title: Role of the reprogramming factors in inducing pluripotency

status: Public on Jan 28 2009

first: Kathrin

last: Plath

address: 615 Charles E. Young Drive South

department: Biological Chemistry

type: Genome binding/occupancy profiling by array

summary: Induced pluripotent stem (iPS) cells can be obtained from fibroblasts by expression of Oct4, Sox2, Klf4, and c-Myc. To determine how these factors induce this change in cell identity, we carried out genomewide promoter analysis of their binding in iPS and partially reprogrammed cells. Most targets in iPS cells are shared with ES cells and the factors cooperate to activate the ES-like expression program. In partially reprogrammed cells, genes bound by c-Myc have achieved a more ES-like binding and expression pattern. In contrast, genes that are co-bound by Oct4, Sox2, and Klf4 in ES cells and that encode pluripotency regulators show severe lack of both binding and transcriptional activation. Among the factors, c-Myc has a pivotal effect on the initiation of the ES transcription program, including the repression of fibroblast-specific genes. Our analysis begins to unravel how the four factors function together and suggests a temporal and separable order of their effects during reprogramming.

overall_design:
For genome wide expression analysis:
A.  ES/iPS/partial iPS cells were analyzed in duplicates from 2 different cell lines (e.g four samples per cell type)
B.  tet inducible factors (tetO/tetS/tetC/tetK) were analyzed individually, a control was an uninduced tet line.
C.  OCK expression was performed in duplicate with 2 different clones.

For genome wide location analysis (ChIP-chip):
Oct4/Sox2/c-Myc/Klf4 were performed with biological duplicates (2 clonally isolated iPS/partial iPS lines and ES cells were performed with v6.5 and E14 cell lines)

first: Rupa

last: Sridharan

first: Jason

last: Tchieu

first: Mike

last: Mason

first: Steve

last: Horvath

first: Qing

last: Zhou


title: Expression data from BAT and liver of the KRAP deficient mice

status: Public on Jan 22 2009

city: Fukuoka

first: takahiro

last: fujimoto

state: Fukuoka

address: 7-45-1 nanakuma,jonan-ku

department: Faculty of medicine,Department of cell biology

country: Japan

institute: fukuoka university

summary:
KRAP (Ki-ras-induced actin-interacting protein) is a cytoskeleton-associated protein and a ubiquitous protein among tissues, originally identified as a cancer-related molecule.  KRAP-deficient (KRAP-/-) mice show enhanced metabolic rate, decreased adiposity, improved glucose tolerance, hypoinsulinemia and hypoleptinemia.  KRAP-/- mice are also protected against high-fat diet-induced obesity and insulin resistance despite of hyperphagia.

This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Gene expression comparisons of T helper cells

status: Public on Jan 27 2009

city: Birmingham

first: Dongquan

last: Chen

state: AL

address: 1717 11th Ave South

department: Medicine

country: USA

institute: Univ of Alabama at Birmingham

summary: This is to compare the gene expression profile of Th1 and Th17 cells.

overall_design: Two replicates (rep1, rep2) in two groups (Th1, Th17).

first: Casey

middle: T

last: Weaver


title: Oligodendroglial precursor cell line [Oli-neu] undergoing differentiation into myelin basic protein-producing cells

status: Public on Jan 31 2009

city: Geneva

first: Marc

last: Lamarine

state: Geneva

address: 9 Chemin des Mines

country: Switzerland

institute: Merck Serono S.A. · Geneva

summary:
Inadequate remyelination of brain white matter lesions has been associated with a failure of oligodendrocyte precursors to differentiate into mature, myelin-producing cells. In order to better understand which genes play a specific role in oligodendrocyte differentiation we performed time dependent, genome-wide gene expression studies of mouse Oli-neu cells as they differentiate into myelin basic protein-producing cells, following treatment with three different agents. Our data indicate that different inducers activate distinct pathways that ultimately converge into the differentiated state where regulated gene sets overlap maximally.
In order to also gain insight into the functional role of genes that are regulated in this process, we silenced 88 of these genes using siRNA, and identified multiple repressors of spontaneous differentiation of Oli-neu, most of which were confirmed in rat primary oligodendrocyte precursors cells. Among these repressors were CNPase, a well-known myelin constituent, and three phosphatases, each known to negatively control MAP kinase cascades. We show that a novel inhibitor for one of the identified genes, dual-specificity phosphatase DUSP10/MKP5, was also capable of inducing oligodendrocyte differentiation in primary oligodendrocyte precursors. Oligodendrocytic differentiation feedback loops may therefore yield pharmacological targets to treat disease related to dysfunctional myelin deposition

Keywords: time course

overall_design: triplicates for  3 times points 10h, 24h, 72h in  6 conditions, Forskolin, Insulin, Dexamethasone, Retinoic Acid, PD174265, Untreated. Arrays were done in two distinct experiments 1 and 2. Some replicates are missing because of lab operating issues

first: Rosanna

middle: P

last: Gobert

first: Lara

last: Joubert

first: Marie-Laure

last: Curchod

first: Catherine

last: Salvat

first: Isabelle

last: Foucault

last: Jorand-Lebrun

first: Hélène

last: Peixoto

first: Chloé

last: Vignaud

first: Christèle

last: Frémaux

first: Thérè

last: se Jomotte

first: Bernard

last: Françon

first: Chantal

last: Alliod

first: Lilia

last: Bernasconi

first: Hadi

last: Abderrahim

first: Dominique

last: Perrin

first: Agnes

last: Bombrun

first: Francisca

last: Zanoguera

first: Christian

last: Rommel

first: Rob

middle: H

last: van Huijsduijnen


title: Mouse mpkCCD cells, Rat Kidney Proximal Tubule, and Rat Kidney Medullary Thick Ascending Limb

status: Public on Jan 26 2009

city: Taipei

first: Ming-Jiun

last: Yu

address: Rm 816, No. 1 Ren-Ai Road Section 1

department: Institute of Biochemistry and Molecular Biology

country: Taiwan

institute: National Taiwan University College of Medicine

summary:
A series contains a set of transcript intensity values measured by Affymetrix microarray.

This SuperSeries is composed of the SubSeries listed below.

sample_organism:
Mus musculus
Rattus norvegicus

platform_organism:
Mus musculus
Rattus norvegicus

overall_design:
We used a systems biology-based approach to investigate the basis of cell-specific expression of the water channel aquaporin-2 (AQP2) in the renal collecting duct. Computational analysis of the 5’-flanking region of the AQP2 gene (GenomatixTM) revealed two conserved clusters of putative transcriptional regulator (TR) binding elements (BEs) at -513 bp
(corresponding to SF1, NFAT and FKHD TR families) and -224 bp(correspnding to AP2, SRF, CREB, GATA, and HOX TR families). Three other conserved motifs corresponded to ETS, EBOX, and RXR TR families. To identify TRs that potentially bind to these BEs, we carried out mRNA profiling (Affymetrix) in mouse mpkCCDc14 collecting duct cells, revealing expression of 25 TRs that are also expressed in native inner medullary collecting duct (“IMCD Transcriptome Database”). One showed a significant positive correlation with AQP2 mRNA abundance among mpkCCD subclones (Ets1) and two showed a significant negative correlation (Elf1 and an orphan nuclear receptor Nr1h2). Transcriptomic profiling in native proximal tubules (PT), medullary thick ascending limbs (MTAL) and IMCDs from kidney identified 14 TRs (including Ets1 and HoxD3) expressed in the IMCD but not PT or TAL (candidate AQP2 enhancers), and 5 TRs (including HoxA5, HoxA9 and HoxA10) expressed in PT and TAL but not in IMCD (candidate AQP2 repressors). In luciferase reporter assays, overexpression of three ETS family TRs transactivated the mouse proximal AQP2 promoter. The results implicate ETS family TRs in cell-specific expression of AQP2 and point to HOX, RXR, CREB and GATA family TRs as playing likely additional roles.


title: mRNP-mRNA Association Map (Tier I - G10, HuR, Imp, PABP)

status: Public on Jan 24 2009

city: Rensselaer

first: Sridar

middle: V

last: Chittur

state: NY

address: One Discovery Drive, CRC 342G

department: Center for Functional Genomics

institute: SUNY-University at Albany

summary:
In eukaryotic organisms gene regulatory networks require an additional level of coordination that links transcriptional and post-transcriptional processes. Messenger RNAs have traditionally been viewed as passive molecules in the pathway from transcription to translation. However, it is now clear that RNA-binding proteins play a major role in regulating multiple mRNAs in order to facilitate gene expression patterns. These tracks show the associated mRNAs that co-precipitated with the targeted RNA-binding proteins HuR, IMP-1 and PABP using RIP-Chip (Ribonomic) profiling

Keywords: RIP-Chip

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and  http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: Replicates for IPs comparable IP-inputs performed independently in each of the ENCODE Tier 1 cell lines.


title: Expression data from liver of the KRAP deficient mice

first: takahiro

last: fujimoto

summary: KRAP (Ki-ras-induced actin-interacting protein) is a cytoskeleton-associated protein and a ubiquitous protein among tissues, originally identified as a cancer-related molecule.  KRAP-deficient (KRAP-/-) mice show enhanced metabolic rate, decreased adiposity, improved glucose tolerance, hypoinsulinemia and hypoleptinemia.  KRAP-/- mice are also protected against high-fat diet-induced obesity and insulin resistance despite of hyperphagia.

overall_design: Total RNA was extracted from livers of three pairs of littermates (KO1 vs. WT1, KO2 vs. WT2 and KO3 vs. WT3) fed normal chow.

first: midori

last: koyanagi

first: keiko

last: doi

first: toshiyuki

last: tsunoda

first: senji

last: shirasawa


title: Expression data from BAT of the KRAP deficient mice

overall_design: Total RNA was extracted from BAT of three pairs of littermates (KO1 vs. WT1, KO2 vs. WT2 and KO3 vs. WT3) fed normal chow.


title: MicroRNAs as modulators of smoking-induced gene expression changes in human airway epithelium

status: Public on Jan 29 2009

city: Gaithersburg

first: Sriram

last: Sridhar

state: MD

address: 1 MedImmune Way

department: Translational Medicine

institute: MedImmune

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

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

platform_organism:
Caenorhabditis elegans
Drosophila melanogaster
Danio rerio
Homo sapiens
Mus musculus
Rattus norvegicus


title: Differential gene expression in ADAM10 over-expressing transgenic mice

city: München-Neuherberg

first: Dietrich

last: Trümbach

address: Ingolstädter Landstraße 1

department: Institute for Developmental Genetics

country: Germany

institute: Helmholtz Zentrum München German Research Center for Environmental Health

summary:
In a transgenic mouse model of Alzheimer disease (AD), cleavage of the amyloid precursor protein (APP) by the α-secretase ADAM10 prevented amyloid plaque formation and alleviated cognitive deficits. Furthermore, there was a positive influence of ADAM10 over-expression on neurotransmitter-specific formation of synapses and on synaptic plasticity.
To assess the influence of ADAM10 on the gene expression profile in the brain we performed microarray analysis using RNA isolated from brains of five month old mice over-expressing either the α-secretase ADAM10 or a dominant-negative mutant (dn) of this enzyme. As compared to non-transgenic wild-type mice, 355 genes were found to be differentially expressed in ADAM10 transgenic mice and 143 genes in dnADAM10 mice. A higher number of genes was found to be differentially regulated in double-transgenic mouse strains additionally expressing the human APP V717I mutant (APP[V717I]). Thus, α-secretase cleavage of over-expressed APP[V717I] alters CNS gene expression additionally.
Keywords: genetic modification

overall_design:
We performed microarray analysis with cDNA transcribed from total RNA of brains from five month old mice. Mono-transgenic ADAM10 as well as dnADAM10 mice were investigated in comparison to non-transgenic FVB/N wild-type mice (n = 3 females), to analyze the influence of the a -secretase ADAM10 or its catalytically inactive form (dnADAM10) on the gene expression profile of the CNS. To elucidate the effect of ADAM10 and dnADAM10 on gene expression we compared samples derived from double-transgenic ADAM10/APP[V717I] and dnADAM10/APP[V717I] mice to those from mono-transgenic APP[V717I] mice (n = 3 females and n = 3 males). At the age of 5 months, APP[V717I] show cognitive deficits, whereas amyloid plaque formation occurs several months later (Moechars et al., 1999). Both were investigated in order to examine an influence of sex.

