title: Epigenetic regulation of type 1 diabetes in nonobese diabetic mice

first: Sundararajan

last: Jayaraman

address: 909 South Wolcott Avenue

institute: University of Illinois at Chicago

summary:
Background: Epigenetic alteration of the genome has been shown to provide palliative effects in mouse models of certain human autoimmune disorders. We have investigated whether chromatin remodeling could provide protection against autoimmune diabetes in nonobese diabetic (NOD) mice. Treatment of female mice during the transition from prediabetic to diabetic stage (18-24 weeks of age) with the well-characterized histone deacetylase inhibitor, Trichostatin A (TSA) effectively reduced the incidence of diabetes and abrogated the ability of splenocytes to adoptively transfer the disease into immunodeficient NOD.scid mice. Protection against diabetes was accompanied by histone hyperacetylation in pancreas and spleen, increased frequency of CD4+ CD62L+ cells in the spleen, reduction in cellular infiltration of islets, restoration of normoglycemia and glucose-induced insulin release by beta cells. In vitro activation of splenic T lymphocytes derived from protected mice resulted in enhanced expression of IFN-gamma mRNA and protein without altering the expression of Il4, Il17, Il18, Inos, and Tnfa genes nor the secretion of IL-2, IL-4, IL-17 and TNF-alpha proteins. Consistently, expression of the transcription factor involved in Ifng transcription, Tbet/Tbx21 but not Gata3 and Rorgt, respectively required for the transcription of Il4 and Il17, was upregulated in activated splenocytes of protected mice. These data indicate that abrogation of autoimmune diabetes is associated with the selective upregulation of certain inducible genes in T lymphocytes.
Microarray analysis was performed to determine the changes in global gene expression underlying abrogation of autoimmune diabetes by TSA-mediated epigenetic modulation and identified a distinct group of genes down-regulated during this process.

overall_design:
Female NOD mice were treated subcutaneously with TSA (500 µg/Kg body weight) during the transition from prediabetic to diabetic stage (18-24 weeks of age), at weekly intervals. Since we sought to determine the modulation of global gene expression associated with long-term protection against diabetes, TSA treated mice were killed between 32 and 36 weeks of age and total RNA was extracted from uninduced splenocytes. RNA was also extracted from splenocytes of untreated mice that became diabetic and those that did not develop diabetes till 36 weeks of age. Blood glucose levels were determined weekly to monitor the glycemic condition in untreated and TSA-treated mice. To minimize the variability in gene expression among individual mice, RNA was extracted from splenocytes of 3 to 5 mice per group and pooled. Each sample was hybridized to microchips in duplicate.
Female NOD mice  were treated with Trichostatin A (500 µg/Kg body weight) between 18-24 weeks of age or left untreated.

first: Jayaraman

last: Sundararajan


title: Mammalian cells acquire epigenetic hallmarks of human cancer during immortalization

status: Public on Nov 29 2012

city: Duarte

first: Xiwei

last: Wu

state: CA

address: 1500 E. Duarte Rd.

department: Computational and Quantitative Medicine

country: USA

institute: City of Hope National Medical Center

type: Methylation profiling by genome tiling array

summary: Progression to malignancy requires cells to overcome senescence and switch to an immortal phenotype. Thus, exploring the genetic and epigenetic changes that occur during senescence/immortalization may help elucidate crucial events that lead to cell transformation. In the present study, we have globally profiled DNA methylation in relation to gene expression in primary, senescent and immortalized mouse embryonic fibroblasts.

overall_design: Primary, senescent and immortalized mouse fibroblasts obtained from three independent embryos. Compare immortalized versus primary and senescent versus primary cells.

first: Stella

last: Tommasi

first: Albert

last: Zheng

first: Annette

last: Weninger

first: Steve

middle: E

last: Bates

first: Arthur

middle: X

last: Li

first: Monica

last: Hollstein

first: Ahmad

last: Besaratinia


title: Impaired intrinsic immunity to HSV-1  in human iPSC-derived TLR3-deficient CNS cells

city: New York

first: Jeffrey

last: Zhao

state: NY

address: 1275 York Avenue

department: Genomics Core

institute: Memorial Sloan Kettering Cancer Center

summary: In the course of primary infection with herpes simplex virus 1 (HSV-1), children with inborn errors of the TLR3- and UNC-93B-dependent induction of IFN-α/β and/or IFN-λ immunity are prone to HSV-1 encephalitis (HSE) 1-3. The cells responsible for HSE in these children have yet to be identified. We tested the hypothesis that the pathogenesis of HSE involves non hematopoietic central nervous system (CNS)-resident cells. We derived induced pluripotent stem cells (iPSCs) from the dermal fibroblasts of TLR3- and UNC-93B-deficient patients and from controls. These iPSCs were allowed to differentiate into highly purified populations of neural stem cells (NSCs), neurons, astrocytes and oligodendrocytes. The induction of IFN-β and/or IFN-λ1 in response to poly(I:C) stimulation was dependent on TLR3 and UNC-93B in all cells tested. However, the induction of IFN-β and IFN-λ1 in response to HSV-1 infection was impaired selectively in UNC-93B-deficient neurons and oligodendrocytes. These cells were also much more susceptible to HSV-1 infection than control cells, whereas UNC-93B-deficient NSCs and astrocytes were not. The rescue of UNC-93B-deficient cells with the wild-type UNC93B1 allele demonstrated the genetic defect as the cause of the poly(I:C) and HSV-1 phenotypes. The viral infection phenotype was further rescued by treatment with exogenous IFN-α/β, but not IFN-λ1. TLR3-deficient neurons were also found to be susceptible to HSV-1 infection, a phenotype rescued by wild-type TLR3. Thus, impaired TLR3- and UNC-93B-dependent IFN-α/β intrinsic immunity to HSV-1 in the CNS, in neurons and oligodendrocytes in particular, may underlie the pathogenesis of HSE in children with TLR3 pathway deficiencies

overall_design: One human ESC line (H9) was differentiated into 4 different cell types, neural rosettes, CNS neurons, astrocytes and immature oligodendrocytes. Rosettes were purified manually, neurons were sorted negatively for the surface markers EGFR and CD44, oligodendrocyte cells were positively sorted for the surface marker O4 while astrocytes were enriched by growth in serum containing medium. All cell types were subjected to RNA extraction and hybridization on Illumina microarrays. Each sample has 3 biological repeats, except rosettes which has 2 repeats. In a seperate experiement, undifferentiated H9 cells along with H9-derived neurons and astrocyes as well as UNC93B-/- iPS derived neurons and astrocytes were also subjected to RNA extraction and hybridization on Illumina microarrays.

first: Fabien

last: Lafaille

first: Lorenz

last: Studer


title: Expression data from leptin administration to Lepob/Lepob mice and  Lepmkyo/Lepmkyo rats

status: Public on Nov 28 2012

city: Kyoto

first: MEGUMI

last: AIZAWA-ABE

address: Shokogin Kawahara-cho

department: Translational Research Center

country: Japan

institute: Kyoto University Hospital

summary:
Leptin-responsive genes in the pathway of a leptin signal from the hypothalamus to the liver has not been detected.
We used microarray to detailed the expression of gene in liver in the status of leptin deficiency, and leptin administration. As leptin deficient status, we use  Lepmkyo/Lepmkyo rats or Lepob/Lepob mice and  their wild type littermates.

sample_organism:
Mus musculus
Rattus norvegicus

platform_organism:
Mus musculus
Rattus norvegicus

overall_design: Recombinant murine leptin (1 microg/mg) and saline was intraperitonealy administrated in 20 weeks old Lepob/Lepob mice and their control littermates, and 20 weeks old Lepmkyo/Lepmkyo rats and their control littermates. In order to detect the early response genes whose expression level were changed before the food intake and body weight would change, we took liver samples 6 hours after administration.

first: Megumi

last: Aizawa-Abe

first: Ken

last: Ebihara

first: Tomoji

last: Mashimo

first: Tadao

last: Serikawa

first: Kazuwa

last: Nakao


title: Expression data from neutrophils from wild-type and Jdp2-/- mice

status: Public on Nov 30 2012

city: Suita

first: Kenta

last: Maruyama

address: yamada-oka 3-1

institute: Osaka university

summary: Jdp2 is a member of the AP-1 family and suppresses histone acetyltransferase activity. We used microarrays to examine the gene expression pattern of neutrophil form Jdp2-/- mice.

overall_design: Bone marrow CD11b+Ly6Clo Ly6G+ neutrophils form wild-type and Jdp2-/-mice were sorted by FACS, followed by RNA extraction. Affymetrix microarrays were used to analyze the mRNA expression.

first: Shizuo

last: Akira


title: Expression data from murine bone marrow erythroid progenitor cells at two early stages of development.

status: Public on Nov 17 2012

city: Bangalore

first: Aishwarya

last: Narayanan

address: 5th Floor, KBP, Bellary Road

country: India

institute: Strand Life Sciences

summary: This study was designed to define erythropoietin (EPO) regulated genes in murine bone marrow erythroid progenitor cells at two stages of development, designated E1, and E2. E1 cells correspond to CFUe- like progenitors, while E2 cells are proerythroblasts.

overall_design: 14 samples were analyzed. 8 samples belong to the E1 stage and the remaning 6 samples correspond to the E2 stage. In the E1 stage, there are 4 controls and 4 treatment samples. The 4 samples in each group are biological replicates. Likewise in the E2 stage, there are 3 control and 3 treatment samples and the 3 samples in each group are biological replicates.

first: Don

middle: M

last: Wojchowski


title: Effect of Th-POK deficiency on global gene expression in liver Va14i NKT cells

status: Public on Dec 01 2012

city: La Jolla

first: Mitch

last: Kronenberg

address: 9420 Athena Circle

institute: LIAI

summary: We sought to identify genes regulated by the transcription factor Th-POK (Zbtb7b) in liver Va14i NKT cells, by RNA microarray analysis of global gene expression in Va14i NKT cells from mice homozygous for the Th-POK-inactivating hd point mutation as compared with the same cell population isolated from heterozygous or wild-type age-matched mice.

overall_design: Two sample set pairs of hd/hd and either hd/+ or +/+ age-matched Va14i NKT cells were prepared via magnetic selection and cell sorting, and total RNA prepared using a Qiagen Rneasy mini kit.  IVT probe generation and hybridization to Affymetrix Mouse Genome 430 2.0 arrays was carried out by the Veterans Medical Research Foundation GeneChipTM Microarray located at UCSD.

first: Mitchell

first: Isaac

last: Engel


title: The circadian clock coordinates ribosome biogenesis.

city: St Lucia

first: Frédéric

last: Gachon

state: QLD

address: 306 Carmody Road

department: Institute for Molecular Bioscience

country: Australia

institute: University Of Queensland

summary: Evolutionary conserved biological rhythms play a fundamental role in the physiology and behavior of all light-sensitive organisms. Generation of rhythmic expression of clock-controlled genes is orchestrated by a molecular circadian clock constitutes by interconnected negative feedback loops of transcription factors. In this study, we want to characterize gene which also present a rhythmic translation through the characterization of genes with a rhythmic polysomal/total RNA ratio.

