each sample, for a total of 9 samples.

first: Luca

last: Azzolin

first: Tito

last: Panciera

first: Daniele

last: Di Biagio

first: Atsushi

last: Fujimura

first: Michelangelo

last: Cordenonsi

first: Stefano

last: Piccolo


title: De novo generation of somatic stem cells from differentiated cells


title: Gene expression profiling of mice given orally a supplement with special amino acid composition of Vespa larval saliva origin (DW vs VAAM)

status: Public on Sep 06 2016

city: Kawasaki

first: Fumika

last: SHINOZAKI

address: 3-25-13 Tonomachi, Kawasaki-ku

institute: Kanagawa Institute of Industrial Science and Technology

summary: VAAM stands for an amino acid mixture simulating the composition of Vespa, a hornet larval saliva. We conducted a comparative study on metabolism-regulatory roles of VAAM, casein-simulating amino acid mixture (CAAM), and pure water on murine hepatic and adipose tissue transcriptomes. Mice were orally fed VAAM solution ( 0.675 g/ kg BW = 2% of food-derived amino acids = 0.38% of total food energy/ day), CAAM solution ( 0.675 g / kg BW/ day) or water under ad libitum for five days. Hepatic transcriptome comparison of VAAM, CAAM and water-treated groups revealed a VAAM-specific regulation of the metabolic pathway, i.e., the down-regulation of glycolysis and fatty acid oxidation, and up-regulation of poly unsaturated fatty acid synthesis and glycogenic amino acids utilization in TCA cycle. Similar transcriptomic analysis of white and brown adipose tissues (WAT and BAT) suggested the up-regulation of phospholipid synthesis in WAT and the negative regulation of cellular processes in BAT. Because these coordinated regulations of tissue transcriptomes implicated the presence of upstream signaling common to these tissues, we conducted Ingenuity Pathways Analysis of these transcriptomes with the results that estrogenic and glucagon signals seemed to be activated in liver and WAT as well as beta-adrenergic signaling did in the three tissues by administration of VAAM. Our data provide a clue to understanding the role of VAAM in metabolic regulation of multiple tissues.

overall_design: Mice were divided randomly into three groups, VAAM, CAAM or water administered group. VAAM, CAAM or water was orally administrated five times once a day using feeding tube. The dosage of 1.8%VAAM, 1.8%CAAM or water was 37.5 microliter per gram of body weight. On day of last administration, food was removed and mice were moved to clean cages at 8:00. The last administrations started at 10:00. At 4 hours later after last administration, mice were sacrificed by cervical dislocation to collect blood, liver, white adipose tissue (WAT) and brown adipose tissue (BAT). Small hepatic pieces were immersed into RNAlater. WAT and BAT were frozen immediately after extraction using liquid nitrogen. All samples were extracted total RNA and hybridized on Affymetrix microarrays.


title: Gene expression profiling of mice given orally a supplement with special amino acid composition of Vespa larval saliva origin


title: Gene expression profiles in mouse embryonic fibroblasts (MEFs) derived from BCL11B-KO mice

status: Public on Sep 05 2016

city: Aomori

first: Yuji

last: Nakai

state: Aomori

address: 2-1-1, Yanagawa

department: Institute of Regional Innovation

institute: Hirosaki University

summary: The differentiation of preadipocytes into adipocytes is controlled by several transcription factors, including peroxisome proliferator-activated receptor γ (PPARγ) and CCAAT/enhancer-binding protein α (C/EBPα), which are known as master regulators of adipogenesis. BCL11B is a zinc finger-type transcription factor that regulates the development of the skin and central nervous and immune systems. Here, we found that BCL11B was expressed in the white adipose tissue (WAT), particularly the subcutaneous WAT and that BCL11B−/− mice had a reduced amount of subcutaneous WAT. During adipogenesis, BCL11B expression transiently increased in 3T3-L1 preadipocytes and mouse embryonic fibroblasts (MEFs). The ability for adipogenesis was reduced in BCL11B knockdown 3T3-L1 cells and BCL11B−/− MEFs, whereas the ability for osteoblastogenesis was unaffected in BCL11B−/− MEFs. Luciferase reporter gene assays revealed that BCL11B stimulated C/EBPβ activity. Furthermore, the expression of downstream genes of the Wnt/β-catenin signaling pathway was not suppressed in BCL11B−/− MEFs during adipogenesis. Thus, this study identifies BCL11B as a novel regulator of adipogenesis, which works, at least in part, by stimulating C/EBPβ activity and suppressing the Wnt/β-catenin signaling pathway.

overall_design: MEFs were derived from embryonic day 12.5 BCL11B+/+ and BCL11B−/− C57BL6 mice embryos. After 2 times passage, MEFs were differentiated using the adipocyte differentiation medium and 10 μM pioglitazone. After 12 h of adipocyte differentiation, gene expression profiles were analyzed by DNA microarray.