ChipInspector carries out significance analysis on the single probe level.  Normalized probe set level data not provided for individual Sample records. Processed data is available on Series record.

first: Claudia

last: Prinzen

first: Wolfgang

last: Wurst

first: Kristina

last: Endres

first: Rolf

last: Postina

first: Falk

last: Fahrenholz


title: Gene expression profiles of E15.5 cap mesenchyme isolated from Six2 transgenic mice using FACS. (GUDMAP Series ID: 23)

status: Public on Jan 16 2009

city: Edinburgh

first: GUDMAP

last: Developers

address: Crewe Road

country: United Kingdom

institute: IGMM MRC Human Genetics Unit

summary:
The long term objective is to create an encyclopedia of the expression levels of all genes in multiple components of the developing kidney. The central thesis is straightforward. The combination of fluorescent activated cell sorting (FACS) plus microarray analysis offers a powerful, efficient and effective method for the creation of a global gene expression atlas of the developing kidney. Microarrays with essentially complete genome coverage can be used to quantitate expression levels of every gene in FACS isolated components of the developing kidney. The ensuing rapid read-out provides an expression atlas that is more sensitive, more economical and more complete than would be possible by in situ hybridizations alone.

Keywords: Comparison of kidney components.

overall_design: At different developmental time points we isolate discrete elements of the kidney by using fluorescent activated cell sorting (FACS) and then define their gene expression profiles with microarrays.

first: Steve

last: Potter

first: Eric

last: Brunskill


title: Loss of Caveolin-3 Induces the Development of a Lactogenic Microenvironment

city: Philadelphia

first: Mathew

last: Casimiro

state: PA

address: 1035 BLSB, 233 South 10th street

department: Cancer Biology

institute: Thomas Jefferson University

summary: Here, we show that functional loss of a single gene is sufficient to confer constitutive milk protein production and protection against mammary tumor formation. Caveolin-3 (Cav-3), a muscle-specific caveolin-related gene, is highly expressed in striated and smooth muscle cells. We demonstrate that Cav-3 is also expressed in myoepithelial cells within the mammary gland. To determine if genetic ablation of Cav-3 expression affects adult mammary gland development, we next studied the phenotype(s) of Cav-3 (-/-) null mice. Interestingly, detailed analysis of Cav-3 (-/-) virgin mammary glands shows dramatic increases in ductal thickness, side-branching, and the development of extensive lobulo-alveolar hyperplasia, akin to the changes normally observed during pregnancy and lactation. Analysis by genome-wide expression profiling reveals the upregulation of gene transcripts associated with pregnancy/lactation, mammary stem cells, and human breast cancers, consistent with a constitutive lactogenic phenotype. The expression levels of three key transcriptional regulators of lactation, namely Elf5, Stat5a, and c-Myc are also significantly elevated. Experiments with pregnant mice directly show that Cav-3 (-/-) mice undergo precocious lactation. Finally, using orthotopic implantation of a transformed mammary cell line (known as Met-1), we demonstrate that virgin Cav-3 (-/-) mice are dramatically protected against mammary tumor formation. Interestingly, Cav-3 (+/-) mice also show similar protection, indicating that even reductions in Cav-3 levels are sufficient to render these mice resistant to tumorigenesis. Thus, Cav-3 (-/-) mice are a novel preclinical model to study the protective effects of a constitutive lactogenic microenviroment on mammary tumor onset and progression. Our current studies have broad implications for using the lactogenic micro-environment as a paradigm to discover new therapies for the prevention and/or treatment of human breast cancers. Most importantly, a lactation-based therapeutic strategy would provide a more natural and nontoxic approach to the development of novel anti-cancer therapies.

overall_design: All WT and Cav-3 knockout (KO) mice used in this study were in the FVB/N genetic background. 4-month old virgin female mice were utilized in a micro array study between 3 wildtype and 3 Caveolin-3 knock-out mammary glands.

first: Federica

last: Sotgia

first: Gloria

last: Bonnucelli

first: Isabelle

last: Mercier

first: Franco

last: Capozza

first: Philippe

middle: G

last: Frank

middle: C

first: Michael

last: Lisanti


title: ICSBP-mediated immune protection against BCR-ABL-induced leukemia requires the CCL6 and CCL9 chemokines

status: Public on Jan 15 2009

city: Boston

first: George

middle: Q

last: Daley

state: MA

address: 300 Longwood Avenue

institute: Children's Hospital

summary: Interferon is effective at inducing complete remissions in patients with Chronic Myelogenous Leukemia (CML), and evidence supports an immune mechanism. Here we show that the Type I Interferons (alpha and beta) regulate expression of the Interferon consensus sequence binding protein (ICSBP) in bcr-abl transformed cells and as shown previously for ICSBP, induce a vaccine-like immunoprotective effect in a murine model of bcr-abl induced leukemia. We identify the chemokines CCL6 and CCL9 as genes prominently induced by the Type I Interferons and ICSBP, and demonstrate that these immunomodulators are required for the immunoprotective effect of ICSBP expression. Insights into the role of these chemokines in the anti-leukemic response of interferons suggest new strategies for immunotherapy of CML.

overall_design: Total RNA was isolated from parental BaF3 cells as well as BaF3 cells expressing BCR-ABL, ICSBP, or both BCR-ABL and ICSBP. Using standard Affymetrix protocols the RNA samples were analyzed for gene expression using Affymetrix mouse 430_2 whole genome microarrays arrays. A threshold value of 50 was set for all genes and the list of genes filtered to include only those that had at least one Present flag ("P" flag) in one of the 4 conditions. For each gene, the ratio of its expression in a particular condition and its expression in parental BaF3 cells was determined. Only genes that had at least a 3-fold up or down change in expression were considered, leaving a set of 1431 genes for further analysis. K-means clustering with Gene cluster 3.0 was used to group these 1431 genes into 15 clusters and JavaTree was used to visualize the results.

first: Valentina

last: Nardi

first: Olaia

last: Naveiras

first: Mohammad

last: Azam


title: SCL knockouts in mouse megakaryocytes

city: Los Angeles

first: matteo

last: Pellegrini

state: CA

address: 621 Charles Young Drive South

department: MCD Biology

institute: UCLA

summary: The bHLH transcription factor stem cell leukemia gene (Scl) is a master regulator for hematopoiesis essential for hematopoietic specification and proper differentiation of the erythroid and megakaryocyte lineages. However, the critical downstream targets of Scl remain undefined. Here, we identified a novel Scl target gene, transcription factor myocyte enhancer factor 2 C (Mef2C) from Sclfl/fl fetal liver progenitor cell lines. Analysis of Mef2C-/- embryos showed that Mef2C, in contrast to Scl, is not essential for specification into primitive or definitive hematopoietic lineages. However, adult VavCre+Mef2Cfl/fl mice exhibited platelet defects similar to those observed in Scl deficient mice. The platelet counts were reduced, while platelet size was increased and the platelet shape and granularity was altered. Furthermore, megakaryopoiesis was severely impaired in vitro. ChIP-on-chip analysis revealed that Mef2C is directly regulated by Scl in megakaryocytic cells, but not in erythroid cells. In addition, an Scl independent requirement for Mef2C in B-lymphoid homeostasis was observed in Mef2C-deficient mice, characterized as severe age-dependent reduction of specific B cell progenitor populations reminiscent of premature aging. In summary, this work identifies Mef2C as an integral member of hematopoietic transcription factors with distinct upstream regulatory mechanisms and functional requirements in megakaryocyte and B-lymphoid lineages.

overall_design:
Sclfl/fl hematopoietic progenitor lines were generated from fetal liver progenitors from E12.5 Sclfl/fl embryos9 by immortalization with Hox11 retrovirus.17 Sclfl/fl progenitor cells were cultured with IL3, and a clonal line containing cells with megakaryocyte morphology and acetylcholinesterase (AchE) activity was selected. The Sclfl/fl cell line was transduced with Cre- GFP retrovirus to generate the Scl
Δ/Δ  cell line, and the Scl Δ/Δ  cell line was transduced with Scl retrovirus to re-introduce Scl expression (Scl Δ/Δ +Scl cell line). Megakaryocyte differentiation was enhanced by adding Tpo for 5 days before harvesting the cells. RNA was extracted with Trizol (Gibco BRL) and RNEasy (Qiagen) kits. Differential gene expression between Sclfl/fl, Scl Δ/Δ and Scl Δ/Δ +Scl cell lines was analyzed by Affymetrix MOE430_2 microarray in the microarray core facility at the Dana-Farber Cancer Institute.

first: Christos

last: Gekas

first: Katrin

middle: E

last: Rhodes

first: Laurraine

middle: M

last: Gereige

first: Hildur

last: Helgadottir

first: Matteo

first: Hanna

middle: K

last: Mikkola


title: Gene expression profiles of E13 bladder compartments. (GUDMAP Series ID: 24)

first: GUDMAP

last: Developers

summary:
The long term objective is to create an encyclopedia of the expression levels of all genes in multiple components of the developing bladder.  The central thesis is straightforward. The combination of microdissected tissues and FACS sorted cells plus microarray analysis offers a powerful, efficient and effective method for the creation of a global gene expression atlas of the developing urogenital system. Microarrays with essentially complete genome coverage can be used to quantitate expression levels of every gene. The ensuing rapid read-out provides an expression atlas that is more sensitive, more economical and more complete than would be possible by in situ hybridizations alone. The data submitted here delineates the gene expression profiles of the mesenchymal and epithelial compartments of the e13 mouse bladder.