overall_design: Analyze of gene expression in liver total RNA and polysomal RNA harvested every 2 hrs during 2 series of 48 hrs, 2 mice per samples

first: Céline

last: Jouffe

first: Gaspard

last: Cretenet

first: Laura

last: Symul

first: Felix

last: Naef


title: Deletion of miRNA processing enzyme Dicer in POMC-expressing cells leads to neurodegeneration and development of obesity

status: Public on Nov 16 2012

city: Genève

first: Jordi

last: Altirriba

address: Rue Michel-Servet 1

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

country: Switzerland

institute: Centre Médical Universitaire de Genève

summary: The activity of the endoribonuclease Dicer is crucial to produce the mature form of most microRNAs (miRNAs). Recent studies indicate that lack of miRNAs in different neuronal types results in a range of anatomical and behavioural phenotypes. In the present study we aimed to investigate the developmental and metabolic consequences of miRNA ablation in hypothalamic POMC neurons studying mice with a conditional deletion of Dicer in this population of neurons (POMCDicerKO). These mice exhibited a progressive obese phenotype characterized by hyperphagia, increased adiposity, hyperleptinemia, defective glucose metabolism and alterations in the pituitary-adrenal axis. The development of the obese phenotype was paralleled by a POMC neuron degenerative process that was complete by 6 weeks of age. Furthermore, immunohistochemistry and gene expression studies in control C57Bl/6 adult mice showed that Dicer was expressed in relevant hypothalamic areas and neurons implicated in energy balance, and that its expression was regulated by nutrient availability. Collectively, our results highlight a crucial role for miRNAs in POMC neuron survival and the consequent development of neurodegenerative obesity.

overall_design: Total RNA was extracted from hypothalamic microdissections of 2-week old control and POMCDicerKO mice using the RNeasy micro spin columns (Qiagen, Venlo, The Netherlands). Ten micrograms of total RNA were converted into cRNA, biotinylated, fragmented, and hybridized to GeneChip Mouse Genome 430 2.0 (Affymetrix, Santa Clara, CA). Six microarrays were hybridized with three independent samples from control and POMCDicerKO mice.

first: M

last: Schneeberger

first: J

first: A

last: Garcia

first: Y

last: Esteban

first: C

last: Castaño

last: Garcia-Lavandeira

middle: V

last: Álvarez

first: R

last: Gomis

last: Claret


title: Transcriptome Sequence Analysis of Pediatric Acute Megakaryoblastic Leukemia Identifies An Inv(16)(p13.3;q24.3)-Encoded CBFA2T3-GLIS2 Fusion Protein As a Recurrent Lesion in 39% of Non-Infant Cases [2010]

status: Public on Nov 20 2012

city: Memphis

first: Tanja

middle: Andrea

last: Gruber

state: TN

address: 262 Danny Thomas Place

department: Oncology

institute: St. Jude Childrens Research Hospital

summary:
Transcriptome Sequence Analysis of Pediatric Acute Megakaryoblastic Leukemia Identifies An Inv(16)(p13.3;q24.3)-Encoded CBFA2T3-GLIS2 Fusion Protein As a Recurrent Lesion in 39% of Non-Infant Cases:  A Report From the St. Jude Children’s Research Hospital – Washington University Pediatric Cancer Genome Project.
Acute Megakaryoblastic Leukemia (AMKL) accounts for ~10% of childhood acute myeloid leukemia (AML).  Although AMKL patients with down syndrome (DS-AMKL) have an excellent 5 year event-free survival (EFS), non-DS-AMKL patients have an extremely poor outcome with a 3 year EFS of less than 40%. With the exception of the t(1;22) translocation seen in infant non-DS-AMKL, little is known about the molecular genetic lesions that underlie this leukemia subtype. To define the landscape of mutations that occur in non-DS-AMKL, we performed transcriptome sequencing on diagnostic blasts from 14 cases (discovery cohort) using the illumina platform. Our results identified chromosomal rearrangements resulting in the expression of novel fusion transcripts in 12/14 cases. Remarkably, in 7/14 cases we detected an inversion on chromosome 16 [inv(16)(p13.3;q24.3)] that resulted in the juxtaposition of the CBFA2T3, a member of the ETO family of transcription factors, next to GLIS2 resulting in a CBFA2T3-GLIS2 chimeric gene encoding an in frame fusion protein. 6 cases in the discovery cohort fused exon 10 of CBFA2T3 to exon 3 of GLIS2, while 1 case carried a larger product that fused exon 11 of CBFA2T3 to exon 1 of GLIS2.  Both products retain the 3 CBFA2T3 N-terminal nervy homology regions that mediate protein interactions, and the 5 GLIS2 C-terminal zinc finger domains that bind the Glis DNA consensus sequence, along with one of its N-terminal transcriptional regulatory domains.  GLIS2 is a member of the GLI super family of transcription factors and has been demonstrated to play a role in regulating expression of GLI target genes as well as inhibiting WNT signaling through the binding of beta catenin.  Although GLIS2 is not normally expressed in hematopoietic cells, the translocation results in high level expression of the CBFA2T3-GLIS2 fusion protein. In addition to CBFA2T3-GLIS2, chimeric transcripts were detected in 6/7 cases that lacked evidence of the inv(16)(p13.3;q24.3).  Specifically, we detected GATA2-HOXA9, MN1-FLI1, NIPBL-HOXB9, NUP98-KDM5A, GRB10-SDK1 and C8orf76-HOXA11AS, each in an individual case.  Importantly, several of the genes involved in these translocations either play a direct role in normal megakaryocytic differentiation (GATA2 and FLI1), or have been previously shown to be involved in leukemogenesis (HOXA9, MN1, HOXB9).  Evaluation of a recurrency cohort of 42 samples including 14 additional pediatric cases and 28 adult cases by RT-PCR revealed 4 additional pediatric samples carrying CBFA2T3-GLIS2 for an overall frequency of 39% in pediatric AMKL.  In addition to these somatic structural variations, we also identified mutations in genes previously shown to play a role in megakaryoblastic leukemia including activating mutations in JAK2 and MPL (36%).
To gain insight into the mechanism whereby CBFA2T3-GLIS2 promotes leukemogenesis, we introduced the fusion into murine hematopoietic cells and assessed its effect on in vitro colony replating as a surrogate measure of self-renewal. Hematopoietic cells transduced with a mCherry expressing retroviral vector failed to form colonies after the second replating. By contrast, expression of either wild-type GLIS2 or the CBFA2T3-GLIS2 fusion resulted in a marked increase in the self-renewal capacity, with colony formation persisting through eight replatings.  Immunophenotypic analysis of the CBFA2T3-GLIS2 expressing colonies revealed evidence of megakaryocytic differentiation. Importantly, the CBFA2T3-GLIS2 cells remained growth factor dependent suggesting that cooperating mutations in growth factor signaling pathways are required for full leukemic transformation.
Taken together these data identify a novel cryptic inv(16)-encoded CBFA2T3-GLIS2 fusion protein as a recurrent driver mutation in approximately 40% of non-infant pediatric non-DS-AMKLs. Moreover, the majority of pediatric cases that lacked this lesion were shown by transcriptome sequence analysis to contain other chromosomal rearrangements that encoded fusion proteins that directly alter megakaryocytic differentiation and/or myeloid cell growth. The alteration of a key transcriptional regulator within the hedgehog signaling pathways in a substantial percentage of pediatric AMKL raises the possibility that inhibition of this pathway may have a therapeutic benefit in this aggressive form of AML.

overall_design: Gene expression profiling was performed on 14 single diagnosis tumor samples

middle: A

first: Amanda

middle: L

last: Gedman

first: Jinghui

last: Zhang

first: Cary

last: Koss

first: Suresh

last: Marada

first: Huy

middle: Q

last: Ta

first: Shann-Ching

last: Chen

first: Xiaoping

last: Su

first: Stacey

last: Ogden

first: Jinjun

last: Dang

first: Vedant

last: Gupta

first: Anna

middle: K

last: Andersson

first: Stanley

last: Pounds

first: Lei

last: Shi

first: John

last: Easton

first: Jianmin

last: Wang

first: Michael

last: Rusch

first: Ramapriya

last: Ganti

first: Jing

last: Ma

first: Ina

last: Radtke

first: Li

last: Ding

first: Giovanni

last: Cazzaniga

first: Andrea

last: Biondis

first: Steven

last: Kornblau

first: Farhad

last: Ravandi-Kashani

first: Hagop

last: Kantarjian

first: Stephen

middle: D

last: Nimer

first: Konstanze

last: Doehner

first: Hartmut

first: Timothy

middle: J

last: Ley

first: Paola

last: Ballerini

first: Thomas

last: Mercher

first: Sheila

last: Shurtleff

first: Lee-Yung

last: Shih

first: Der-Cherng

last: Liang

first: Jeffrey

last: Rubnitz

first: Ching-Hon

last: Pui

first: Elaine

middle: R

last: Mardis

first: Richard

last: Wilson

first: James


title: Expression data from Middle Ear Mucosal Metaplasia in Mice

status: Public on Nov 13 2012

city: Washington

first: Svetlana

last: Ghimbovschi

state: DC

address: 111 Michigan Ave., NW

department: Research Center for Genetic Medicine

institute: Children's National Medical Center

summary:
Chronic Otitis Media (OM) develops after sustained inflammation and is characterized by secretory middle ear epithelial metaplasia and effusion, most frequently mucoid. Non-typeable Haemophilus influenzae (NTHi), the most common acute OM pathogen, is known to activate inflammation and mucin expression in vitro and in animal models of OM. The goals of this study were to:  examine expression profiling epithelial effects of NTHi challenge in murine middle ears.
We used microarrays to detail examine the global programme of gene expression underlying  epithelial effects of NTHi challenge in murine middle ears during this study.

overall_design: Weekly transtympanic inoculation of Balb/c mice with 300 µg/ml of NTHi lysates vs saline was performed. Bacteria were grown on chocolate agar at 37ºC in 5% CO2 overnight and inoculated in brain heart infusion (BHI) broth supplemented with 3.5 mg of nicotinamide adenine dinucleotide per ml. After overnight incubation, bacteria were subcultured into 5 ml of fresh brain heart infusion (BHI) and upon reaching log phase growth, NTHi were washed and suspended in phosphate-buffered saline (PBS) followed by sonication for lysis. Three transtympanic inoculation of 6 Balb/c mice middle ears (3 animals, 6 ears) with 50 uL of 300 ug/ml of NTHi bacterial lysate and 6 Balb/c mice middle ears (3 animals, 6 ears) with 50 uL of 1X phosphate buffered saline (PBS) were carried out weekly over 4 weeks (injection on days 7, 14, and 21). On day 28, the mice were euthanized and their bullae harvested. Expression microarray analysis was performed at 1 and 7 days.  Microarray findings were validated in independent animal samples and in a cultured murine middle ear epithelial cell (mMEEC) line.

first: Diego

last: Preciado


title: Genome-Wide Analysis of Gene Program Activation by Defined Cardiac Transcription Factor Tbx5, Gata4 and Myocardin

city: Houston

first: Lei

last: Zhou

address: 6700 Bertner Avenue

institute: Texas Heart Institute

summary:
Background: Cardiac transcription factors are master regulators during heart development. Recently, some were shown to transdifferentiate noncardiac mesoderm cells and cardiac fibroblasts into cardiomyocytes. However, the individual roles of each transcription factors in activating cardiac gene program have not been elucidated. We examined cardiac-specific and genome-wide gene expression in fibroblasts induced with cardiac transcription factors Nkx2.5 (N), Tbx5 (T), Gata4 (G), Myocardin (M) alone or different combinations.

Methodology/Principal Findings: We applied different combinations of human Nkx2.5 (N), Tbx5 (T), Gata4 (G) and Myocardin (M) lentiviruses into 10T1/2 fibroblasts. Immunostaining and quantitative reverse transcription polymerase chain reaction (qRT-PCR) showed that N, T, G or M alone did not induce expression of cardiac marker genes α-myosin heavy chain (αMHC) and cardiac troponin T (cTnT). Only T+M and T+G+M combinations induced αMHC and cTnT expression. Microarray-based gene ontology analysis revealed that T alone inhibited most genes involved in cardiac-related processes and activated genes involved in Wnt receptor signaling pathway and in aberrant processes. M alone inhibited genes involved in Wnt receptor signaling pathway and activated genes involved in cardiac-related processes and in aberrant processes. G alone inhibited genes involved in ectoderm development. T+G+M combination was the most effective activator of genes associated with cardiac-related processes including muscle cell differentiation, sarcomere, striated muscle contraction, regulation of heart contraction, and glucose metabolism and fatty acid oxidation (two significant forms of cardiomyocyte energy metabolism). And unlike T, M, G alone or T+M, T+G+M did not activate genes associated with aberrant processes.