first: Jun

last: Inoue

first: Yusuke

last: Ihara

first: Daisuke

last: Tsukamoto

first: Keisuke

last: Yasumoto

first: Tsutomu

last: Hashidume

first: Kenya

last: Kamimura

first: Shigeki

last: Hirano

first: Makoto

last: Shimizu

first: Ryo

last: Kominami

first: Ryuichiro

last: Sato


title: Chronic activation of hepatic Nrf2 has no major effect on fatty acid and glucose metabolism in adult mice

status: Public on Sep 01 2016

city: Frankfurt am Main

first: Daniel

last: Margerie

address: Industrial Park Hoechst, Building H831

department: R&D, Digital Data Sciences

institute: Sanofi-Aventis Deutschland GmbH

summary: The transcription factor NF-E2-related factor 2 (Nrf2) induces cytoprotective genes, but has also been linked to the regulation of hepatic energy metabolism. In order to assess the pharmacological potential of hepatic Nrf2 activation in metabolic disease, Nrf2 was activated over 8 weeks in mice on Western diet using two different siRNAs against kelch-like ECH-associated protein 1 (Keap1), the inhibitory protein of Nrf2. Whole genome expression analysis followed by pathway analysis demonstrated that the suppression of Keap1 expression induced genes that are involved in anti-oxidative stress defense and biotransformation, pathways proving the activation of Nrf2 by the siRNAs against Keap1. The expression of neither fatty acid- nor carbohydrate-handling proteins was regulated by the suppression of Keap1. Metabolic profiling of the animals did also not show effects on plasma and hepatic lipids, energy expenditure or glucose tolerance by the activation of Nrf2. The data indicate that hepatic Nrf2 is not a major regulator of intermediary metabolism in mice.

overall_design: Gene expression profile of mouse liver samples from 8-week-old male C57BL6/J mice (N=24) treated with liver-selective Keap1-specific siRNA (group 1: siKeap1-1, N=8; group 2: siKeap1-2, N=8) or unspecific scrambled control siRNA (group 3: siControl, N=8)

first: Sebastian

last: Brachs

first: Dieter

last: Schmoll


title: Expression data for CD8 TILs subpopulations sorted by Tim3 and PD1

status: Public on Sep 07 2016

city: CAMBRIDGE

first: Meromit

last: Singer

state: MASSACHUSETTS

address: 415 main st, ROOM 6031

institute: Broad Institute of MIT and Harvard

summary: Reversing the dysfunctional T cell state that arises in cancer and chronic viral infections is the focus of therapeutic interventions; however, current therapies are effective in only some patients and some tumor types. To gain a deeper molecular understanding of the dysfunctional T cell state, we analyzed population and single-cell RNA profiles of CD8+ tumor-infiltrating lymphocytes (TILs) and used genetic perturbations to identify a distinct gene module for T cell dysfunction that can be uncoupled from T cell activation. This distinct dysfunction module is downstream of intracellular metallothioneins that regulate zinc metabolism and can be identified at single-cell resolution. We further identify Gata-3, a zinc-finger transcription factor in the dysfunctional module, as a regulator of dysfunction, and use CRISPR/Cas9 genome editing to show that it drives a dysfunctional phenotype in CD8+ TILs. Our results open novel avenues for targeting dysfunctional T cell states, while leaving activation programs intact.

overall_design: Samples were generated of naive (CD62LhiCD44low) and effector/memory (CD62LlowCD44hi) CD8+ cells from non tumor-bearing Balb/c mice, CD8+Tim3-PD1- (DN) TILs, CD8+Tim3-PD1+(SP), and CD8+Tim3+PD1+ (DP) TILs. Batch indicated in sample name (2157, 1962, 1635, 1655 and 1716).


title: Transcriptional profiling of mouse liver after short-term in vivo exposure (up to 56 days) of C57BL-mice to carcinogenic and non-carcinogenic chemicals

status: Public on Aug 26 2016

city: Basel

first: Jonathan

last: Moggs

address: Fabrikstrasse 2

institute: Novartis

summary: To further our investigations for early biomarkers of non-genotoxic carcinogenesis, groups of mice were treated with a range of known or suspected non-genotoxic carcinogens for a period of 28 or 56d and liver tissue harvested for expression profiling. Control groups were treated with appropriate vehicles.

overall_design: Group size was 5 mice (mus musculus, C57BL/6J, randomly assigned); all chemicals were of the highest quality available, and were administered by experienced personnel.

first: Colin

last: Henderson

first: Michael

last: Römer

first: Rita

last: Moreno

first: Lynsey

last: Chatham

first: Amy

last: Cameron

first: Jennifer

last: Grant

first: Roland

last: Wolf


title: Microarray data of dermal cells from ventral or dorsal skin of virgin and pregnant mice

status: Public on Aug 30 2016

city: Bunkyo-ku

first: Fumiko

last: Toyoshima

state: Tokyo

address: 1-5-45 Yushima

department: Medical Research Laboratory

institute: Institute of Science Tokyo

summary: To identify genes expressed predominantly in the ventral skin dermis of pregnant mice, we performed DNA microarray analysis by using isolated dermal tissues from ventral skin at 0 and 15 dpc, PP2-injected ventral skin at 15 dpc, and dorsal skin at 15 dpc.

overall_design: 8-12-week-old C57BL/6 virgin or pregnant (at 12 dpc) female mice were intradermally injected with PP2 or control DMSO twice a day for 4 days. At 0 or 15 dpc, the dermal cells were isolated from ventral or dorsal skin. Total RNA was isolated from the dermal cells and subjected to Affymetrix microarray using GeneChip 3'IVT Expression Kit.

last: Ichijo


title: De novo generation of somatic stem cells from differentiated cells [neuron]

first: Silvio

last: Bicciato

summary: To investigate the role of YAP/TAZ as factors able to convert differentiated cells into stem cells of the same tissue, we compared the expression profiles of neural stem cells (NSCs) obtained by doxycycline-inducible expression of YAP (yNSCs) in neurons with original neurons and neural stem cells (NSCs) treated in the same way.

overall_design: We collected RNA from NSCs, yNSCs, and neurons. Samples were then processed for total RNA extraction and hybridization on Affymetrix microarrays. Three biological replicas (A, B, C) were used for each sample, for a total of 9 samples.

first: Atsushi

last: Fujimura

first: Luca

last: Azzolin

first: Tito

last: Panciera

first: Daniele

last: Di Biagio

first: Michelangelo

last: Cordenonsi

first: Stefano

last: Piccolo