Keywords: Mouse embryonic day 13 bladder mesenchyme and epithelium.

overall_design: FVB/N mice were time mated. At embryonic day 13 mice were euthanized by decapitation and the bladders were microdissected, cut just above the ureters, and treated with 20 µM EDTA for 20 minutes. Mesenchymal and epithelial compartments were then separated by rimming the bladder with a needle and harvested in RLT. Total RNA was isolated for gene expression analysis using the Affymetrix MOE430 microarray chip

first: James

last: Lessard

first: Alfor

last: Lewis


title: Hippocampal gene expression changes during age-related cognitive decline

city: Greenwood

first: Traci

middle: L

last: Pawlowski

state: SC

address: 113 Gregor Mendel Circle

department: molecular research

institute: Greenwood Genetic Center

summary: Comparison of hippocampal gene expression between normal young animals and older animals with good spatial memory and older animals with poor spatial memory

overall_design: The hippocampus from animals with good spatial memory (unimpaired) were compared to animals with poor spartial memory (impaired)

first: Linda

last: Bellush

first: Amy

middle: W

last: Wright

first: Jon

last: Walker

first: Robert

middle: A

last: Colvin

first: Matthew

middle: J

last: Huentelman


title: Expression data from Murine T cell in response to cycloheximide treatment

status: Public on Jan 10 2009

city: Livermore

first: Zhaoduo

last: Zhang

address: 7011 East Ave

department: Biosystems

institute: Sandia National Labs

summary:
Cycloheximide has been used for inhibiting protein synthesis in order to identify IL-2 direct targeted genes in T cells, but the effects of cycloheximide itself on genomewide genes are not well defined
We conducted a global analysis of cycloheximide regulated genes in mouse T cell line CTLL-2 using Affymetrix mouse genome array, and identified 213 genes differentially expressed (?1.5-fold change) in response to cycloheximide 30min after adding cylcoheximide to T cells cultured without IL-2 for 14 hours. These genes involve in a number biological processes.
Keywords: stress response

overall_design: Murine cytotoxic T lymphocyte cell line CTLL-2, derived from a C57BL/6 mouse, is an IL-2 dependent cell line. Cells were cultured in D10 medium in an incubator with 5% CO2 at 37oC to mid-log phase (~2 X 105 cells/mL), and collected by centrifugation, washed with phosphate buffered saline (PBS) (Invitrogen), resuspended at 1 X 106 cells/mL in the medium without IL-2 (IL-2 starvation) and cultured for 14 hours (No IL-2 stimulation, T0, 5 reps), followed by adding cycloheximide (20 ?g/mL) for 30min (T4-CHX, 4 reps). Total RNA were extracted from the cells and was hybridized on Affymetrix GeneChip Mouse Genome 430 2.0 Array.

first: Anthony

last: Martino

first: Jean-Loup

last: Faulon


title: Effect of BDNF on the APP transgenic mouse model of Alzheimer's disease

status: Public on Jan 23 2009

first: Giovanni

last: Coppola

address: 1524 Gonda, 695 Charles Young Drive South

department: Psychiatry and Neurology

summary:
We examined transgenic (TG) mice expressing human APP695 bearing the double Swedish (671KM>NL) and Indiana (717V>F) amyloid precursor protein (APP) mutations. Lentiviral vectors constitutively expressing BDNF-GFP under control of the CMV/ß-actin hybrid promoter or GFP alone were injected into the entorhinal cortices of TG mice bilaterally at age 6 months, a time point by which neuropathological degeneration and cell loss are established. Age-matched wild-type littermates underwent sham surgery or injection of lentivirus expressing GFP into the entorhinal cortices bilaterally.

Keywords: Treatment effect

overall_design: 26 Samples total: 4 biological replicates of APP transgenic mice BDNF treated, 4 biological replicates of APP transgenic mice GFP treated, 3 biological replicates of non-trangenic mice sham lesion and 2 biological replicates of non-transgenic mice GFP treated for both tissues: Entorhinal cortex and hippocampus.

first: A

last: Nagahara

first: D

last: Merrill

first: G

first: S

last: Tsukada

first: B

last: Schroeder

last: Shaked

first: L

last: Wang

last: Blesch

last: Kim

first: J

last: Conner

first: E

last: Rockenstein

first: M

last: Chao

last: Koo

last: Geschwind

last: Masliah

last: Chiba

last: Tuszynski


title: Small molecule inducers of pancreatic beta-cell expansion

status: Public on Jan 19 2009

city: San Diego

first: John

middle: R

last: Walker

address: 10675 John Jay Hopkins

institute: Genomics Institute of the Novartis Research Foundation

summary:
New insulin-producing pancreatic beta-cells are formed primarily by self-replication during adult life. To identify small molecules that can induce beta cell replication, a large chemical library was screened for proliferation of growth-arrested, reversibly immortalized mouse beta-cells using an automated high-throughput screening platform. A number of structurally diverse, active compounds were identified including phorbol esters, which likely act through protein kinase C, and a group of thiophene-pyrimidines that stimulate beta-cell proliferation by activating the Wnt signaling pathway. A group of dihydropyridine (DHP) derivatives was also shown to reversibly induce beta-cell replication in vitro by activating L-type calcium channels (LTCCs). Our data indicate that the LTCC agonist 2a affects the expression of genes involved in cell cycle progression and cellular proliferation. Furthermore, treatment of beta-cells with both LTCC agonist 2a and the Glp-1 receptor agonist Ex-4 showed an additive effect on beta-cell replication. The identification of small molecules that induce beta-cell proliferation suggests that it may be possible to reversibly expand other quiescent cells to overcome deficits associated with degenerative and/or autoimmune diseases.

Keywords: treatment and time course

overall_design: compound treatment and time course

first: Weidong

first: Xia

last: Tremblay

first: Jae

last: Lee

first: Xu

last: Wu

first: Peter

last: Schultz


title: Epigenetic Mechanisms Underlie T Cell Plasticity

status: Public on Jan 08 2009

city: Bethesda

first: Lai

last: Wei

address: 10 Center Dr. Room 2B47

institute: NIH/NEI/NCCAM

summary: Multipotential naïve CD4+ T cells differentiate into distinct lineages including T helper 1 (Th1), Th2, Th17, and inducible T regulatory (iTreg) cells. The remarkable diversity of CD4+ T cells begs the question whether the observed changes reflect terminal differentiation with heritable epigenetic modifications or plasticity in T cell responses. We generated genome-wide histone H3 lysine 4 (H3K4) and lysine 27 (H3K27) trimethylation maps in naïve, Th1, Th2, Th17, iTreg, and natural (n)Treg cells. We found that although modifications of signature cytokine genes (Ifng, Il4, and Il17) partially conform to the expectation of lineage commitment, critical transcription factors such as Tbx21 exhibit a broad spectrum of epigenetic states, consistent with our demonstration of T-bet and IFN-gamma induction in nTreg cells. Our data suggest an epigenetic mechanism underlying the specificity and plasticity of effector and regulatory T cells and also provide a framework for understanding complexity of CD4+ T helper cell differentiation.

overall_design: Different T helper subsets are profiled for mRNA expression.

first: Gang

first: Jinfang

last: Zhu

first: Jane

last: Hu-Li

last: O'Shea

first: Keji

last: Zhao


title: Transcriptional response in skin of mouse 24 hours after intradermal infection with Trypanosoma cruzi

status: Public on Jan 02 2009

first: Barbara

last: Burleigh

address: 665 Huntington Ave

department: Immunology and Infectious Diseases

institute: Harvard School of Public Health

summary:
To investigate the early host response triggered by three different strains of Trypanosoma cruzi at a local infection site, changes in host gene expression were monitored in a murine intradermal infection model using Affymetrix oligonucleotide arrays. Robust induction of IFN-stimulated genes (ISGs) was observed in excised skin 24 hours post-infection where the level of ISG induction was parasite strain-dependent with the least virulent strain triggering a muted IFN response. Infection of mice immunodepleted of IFNγ-producing cells or infection of IFNγ-deficient mice had minimal impact on the IFN response generated in T. cruzi infected mice. In contrast, infection of mice lacking the type I IFN receptor demonstrated that type I IFNs are largely responsible for the IFN response generated at the site of infection. These data highlight type I IFNs as important components of the innate immune response to T. cruzi the site of inoculation and their role in shaping the early transcriptional response to this pathogen.
We used microarrays to detail the local host transcriptional response to intradermal T. cruzi infection in WT mice and mice depleted of NK cells, or deficient in IFN-gamma or type I IFN responses. Additionally we compared the local host-transcriptional response generated to infection with 3 different strains of Trypanosoma cruzi (Y, Brazil, and G).

Keywords: disease state analysis

overall_design: Mice were infected by intradermal injection of 10^6 T. cruzi trypomastigotes in 100uL of saline split between 2 adjacent sites on the shaved side flank.  Control mice were injected with an equal volume of saline. 24 hours post-injection approximately 75mm^2 of skin immediately surrounding the injection site was excised and RNA was isolated from the tissue. Balb/c mice were used for most experiments and IFN-gamma KO mice were on the Balb/c background. WT 129 mice were also used as IFNAR-/- mice were on the 129 background. In total 33 arrays were performed. 7 WT (Balb/c) control, 3 Y strain infected, 3 Brazil strain infected, 3 G strain infected, 2 IFN-gamma KO control, 2 IFN-gamma KO infected, 1 NK cell depleted control, 1 NK cell depleted infected, 3 WT (129) control, 3 WT (129) infected, 3 IFNAR KO control, 3 IFNAR KO infected


title: FoxO RNAi in C2C12 cells

status: Public on Dec 31 2008

city: Berkeley

first: Ping

last: Hu

address: Hearst & Oxford

department: MCB

institute: University of California, Berkeley

summary: C2C12 cells are mouse skeletal muscle cells.  These cells were transfected with shRNA against FoxO1, FoxO3, and FoxO4.  FoxO1, FoxO3, and FoxO4 are the known paralogues expressed in this cell line.

overall_design: C2C12 cells are transfected with shRNA against FoxO1, FoxO3, and FoxO4, respectively.  Colonies were selected for the best depletion of the target FoxOs, respectively.  Cells were grown in DMEM medium.  Total RNA was extracted from each line.  Microarray analysis was performed by following the Affymetrix protocols.  The data were analyzed by GCOS system.  The target genes that we are interested in were further confirmed by qRT-PCR, reporter assay, and other biochemical and molecular biology assays.

first: Kenneth

last: Geles

first: Ji-Hye

last: Pairk

first: Ronald

last: DePinho

first: Robert

last: Tjian


title: Expression data from 3T3-MEFs derived from wild-type and SMRT RID mutant mice

status: Public on Jan 07 2009

city: La Jolla

first: Ruth

last: Yu

address: 10010 N Torrey Pines Rd

department: Gene Expression Lab

institute: Salk Institute

summary:
SMRT (silencing mediator of retinoid and thyroid hormone receptors) is recruited by numerous transcription factors to mediate lineage and signal dependent transcriptional repression.  We generated a knock-in mutation in the receptor interaction domain (RID) of SMRT (SMRTmRID) that solely disrupts its interaction with nuclear hormone receptors.  SMRTmRID-derived 3T3-MEFs display a dramatically increased adipogenic capacity and accelerated differentiation rate.  We measured global gene expression in wild-type versus SMRTmRID-derived 3T3-MEFs in the undifferentiated state to examine which pathways were altered. Our results demonstrate that SMRT-RID dependent repression is a key determinant of the adipogenic set point.