Conclusions: Tbx5, Gata4 and Myocardin play different roles in activating cardiac gene program and in avoiding aberrant gene program activation. The combination of T+G+M activated cardiac gene program and avoided aberrant gene program activation.

overall_design: Two weeks after doxycline induction, total RNA was isolated from 10T1/2-tTA cells infected with different combinations of Tbx5, Gata4, and Myocardin lentiviruses. Biological triplicated.

first: Yu

last: Liu

last: Dixon

first: Li

last: Lu


title: Transcriptome Sequence Analysis of Pediatric Acute Megakaryoblastic Leukemia Identifies An Inv(16)(p13.3;q24.3)-Encoded CBFA2T3-GLIS2 Fusion Protein As a Recurrent Lesion in 39% of Non-Infant Cases [2007]

first: Tanja

last: Gruber

overall_design: Gene expression profiling was performed on 29 single diagnosis tumor samples

first: Amanda

last: Gedman

first: Jinghui

last: Zhang

first: Cary

last: Koss

first: Suresh

last: Marada

first: Huy

last: Ta

first: Shann-Ching

last: Chen

first: Xiaoping

last: Su

first: Stacey

last: Ogden

first: Jinjun

last: Dang

first: Vedant

last: Gupta

first: Anna

last: Andersson

first: Stanley

last: Pounds

last: Shi

first: John

last: Easton

first: Jianmin

last: Wang

first: Michael

last: Rusch

first: Ramapriya

last: Ganti

first: Jing

last: Ma

first: Ina

last: Radtke

last: Ding

first: Giovanni

last: Cazzaniga

first: Andrea

last: Biondi

first: Steven

last: Kornblau

first: Farhad

last: Ravandi-Kashani

first: Hagop

last: Kantarjian

first: Stephen

last: Nimer

first: Konstanze

last: Doehner

first: Hartmut


title: Transcriptome Sequence Analysis of Pediatric Acute Megakaryoblastic Leukemia Identifies An Inv(16)(p13.3;q24.3)-Encoded CBFA2T3-GLIS2 Fusion Protein As a Recurrent Lesion in 39% of Non-Infant Cases

first: Tanja

last: Gruber

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

overall_design: Refer to individual Series


title: The role of Raf-1 kinase inhibitor protein in the regulation of pancreatic beta cell proliferation in mice

status: Public on Nov 19 2012

first: Jordi

last: Altirriba

summary:
AIMS/HYPOTHESIS: Manoeuvres aimed at increasing beta cell mass have been proposed as regenerative medicine strategies for diabetes treatment. Raf-1 kinase inhibitor protein 1 (RKIP1) is a common regulatory node of the mitogen-activated protein kinase (MAPK) and nuclear factor κB (NF-κB) pathways and therefore may be involved in regulation of beta cell homeostasis. The aim of this study was to investigate the involvement of RKIP1 in the control of beta cell mass and function.
METHODS: Rkip1 (also known as Pebp1) knockout (Rkip1 (-/-)) mice were characterised in terms of pancreatic and glucose homeostasis, including morphological and functional analysis. Glucose tolerance and insulin sensitivity were examined, followed by assessment of glucose-induced insulin secretion in isolated islets and beta cell mass quantification through morphometry. Further characterisation included determination of endocrine and exocrine proliferation, apoptosis, MAPK activation and whole genome gene expression assays. Capacity to reverse a diabetic phenotype was assessed in adult Rkip1 (-/-) mice after streptozotocin treatment.
RESULTS: Rkip1 (-/-) mice exhibit a moderately larger pancreas and increased beta cell mass and pancreatic insulin content, which correlate with an overall improvement in whole body glucose tolerance. This phenotype is established in young postnatal stages and involves enhanced cellular proliferation without significant alterations in cell death. Importantly, adult Rkip1 (-/-) mice exhibit rapid reversal of streptozotocin-induced diabetes compared with control mice.
CONCLUSIONS/INTERPRETATION: These data implicate RKIP1 in the regulation of pancreatic growth and beta cell expansion, thus revealing RKIP1 as a potential pharmacological target to promote beta cell regeneration.

overall_design: Pancreatic gene expression of Rkip-1 (Raf kinase inhibitor 1) knockout (KO) and wild type (WT) mice, including three biological replicates in each group.

first: Fabian

middle: N

last: Pardo

first: Marta

last: Pradas-Juni

first: Ainhoa

last: García

first: Ulf

last: Ahlgren

first: Albert

last: Barberà

first: Juan

middle: C

last: Slebe

first: Alejandro

last: Yañez

first: Ramon

last: Gomis

first: Rosa

last: Gasa


title: C/EBPa controls acquisition and maintenance of adult hematopoietic stem cell quiescence

status: Public on Nov 14 2012

city: Singapore

first: Henry

last: Yang

address: 28 Medical Drive

country: Singapore

institute: Cancer Science Institute of Singapore

summary: In blood, the transcription factor C/EBPa is essential for myeloid differentiation and has been implicated in regulating self-renewal of fetal liver hematopoietic stem cells (HSCs). However, its function in adult HSCs is unknown. Here, using an inducible knockout model, we found that C/EBPa deficient adult HSCs underwent a pronounced expansion with enhanced proliferation, characteristics resembling fetal liver HSCs. Consistently, transcription profiling of C/EBPa deficient HSCs revealed a gene expression program similar to fetal liver HSCs. Moreover we observed that age-specific C/EBPa expression correlated with its inhibitory effect on the HSC cell cycle. Mechanistically, we identified N-Myc as a C/EBPa downstream target. C/EBPa upregulation during HSC transition from an active fetal state to a quiescent adult state was accompanied by down-regulation of N-Myc, and loss of C/EBPa resulted in de-repression of NMyc. Our data establish that C/EBPa acts as a molecular switch between fetal and adult states of HSC in part via transcriptional repression of the proto-oncogene N-Myc.

overall_design: HSCs of Pu.1 knock-in (PU.1ki/ki) mice were used for RNA extraction and hybridization on Affymetrix microarrays. We compared these microarray samples with the corresponding wild type.

first: Min

last: Ye

first: Hong

last: Zhang

first: Giovanni

last: Amabile

first: Philipp

middle: B

last: Staber

first: Elena

last: Levantini

first: Pu

first: Meritxell

last: Alberich-Jorda

first: Junyan

first: Akira

last: Kawasaki

first: Daniel

middle: G

last: Tenen


title: Dynamic regulation of miRNA and mRNA signatures during in vitro pancreatic differentiation

status: Public on Nov 07 2012

first: Xiaoyan

last: Liao

address: 200 W Arbor Street

department: Reproductive Medicine

institute: University of California, San Diego

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


title: Profile of testicular polysomal gene expression regulated by Gonadotropin Regulated Testicular RNA helicase in adult mice

status: Public on Nov 21 2012

city: Bethesda

first: Chon-Hwa

last: Tsai-Morris

state: Md

address: Bldg. 49, Rm 6B03, 49 Convent Drive

department: PDEGEN, NICHD, NIH

summary:
The down-regulation of known genes concerned with spermatogenesis at polysomal sites in GRTH KO and their association with GRTH in WT coupled with early findings of minor or unchanged total mRNAs and abolition of their protein expression in KO, underscore the relevance of GRTH in translation.
Studies showed the association of GRTH bound polysome genes with the ubiquitin-proteasome-heat shock protein signaling network pathway and NFκB/TP53/TGFB1 signaling networks were derived from the differentially expressed gene analysis.

overall_design: Microarray differential gene expression analysis was performed using polysome-bound RNA isolated from testes of wild type (WT) and GRTH KO mice.

first: Hisashi

last: Sato

first: Ravi

last: Gutti

first: Maria

last: Dufau


title: Dynamic regulation of miRNA and mRNA signatures during in vitro pancreatic differentiation (miRNA)

summary: The remarkable differentiation capacity of pluripotent stem cells into any adult cell types have enabled researchers to model human embryonic development and disease process in dishes, as well as deriving specialized cells for replacing damaged tissues. Type 1 diabetes is a degenerative disease characterized by autoimmune destruction of the insulin-producing beta islet cells in the pancreas. Recent advances have led to the establishment of different methods to direct differentiation of human or mouse pluripotent stem cells toward beta cell lineages. However, existing strategies have not yet succeeded in generating fully functional beta cells in vitro. Thus, it remains a major challenge to identify novel regulators of beta cell differentiation and maturation, and the islet-specific genetic and epigenetic regulatory networks are logical targets.

overall_design: To obtain a comprehensive view of the microRNA expression pattern during in vitro directed differentiation of hPSC into pancreatic beta islet cells, we collected 16 samples of 6 stages of differentiated derivatives, 2 samples of human fetal pancreas and 5 samples of purified human beta islet cells for analysis. With these samples, we performed genome-wide microRNA expression profiling using the Illumina Human v2 MicroRNA Expression BeadChips (1,146 assays).

first: Haipeng

last: Xue

first: Yu

last: Wang

first: Kristopher

last: Nazor

first: Neha

last: Trivedi

first: Suzanne

last: Peterson

first: Ying

last: Liu

first: Jeanne

middle: F

last: Loring

first: Louise

last: Laurent


title: Expression data from preimplantation mouse embryos

status: Public on Nov 09 2012

city: Stanford

first: Kin Fai

last: Au

address: James H. Clark Center, 1st Floor East, 318 Campus Drive,

department: Statistics

institute: Stanford

summary:
Landmark events occur in a coordinated manner during preimplantation development of the mammalian embryo, yet the regulatory network that orchestrates these events remains largely unknown.
We delineated the regulons of Oct4, Sall4, and Nanog using morpholino (MO)-mediated gene knockdowns followed by microarray analysis of pooled embryos.

overall_design: 1-cell fertilized mouse embryos were injected with a morpholino and were collected at either 20 hours or at 44 hours after microinjection.

first: Meng

middle: H

last: Tan

first: Kin


title: Hsp70 and a Novel Axis of Type 1 Interferon-Dependent Antiviral Immunity in the Measles Virus-Infected Brain

city: Columbus

first: Lianbo

last: Yu

state: OH

address: 1800 Cannon Drive

department: Center for Biostatistics

institute: The Ohio State University

summary: The major inducible 70 kDa heat shock protein (hsp70) is host protective in a mouse model of measles virus (MeV) brain infection. Transgenic constitutive expression of hsp70 in neurons, the primary target of MeV infection, abrogates neurovirulence in neonatal H-2d congenic C57BL/6 mice. A significant level of protection is retained after depletion of T lymphocytes, implicating innate immune mechanisms. Focus of the present work was to elucidate the basis for hsp70-dependent innate immunity using this model. Transcriptome analysis of brains from transgenic (TG) and non-transgenic (NT) mice 5 days after infection identified type 1 interferon (IFN) signaling and macrophage activation/antigen presentation as the main differences linked to survival. The pivotal role for type 1 IFN in hsp70-mediated protection was demonstrated in mice with a genetically disrupted type 1 IFN receptor (IFNAR-/-), where IFNAR-/- eliminated the difference in survival between TG and NT mice. Brain macrophages, not neurons, are the predominant source of type 1 IFN in the virus-infected brain, and in vitro studies provided a mechanistic basis by which MeV-infected neurons can induce IFN-β in uninfected microglia in an hsp70-dependent manner. MeV infection induced extracellular release of hsp70 from mouse neuronal cells that constitutively express hsp70, and extracellular hsp70 induced IFN-β transcription in mouse microglial cells through Toll-like receptors 2 and 4. Collectively, results support a novel axis of type 1 IFN-dependent antiviral immunity in the virus-infected brain that is driven by hsp70.

overall_design:
Hsp70 expression in mice enhances gene expression related to antiviral immune response against MeV neurovirulence. We performed microarrays on whole brain tissues in mice to obtain an unbiased picture of how hsp70 alters host innate responses to viral infection.
Hsp70-overexpressing transgenic (TG) and non-transgenic (NT) mice were infected with MeV intracranially, and total brain mRNA harvested at 5 and 10 days post infection (d.p.i.) was analyzed, sampling the hemisphere opposite the side of viral inoculation. Analysis includes 6 groups: infected TG at 5 d.p.i. (n=4), infected TG at 10 d.p.i. (n=5), infected NT at 5 d.p.i. (n=4), infected NT at 10 d.p.i. (n=5), uninfected TG at 5 d.p.i. (n=4), and uninfected NT at 5 d.p.i. (n=4).

first: Michael

last: Oglesbee

first: Jianying

last: Zhang


title: Offspring from oocytes derived from in vitro primordial germ cell-like cells in mice

status: Public on Nov 05 2012

city: Nara

first: Kazuki

last: Kurimoto

address: 840 Shijo-Cho, Kashihara

department: School of medicine

institute: Nara Medical University

summary: Reconstitution of female germ-cell development in vitro is a key challenge in reproductive biology and medicine. We show here that female (XX) embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs) in mice are induced into primordial germ cell-like cells (PGCLCs), which, when aggregated with female gonadal somatic cells as reconstituted ovaries, develop pre-meiotic germ cell characteristics, including X-reactivation, imprint erasure, and cyst formation. Upon transplantation under ovarian bursa, PGCLCs in the reconstituted ovaries mature into germinal vesicle-stage oocytes, which, through in vitro maturation and fertilization, contribute to fertile offspring. Our culture system serves as a robust foundation for the investigation of key properties of female germ cells, including the acquisition of totipotency, and for the reconstitution of whole female germ-cell development in vitro.

overall_design: We performed expression analysis of female PGC-like cells [PGCLCs; day 3 (d3), day 6 (d6), and day 3 followed by day 6 in aggregation with female embryonic day (E) 12.5 gonadal somatic cells (d3ag6)] in comparison to in vivo embryonic PGCs (E12.5 female PGCs and E9.5 PGCs) and male d6 PGCLCs. PGCLCs were marked with fluorescence of Blimp1-mVenus, stella-ECFP transgenic reporters (BVSC). PGCs were marked with fluorescence of the stella-EGFP transgenic reporter.

first: Katushiko

last: Hayashi

first: Sugako

last: Ogushi

first: So

last: Shimamoto

first: Hiroshi

last: Ohta

first: Mtinori

last: Saitou


title: Comparison of microarray platforms for measuring differential microRNA expression (Illumina data)

status: Public on Nov 26 2012

city: Milan

first: Loris

last: De Cecco

address: via Venezian 1

country: Italy

institute: IRCSS Istituto Nazionale Tumori

summary:
Microarray technology applied to miRNA profiling is a promising tool in many research fields. At present, only few studies have addressed intra- and inter-platform reproducibility by using tissues/cell-lines of different origin to maximize differences in miRNA content. Although the approach might provide an useful system to address technical issues since, for sure, a huge modulation can be evaluated, it  does not reflect the common experimental practice in laboratory. As a matter of fact, from all these studies it is not know how concordant can be expected the results obtained by different platforms starting from biological meaningful specimens.  We investigated the issue of inter-platform reproducibility using four miRNA microarray platforms and nine paired tumor/normal colon tissues.
The tumor and the normal counter-part samples were prospectively collected from 9 patients who underwent surgical resection at the INT-MI. Neoplastic samples were obtained from the central area of the neoplasia, avoiding to select necrotic material or transition zones with healthy mucosa. Samples of colonic healthy mucosa were resected at least 20 centimeters far from the neoplasia and distant from the surgical resection margins. Tissue samples were stored in liquid nitrogen until RNA extraction. Total RNA was extracted from 10–20 mg of tumor samples and from 30–40 mg of normal samples.

overall_design: Nine paired tumor/normal colon tissues on Illumina Human_v2 microRNA expression Beadchips

first: Maurizio

last: Callari


title: hyperlipidemia impaired innate response

city: Fuzhou

first: Lang

last: Lei

state: Fujian

address: 246# Yangqiaozhong Road, Gulou District

country: China

institute: Fujian Medical University

summary: To explore the effect of hyperlipidemia on macrophages' innate immune response to Porphyromonas gingivalis invasion

overall_design: 12 samples, 3 replicates in 4 groups, with cells from hyperlipidemic ApoE deficient mice and nonhyperlipidemic C57BL/6 mice stimulate with or without P.gingivalis(Pg)

first: Houxuan

last: Li

first: Fuhua

last: Yan

first: Yin

last: Xiao


title: Cerebellar Granule Neuron Temporal-NFI Microarray Data

city: Worcester

first: Baojin

last: Ding

state: MA

address: 55 Lake AVE. N.

department: Microbiology and Physiological Systems

institute: UMASS Medical School

summary:
Dendrite and synapse development are critical for establishing appropriate neuronal circuits, and disrupted timing of these events can alter connectivity leading to disordered neural function.
In early postnatal development of cerebellar granule neurons (CGNs), the expression of many genes is temporally regulated. Further, NFI (Nuclear Factor I) proteins have been shown to play important roles in the regulation of gene expression in developing CGNs.
To identify NFI-regulated genome-wide targets involved in late maturation of mouse CGNs, we performed two groups of microarray expression analysis: (1) temporal expression arrays using 1.5 and 6 day cultures of mouse CGNs representing immature and more mature CGNs, respectively, which identified 844 Temporal-Up or Down genes; and (2) NFI-regulated genes in 6 day CGN cultures that were infected at the time of plating with lentiviral vectors expressing either NFI dominant repressor (NFI-EnR) or EnR control protein. This identified 686 NFI-Up (NFI-EnR down-regulated) or NFI-Down (NFI-EnR up-regulated) genes.
Overlap analysis identified 212 temporal genes that were regulated by NFI. These results indicated that NFI plays a pivotal role in the regulation of late CGN maturation.

overall_design: For temporal arrays,  mouse CGN progenitors were purified from P6 mouse cerebellum and cultured for either 1.5 or 6 days. Three biological replicates were analyzed for each time point. For NFI arrays, CGN progenitors from P6 mice were transduced upon plating with either NFI-EnR or EnR control lentivirus and cultured 6 days. Four pairs of biological replicates were performed.

first: Wei

last: Wang

first: Hualin

middle: S

last: Xi

first: Daniel

last: Kilpatrick


status: Public on Nov 01 2012

city: Rotterdam

first: Su Ming

last: Sun

address: Dr. Molewaterplein 50

department: Hematology

country: Netherlands

institute: Erasmus University Medical Center

summary:
Overexpression of miR-9 and miR-9* in 32D cells, cells grown under IL-3 conditions and miR-9 and miR-9* were introduced with retroviral vectors containing about ~150 bp up and downstream of mmu-mir-9-2.
Expression was determined to find out the effect of miR-9/9*overexpression on the transcriptome level compared to introduction of empty vector control.

overall_design: Transcriptome levels were determined for 32D cells expressing miR-9 and miR-9* and empty vector control. Experiment performed in three independent replicates.

first: Su

middle: M


title: Treatment of CHRF288-11 Megakaryocytic Cells with Wnt compounds

city: Dublin

first: Patricia

last: Maguire

address: Belfield

department: Conway Institute

country: United Kingdom

institute: University College Dublin

summary:
CHRF288-11 cells were treated with Wnt3a (150ng/ml) and/ot Wnt5a (1200ng/ml) and RNA was harvested after 8 hours of treatment
Gene expression was analysed using Human WG6 V3 Illumina Beadarrays

overall_design: There are four experimental groups (Wnt3a Treated, Wnt5a Treated, Wnt3a + Wnt5a treated and Untreated (control)), each with three biological replicates

first: Iain

last: Macaulay


title: Comparison of expression profiles of Foxp3(+)epigenetics(-) T cells, Foxp3(-)epigenetics(+) T cells, and Foxp3(+)epigenetics(+) T cells

city: Suita

first: Hiromasa

last: Morikawa

state: Osaka

address: 3-1 Yamadaoka

department: IFReC

institute: Osaka university

summary: Analysis of Foxp3(+)epigenetics(-) T cells, Foxp3(-)epigenetics(+) T cells, and Foxp3(+)epigenetics(+) T cells. Results indicate regulatory T cell (Treg) ontogenesis requires two independent processes, expression of the transcription factor Foxp3 and establishment of Treg epigenetic programs induced by T cell receptor (TCR) stimulation.

overall_design: GFP+CD4+ and GFP-CD4+ splenocytes were sorted from DEREG and DEREG/Scurfy mice. These cells were activated with anti-CD3/CD28 antibodies, and then transduced with Foxp3-expressing retrovirus (pGCSamIN, NGFR marker). NGFR+ T cells sorted were subjected to microarray analysis (Affymetrix, mouse genome 430 2.0 array). To normalize the experimental conditions, Tregs (GFP+ T cells from DEREG) and Tconv (GFP- T cells from DEREG) were also activated and transduced with empty vector. Two replicates each.


title: Differential regulation of extracellular matrix constituents in myocardial remodeling with and without heart failure following pressure overload

city: Oslo

first: Ståle

last: Nygård

address: Institute for Experimental Medical Research, Oslo University Hospital - Ulleval

country: Norway

institute: University of Oslo

summary:
The aim of the present study was to examine potential differences in the regulation of myocardial ECM constituents, in mice that develop hypertrophy only (ABnonHF) and in mice that develop overt heart failure (ABHF) as response to pressure overload.
Seven weeks old male C57BL/6 mice were subjected to aortic banding (AB) or sham operation (sAB), with sacrifice 4 weeks after banding. Prior to sacrifice, cardiac function and geometry were evaluated by echocardiography. Animals with comparable gradients over the banded ascending aorta, comparable cardiac output and heart rate were divided into two groups: ABnonHF and ABHF. Our criterion for dividing AB animals into these two groups was based on lung weight and left atrial diameter (LAD), as an increase in these parameters most likely is due to pulmonary congestion. Heart failure (HF) was defined as an increase in lung weight and LAD defining ABnonHF as lung weight/tibia length ≤ 10.5 mg/mm and LAD ≤ 2.0 mm and ABHF as lung weight/tibia length ≥ 15 mg/mm and LAD ≥ 2.4 mm.

overall_design: Microarray screening was performed in 7 mice from each AB group and in 5 sAB mice. Sham was used as control.