Keywords: SMRTmRID expression compared to wild-type

overall_design: 3T3 cells derived from wild-type and SMRT RID MEFs were cultured under pre-differentiated conditions prior to harvesting for RNA.

first: Russell

last: Nofsinger

last: Evans


title: Analysis of OBF-1 overexpression in early B cells

status: Public on Jan 05 2009

city: Basel

first: Edward

middle: James

last: Oakeley

address: Maulbeerstrasse 66

institute: Friedrich Miescher Institute for Biomedical Research

summary: OBF1, also known as Bob.1 or OCA-B, is a B lymphocyte-specific transcription factor which coactivates Oct1 and Oct2 on B cell specific promoters. So far, the function of OBF1 has been mainly identified in late stage B cell populations. The central defect of OBF1 deficient mice is a severely reduced immune response to T cell-dependent antigens and a lack of germinal center formation in the spleen. Relatively little is known about a potential function of OBF1 in developing B cells. Here we have generated transgenic mice overexpressing OBF1 in B cells under the control of the immunoglobulin heavy chain promoter and enhancer. Surprisingly, these mice have greatly reduced numbers of follicular B cells in the periphery and have a compromised immune response. Furthermore, B cell differentiation is impaired at an early stage in the bone marrow. A first block is observed during B cell commitment and a second differentiation block is seen at the large preB2 cell stage. The cells that succeed to escape the block and to differentiate into mature B cells have post-translationally downregulated the expression of transgene, indicating that expression of OBF1 beyond the normal level early in B cell development is deleterious. Indeed ID3, which is a negative regulator of B cell differentiation, is upregulated in the EPLM and preB cells of the transgenic mice. Furthermore ID3 promoter contains an octamer site suggesting that it is a potential OBF-1 direct target gene. These results provide evidence that OBF1 expression has to be tightly regulated in early B cells to allow efficient B lymphocyte differentiation.

overall_design: OBF-1 was overexpressed in the B cell lineage and the gene expression profiles of the early progenitors with lymphoid and myeloid developmental potential (EPLM) and Large PreB cells investigated using Affymetrix arrays

first: Alain

last: Bordon

first: Patrick

last: Matthias


title: lincRNA Expression

status: Public on Jan 01 2009

city: Cambridge

first: Mitchell

last: Guttman

address: 7 Cambridge Center

institute: Broad Institute

type: Non-coding RNA profiling by genome tiling array

summary: There is growing recognition that mammalian cells produce many thousands of large intergenic transcripts. However, the functional significance of these transcripts has been particularly controversial. While there are some well-characterized examples, the vast majority (>95%) show little evidence of evolutionary conservation and have been suggested to represent transcriptional noise. Here, we report a new approach to identifying large non-coding RNAs (ncRNAs) by using chromatin-state maps to discover discrete transcriptional units intervening known protein-coding loci. Our approach identified ~1600 large multi-exonic RNAs across four mouse cell types. In sharp contrast to previous collections, these large intervening ncRNAs (lincRNAs) exhibit strong purifying selection in their genomic loci, exonic sequences, and promoter regions – with greater than 95% showing clear evolutionary conservation. We also developed a novel functional genomics approach that assigns putative functions to each lincRNA, revealing a diverse range of roles for lincRNAs in processes from ES pluripotency to cell proliferation. We obtained independent functional validation for the predictions for over 100 lincRNAs, using cell-based assays. In particular, we demonstrate that specific lincRNAs are transcriptionally regulated by key transcription factors in these processes such as p53, NFKB, Sox2, Oc4, and Nanog. Together, these results define a unique collection of functional lincRNAs that are highly conserved and implicated in diverse biological processes.

overall_design:
lincRNA expression patterns were generated across a compendium of mouse tissues, cell types, and conditions.
lincRNA expression profiles were generated on custom NimbleGen arrays (Samples GSM346609..GSM346650) and correlated with known  protein coding genes on Affymetrix gene expression arrays (Samples GSM347910..GSM347943).

first: John

last: Rinn

first: Eric

middle: S

last: Lander


title: Gene expression following miR-30a knockdown in bipotential mouse embryonic liver (BMEL) cells

first: Joshua

last: Friedman

address: ARC 1007B, 3615 Civic Center Blvd.

department: Pediatrics

institute: University of Pennsylvania School of Medicine

summary:
The goal was to identify genes targeted by miR-30a.

Keywords: Transfection of cultured cells with antisense oligonucleotide

overall_design: RNA was isolated from BMELs tranfected with a locked nucleic acid (LNA) antisense oligonucleotide to miR-30a or with a scrambled control oligo.


title: IFNa activates dormant HSCs in vivo

city: Heidelberg

first: Andreas

last: Trumpp

address: Im Neuenheimer Feld 280

department: Division of Stem Cells and Cancer

institute: Deutsches Krebsforschungszentrum (DKFZ)

summary: Maintenance of the blood system is dependent on dormant haematopoietic stem cells (HSCs) with long-term self-renewal capacity. Upon injury these cells are induced to proliferate in order to quickly re-establish homeostasis. The signalling molecules promoting the exit of HSCs out of the dormant stage remain largely unknown. Here we show that in response to treatment of mice with interferon-alpha (IFNα), HSCs efficiently exit G0 and enter an active cell cycle. HSCs respond to IFNα treatment by increased phosphorylation of STAT1 and PKB/Akt, expression of IFNα target genes and up-regulation of stem cell antigen-1 (Sca-1). HSCs lacking either the interferon-α/β receptor (IFNAR), STAT1 or Sca-1 are insensitive to IFNα stimulation, demonstrating that STAT1 and Sca-1 mediate IFNα induced HSC proliferation. Although dormant HSCs are resistant to the anti-proliferative chemotherapeutic agent 5-FU1, HSCs pre-treated (primed) with IFNα and thus induced to proliferate are efficiently eliminated by 5-FU exposure in vivo. Conversely, HSCs chronically activated by IFNα are functionally compromised and are rapidly out competed by non-activatable IFNAR-/- cells in competitive repopulation assays. In summary, while chronic activation of the IFNα pathway in HSCs impairs their function, acute IFNα treatment promotes the proliferation of dormant HSCs in vivo. These data may help to clarify the so far unexplained clinical effects of IFNα on leukemic cells and raise the possibility for novel applications of type I interferons to target cancer stem cells.

overall_design: cDNA microarray analysis was performed on sorted Lin neg, cKit+, CD150+, CD48neg HSCs from IFNα treated (16h after treatment) and untreated (littermate) mice. Per condition 3 independent biological replicates were analysed.

first: Marieke

last: Essers

first: Sandra

last: Offner

first: William

last: Blanco-Bose

first: Zoe

last: Waibler

first: Ulrich

last: Kalinke

first: Michel

last: Duchosal


title: mRNA stability influences the temporal order of inflammatory gene induction

city: PASADENA

first: Shengli

last: Hao

address: 1200 E. California Blvd,

department: Biology Division

institute: California Institute of Technology

summary: The inflammatory response plays out over time in a reproducible and organized manner after an initiating stimulus. Here we showed that the genes activated in cultured mouse fibroblasts in response to the proinflammatory cytokine tumor necrosis factor can be divided roughly into three groups, each with different induction kinetics. Whereas differential transcription is important in determining the grouping of these genes, differential mRNA stability also exerted strong influence in some cases overriding that of transcriptional control elements on the temporal order of gene expression. mRNA transcripts expressed early after TNF stimulation have abundant AU-rich elements in their 3'-untranslated regions whereas those expressed later are contain fewer AU-rich sequences. Thus mRNA stability and transcriptional control, two intrinsic characteristics of genes, control the kinetics of proinflammatory cytokine-induced gene expression.

overall_design: The gene expression levels were monitored in the mouse embryonic cells stimulated with TNF for 0, 0.5h, 2h and 12 hours.

first: David

last: Baltimore


title: Genetic architecture of murine skin inflammation and tumor susceptibility

city: San Francisco

last: Quigley

address: 1450 Third St. Room 207

department: Helen Diller Comprehensive Cancer Center

institute: UCSF

summary:
Gene expression in self-renewing epithelial tissues is controlled by cis- and trans-activating regulatory factors that mediate responses to exogenous agents capable of causing tissue damage, infection, inflammation, or tumorigenesis.  We used network construction methods to analyze the genetic architecture of gene expression in normal mouse skin in a cross between tumor-susceptible Mus musculus and tumor-resistant Mus spretus. We demonstrate that gene expression motifs representing different constituent cell types within the skin such as hair follicle cells, haematopoietic cells, and melanocytes are under separate genetic control. Motifs associated with inflammation, epidermal barrier function and proliferation are differentially regulated in mice susceptible or resistant to tumor development. The intestinal stem cell marker Lgr5 is identified as a candidate master regulator of hair follicle gene expression, and the Vitamin D receptor (Vdr) links epidermal barrier function, inflammation, and tumor susceptibility.

Keywords: Expression Quantitative Trait Loci

sample_organism:
Mus musculus
Mus spretus
Mus musculus x Mus spretus

overall_design: A backcross was generated using male Mus spretus and female FVB/N mice; female F1 hybrids were mated with male FVB/N mice. Seventy-one backcross mice (8-12 weeks old) received a single dose of DMBA (25 µg per mouse in 200 µl acetone). Starting one week after the initiation tumors were promoted with TPA (200 µl of 10-4 M solution in acetone) twice weekly for 20 weeks. Initiation and promotion were performed on doral back skin. Normal tail skin was snap frozen when the animals were sacrificed.  Tail epidermis from completely untreated Spretus, FVB, and Spretus x FVB F1 mice was also analyzed.

first: Minh

middle: D

last: To

first: Jesús

last: Pérez-Losada

first: Jian-Hua

last: Mao

first: Hiroki

last: Nagase

last: Ginzinger

first: Allan

last: Balmain


first: BIDMC

last: GENOMICS

address: 4 BlackFan Circle

department: Genomics Center

institute: Beth Israel Deaconess Medical Center

summary:
Gene expression profile of Transgenic Adenocarcinoma of the Mouse Prostate (TRAMP) reveals murine targets for preclinical development of human prostate cancer therapy

In this study, we have generated an open source TRAMP microarray dataset to identify differentially expressed genes from human prostate cancer that have concordant expression in TRAMP tumors, and thereby represent lead targets for preclinical therapy development. Affymetrix Mouse 430 2.0 chips were used for microarrays of total RNA from 9 TRAMP tumors and 9 normal prostates (ventral and dorsolateral lobes).
Keywords: prostate cancer, TRAMP

overall_design: normal prostate vs. TRAMP

first: Kerstyn

last: Haram

first: Heidi

last: Peltier

first: Bin

last: Lu

first: Mohamed

last: Arredouani

first: Hasan

last: Out

first: Bob

last: Choy

first: Manoj

last: Bhasin

first: Meredith

last: Regan

first: Gary

last: Latham

first: Towia

last: Libermann

first: Martin

last: Sanda


title: WT vs Klf5 KO ES

city: Tsukuba

first: Kazuhiko

last: Uchida

state: Ibaraki

address: 1-1-1 Tennnoudai

department: Institute of Basic Medical Sciences

institute: University of Tsukuba

summary:
Homozygous disruption of Bteb2/Klf5, a homolog of Drosophila gap gene Krüppel, led to increased expression of various differentiation marker genes, such as Fgf5, Cdx2, and Brachyury in mouse ES cells without compromising their ability to differentiate into all three germ layers. Upon removal of LIF, Klf5-deficient ES cells showed faster differentiation kinetics than wild-type ES cells. In contrast, overexpression of Klf5 in ES cells suppressed the transcription of differentiation marker genes, and maintained pluripotency in the absence of LIF. In order to search downstream genes of Klf5, we surveyed genes implicated in ES cell proliferation by microarray analysis
Keywords: cell type comparison

overall_design: WT (clone 1 and 2) and Klf5 KO (clone 1 and 2) ES cells were maintained in ES medium + 15%FBS + LIF. Total RNAs from those ES cells were prepared using RNeasy Kit. Genes down-regulated in Klf5 KO ES cells were searched by GeneSpring software.

first: Masatsugu

last: Ema


title: Curative and beta cell regenerative effects of alpha1 antitrypsin treatment in autoimmune diabetic NOD mice

first: Terry

middle: B

last: Strom

address: 77 Avenue Louis Pasteur

summary:
In this study, we performed the gene expression analysis of the Normal, Diabetic and AAT treated NOD mice to elucidate the transcriptional changes induced by AAT. This will assist in identifying the biological processes / pathways involved in curative mechanism of AAT.
Keywords: alpha1 antitrypsin treatment

overall_design: Duplicate samples of Normal, Diabetic and AAT treated NOD mice were analyzed.

first: Maria

last: Koulmanda


title: Analysis of the retinal gene expression after hypoxic preconditioning identifies candidate genes for neuroprotection

city: Illkirch/Strasbourg

first: Wolfgang

last: Raffelsberger

address: 1 rue Laurent Fries

department: DBGS

country: France

institute: IGBMC

summary:
Neuroprotective therapies for retinal degeneration may be used to rescue retinal cells and preserve vision. Hypoxic preconditioning stabilizes the transcription factor HIF-1α in the retina and strongly protects photoreceptors in an animal model of light-induced retinal degeneration.
Our data suggest that neuroprotection after hypoxic preconditioning of the retina is the result of the differential expression of a multitude of genes which may act in concert to protect visual cells against a toxic insult.