first: Biljana

last: Skrbic

last: Nygard

first: Johannes

last: Bjornstad

first: Theis

last: Tonnessen


title: Female Mice Lacking p47phox Have Altered Adipose Tissue Gene Expression and are Protected against High Fat-Induced Obesity and Metabolic Syndrome

city: Little Rock

first: Horacio

last: Gomez-Acevedo

state: Arkansas

address: 4301 W. Markham St

department: Biomedical Informatics

institute: University of Arkansas for Medical Sciences

summary: Oxidative stress in adipose tissue and liver has been linked to the development of obesity.  NADPH oxidases (NOX) enzymes are a major source of reactive oxygen species (ROS). The current study was designed to determine if NOX2-generated ROS play a role in development of obesity and metabolic syndrome after high fat feeding. Wild type (WT) mice and mice lacking the cytosolic NOX2 activated protein p47phox (P47KO) were fed AIN-93G diets or high fat diets (HFD) containing 45% fat and 0.5% cholesterol for 13 weeks from weaning. Affymetrix array analysis revealed dramatically less expression of mRNA of genes linked to energy metabolism,  adipocyte differentiation (PPARγ, Runx2) and fatty acid uptake (CD36, lipoprotein lipase) in fat pads from female HFD-P47KO mice compared to HFD-WT females. These data suggest that NOX2 is an important regulator of metabolic homeostasis and that NOX2-associated ROS plays an important role in development of diet-induced obesity particularly in the female

overall_design: fat pads from p47phox and wild type fed a high fat or control diet

first: Martin

last: Ronis

first: Neha

last: Sharma

first: Jamie

last: Vantrease

first: Sarah

last: Borengasser

first: Matthew

last: Ferguson

first: Thomas

last: Badger


title: Comparison of microarray platforms for measuring differential microRNA expression

first: Loris

last: De Cecco

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

platform_organism:
Homo sapiens
synthetic construct


title: Microarray analysis of T-cell death-associated gene 8 (TDAG8)-mediated gene expression in mouse Lewis lung carcinoma (LLC) cells.

city: Tokyo

first: Satoshi

last: Ishii

address: 7-3-1 Hongo, Bunkyo

department: Department of Biochem. & Mol. Biol.

institute: The University of Tokyo

summary: We previously identified an extracellular pH-sensing G protein-coupled receptor T cell death associated gene 8 (TDAG8) as an extracellular pH sensor of tumor cells that promotes cell growth/survival in vitro and tumor development in vivo. To determine genes regulated by TDAG8 in vitro, mouse Lewis lung carcinoma (LLC) cells stably expressing TDAG8 (TDAG8-LLC cells) and control vector (control LLC cells) were cultured under acidic conditions. Transcriptome microarray analysis using Affymetrix GeneChip Mouse Genome 430 2.0 Arrays was performed with total RNA prepared from these cells.

overall_design: To determine genes regulated by TDAG8 in vitro, mouse Lewis lung carcinoma (LLC) cells stably expressing TDAG8 (TDAG8-LLC cells) and control vector (control LLC cells) were cultured under acidic conditions. Transcriptome microarray analysis using Affymetrix GeneChip Mouse Genome 430 2.0 Arrays was performed with a mixture of equal amounts of total RNA samples from four independent cell cultures.

first: Yuichro

last: Ihara

first: Hiroyuki

last: Aburatani

first: Takao

last: Shimizu


title: The transcriptional landscape of hematopoietic stem cell ontogeny

city: Baltimore

first: Patrick

last: Cahan

state: MD

address: 733 North Broadway, MRB 653

department: ICE and Biomedical Engineering

institute: Johns Hopkins University School of Medicine

summary: Transcriptome analysis of adult hematopoietic stem cells (HSC) and their progeny has informed our understanding of blood differentiation and leukemogenesis, but a similarly transformative analysis of the embryonic origins of hematopoiesis is lacking.  To address this issue, we acquired gene expression profiles of developing HSC purified from over 2500 dissected murine embryos and adult mice, and applied a network biology-based analysis to reconstruct the gene regulatory networks of sequential stages of HSC development. We found that embryonic hematopoietic elements clustered into three distinct transcriptional states characteristic of the definitive yolk sac, HSCs emerging from hemogenic endothelium, and definitive HSCs. We functionally validated several candidate transcriptional regulators of HSC ontogeny by morpholino-mediated knock-down in zebrafish embryos, confirming changes in the expression of HSC markers runx1 and c-myb in the aorta-gonads-mesonephros (AGM), the site of definitive HSC specification. Moreover, we found that HSCs derived from differentiating embryonic stem cells in vitro (ESC-HSC) most closely resemble definitive HSC, yet lack a signature indicative of specification by Notch signaling, which likely accounts for their deficient lymphoid development. Our analysis and accompanying web resource will accelerate the characterization of regulators of HSC ontogeny, facilitate efforts to direct hematopoietic differentiation and cell fate conversion, and serve as a model to study the origins of other adult stem cells.

overall_design: Hematopoietic stem cells and their precursors were isolated from mouse embryos and distinct stages and sites during development, purified by fluorescence activated cell sorting, and gene expression profiled on Affymetrix arrays.  We also profiled HSCs and their precurors derived by in vitro differentitation of embryonic stem cells [expression data from GSE16925 and GSE14012 was used for mESCs, available at http://hsc.hms.harvard.edu/].

first: Shannon

last: McKinney-Freeman

first: Hu

last: Li

first: George

last: Daley


title: Expression data from control and LRF (leukemia/lymphoma related factor)-deficient mouse LT-HSCs

status: Public on Oct 26 2012

city: Boston

first: Takahiro

last: Maeda

address: One Blackfan Circle

institute: Brigham and Women's Hospital

summary: LRF, which is encoded by the ZBTB7A gene and formerly known as POKEMON (POK erythroid myeloid ontogenic factor), was originally identified as a PLZF (promyelocytic leukemia zinc finger) homologue interacting with BCL6 (B-cell lymphoma 6). LRF is a transcription factor that is broadly expressed in hematopoietic lineage cells, but its expression is particularly high in erythroblasts and germinal center (GC) B-cells. The goal of this study is to assess the effect of LRF loss on the LT-HSC transcriptome. Nine days after injection of adult mice with polyinosinic polycytidylic acid (pIpc) to activate Cre, total RNAs were isolated from double-sorted LT-HSCs from LRF Flox/+ Mx1-Cre+ and LRF Flox/Flox Mx1-Cre+ mice and processed for microarray analysis.

overall_design: We performed gene expression microarray analysis of FACS-sorted LT-HSCs (LSK IL7Ra-Flt3-CD150+CD48-) to assess the effect of Lrf loss on the LT-HSC transcriptome. Zbtb7a Flox/+ Mx1-Cre+ mice were used as a control to normalize the potential effects of Cre recombinase. LT-HSCs were FACS-sorted from three Lrf knockout (Zbtb7a Flox/Flox Mx1-Cre+) and two control (Zbtb7a Flox/+ Mx1-Cre+) mice, nine days after the first pIpC injection.

first: Sung

middle: U

last: Lee

first: Sierra


title: Data from a time course study of gene expression in a mouse model of osteoarthritis

city: Winston-Salem

first: Richard

middle: F.

last: Loeser

state: NC

address: Medical Center Blvd.

department: Molecular Medicine

institute: Wake Forest School of Medicine

summary: The purpose of this study was to characterize the histologic development of OA in a mouse model where OA is induced by destabilization of the medial meniscus (DMM model) and to identify genes regulated during different stages of the disease, using RNA isolated from the joint “organ” and analyzed using microarrays.427 genes from the microarrays passed consistency and significance filters. There was an initial up-regulation at 2 and 4 weeks of genes involved in morphogenesis, differentiation, and development, including growth factor and matrix genes, as well as transcription factors including Atf2, Creb3l1, and Erg. Most genes were off or down-regulated at 8 weeks with the most highly down-regulated genes involved in cell division and the cytoskeleton. Gene expression increased at 16 weeks, in particular extracellular matrix genes including Prelp, Col3a1 and fibromodulin.The results support a phasic development of OA with early matrix remodelling and transcriptional activity followed by a more quiescent period that is not maintained.

overall_design:
A group of 9 mice was used for collection of RNA at time 0 (before surgery) when the animals were 12 weeks old. For the other time points, 9 DMM and 9 sham controls were sacrificed at 2, 4, 8, and 16 weeks after surgery for RNA isolation. The tissue included tibial plateau and femoral condyle articular cartilage, subchondral bone with any osteophytes, meniscus, and the joint capsule with synovium was used for RNA isolation. The tissue was treated with RNAlater® (Invitrogen) prior to freezing and storage at -800 C. RNA was extracted by homogenization using the Precellys 24 tissue homogenizer (Bertin Technologies purchased from MO BIO) and the amount and quality of the RNA was determined using an Agilent 2100 Bioanalyzer.
RNA was pooled prior to microarray analysis such that 3 randomly selected samples from each surgical group and time point were pooled to create each biological replicate. Because 9 mice were used for each experimental group, a total of three biological replicates per group were analyzed using the Affymetrix Mouse Genome 430 2.0 oligonucleotide arrays as described. One replicate pool, which was from week two DMM mice, did not meet the RNA integrity level needed for microarray analysis; thus, this pool was not analyzed further, leaving two pools for the week two DMM mice.

first: Jeff

middle: W

last: Chou


title: Expression data from mouse kidney tissue

city: Hamburg

last: Streichert

address: Martinistr. 52, Campus Forschung N27, 2. OG

department: Institute For Clinical Chemistry / Central Laboratories

country: Germany

institute: University Medical Center Hamburg-Eppendorf

summary:
The role of the renin-angiotensin system in chronic kidney disease involves multiple peptides and receptors. Exerting antipodal pathophysiological mechanisms, renin inhibition and AT1 antagonism ameliorate renal damage.
This is a comparison between the renin inhibitor aliskiren with the At1 antagonist losartan in mice with chronic kidney disease due to renal ablation.

overall_design: Renal tissue from ablated mice was used after 6-week treatment with either 500 mg/l losartan or 50 mg/kg aliskiren per day (n = 5)

first: Christoph

last: Fraune

first: Ulrich

middle: O

last: Wenzel


title: Gene Expression in Myotonic Dystrophy

status: Public on Oct 21 2012

city: Cleveland

first: Erik

last: van Lunteren

address: 10701 East Boulevard

department: Pulmonary 111J(W)

institute: Cleveland VA Medical Center

summary:
In order to examine the changes in gene expression between normal and myotonic dystrophic animals, gene expression array studies were done with extensor digitorum longus (EDL) of transgenic HSALR line 20b mice using Affymetrix MOE430 2.0 microarrays.
We used EDL muscle from transgenic HSALR line 20b mice, maintained as homozygotes in an FVB inbred background and wild-type FVB mice purchased from Taconic.

overall_design: Affymetrix gene expression arrays were performed on HSALR and wild type EDL muscle

first: Michelle

last: Moyer

first: Dara

last: Berger

first: Gregory

last: Kliment

first: Andrea

last: Ladd


title: Comparative expression data of PD21 Pik3cd+/- and Pik3cd-/- female mice ovaries responsed to exogenous gonadotropins.

status: Public on Oct 23 2012

city: Nanjing

first: Qian

address: Hanzhong Road 140

institute: Nanjing Medical University

summary:
The Pik3cd null females are subfertile and have less growing follicles than their heterozygous littermates in the ovary. These mice poorly respond to the exogenous gonadotropins and ovulate much less oocytes than controls. In addition, the estrodial stimulated GC proliferation in preantral follicles is also impaired in Pik3cd null ovaries. FSH and E2 dramatically activates PI3K/AKT pathway in GCs of wild type mice, but not in the Pik3cd null mice.
we used microarray to identify those genes regulated by Pik3cd in response to PMSG (Pregnant Mare Serum Gonadotropin) and E2 treatment in ovary.

overall_design: We set 3 treatment groups of both Pik3cd+/- and Pik3cd-/- female mice, including PD21 untreatment, PD21 after PMSG administration for 44 hours, PD21 after E2 administration for 72 hours, each group contained three biological repeats. The genes up/down-regulated significantly (not less than 2 fold change) in Pik3cd+/- mice after PMSG and E2 treatment were listed out as PMSG or E2 target genes, in which, those had not the same change trends in Pik3cd-/- were considered as Pik3cd-dependent genes.

first: HengYu

last: Fan


title: Microarray analysis of WT and Drd2-/- striatal tissue from C57BL/6 mice

status: Public on Oct 25 2012

city: shanghai

first: Jia-wei

last: Zhou

address: room. 319, building 23#, yueyang road No.320

institute: Institute of Neuroscience

summary: Drd2 regulates striatal gene networks.

overall_design: WT and KO striatal tissue were dissected from 2-month-old naïve male C57BL/6 genetic background mice and subjected to microarray analysis.

first: W

last: Shao

first: S

middle: Z

last: Zhang

first: J


title: Expression data from adult (9 month-old) and young (4 month-old) hearts from C57BL/6J mice

city: Madrid

first: Lucas

last: Elisa

state: Madrid

address: Nicolas Cabrera 1

department: Molecular Biology

country: Spain

institute: Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM)

summary:
G protein-coupled receptor kinase 2 (GRK2) has emerged as a key regulator of cardiac function and myocardial structure. Cardiac GRK2 is increased in heart failure and ischemia in humans, whereas genetic inhibition of GRK2 is cardioprotective in animal models of these pathologies. However, the mechanistic basis underlying these effects are not fully understood. We have used adult GRK2 hemizygous mice (GRK2+/-) as a model to assess the effects of a sustained systemic inhibition of GRK2 in heart tissue with age.
We used microarrays to determine the global programme of gene expression underlying cardioprotection with age in GRK2 hemizygous mice in comparation with their wild-type littermates.

overall_design: 9 month-old and 4 month-old mice hearts were collected for RNA extraction and hybridization on Affymetrix microarrays.

first: Maria

last: Jurado-Pueyo

first: E

last: Lucas


title: Expression data from young (4 month-old) hearts from GRK2 heterozygous C57BL/6J mice and its wild type littermates

summary:
G protein-coupled receptor kinase 2 (GRK2) has emerged as a key regulator of cardiac function and myocardial structure. Cardiac GRK2 is increased in heart failure and ischemia in humans, whereas genetic inhibition of GRK2 is cardioprotective in animal models of these pathologies. However, the mechanistic basis underlying these effects are not fully understood. We have used adult GRK2 hemizygous mice (GRK2+/-) as a model to assess the effects of a sustained systemic inhibition of GRK2 in heart tissue with age.
We used microarrays to determine the global programme of gene expression underlying cardioprotection in GRK2 hemizygous mice.

overall_design: 4 month-old mice hearts were collected for RNA extraction and hybridization on Affymetrix microarrays.


title: Expression data from adult (9 month-old) and young (4 month-old) hearts from GRK2 heterozygous C57BL/6J mice.

summary:
G protein-coupled receptor kinase 2 (GRK2) has emerged as a key regulator of cardiac function and myocardial structure. Cardiac GRK2 is increased in heart failure and ischemia in humans, whereas genetic inhibition of GRK2 is cardioprotective in animal models of these pathologies. However, the mechanistic basis underlying these effects are not fully understood. We have used adult GRK2 hemizygous mice (GRK2+/-) as a model to assess the effects of a sustained systemic inhibition of GRK2 in heart tissue with age.
We used microarrays to determine the global programme of gene expression underlying cardioprotection in GRK2 hemizygous mice with age.


title: Expression data from adult (9 month-old) hearts from GRK2 heterozygous C57BL/6J mice and its wild type littermates

status: Public on Oct 20 2012

overall_design: 9 month-old mice hearts were collected for RNA extraction and hybridization on Affymetrix microarrays.

first: Elisa


title: Genome-wide expression study of the responses of murine NK cells and dendritic cell subsets to MCMV infection

status: Public on Oct 17 2012

city: marseille

first: Thien-Phong

last: Vu Manh

address: 163 avenue de Luminy

country: France

institute: CIML

summary:
Murine Cytomegalovirus (MCMV) infection leads to the activation of various immune cells, including dendritic cells (DCs) and Natural Killer (NK) cells. This activation is partly driven by innate cytokines including IFN-I, which are induced early after infection. The objective was to address the role of different innate cytokines in shaping DC subsets and NK cell responses, in particular  the role of cell intrinsic responses to IFN-I.
In order to decipher the specific impact of cell-intrinsic IFN-I on cell subsets, we performed a genome-wide expression analysis on CD45.1 WT and CD45.2 IFNAR-/- splenic conventional DC (cDC) subsets and NK cells isolated from C57BL/6 [CD45.1 WT / CD45.2 IFNAR-KO] mixed bone marow chimera mice.

overall_design: This study includes data from cDC subsets (CD8a and CD11b) and NK cells purified by flow cytometry sorting from the spleen of bone marrow chimera (BMC) mice, under steady-state or MCMV condition. Two independent replicates were made for each cell type, from two independent pools of spleens from uninfected or d1.5 MCMV-infected BMC 5-8 mice,  and were hybridized on 3 separate batches of gene chips.

first: T

last: Baranek

first: TP

first: M

last: Dalod


title: DNA repair genes: Alternative transcription and gene expression at the exon level in response to the DNA damaging agent, ionizing radiation

city: East Melbourne

first: Jason

last: Li

address: St Andrews Pl

institute: Peter MacCallum Cancer Centre

summary: DNA repair is an essential cellular process required to maintain genomic stability. Every cell is subjected to thousands of DNA lesions daily under normal changes in transcription. Transcription is a primary process where protein amount and function can be regulated. One aspect of the transcriptional IR response that little is known about on a whole genome basis is alternative transcription. These investigations focus on the response to IR at the exon level in human cells but also at the whole gene level. Whole genome exon arrays were utilized to comprehensively characterize radiation-induced transcriptional expression products in two human cell types, namely EBV-transformed lymphoblast and primary fibroblast cell lines.

overall_design: 12 human primary fibroblast cell lines and 12 primary lymphoblast cell line samples were used for two doses (0 and 10 Gy) and two time points (0 and 4hr). Additional doses ( 1 Gy, 2 Gy, 5 Gy, and 20 Gy) and time points ( 1hr, 2hr, 8hr, 24hr and 48hr) were assessed in four primary lymphoblast cell lines and four primary fibroblasts.

first: Carl

last: Sprung


title: GRK2 deficiency confers cardioprotective profile.

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

overall_design: Refer to individual Series


title: Transcriptional reprogramming of tumor-associated endothelial cells by disruption of TNF-α signaling

city: Chicago

first: Sean

middle: Pravin

last: Pitroda

state: IL

address: 5841 South Maryland Avenue, MC 1105

department: Radiation and Cellular Oncology

institute: The University of Chicago

summary: Endothelial inflammation contributes to the pathogenesis of numerous human diseases; however, the role of tumor endothelial inflammation in the growth of experimental tumors and its influence on the prognosis of human cancers is less understood. TNF-α, an important mediator of tumor stromal inflammation, is known to target the tumor vasculature. In this study, we demonstrate that B16-F1 melanomas grew more rapidly in C57BL/6 wild-type (WT) mice than in syngeneic mice with germline deletions of both TNF-α receptors (KO). This enhanced tumor growth was associated with increased COX2 inflammatory expression in WT tumor endothelium compared to endothelium in KO mice. We purified endothelial cells from WT and KO tumors and characterized dysregulated gene expression, which ultimately formed the basis of a 6-gene Inflammation-Related Endothelial-derived Gene (IREG) signature. This inflammatory signature expressed in WT tumor endothelial cells was trained in human cancer datasets and predicted a poor clinical outcome in breast cancer, colon cancer, lung cancer and glioma. Consistent with this observation, conditioned media from human endothelial cells treated with pro-inflammatory cytokines (TNF-α and interferons) accelerated the growth of human colon and breast tumors in immune-deprived mice as compared with conditioned media from untreated endothelial cells. These findings demonstrate that activation of endothelial inflammatory pathways contributes to tumor growth and progression in diverse human cancers.

overall_design: To investigate the genes associated with TNF-α signaling in tumor endothelium, we performed expression profiling of tumor-associated endothelial cells isolated from B16F1 tumors grown in syngeneic TNFR 1, 2 -/- (KO) and C57BL/6 (WT) mice. Tumor endothelial cells were isolated from WT and KO tumors when tumor volumes were ~180 mm^3. This was based on a stepwise immunopurification of combined tumor tissue (Seaman, S. et al. Genes that distinguish physiological and pathological angiogenesis. Cancer Cell 11, 539-54 (2007)). Tumor endothelial cells were lysed to collect total RNA and analyzed in duplicates with Affymetrix GeneChip® Mouse Genome 430 2.0 Arrays.

middle: P

first: Edwardine

last: Labay

first: Michael

middle: A

last: Beckett

first: Helena

last: Mauceri

first: Nikolai

last: Khodarev

first: Ralph

last: Weichselbaum


title: Gene expression profile of mouse breast cancer V720 cells treated with vehicle or PD 0332991

status: Public on Oct 16 2012

first: Takaomi

last: Sanda

address: 450 Brookline Ave

institute: Dana-Farber Cancer Institute

summary: D-cyclins represent components of cell cycle machinery. To test the efficacy of targeting D-cyclins in cancer treatment, we engineered mouse strains which allow acute and global ablation of individual D-cyclins in a living animal. Ubiquitous shutdown of cyclin D1 or inhibition of cyclin D associated kinase activity in mice bearing ErbB2-driven mammary carcinomas halted cancer progression and triggered tumor-specific senescence, without compromising the animals' health. Ablation of cyclin D3 in mice bearing T-cell acute lymphoblastic leukemias (T-ALL) triggered tumorspecific apoptosis. Such selective killing of leukemic cells can be also achieved by inhibiting cyclin D associated kinase activity in mouse and human T-ALL models. Hence, contrary to what one might expect from ablation of a cell cycle protein, acute shutdown of a D-cyclin leads not only to cell cycle arrest, but it also triggers tumor cell senescence or apoptosis, and it affects different tumor types through distinct cellular mechanisms. Inhibiting cyclin D-activity represents a highly-selective anticancer strategy which specifically targets cancer cells without significantly affecting normal tissues.

overall_design: Mouse breast cancer V720 cells were cultured in the presence of the CDK4/6 inhibitor PD 0332991 (PD; 1 microM) or vehicle (VO) for 24 hrs. Experiment was done in biological triplicate. A total of 6 RNA samples (3 vehicle treated and 3 PD 0332991 treated samples) were used for microarray expression analysis.

first: Yoon

middle: J

last: Choi

first: Xiaoyu

first: Per

last: Hydbring

first: Joanna

last: Stefano

first: Amanda

middle: L

last: Christie

first: Sabina

last: Signoretti

first: Thomas

last: Look

first: Andrew

last: Kung

first: Harald

last: von Boehmer

first: Piotr

last: Sicinski


title: 5AZA-induced Gene Expression in Human Breast Cancer Cell Lines and Benign Primary Mammary Epithelial Cell Cultures

status: Public on Oct 19 2012

city: Dallas

first: David

last: Euhus

state: TX

address: 5323 Harrry Hines Blvd

department: Surgery

institute: UT Southwestern Medical Center

summary:
The goal of this experiment was to identify genes that were expressed at higher levels in benign human  mammary epithelial cells than in breast cancer cell lines and that were induced by 5AZA treatment in breast cancer cell lines. Six breast cancer cell lines were selected for demethylation studies based on known tumor suppressor gene expression regulation by promoter region hypermethylation:  HCC1569 (CCND2), HCC1954 (SCGB3A1, APC, RASSF1A), MCF-7 (RAR-beta2), MDA-MB-231 (ESR1), UACC3199 (BRCA1), and BT-549 (hypermethylator phenotype).  Other than MCF10A we specifically avoided immortalized benign human mammary epithelial cell lines for this experiment as these cells frequently show tumor suppressor gene methylation (e.g. p16) and gene expression profiles that are intermediate between normal breast epithelial cells and breast cancer. Instead, we opted to test six first-passage benign human mammary epithelial cell cultures (HME) generated in serum-free media from small fragments of normal breast tissue obtained from young women undergoing fibroadenoma excision.
The 5AZA dose (0.5 microM) was selected based on evaluation of growth curves and induction of BNC1, SERPINB, and TKTL1 gene expression measured by RT-PCR in benign and malignant cells.  The breast cancer cell lines, HME cultures, and MC10A cells were treated with 0.5 microM 5AZA (Sigma-Aldrich, St. Louis, MO) in DMSO or DMSO alone for six days after which the cells were harvested, and RNA prepared  using the Illumina TotalPrep kit (AMIL1791, Life Technologies, Grand Island, NY).  Whole genome expression was assessed using the Illumina HumanWG-6-v3 chip

overall_design: Gene expression was evaluated in 6 breast cancer cell lines, 6 primary breast epithelial cell cultures, and MCF10A cells after 6 days in DMSO or DMSO plus 0.5 microM 5AZA.