Keywords: hypoxic preconditioning, neuroprotection, transcription-profile, retina

overall_design: In total 24 samples were analyzed on Affymetrix mouse 430.2 arrays, the samples represent different durations of regeneration (none = 0 h, 2 h, 4 h and 16 h) from hypoxic or normoxic treatments, that were tested in triplicates.

first: Markus

last: Thiersch

first: Rico

last: Frigg

first: Marijana

last: Samardzija

first: Andreas

last: Wenzel

first: Olivier

last: Poch

first: Christian

last: Grimm


title: AC61 Vector vs. pRb

city: Kyoto

first: Chiaki

last: Takahashi

state: Kyoto

address: Yosida-Knoe-cho, Sakyo-ku,

department: Molecular Oncology

institute: Kyoto University Graduate School of Medicine

summary: This experiment is to identify genes that are regulated by pRb in AC61 cells. AC61 cells were derived from a C-cell adenocarcinoma developed in an Rb+/-N-ras-/- mouse.

overall_design: AC61 cells were infected with retrovirus derived from pLXSB or pLSXB-Rb and selected with balsticidin for 36 hours. At 72 hour after infection, cells were quickly frozen.

first: Awad

last: Shamma


title: Gene Expression Profiling of the SSC-Enriched Thy1+ and SSC-Depleted Thy1- Fractions of Prepubertal Mouse Testes

status: Public on Dec 30 2008

city: University Park

first: Jon

last: Oatley

address: 324 Henning

department: Dairy and Animal Science

institute: Pennsylvania State University

summary: Self-renewal and differentiation of spermatogonial stem cells (SSCs) provides the foundation for testis homeostasis, yet mechanisms that control their functions in mammals are poorly defined. We used microarray transcript profiling to identify specific genes whose expression are augmented in the SSC-enriched Thy1+ germ cell fraction of mouse pup testes. Comparisons of gene expression in the Thy1+ germ cell fraction to the Thy1-depeleted testis cell population identified 202 genes that are expressed 10-fold or higher in Thy1+ cells. This database provided a mining tool to investigate specific characteristics of SSCs and identify novel mechanisms that potentially influence their functions.

overall_design: Testis cell fractions with different spermatogonial stem cell contents from mouse testes were collected using a modified MACS isolation. Three replicate samples were collected for each fraction from independent donor preparations. The stem cell contents of these cell fractions were determined using functional germ cell transplantation which showed a >25-fold enrichement of stem cells in the Thy1+ fration. Gene expression profiles were evaluated using DNA microarray analysis and genes expressed 10-fold or greater in the Thy1+ fraction compared to the Thy1- population were identified.

first: Melissa

first: Mary

last: Avarbock

first: John

last: Tobias

first: Ralph

last: Brinster


title: Genome wide expression analysis in AtT-20 cells following Dnmt1 knockdown

city: Stoke on Trent

first: Kevin

middle: John

last: Dudley

state: Staffordshire

address: Thornburrow Drive

department: Institute of Science and Technology in Medicine

institute: University of Keele

summary:
Efficient and sustained knockdown of DNMT1 transcript and protein was achieved using a consecutive transfection protocol in the mouse pituitary adenoma cell line, AtT-20.  Genome wide microarray analysis identified 91 transcripts that were significantly differentially expressed relative to cells treated with a non-targeting control.
Keywords: Differential expression

overall_design: AtT-20 cells were repeatedly treated with 20 nM siRNA (siDNMT1 or siNT) over an eight day period.  After eight days total RNA was extracted and prepared for microarray analysis.  The procedure was repeated three times independently.


title: Testicular germ cell tumor susceptibility genes from the consomic 129.MOLF-Chr19 mouse strain

status: Public on Jan 13 2009

city: Houston

first: Rui

last: Zhu

state: TX

address: 1515 Holcombe Blvd.

department: Genetics

institute: UT MD Anderson Cancer Center

summary: Chromosome substitution strains (CSS or consomic strains) are useful for mapping phenotypes to chromosomes.  However, huge efforts are needed to identify the gene(s) responsible for the phenotype in the complex context of the chromosome.  Here, we report the identification of candidate disease genes from a CSS using a combination of genetic and genomic approaches as well as by using knowledge about the germ cell tumor disease etiology.   We utilized the CSS, 129.MOLF-Chr 19 chromosome substitution strain (or M19), in which males develop germ cell tumors of the testes at an extremely high rate.  We are able to identify 3 protein-coding genes and 1 microRNA on chromosome 19 that have previously not been implicated to be testicular tumor susceptibility genes.   Our findings suggest that changes in gene expression levels in the gonadal tissues of multiple genes from Chr 19 likely contribute to the high TGCT incidence of the M19 strain.  Our data advances the use of CSS to identify disease susceptibility genes and demonstrates that the 129.MOLF-Chr 19 strain serves as a useful model to elucidate the genetics and biology of germ cell transformation and tumor development.

overall_design:
For gene expression profiling, we used male gonads from different developmental stages, E13.5 and PN1, from the M19 and 129 strains.  The idea was to detect the common gene expression changes in the gonads at stages when germ cells are known to transform to embryonal carcinoma (EC) cells.  E13.5 stage was chosen because tumor development is reported to start around E13.5 in 129 strains (Stevens 1973b; Stevens and Hummel 1957).   PN1 stage gonads were chosen because our studies with M19;Oct4-GFP mice, as described above, showed that both germ cells and EC cells are present at this stage suggesting that germ cell transformation may also be ongoing at this stage in the testes of M19 strain.
We also compared gene expression differences in gonads to that of embryos to determine whether gene expression differences are specific to the gonads.   Our goal was to identify gene(s) whose expression is consistently changed in the gonads at E13.5 and PN1 in the M19 as these would likely be candidate TGCT susceptibility gene(s).
Fig. 3A indicates the 3 different tissue samples collected from the M19 and 129 strains: gonads (genital ridges) dissected from male E13.5 embryos and from PN1 mice and male embryos at E13.  Because tumor incidence in M19 is approximately 80% we anticipated that gene expression changes could be masked because ~20% of cells/tissues within a sample may have normal levels of gene expression or 20% of the testes may have normal gene expression.  Moreover, the amount of RNA extracted from a single genital ridge or PN1 testis is insufficient for a microarray experiment.  To minimize the effect of individual samples and to isolate sufficient RNA for microarray analysis from these small sized gonads, we pooled RNA from multiple samples (Table 1).
Six RNA pooled samples were prepared (Fig.3A and Supplementary Table 2): E13.5 gonad RNA from males of 129 (129-GR) and M19 (M1-GR); PN1 testes RNA from 129 (129-NBT) and M19 (M1-NBT); E13.5 embryo RNA from males of 129 (129-E) and M19 (M1-E).  The six RNA samples were hybridized to six Affymetrix mouse genome genechips individually.  Hierarchical clustering analysis revealed a dendrogram in which gene expression profiles of the same tissue type clustered together (Fig. 3B).  Profiles of the gonads, E13.5 and PN1, were related more closely than to those of embryos.
Comparison of the expression profiles of E13.5 gonads from M19 and 129 revealed 10 genes with more than a 2-fold difference in expression levels (Fig. 3A and Supplementary Table 3A).  Six of the 10 genes mapped to Chr 19.  For the PN1 testes, 266 genes showed significant fold changes between the two strains and of these 13 genes mapped to Chr 19 (Fig. 3A and Supplementary Table 3C).
 For the E13.5 embryos, 35 genes showed greater than a 2-fold change in expression between the M19 and 129 and 5 out of 35 genes mapped to Chr 19 (Fig. 3A and Supplementary Table 3B).
By analyzing the data of differentially expressed genes present in the 3 samples, as well as selecting those that map to Chr 19, we were able to exclude a majority of the genes but found 3 genes in common.  The 3 genes map to Chr 19 and were found to be downregulated in the M19 strain E13.5 and PN1 gonads as well as E13.5 embryos.  These are Zfp162, D19Bwg1357e and Cox15.   These 3 genes have not been previously implicated in testicular tumorigenesis and are novel TGCT candidate susceptibility genes.

first: Yuan

last: Ji

first: Lianchun

last: Xiao

first: Angabin

last: Matin


title: Gene expression of growth plate of mouse.

status: Public on Dec 23 2008

city: Komaba

first: Shuichi

last: Tsutsumi

institute: The University of Tokyo

summary: The growth plate is histomorphologically classified into four zones {resting zone (RZ), proliferating zone (PZ), maturing zone (MZ) and hypertrophic zone (HZ)}. Gene expression profile analyses of 4 zones were performed using microarrays.

overall_design: We performed global analysis of gene expression in tibias from nine-day-old mice.  Chondrocytes layer was microdissected en-block from four anatomically distinct growth plate zones, and RNA expression was analyzed using microarrays.Chondrocytes from four anatomical zones were isolated from tibias of two mice.  The eight samples were named after the mouse (1 or 2) and the growth plate zone, such as resting zone of 1st mouse (RZ01), 2nd mouse (RZ02), proliferation zone (PZ01, PZ02), maturing zone (MZ01, MZ02) and hypertrophic zone (HZ01, HZ02).

first: Honoka

last: Isshiki

first: Kazuki

last: Sato

first: Hiroaki

last: Takano

first: Makoto

last: Kano

first: Hiroyasu

last: Ikegami

first: Hitoshi

last: Abe

first: Akihiro

last: Umezawa

first: Hiroyuki

last: Aburatani

first: Yoshiaki

last: Toyama


title: Comparison of gamma delta intraepithelial lymphocytes from DSS-treated and untreated colon

status: Public on Dec 18 2008

city: Dallas

first: Lora

middle: V

last: Hooper

address: 5323 Harry Hines Blvd.

department: Immunology

institute: The University of Texas Southwestern Medical Center at Dallas

summary: gamma delta intraepithelial lymphocytes were isolated from the colons of DSS-treated and untreated mice. Total RNAs were isolated and compared by Affymetrix DNA microarray.

overall_design: Duplicate comparisons were made between DSS-treated and untreated gamma delta intraepithelial lymphocytes.

first: Anisa

last: Ismail

first: Cassie

last: Behrendt


title: Gene expression profiles of CD4+CD25+ Tregs from NOD and B6.H2g7 mice

status: Public on Dec 19 2008

city: Boston

first: CBDM

last: Lab

department: Microbiology and Immunobiology

institute: Harvard Medical School

summary:
The NOD (nonobese diabetic) mouse strain develops a characteristic autoimmune syndrome that closely resembles human type I diabetes.  It has been suggested that NOD mice exhibit both numerical deficiency in CD4+CD25+ regulatory T cells (Treg) and reduced suppressive activity.  We compared sorted CD4+CD25+ Tregs from the spleens of 6-7 week-old female NOD and nondiabetic B6.H2g7 mice.  Tregs were 93±2% and 95±1% Foxp3+ in NOD and B6.H2g7 cells, respectively, on post-sort reanalysis.  "Conventional" CD4+CD25- T cells (Tconv) are included as reference populations.  Surprisingly, Treg "signature" is similar between the two strains, with only a few probesets that subtly deviate.
Keywords: Cell population comparison from two mouse strains.

overall_design: For each strain (NOD and B6.g7), we analyzed two populations: CD4+CD25+ Treg and CD4+CD25- Tconv cells, for a total of four distinct populations.  RNA from three mice were pooled for each replicate; there are three independent replicates for each population.  After RMA normalization, intensity values were averaged across the three replicates and analyzed.  We calculated the ratio of Treg/Tconv intensity values for each strain and compared the results.

first: Vincent

last: Auyeung

first: Markus

last: Feuerer

first: Jonathan

last: Hill

first: Phil

last: Holler

first: Wenyu

last: Jiang

first: Christopher

last: Campbell

first: Diane

last: Mathis

first: Christophe

last: Benoist


title: An essential role for the antiviral endoribonuclease, RNase-L, in antibacterial immunity.

city: blacksburg

first: Saroj

last: Mohapatra

state: VA

address: washington Street

department: VBI

institute: Virginia Tech

summary:
Type I interferons were discovered as the primary antiviral cytokines and are now known to serve critical functions in host defense against bacterial pathogens. Accordingly, established mediators of interferon antiviral activity may mediate previously unrecognized antibacterial functions. RNase-L is the terminal component of an RNA decay pathway that is an important mediator of interferon-induced antiviral activity. Here we identify a novel role for RNase-L in the host antibacterial response. RNase-L-/- mice exhibited a dramatic increase in mortality following
challenge with Bacillus anthracis and Escherichia coli; this increased susceptibility was due to a compromised immune response resulting in increased bacterial load. Investigation of the mechanisms of RNase-L antibacterial activity indicated that RNase-L is required for the optimal induction of proinflammatory cytokines that play essential roles in host defense from bacterial pathogens. RNase-L also regulated the expression of the endolysosomal protease, cathepsin-E, and endosome-associated activities, that function to eliminate internalized bacteria and may contribute to RNase-L antimicrobial action. Our results reveal a unique role for RNase-L in the antibacterial response that is mediated through multiple mechanisms. As a regulator of fundamental components of the innate immune response, RNase-L represents a viable therapeutic target to augment host defense against diverse microbial pathogens.

overall_design: two strains: wildtype and knockout, three time points: untreated, 2hours, and 8hours. three replication for each group. Totally 18 samples.

first: Xiao-Ling

last: Li

first: Heather

last: Ezelle

first: Tae-Jin

last: Kang

first: Lei

last: Zhang

first: Kari

last: Shirey

first: Janette

last: Harro

first: Jeffrey

last: Hasday

first: Oswald

last: Crasta

first: Stefanie

middle: N

last: Vogel

first: Alan

last: Cross

first: Bret

last: Hassel


status: Public on Dec 16 2008

city: Hørsholm

first: Morten

last: Lindow

address: Bøge Alle 3

department: microRNA

country: Denmark

institute: Santaris Pharma A/S

summary:
Antagonism of microRNA-122 in mice by systemically administered LNA-antimiR leads to up-regulation of a large set of predicted target mRNAs in the liver

MicroRNA-122 (miR-122) is an abundant liver-specific miRNA, implicated in fatty acid and cholesterol metabolism as well as hepatitis C viral replication. Here, we report that a systemically administered 16-nt, unconjugated LNA (locked nucleic acid)-antimiR oligonucleotide complementary to the 5' end of miR-122 leads to specific, dose-dependent silencing of miR-122 and shows no hepatotoxicity in mice. Antagonism of miR-122 is due to formation of stable heteroduplexes between the LNA-antimiR and miR-122 as detected by northern analysis. Fluorescence in situ hybridization demonstrated uptake of the LNA-antimiR in mouse liver cells, which was accompanied by markedly reduced hybridization signals for mature miR-122 in treated mice. Functional antagonism of miR-122 was inferred from a low cholesterol phenotype and de-repression within 24 h of 199 liver mRNAs showing significant enrichment for miR-122 seed matches in their 3' UTRs. Expression profiling extended to 3 weeks after the last LNA-antimiR dose revealed that most of the changes in liver gene expression were normalized to saline control levels coinciding with normalized miR-122 and plasma cholesterol levels. Combined, these data suggest that miRNA antagonists comprised of LNA are valuable tools for identifying miRNA targets in vivo and for studying the biological role of miRNAs and miRNA-associated gene-regulatory networks in a physiological context.

Keywords: compound treatment

overall_design: Female NMRI mice were treated at day 2 with either 25mg/kg antimiR-122 (SPC3372) or vehicle (saline). Mice were sacrificied at day 3, 9 and 23 and liver RNA assayed. Three biological replicates for each of the six groups.


title: Global gene expression profiles in Oct4-knockdown and Ccna2-knockdown mouse embryos.

city: Stanford

first: Bokyung

last: Choi

address: 318 Campus Drive

department: Applied physics

institute: Stanford University

summary:
Gene regulation at the maternal-embryonic transition in the pre-implantation mouse embryo is not well understood.  We knock down Ccna2 to establish proof-of-concept that antisense morpholino oligonucleotides can be used to target specific genes.  We applied this strategy to study Oct4 and discovered that Oct4 is required prior to blastocyst development.  Specifically, gene expression is altered as early as the 2-cell stage in Oct4-knockdown embryos.
Distinct subsets of genes are differentially expressed between Oct4 and Ccna2-knockdown embryos, and indicated differential functions.  Further, a large panel of genes were confirmed to be differentially-expressed in Oct4-knockdown embryos by quantitative, real time RT-PCR.

Keywords: gene knockdown

overall_design: 3-5 week old wild type F1 (C57BL6xDBA/2) females (Charles River) were superovulated by intraperitonial injections of 5 IU of pregnant mare’s serum gonadotropin (Sigma) followed by 5 IU of human chorionic gonadotropin (Sigma) 48 hours later, and mated overnight with wild type males. Mice were sacrificed by cervical dislocation 17 hours after hCG injection, and 1-cell embryos were released from oviducts. Cumulus cells were removed by hyaluronidase (Sigma) treatment and pipetting. Pre-implantation embryos at the two pronuclei stage were recovered, pooled from 3-6 females in M2 media (Chemicon International), followed by immediate cytoplasmic microinjection of gene-specific antisense morpholino oligonucleotides and culture in Human Tubal Fluid with 10% serum supplement (In-Vitro Fertilization, Inc.) microdrops under mineral oil (Sigma) in mixed gas (90% nitrogen, 5% oxygen, 5% carbon dioxide; Praxair) at 37°C, and cultured at ten embryos per 20 μL drop. Uninjected control embryos derived from the same embryo pool, and were placed in identical conditions in parallel, except that they were not injected.

first: Kira

last: Foygel

first: Sunny

last: Jun

first: Denise

last: Leong

last: Lee

first: Connie

middle: C

last: Wong

first: Elizabeth

last: Zuo

first: Michael

last: Eckart

first: Renne

last: Rejio Pera

first: Wing

middle: H

first: Mylene

last: Yao


title: Expression profiles of Embryonic stem cells derived from normal fertilization and parthenogenesis

city: Seoul

first: heebal

last: kim

address: San 56-1 Sillim-dong Gwanak-gu

country: South Korea

institute: Seoul National University

summary:
To identify the imprinting loci, we designed microarray analysis on the parthenogenetic embryonic stem cells and normal embryos. We could predict 217 imprinting domains associated with embryo development and maternal imprinting.
Keywords: Cell type comparison

overall_design: Five embryonic stem (ES) cell lines were derived from two F1 hybrid strains that were produced by mating female C57BL6 mice with male DBA2 or CBA/Ca mice. Two-week-old prepubertal female was used for follicle retrieval. All procedures for animal management, breeding, and surgery followed the standard protocols of Seoul National University, Korea. The Institutional Animal Care and Use Committee Review Board at Seoul National University approved our research proposal in April 2005 (approval number: SNU0050331-02). Three parthonogenetic ES embryo cell lines were established from parthenogenetic activation on naturally ovulated oocytes (OpB6D2-SNU-1) and in vitro-growth oocytes (FpB6CBA-SNU8 and FpB6D2-SNU2). Two normal ES embryo cell lines were derived from mating naturally ovulated female mice in estrus with male mice (NmB6D2-SNU-1) and purchased from ATCC. Detailed procedures, including establishment of ES cell lines can be found elsewhere (FpB6CBA-SNU8, FpB6D2-SNU2 and OpB6D2-SNU-1 for and NmB6D2-SNU-1 and OP1 for manuscript in preparation).

first: Sunjin

last: Moon

first: Seung

middle: P

last: Gong

first: Eun

first: Woon

first: Jeoung

last: Lim

first: Heebal

last: Kim


title: Expression data from mouse ES cells and various differentiated cell types

status: Public on Dec 12 2008

first: Xiaohua

last: Shen

address: 44 Binney Street

department: Pediatric Oncology

institute: Dana Farber Cancer Institute

summary:
We used microarrays to detail the role of Polycomb proteins including Ezh2 and Eed in maintaining ES cell identity and executing pluripotency.