title: Transcriptomic Dose Response Changes in Female Mouse and Rat Lungs following Chloroprene Exposure

status: Public on Oct 12 2012

city: RTP

first: Longlong

last: Yang

address: 6 Davis Dr.

institute: CIIT Centers for Health Research

summary: ß-chloroprene (2-chloro-1,3-butadiene), a monomer used in the production of neoprene elastomers, is of regulatory interest due to the production of multi-organ tumors in mouse and rat cancer bioassays.  A significant increase in female mouse lung tumors was observed at the lowest exposure concentration of 12.8 ppm while a small, but not statistically significant, increase was observed in female rats only at the highest exposure concentration of 80 ppm.  The metabolism of chloroprene results in the generation of reactive epoxides and the rate of overall chloroprene metabolism is highly species dependent. To identify potential key events in the mode-of-action of chloroprene lung tumorigenesis, dose response and time course gene expression microarray measurements were made in the lungs of female mice and female rats.  The gene expression changes were analyzed using both a traditional analysis of variance approach followed by pathway enrichment analysis and a pathway-based benchmark dose (BMD) analysis approach.  Pathways related to glutathione biosynthesis and metabolism were the primary pathways consistent with cross-species differences in tumor incidence and transcriptional BMD values for the pathway were more similar to differences in tumor response than were estimated target tissue dose surrogates based on the total amount of chloroprene metabolized per unit mass of lung tissue per day. The closer correspondence of the transcriptional changes with the tumor response are likely due to their reflection of the overall balance between metabolic activation and detoxication reactions whereas the current tissue dose surrogate reflects only oxidative metabolism.

overall_design: Female mice (B6C3F1/Crl) were exposed to chloroprene (CAS 126-99-8) by whole-body inhalation exposure at 0, 0.3, 2, 13, or 90 ppm.  Exposures were performed for 6 hr/day, 5 days per week.  The animals were sacrified at 5 days or 19 days (15 exposure days) post initiation of exposure. The right lung was excised and gene expression microarray analysis was performed using Affymetrix Mouse 430_2 arrays. Female rats (F344/NCrl) were exposed to chloroprene (CAS 126-99-8) by whole-body inhalation exposure at 0, 5, 30, 90, or 200 ppm.  Exposures were performed for 6 hr/day, 5 days per week.  The animals were sacrified at 5 days or 19 days (15 exposure days) post initiation of exposure. The right lung was excised and gene expression microarray analysis was performed using Affymetrix Rat 230_2 arrays.

first: Russell

last: Thomas


title: Analysis of early dendritic cell, natural killer cell and B lymphocyte responses to murine cytomegalovirus (MCMV) infection by genome-wide expression profiling

city: Marseille

first: Marc

last: DALOD

address: Parc scientifique de Luminy, Case 906

department: Dendritic cells and antiviral defense

institute: Center of Immunology of Marseille Luminy (CIML)

type:
Expression profiling by array
Third-party reanalysis

summary:
Dendritic cells (DCs) are a complex group of cells which play a critical role in vertebrate immunity. They are subdivided into conventional DC (cDC) subsets (CD11b and CD8alpha in mouse) and plasmacytoid DCs (pDCs). Natural killer cells are innate lymphocytes involved in the recognition and killing of abnormal self cells, including virally infected cells or tumor cells. DCs and NK cells are activated very early upon viral infections and regulate one another. However, the global responses of DC and NK cells early after viral infection in vivo and their molecular regulation are not entirely characterized. The goal of this experiment was to use global gene expression profiling to assess the global genetic reprogramming of DC and NK cells during a viral infection in vivo, as compared to B lymphocytes, and to investigate the underlying molecular mechanisms

This study includes data from cell sort purified DCs, NK cells and B cells isolated from the spleen of MCMV-infected mice. 2 independent replicates were made for each cell type except B cells. The control dataset for cells isolated from uninfected control animals has been previously published and is available in the GEO database as GSE9810.

The complete dataset representing: (1) the infected Samples and (2) the uninfected control Samples from Series GSE9810 (re-processed using RMA), is linked below as a supplementary file.

overall_design: Comparison of the gene expression programs of wild-type spleen leukocyte subsets, including plasmacytoid DCs, CD8alpha conventional DCs,  CD11b conventional DCs and NK cells, isolated from MCMV-infected versus control animals.

first: T

last: VU MANH

first: M

first: K

last: CROZAT

last: BARANEK

first: N

last: ZUCCHINI

first: SH

last: ROBBINS


title: Remote ischemic preconditioning in on-pump coronary artery bypass graft surgery

city: Edmonton

first: Eliana

last: Lucchinetti

address: HMRC 408

country: Canada

institute: University of Alberta

summary: In this placebo-controlled randomized controlled trial, we tested whether remote ischemic preconditioning (RIPC) elicited by four 5-minute cycles of 300 mmHg of cuff inflation/deflation of the lower limb would reduce myocardial necrosis in isoflurane-anesthetized patients undergoing on-pump coronary artery bypass graft surgery. Secondary outcomes were the perioperative release of the biomarkers NTproBNP, hsCRP, S100, atrial transcriptional profiles, and short- and long-term clinical outcomes. RIPC with concomitantly applied isoflurane did not affect the release of biomarkers or clinical outcome. NTproBNP release correlated with isoflurane- but not RIPC-induced transcriptional changes.

overall_design: For eleven randomly selected patients from each group (RIPC/CTL=no RIPC) two atrial samples were collected, one at the time of cannulation (T1) and one fifteen min after releasing the cross clamp (T2). The samples were immediately frozen in liquid nitrogen and later used for RNA isolation and subsequent microarray hybridization. Gene-level analysis was performed. the results of exon-level analysis will be published separately (only preliminary results available so far).

first: Michael

last: Zaugg


title: Pancreatic gene expression associated with cerulein induced chronic pancreatitis in mice

status: Public on Oct 10 2012

city: Saint Louis

first: Audrey

last: Watson

state: Missouri

address: 1100 South Grand

institute: Saint Louis University

summary: A frequently used experimental model of chronic pancreatitis (PC) recapitulating human disease is repeated injection of cerulein to mice. We found that two common substrains of C57BL/6 , C56BL/6J (Jackson) and C57BL/6NHsd (Harlan), exhibit different degree of CP with C57BL/6J beeing more susceptible to repetitive cerulein induced CP. The goal of this study was to identify genes associated with CP and also to identify genes differentially regulated between two substrains as candidates for the CP progression.

overall_design: RNAs were isolated from the pancreas of 8-week old Jackson and Harlan mice after the cerulein induction of chronic pancreatitis and hybridized on Affymetrix microarrays. Saline injected mice were used as controls. Three mice from each experimental and control groups were used in the experiment.


title: SRC-2 Coactivator Deficiency Decreases Functional Reserve in Response to Pressure Overload of Mouse Heart

status: Public on Oct 13 2012

city: Houston

first: Erin

last: Reineke

address: One Baylor PLaza

institute: Baylor College of Medicine

summary: A major component of the cardiac stress response is the simultaneous activation of several gene regulatory networks.  Interestingly, the transcriptional regulator steroid receptor coactivator-2, SRC-2 is often decreased during cardiac failure in humans. We postulated that SRC-2 suppression plays a mechanistic role in the stress response and that SRC-2 activity is an important regulator of the adult heart gene expression profile. Genome-wide microarray analysis, confirmed with targeted gene expression analyses revealed that genetic ablation of SRC-2 activates the “fetal gene program” in adult mice as manifested by shifts in expression of a) metabolic and b) sarcomeric genes, as well as associated modulating transcription factors. While these gene expression changes were not accompanied by changes in left ventricular weight or cardiac function, imposition of transverse aortic constriction (TAC) predisposed SRC-2 knockout (KO) mice to stress-induced cardiac dysfunction.  In addition, SRC-2 KO mice lacked the normal ventricular hypertrophic response as indicated through heart weight, left ventricular wall thickness, and blunted molecular signaling known to activate hypertrophy. Our results indicate that SRC-2 is involved in maintenance of the steady-state adult heart transcriptional profile, with its ablation inducing transcriptional changes that mimic a stressed heart. These results further suggest that SRC-2 deletion interferes with the timing and integration needed to respond efficiently to stress through disruption of metabolic and sarcomeric gene expression and hypertrophic signaling, the three key stress responsive pathways.

overall_design: For microarray analysis, 250ng of RNA isolated from total heart (RNeasy kit, Qiagen) for each sample was labeled using the new standard Affymetrix linear amplification protocol using the 3' IVT Express Kit. This was reverse-transcribed and cRNA was produced and biotinylated via in vitro transcription. A hybridization cocktail containing Affymetrix spike-in controls and 15 μg fragmented, labeled cRNA was loaded onto a GeneChip® Mouse 430 2.0 array.  The array was hybridized for 16 hours at 45°C with rotation at 60 rpm then washed and stained with a strepavidin, R-phycoerythrin conjugate stain using the FS 450_0001 Fluidics protocol setting.  Signal amplification was done using biotinylated antistreptavidin.  The stained array was scanned on the Affymetrix GeneChip® Scanner 3000.  The images were analyzed and quality control metrics recorded using Affymetrix Command Console v3. Experiments were run using Affymetrix MG 430 2.0 chip with 45,101 probesets representing 20,757 unique genes. There were 8 experiments in 2 groups: WT-unstressed – 4 experiments, and KO-unstressed – 4 experiments. QC parameters for all experiments were within the acceptable limits. We used the following software packages for data QC, statistical analysis and presentation of the results: Affymetrix Expression Console (www.affymetrix.com), Partek (www.partek.com), BRB Array Tools (linus.nci.nih.gov/BRB-ArrayTools.html), and dChip (biosun1.harvard.edu/complab/dchip).    Expressions were estimated using the RMA (Multi-Array Analysis) method [38] with Partek software. Differentially expressed genes were found using the RVM (Random Variance Model) t-test, which is designed for small sample size experiments [39]. We used BRB Array Tools software, developed by Dr. Richard Simon and the BRB-ArrayTools Development Team. All genes were included in the comparison. For the genes represented by more than one probeset, we used the most highly expressed probeset. The cutoffs for differentially expressed genes were False Discovery Rate (FDR) = 0.05 [40].


title: Sense exon profiling across human, mouse, and rat

city: Brookings

first: Maurice

last: Ling

department: Mathematics and Statistics

institute: South Dakota State University

summary: Transcription profiling of sense transcripts of 10 tissues each from human, mouse, and rat.

sample_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: We profiled the sense transcription level of 10 tissues each from human, mouse, and rat. Only Affymetrix core probesets were used. Two technical replicates per sample.


title: The expression level of microRNA in CTGF-overexpressed SAS cell line

city: Taipei

first: Muh-Hwa

address: No.155, Sec.2, Li-Nong Street

department: Institute of Clinical Medicine

country: Taiwan

institute: National Yang-Ming University

summary: To screen the microRNA regulated by Connective tissue growth factor (CTGF)

overall_design: Establish stable transfectants of pcDNA3-CTGF in SAS cells and analyze the miRNA expression level of  by microRNA microarray. SAS transfected with pcDNA3 was used as a control experiment.

first: Cheng-Chi

last: Chang


title: Ulipristal and Progesterone Receptor

status: Public on Oct 04 2012

city: Urbana

first: Shanmugasundaram

last: Nallasamy

address: 2001 S Lincoln Ave

department: Comparative Biosciences

institute: University of illinois at Urbana-Champaign


title: Antisense exon profiling across human, mouse, and rat

summary: Transcription profiling of antisense transcripts of 10 tissues each from human, mouse, and rat.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: We profiled the antisense transcription level of 10 tissues each from human, mouse, and rat. Only Affymetrix core probesets were used. Two technical replicates per sample. Reference for protocol: Ge, X., Rubinstein, W.S., Jung, Y.C., and Wu, Q. (2008). Genome-wide analysis of antisense transcription with Affymetrix exon array. BMC Genomics 9, 27.


title: Sense and antisense exon profiling across human, mouse, and rat

summary:
Transcription profiling of sense and antisense transcripts of 10 tissues each from human, mouse, and rat.