Keywords: cell type and time course

overall_design: To assay the global effects of the loss of polycomb proteins (Ezh2 or Eed) in embryonic stem (ES) cells , we compared the expression profiles of homologuous Ezh2 or Eed knockout ES cells to wild-type ES cells in undifferentiated or differentiated condition.

first: Stuart

last: Orkin


title: Novartis 12 Strain Diet Sex Survey

status: Public on Dec 10 2008

city: Bar Harbor

first: Keith

last: Shockley

state: ME

address: 600 Main Street

department: Computational and Systems Biology

institute: The Jackson Laboratory

summary:
High-fat diets are associated with increased obesity and metabolic disease in mice and humans. Here we used analysis of variance (ANOVA) to scrutinize a microarray data set consisting of 10 inbred strains of mice from both sexes fed atherogenic high-fat and control chow diets. An overall F-test was applied to the 40 unique groups of strain-diet-sex to identify 15,288 genes with altered transcription. Bootstrapping k-means clustering separated these changes into four strain-dependent expression patterns, including two sex-related profiles and two diet-related profiles. Sex-induced effects correspond to secretion (males) or fat and energy metabolism (females), whereas diet-induced changes relate to neurological processes (chow) or immune response (high-fat). The full set of pairwise contrasts for differences between strains within sex (90 different statistical tests) uncovered 32,379 total changes. These differences were unevenly distributed across strains and between sexes, indicating that strain-specific responses to high-fat diet differ between sexes. Correlations between expression levels and 8 obesity-related traits identified 5,274 associations between transcript abundance and measured phenotypic endpoints. From this number, 2,678 genes are positively correlated with total cholesterol levels and associate with immune-related categories while 2,596 genes are negatively correlated with cholesterol and connect to cholesterol synthesis.
Keywords: gene expression analysis, strain comparision, effect of dietary fat, sex-specific effects

overall_design: One group of mice was fed an atherogenic high-fat (30% fat) diet containing cholic acid to increase fat uptake and another was fed a low-fat (6% fat) regular chow diet.  Males and females from both diets were studied for mouse strains 129S1/SvImJ, A/J, BALB/cJ, C3H/HeJ, C57BL/6J, CAST/EiJ, DBA/2J, I/LnJ, MRL/MpJ-Tnfrsf6lpr/J, NZB/BINJ, PERA/Ei, and SM/J. All strains were sacrificed between 11- and 13 weeks of age except for CAST and PERA, which were harvested after 50 weeks of age. CAST and PERA were subsequently removed from our analysis based on discrepant harvest age, but can be found in our database (see below). Three replicate animals were used for each combination of diet, strain, and sex, resulting in a total of 120 mice surveyed for gene expression.

first: Gary

last: Churchill

first: Beverly

last: Paigen

first: David

last: Witmer


title: Cancer Stem Cells Are Enriched In The Side-Population Cells In A Mouse Model Of Glioma

status: Public on Dec 15 2008

first: Kyuson

last: Yun

summary: The recent identification of cancer stem cells (CSCs) in multiple human cancers provides a new inroad to understanding tumorigenesis at the cellular level.  CSCs are defined by their characteristics of self-renewal, multipotentiality, and tumor initiation upon transplantation.  By testing for these defining characteristics, we provide evidence for the existence of CSCs in a transgenic mouse model of glioma, S100ß-verbB;Trp53.   In this glioma model, CSCs are enriched in the side-population (SP) cells.  These SP cells have enhanced tumor-initiating capacity, self-renewal, and multipotentiality compared to non-SP cells from the same tumors.  Furthermore, gene expression analysis comparing FACS-sorted cancer SP cells to non-SP cancer cells and normal neural SP cells identified 45 candidate genes that are differentially expressed in glioma stem cells.  We validated the expression of two genes from this list (S100a4 and S100a6) in primary mouse gliomas and human glioma samples.  Analyses of xenografted human GBM (glioblatoma multiforme) cell lines and primary human glioma tissues show that S100A4 and S100A6 are expressed in a small subset of cancer cells and that their abundance is positively correlated to tumor grade.  In conclusion, this study shows that CSCs exist in a mouse glioma model, suggesting that this model can be used to study the molecular and cellular characteristics of CSCs in vivo and to further test the cancer stem cell hypothesis.

overall_design: This study features two factors, injected cell origin (either tumorsphere or neurosphere) and FACS cell population (either side population or non-side population cells).  There were two different tumorspheres, labeled 3447 and 4346 that were isolated from brain tumors in S100beta-verbB;p53-/- or S100beta-verbB;p53+/- mice.  The tumorspheres were injected separately into the brains of NOD.Cg-Prkdc<scid>Il2rg<tm1Wjl>/SzJ mice to generate biological triplicates of each primary tumor.  Tumorspheres were isolated and cultured before FACS sorting to obtain side population and non-side population cells.  As a control, untransformed neurospheres from three independent S100beta-verbB;p53-/- or S100beta-verbB;p53+/- mice were isolated, cultured, and FACS sorted to obtain side population and non-side population cells.  Side population and non-side population cells cultured from three mice injected with the 3447 cultured tumorspheres were assayed for gene expression (six samples).  Side-population stem cells cultured from three mice injected with the 4346 cultured tumorspheres were assayed for gene expression (three samples).  Side-population and non-side population cells cultured from three mice injected with the neurospheres were assayed for gene expression (six samples).

first: Molly

last: Harris

first: Hyuna

last: Yang

first: Benjamin

middle: E

last: Low

first: Joydeep

last: Mukherje

first: Abhijit

last: Guha

first: Roderick

middle: T

last: Bronson

first: Leonard

last: Shultz

first: Mark

last: Israel


title: Re-expression of GATA2 Cooperates with PPAR gamma Depletion to Revert the Adipocyte Phenotype

status: Public on Jan 14 2009

first: Scott

middle: Andrew

last: Ochsner

address: One Baylor Plaza

department: Molecular and Cellular Biology

institute: Baylor College of Medicine

summary:
The nuclear receptor PPAR gamma is required for adipocyte differentiation, but its role in mature adipocytes is less clear.  Here we report that knockdown of PPAR gamma expression in 3T3-L1 adipocytes returned the expression of most adipocyte genes towards preadipocyte levels. Consistently, down regulated but not up regulated genes showed strong enrichment of PPAR gamma binding. Surprisingly, not all adipocyte genes were reversed and the adipocyte morphology was maintained for an extended period after PPAR gamma depletion.  To explain this, we focused on transcriptional regulators whose adipogenic regulation was not reversed upon PPAR gamma depletion. We identified GATA2, a transcription factor whose down-regulation early in adipogenesis is required for preadipocyte differentiation, remaining low after PPAR gamma knockdown. Forced expression of GATA2 in mature adipocytes complemented PPAR gamma depletion and impaired adipocyte functionality with a more preadipocyte- like gene expression profile. Ectopic expression of GATA2 in adipose tissue in vivo had similar effect on adipogenic gene expression. These results suggest that PPAR gamma-independent down regulation of GATA2 prevents reversion of mature adipocytes after PPAR gamma depletion.

Keywords: cell type comparison, Gata2, PPAR gamma, adipocyte, preadipocytes, differentiation

overall_design:
This dataset consists of three sample groups: preadipocytes, control siRNA treated adipocytes, and PPAR gamma siRNA treated adipocytes.  Each sample group consists of three replicates samples.  Each sample was hybridized to a separate array for a total of nine arrays.

Technical replicates: Pread 1, Pread 2, Pread 3
Technical replicates: Cont siRNA 1, Cont siRNA 2, Cont siRNA 3
Technical replicates: PPAR gamma siRNA 1, PPAR gamma siRNA 2, PPAR gamma siRNA 3

first: Michael

last: Schupp

first: Ana

middle: G

last: Cristancho

first: Martina

middle: I

last: Lefterova

first: Elyish

last: Hanniman

first: Erika

last: Briggs

last: Steger

first: Mohammed

last: Qatanani

first: Joshua

last: Curtin

first: Jonathan

last: Schug

first: Neil

last: Mckenna

first: Mitch

last: Lazar


title: Whole heart response to stable HIF-1alpha overexpression

status: Public on Dec 02 2008

city: Honolulu

first: Chad

middle: Brian

last: Walton

state: HI

address: 651 Ilalo Street, JABSOM BSB 222-18

department: Center for Cardiovascular Research

institute: University of Hawaii

summary: An oxygen stable form of HIF-1alpha was overexpressed in the hearts of mice, under tet-off control.

overall_design: Bi-allelic transgenic mice were created by crossing alpha-MHC promoter/tet transactivating protein expressing mice with tet responsive element promter/stable HIF-1alpha protein expressing mice.  Mice were either, maintained on Doxycycline (inhibiting the expression of the HIF-1alpha transgene) or removed from doxycycline (inducing expression) for one or three days.

first: Ralph

last: Shohet

first: Raffi

last: Bekeredijan

first: Fred

last: Kruse

first: Joel

last: Outten

first: David

last: Sutcliffe

first: Richard

middle: K

last: Bruick

first: Robert

last: Gerard


title: Gene expression in Dicer-deficient mouse liver

city: Philadelphia

last: Friedman

address: ARC 1007B, 3615 Civic Center Blvd.

department: Pediatrics

institute: University of Pennsylvania School of Medicine

summary:
Background & Aims: MiRNAs are small (~22 nucleotide), non-coding RNA molecules that regulate gene expression through imperfect complementarity with target messenger RNAs. The function of miRNA in mammalian organogenesis is largely unknown. Conditional loss-of-function of Dicer, the enzyme that processes precursor miRNA transcripts into their mature, active form, has been shown to cause severe defects in a number of organ systems. Here we address the role of Dicer in liver development and function. Methods: Mice lacking Dicer function in hepatocytes were generated using an Afp-Cre strain to drive deletion of a floxed Dicer allele. Deletion of the flox-dicer allele was confirmed by quantitative PCR. Decreased miRNA levels detected by quantitative RT-PCR and in situ hybridization confirmed loss of Dicer function. Gene expression microarray analysis was performed on liver RNA from P28 mutant and control mice. Liver sections from mutant and control mice ranging from embryonic stages through 3-4 months of age were examined and liver function tests were performed on adult mice. Results: Mice lacking hepatocyte Dicer function were born alive at the expected frequency, and had grossly normal appearance and behavior. Despite the loss of mature miRNA, hepatic function was normal, as reflected by normal blood gludose, albumin, cholesterol, and bilirubin. However, mutant mice between 2-4 months of age exhibit progressive hepatocyte damage, elevated ALT/AST, with evidence of balanced proliferation and apoptosis in the lobule. Microarray analysis indicates large-scale changes in gene expression, with increased expression of many miRNA targets, as well as imprinted genes. Conclusions: Loss of miRNA processing in the liver at late gestation has a remarkably mild phenotype, suggesting that miRNAs do not play an essential role in hepatic physiology. However, miRNA deficiency results in hepatocyte apoptosis and balanced hepatocyte regeneration. Finally, microarray analysis of gene expression in mutant liver suggests a previously unrecognized role for Dicer in the repression of imprinted genes.

Keywords: Genetic modification

overall_design: Hepatic RNA was isolated from 5 control and 5 DicerloxP/loxP;Afp-Cre+ mice at P28.

middle: R


title: Estrogen-modulated gene expression in c-kit+ stem cells and CD44+ stromal cells

city: Montréal

first: Caroline

last: Lemieux

state: Québec

address: 5000, Bélanger Est

department: Centre de recherche

country: Canada

institute: Institut de Cardiologie de Montréal

summary:
The recent interest in the role of bone marrow derived endothelial progenitor cells in the benefits of estrogen on cardiovascular health brought us to evaluate if estrogen could affect cardiac repair more broadly by regulating biological processes involved in the functional organization of the bone marrow stem cell niche.
To assess such possibility, we evaluated gene expression profiles of bone marrow c-kit+ stem cells and CD44+ stromal cells, derived from primary whole bone marrow cultured system, after exposure to a physiological concentration of 17β-estradiol (17βE).
Keywords: estrogen treatment response

overall_design: 6 samples per cell type (c-kit+ stem cells or CD44+ stromal cells) were analysed.  Of these, triplicates of 17βE treated and corresponding control non-treated cells are included.

first: Isabelle

last: Cloutier

first: Jean-François

last: Tanguay


title: Mouse Erythroleukemia (MEL) Cells Expressing Tagged Versions of BCL11A

status: Public on Dec 05 2008

first: Vijay

middle: G.

last: Sankaran

address: 300 Longwood Avenue

department: Department of Medicine

institute: Children's Hospital Boston

summary:
Differences in the amount of fetal hemoglobin (HbF) that persists into adulthood affect the severity of sickle cell disease and the beta-thalassemia syndromes. Genetic association studies have identified sequence variants in the gene BCL11A that influence HbF levels. Here we examine BCL11A as a potential regulator of HbF expression. The high HbF BCL11A genotype is associated with reduced BCL11A expression. Moreover, abundant expression of full-length forms of BCL11A is developmentally restricted to adult erythroid cells. Down-regulation of BCL11A expression in primary adult erythroid cells leads to robust HbF expression. Consistent with a direct role of BCL11A in globin gene regulation, we find that BCL11A occupies several discrete sites in the beta-globin gene cluster. BCL11A emerges as a therapeutic target for reactivation of HbF in beta-hemoglobin disorders.
Expression clone label: FBB (4 different subclones, with 2 arrays each), Control label: MelBirA

Keywords: cell type comparsion

overall_design: Microarray expression analysis from parental control mouse erythroleukemia (MEL) cells containing the BirA enzyme (MelBirA cells) and cells containing tagged versions (FLAG-Biotag) of BCL11A.  Two control datasets and eight datasets from four subclones containing tagged BCL11A are included.


title: Gene expression profiles of the lymphoid and non-lymphoid leukemias induced by the Graffi murine leukemia retrovirus

status: Public on Dec 01 2008

city: Montreal

first: Eric

last: Rassart

state: Quebec

address: C.P. 8888 Succursale Centre-Ville

department: Biology

institute: UQAM

summary:
We used the microarrays to obtain the cancerous signatures of T-cell, B-cell, erythroid and megakaryoblastic leukemias in mice.

Keywords: cell type comparison

overall_design: 16 samples are included, 13 corresponding to leukemic samples and 3 corresponding to control samples. Each control sample corresponds to the pooled RNA of 12 mice.

first: Veronique

last: Voisin


title: Expression Data from NKDxIL15tg and IL15 tg NK cells

status: Public on Jan 29 2009

city: Saint Louis

first: John

last: Sunwoo

state: MO

address: 660 S. Euclid Avenue, Campus Box 8115

institute: Washington University School of Medicine

summary:
NK cells from NKDxIL15tg mice spleens and bone marrow were purified by FACS.  NK cells from IL15tg mice spleens were purified by FACS.
Gene expression differences were analyzed to identify genes involved in NK cell development.
Keywords: cell type comparison

overall_design: Immature NK cells from NKDxIL15tg mice and mature NK cells from IL15tg mice were purified by FACS.  RNA was made for target synthesis and hybridization to Affymetrix microarrays.

first: Wayne

middle: M

last: Yokoyama


title: Mitochondrial dysfunction by loss of HtrA2 results in the activation of a brain-specific transcriptional stress response

city: London

first: Kristina

last: Klupsch

address: 44 Lincoln's Inn Fields

department: London Research Institute

institute: Cancer Research UK

summary:
Cellular stress responses can be activated following functional defects in organelles such as mitochondria and the endoplasmic reticulum. Mitochondrial dysfunction caused by loss of the serine protease HtrA2 leads to a progressive movement disorder in mice and has been linked to parkinsonian neurodegeneration in humans. Here we demonstrate that loss of HtrA2 results in transcriptional up-regulation of nuclear genes characteristic of the integrated stress response, including the transcription factor CHOP, selectively in the brain. We also show that loss of HtrA2 results in the accumulation of unfolded proteins in the mitochondria, defective mitochondrial respiration and enhanced production of reactive oxygen species that contribute to the induction of CHOP expression and to neuronal cell death. CHOP expression is also significantly increased in Parkinson’s disease patients’ brain tissue. We therefore propose that this brain-specific transcriptional response to stress may be important in the advance of neurodegenerative diseases.

This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Hematopoietic stem cell (HSC) expression alteration in an ADAR1 mouse model

status: Public on Dec 07 2008

city: New Haven

first: Jun

last: Lu

state: CT

address: 10 Amistad St

department: Yale Stem Cell Center and Department of Genetics

institute: Yale University

summary: Hematopoietic stem cells purified from +/+, +/- and -/- ADAR1 mice were compared with global gene expression analysis.

overall_design: Each sample was purified from one mouse.

first: Jochen

last: Hartner

first: Carl

last: Walkley

first: Todd

last: Golub

first: Stuard

last: Orkin


title: (AKR/J x FVB/NJ)F1 versus (DBA/2J x FVB)F1 spleen expression data

status: Public on Nov 30 2008

city: Bethesda

first: Kent

last: Hunter

address: 37/4048 37 Convent Drive

department: Center for Cancer Research

institute: National Cancer Institute

summary:
F1 hybrids from (AKR/J x FVB/NJ) and (DBA/2J x FVB/NJ) outcrosses display a 20-fold difference in mammary tumor metastatic capacity, due to differences in inherited polymorphisms.  Expression studies were performed to determine whether polymorphism-driven gene expression signatures predictive of outcome could be generated from normal tissues

Keywords: Basal transcription profiles

overall_design: Spleen from adult F1 animals from (AKR/J x FVB/NJ) and (DBA/2J x FVB/NJ) outcrosses was collected and arrayed on Affymetrics chip to identify basal differences in gene expression between the different genotypes

middle: W


title: (AKR/J x FVB/NJ)F1 versus (DBA/2J x FVB)F1 lung expression data

overall_design: Lung from adult F1 animals from (AKR/J x FVB/NJ) and (DBA/2J x FVB/NJ) outcrosses was collected and arrayed on Affymetrics chip to identify basal differences in gene expression between the different genotypes


title: (AKR/J x FVB/NJ)F1 versus (DBA/2J x FVB)F1 blood expression data

overall_design: Whole blood from adult F1 animals from (AKR/J x FVB/NJ) and (DBA/2J x FVB/NJ) outcrosses was collected and arrayed on Affymetrics chip to identify basal differences in gene expression between the different genotypes


title: Expression data from GNMT knockout mice

city: Taipei

first: Yi-Ming

middle: Arthur

last: Chen

state: Taiwan

address: 155, Li-Noun St., Sec. 2

department: AIDS Prevention and Research Center

institute: National Yang-Ming University

summary:
We report that 7 of 7 female Gnmt-/- mice developed hepatocellular carcinoma (HCC), the most common form of liver cancer, at the mean age of 16.1 months. In contrast, only one-third (2/6) of male Gnmt-/- mice had HCC, the remaining had either premature death or liver necrosis.
Microarray analysis showed that genes involved in the following pathways were deregulated in different stages of tumorigenesis: S-adenosylmethionine (SAM)-dependent methyltransferases, metabolism, signal transduction, cell proliferation, cell adhesion and immune responses.
This study reveals that GNMT plays an important role in the prevention of hapatotumorigenesis through regulating DNA methylaiton and oxidative stress signaling pathways. We postulate that GNMT is a stress-responsive protein and its expression may account for the gender difference of the susceptibility to liver cancer.
Keywords: Gnmt knockout

overall_design: Liver tissues from wild-type or Gnmt knockout mice at young ages, devoloping dysplasia nodules or HCC were used for RNA extraction and hybridization on Affymetrix microarrays. For 11 weeks old mice, total RNA were mixed in equal proportion from 3 mice.

middle: A

first: Yi-Jen

last: Liao

first: Shih-Ping

last: Liu

first: Cheng-Ming

last: Lee

first: Ying-Shiuan

last: Li

first: Pei-Chun

last: Chuang

first: Chia-Yen


title: B6_IL1218_WAP

status: Public on Nov 29 2008

city: Munich

first: Reinhard

last: Hoffmann

address: Trogerstr. 30

institute: Institute for medical microbiology

summary:
Dataset of IL-12+IL-18 trated and Yersinia enterocolitica infected C57BL/6 NK cells
Keywords: infection response

overall_design:
NK cells were isolated from mouse spleen, grown on IL-2 in vitro, stimlated wih Y. enterocolitica WA(pYV) or left uninfected.
3 conditions, 3 biological replicates each


title: (AKR/J x FVB/NJ)F1 versus (DBA/2J x FVB)F1 bone marrow expression data

state: MD

overall_design: Bone Marrow from adult F1 animals from (AKR/J x FVB/NJ) and (DBA/2J x FVB/NJ) outcrosses was collected and arrayed on Affymetrics chip to identify basal differences in gene expression between the different genotypes


title: Role of HNF4alpha in the adult colon

city: Sherbrooke

first: Francois

last: Boudreau

address: 3001 12e ave Nord

department: Anatomy and Cell Biology

institute: University of Sherbrooke

summary: Background & Aims: HNF4α is an important transcriptional regulator of hepatocyte and pancreatic function. Hnf4α deletion is embryonically lethal with severe defects in visceral endoderm formation, liver maturation and colon development.  However, the precise role of this transcription factor in maintaining homeostasis of the adult intestine remains unclear.  Herein, we aimed to elucidate the adult intestinal functions of Hnf4α.  Methods: A conditional intestinal epithelial Hnf4α knockout mouse was generated.  Histological abnormality of the colonic mucosa was assessed by immunodetection and Western.  Changes in global gene expression and biological network were analyzed.  Results: Hnf4α intestine null mice developed normally until reaching young adulthood. Crypt distortion became apparent in the Hnf4α null colon at 3 months of age followed by focal areas of crypt dropout, increased immune cell infiltrates, crypt hyperplasia and early signs of polyposis later in life.  A gene profiling analysis identified cell death and cell cycle related to cancer as the most significant sets of genes altered in the Hnf4α colon null mice.  Expression levels of the tight junction proteins claudin 4, 8 and 15 were altered early in the colon epithelium of Hnf4α mutants and correlated with increased barrier permeability to a molecular tracer that does not normally penetrate normal mucosa.  Conclusion: These observations support a functional role for Hnf4α in protecting the colonic mucosa against the initiation of the changes resembling inflammatory bowel diseases and polyp formation.

overall_design: HNF4alpha was conditionally knockout in the mouse epithelial colon with the villin CRE. A total of 3 control and 3 mutant littermates individuals were sacrificed at 1 year of age.  The colon was harvested and Total RNA was isolated from each individuals.  Each RNA sample was independently used to generate probes to screen affymetrix chips.

first: Mathieu

last: Darsigny

first: Jean-Philippe

last: Babeu

first: Andrée-Anne

last: Dupuis

first: Emma

last: Furth

first: Ernest

last: Seidman

first: Emile

last: Levy

first: Fernand-Pierre

last: Gendron


title: The effect of inherited polymorphism on prognostic gene expression signatures

first: Kent

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


title: (AKR/J x FVB/NJ)F1 versus (DBA/2J x FVB)F1 Thymus expression data

overall_design: Thymus from adult F1 animals from (AKR/J x FVB/NJ) and (DBA/2J x FVB/NJ) outcrosses was collected and arrayed on Affymetrics chip to identify basal differences in gene expression between the different genotypes


title: Age-related gene expression changes in mouse neocortex

status: Public on Nov 26 2008

city: Boston

first: Philipp

last: Oberdoerffer

address: 77 Avenue Louis Pasteur

department: Pathology

institute: Harvard Medical School

summary:
Aging is associated with major nuclear changes affecting genomic integrity and gene expression. Here we compare the gene expression profiles in the neocortex of young (5 months old) and old (30 months old) B6xC3 F1 mice.
In a related study, we compare genes that change expression with age to SIRT1 associated genes identified by ChIP on chip (NimbleGen) and find a significant overlap, indicating that SIRT1 target genes are preferentially deregulated with age.

Keywords: gene expression comparison, age-comparison

overall_design: Total neocortex RNA was hybridized on Affymetrix M430 2.0 arrays. RNA was isolated from five young (5 months) and 5 old (30 months) B6xC3 F1 mice, samples were hybridized individually.

first: Tomas

last: Prolla

first: David

last: Sinclair

first: James

last: Vann

first: Sang-Kyu

last: Park