This SuperSeries is composed of the SubSeries listed below.

overall_design: We profiled the sense and antisense transcription level of 10 tissues each from human, mouse, and rat. Only Affymetrix core probesets were used. Two technical replicates per sample. Reference for protocol: Ge, X., Rubinstein, W.S., Jung, Y.C., and Wu, Q. (2008). Genome-wide analysis of antisense transcription with Affymetrix exon array. BMC Genomics 9, 27.

first: Yuguang

last: Ban

first: Xijin

last: Ge


title: Gene expression profiling of ovaries collected from mice treated with or without Ulipristal

summary: Ulipristal acetate (UPA), also referred to as VA/CDB-2914, is a new and promising emergency contraceptive. It is a selective progesterone receptor modulator (SPRM) that has been approved in Europe and the USA for emergency contraception.

overall_design: To experimentally induce ovulation, the immature CD-1 mice (24–28 d old) were injected ip with 5 IU of PMSG and 48 h later by 5 IU of hCG.  Two hour after hCG treatment, mice were administered with UPA/CDB or vehicle/OIL. Ovaries were collected at 11 h and total RNA was analyzed using Affymetrix mouse arrays

first: J

last: Kim

first: Indrani

middle: C

last: Bagchi

first: Milan

middle: K


title: ZR-75-1 microarray expression data

status: Public on Oct 03 2012

city: Woodville South

first: Grant

last: Buchanan

state: South Australia

address: 28 Woodville Road

institute: Basil Hetzel Institute for Translational Health Research, University of Adelaide

summary:
Testing the hormonal response of ZR-75-1 cells to estrogen, androgens, and a combination of both homones, with view determining the crosstalk between the transcriptional programs mediated by these hormones in breast cancer cells, and comparison with matched ChIP sequencing data for AR and ERalpha.
Data analysis demonstrated reciprocal interference between 5α-dihydrotestosterone (DHT)- and estradiol (E2)-induced transcriptional programs. Specifically, regulation of 26% of E2 and 15% of DHT target genes was significantly affected by cotreatment with the other hormone, in the majority of cases (78-83%) antagonistically. Pathway analysis suggested that DHT co-treatment, for example, depleted E2-regulted pathways in cell survival and proliferation.

overall_design: Total RNA was extractd from luminal-like breast cancer ZR-75-1 cells in quadruplicate after treatment for 16h with 10nM of E2, DHT or E2+DHT.

first: Eleanor

last: Need


title: Gene expression profiling  during interference with PPAR gamma signaling in thoracic aorta

city: Iowa City

first: Henry

last: Keen

state: IA

department: Pharmacology

institute: University of Iowa

summary: Pharmacological activation of the transcription factor PPAR gamma lowers blood pressure and improves glucose tolerance in humans.  In contrast, naturally occurring mutations (e.g., P467L, V290M) in the ligand binding domain of PPAR gamma in humans leads to severe insulin resistance and early-onset hypertension. Experimental evidence, including whole genome expression profiling, suggests that these mutant versions of PPAR gamma act in a dominant negative manner. Because PPAR gamma is expressed in a variety of cell types and tissues, we generated a transgenic mouse model (SP467L) specifically targeting dominant negative PPAR gamma to the vascular smooth muscle cells in order to determine the action of PPAR gamma in the blood vessel independent of its systemic metabolic actions.   In the data set provided herein, we examined the gene expression profile in thoracic aorta from SP467L mice and their control littermates using the Affymetrix Mouse Genome 430 2.0 array.

overall_design: We generated transgenic mice specifically targeting expression of mutant dominant negative human PPAR gamma (P467L) to vascular smooth muscle using a smooth muscle-specific promoter (smooth muscle myosin heavy chain or SMMHC).  Thoracic aortas were isolated from male transgenic mice and corresponding non-transgenic littermate controls. Total RNA was prepared using conventional methods and quality was assessed using the Bioanalyzer 2100 (Agilent Technologies). For the microarray hybridizations, 2 samples from control mice and 3 samples from transgenic mice were used. Each sample was an independent biological replicate generated by pooling total RNA from 6-8 separate mouse aortas. All procedures were conducted at the University of Iowa DNA Core facility using standard Affymetrix protocols. In brief, approximately 3-5 ug of total RNA was used as input to a one-step amplification procedure to generate biotin-labeled RNA fragments for hybridization to the Affymetrix Mouse Genome 430 2.0 array.

first: Curt

middle: D

last: Sigmund


title: Expression Profiles of E11.5 Mouse Optic Fissure

status: Public on Oct 02 2012

city: Kansas City

first: Shuyi

last: Chen

state: MO

institute: Stowers Institute for Medical Research

summary: Mice that are mutant for both Fgfr1 and Fgfr2 specifically in the developing retina develop coloboma. To analyze the transcripts that are affected by defective FGF signaling, we micro-dissected the optic fissure region from the control and FGFR condtional mutant mice and did microarray analysis.

overall_design: E11.5 control and Six3Cre+; Fgfr1fx/fx;Fgfr2 fx/fx optic fissures are dissected using laser-assisted micro-dissection microscope, RNAs are extracted and labelled and hybridyzed to chips

first: Ting

last: Xie


title: CWRU Circulating miRNAs in Breast Cancer

city: Cleveland

first: Cheryl

last: Thompson

state: Ohio

address: 10900 Euclid Ave.

institute: Case Western Reserve University

summary: Study investigating the role of miRNAs in breast cancer detection

overall_design: miRNA extracted from plasma on 20 breast cancer patients, 20 controls, 20 post-resection breast cancer patients and 10 lung/colorectal cancer patients, miRNA quanitification using Illumina microarray

first: Rom

last: Leidner


title: Interference of PPAR gamma signaling in thoracic aorta

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

overall_design: Refer to individual Series


title: Serial gene expression profiling in the liver of Pdgf-c Tg mice that developed hepatic fibrosis and tumors

city: Kanazawa

first: Masao

last: Honda

address: Takara-Machi 13-1

department: Gastroenterology

institute: Kanazawa University

summary:
Over expression of PDGF-C in mouse liver resulted in the progression of hepatic fibrosis, steatosis and the development of HCC; this mouse model closely resembles the human HCC that is frequently associated with hepatic fibrosis.
Peretinoin (generic name; code, NIK-333), developed by the Kowa Company, (Tokyo, Japan), is an oral acyclic retinoid (ACR) with a vitamin A-like structure that targets the retinoid nuclear receptor. Peretinoin effectively inhibits the progression of hepatic fibrosis and tumors in Pdgf-c Tg mice. Gene expression profiling was evaluated during the progression of hepatic fibrosis and tumors.

overall_design: After weaning at week 4, Pdgf-c Tg or non-transgenic WT mice were fed a basal diet or a diet containing+0.06% peretinoin respectively. At week 20, mice were sacrificed for the analysis of progression of hepatic fibrosis. At week 48, mice were sacrificed for the analysis of the development of hepatic tumors.

first: Hikari

last: Okada

first: Jean

last: Campbell

first: Yoshio

last: Sakai

first: Taro

last: Yamashita

first: Tatsuya

first: Kuniaki

last: Arai

first: Eishiro

last: Mizukoshi

first: Akito

first: Yuuki

last: Takebuchi

first: Kazuhiro

last: Hata

first: Takayoshi

last: Shirasaki

first: Mikiko

last: Nakamura

first: Hajime

last: Sunakozaka

first: Takuji

last: Tanaka

first: Nelson

last: Fausto

first: Shuichi

last: Kaneko


title: The Mediator MED23 plays opposing roles in directing smooth muscle cell and adipocyte differentiation

status: Public on Oct 01 2012

city: Seoul

first: Jiyeon

last: Park

address: 222, Banpo-daero

department: Catholic Center for Precision Medicine Research

country: South Korea

institute: The Catholic University of Korea

summary: We examined how MED23 regulates SRF-targeted genes by comparing WT and Med23 KO mouse embryonic fibroblasts (MEFs) in the presence or absence of serum-stimulation (for 30 and 90 min). To investigate whether MAL antagonizes MED23 in the adipocyte lineage program, we compared the gene expression changes resulting from Mal overexpression (oxMal) and Med23 deficiency (siMed23) in 10T1/2 cell.

overall_design: In MEF cells, we examined SRF-dependent gene expression in three time points (0, 30, 90min) and two conditions (WT and KO). In 10T1/2 cells, we used three treatment conditions (Mal overexpression, Med23 knockdown, and treatment of both Mal overexpression and Med23 knockdown) with control (no treatment).

first: Jing-wen

last: Yin

first: Ji

middle: Y

first: Bin

last: Tian

first: Gang

last: Wang


title: Global Transcriptional Analysis of Nuclear Reprogramming in the Transition from MEFs to iPSCs

city: guangzhou

first: zhenwei

last: song

address: beisan road

institute: sun yat-sen university

summary: Here, we focused on the intermediate stages of SCR by comparing the somatic cell line induced by OCT4, SOX2, and KLF4 (OSK) for 7 days with mouse embryonic fibroblasts (MEFs), iPSCs, and embryonic stem cells (ESCs). Transcriptional profiles of these four cell lines were analyzed by microarray, and we found that the transition process from day 7 to the formation of iPSCs is crucial for SCR and that the reverse expression patterns can provide more candidate markers to distinguish ESCs and somatic cells iPSC. Data confirmed that the viral infection results in defense innate immunity, DNA damage, and apoptosis in MEFs, which slows down cell proliferation and immortalization to inhibit SCR. Although SCR is initiated by OSK, the p53 signaling pathway can affect the transcriptional regulatory networks through cell cycle and genomic instability as a powerful core node.

overall_design: MEFs were derived from embryonic day 13.5 C57BL6 mice embryos. Cell line day7 is MEF induced by OCT4, SOX2, and KLF4 (OSK) for 7 days with mouse embryonic fibroblasts (MEFs), iPSCs, and embryonic stem cells (ESCs).

first: Fulu

last: Dong

first: Zhenwei

last: Song

first: Youde

last: Lu

first: Chunlei

first: BaoChun

last: Jiang

first: Baole

last: Zhang

first: Peiqing

last: Cong

first: Hongyan

last: Sun

first: Fangxiong

last: Shi

first: Honglin

last: Liu