title: Leukocyte transcript alterations in West-African girls following a booster vaccination with diphtheria-tetanus-pertussis vaccine

city: Aarhus

first: Kasper

last: Thorsen

address: Brendstrupgaardsvej

country: Denmark

institute: Aarhus University Hospital

summary: Observational studies from low-income countries have shown that the vaccination against diphtheria, tetanus and pertussis (DTP) is associated with excess female mortality due to infectious diseases. To investigate possible changes in gene expression after DTP vaccination, we identified a group of nine comparable West African girls, from a biobank of 356 children, who were due to receive DTP booster vaccine at age 18 months. We extracted RNA from blood samples before, and 6 weeks after, vaccination to analyse the coding transcriptome in leukocytes using expression microarrays, and ended up with information from eight girls. The data was further analysed using dedicated array pathway and network software. We aimed to study whether DTP vaccination introduced a systematic alteration in the immune system in girls. We found very few transcripts to alter systematically. Those that did mainly belonged to the interferon (IFN) signalling pathway. We scrutinized this pathway as well as the interleukin pathways. Two out of eight showed a down-regulated IFN pathway and two showed an up-regulated IFN pathway.  The two with down-regulated IFN pathway had also down-regulated IL-6 pathway. In the study of networks, two of the girls stood out as not having the inflammatory response as top altered network. In conclusion, the transcriptome changes following DTP booster vaccination were subtle, but it is possible to identify sub groups that deviate from each other, mainly in the IFN response.

overall_design: Microarrays (Human Exon 1.0 ST Arrays (Affymetrix )) were used to compare the gene expression alteration following DTP-vaccination in 18-19 months old West African girls. The gene expression analysis was based on RNA from venous blood. The blood was drawn immediately before DTP-vaccination (baseline sample) and 6 weeks after (42 -50 days, post-vaccination sample) in a total of eight girls

first: Nikolaj

last: Ørntoft

first: Jane

last: Agergaard


title: Genome-wide analysis of mouse macrophages stimulated with IL-4 (Biogel and thioglycollate macrophages) (Affymetrix)

status: Public on Sep 29 2012

city: Guildford

first: Fernando

middle: O

last: Martinez Estrada

state: Surrey

address: Stag Hill

department: Faculty of Health & Medical Sciences

country: United Kingdom

institute: University of Surrey

summary:
Analysis of alternative activation of macrophages at gene expression level. The study forms part of a wider study where we compare the effects of IL-4 in different human and mouse macrophages. Our results support the notion that in vitro culture conditions greatly affect the macrophage response to IL-4.
Total RNA obtained from Thioglycollate and Biogel elicited peritoneal macrophages exposed to 20 ng/ml of IL-4 for 18 hours.

overall_design: Biogel and thioglycollate elicited macrophages were stimulated with the Th2 cytokine IL-4, for RNA extraction and hybridization on Affymetrix microarrays.

last: Martinez

first: Laura

last: Helming

first: Siamon

last: Gordon


title: Genome-wide analysis of mouse macrophages stimulated with IL-4 (bone marrow macrophages) (Affymetrix)

summary:
Analysis of alternative activation of macrophages at gene expression level. The study forms part of a wider study where we compare the effects of IL-4 in different human and mouse macrophages. Our results support the notion that in vitro culture conditions greatly affect the macrophage response to IL-4.
Total RNA obtained from bone marrow derived macrophages upon exposure to 20 ng/ml of IL-4 for 18 hours.

overall_design: Bone marrow derived macrophages were stimulated with the Th2 cytokine IL-4, for RNA extraction and hybridization on Affymetrix microarrays.


title: Foxp3 exploits a preexistent enhancer landscape for regulatory T cell lineage specification [Expression]

status: Public on Sep 28 2012

city: New York

first: Aaron

last: Arvey

state: NY

country: USA

institute: Memorial Sloan-Kettering Cancer Center

summary: Regulatory T (Treg) cells, whose identity and function are defined by the transcription factor Foxp3, are indispensable for immune homeostasis.  It is unclear whether Foxp3 exerts its Treg lineage specification function through active modification of the chromatin landscape and establishment of new enhancers or by exploiting a pre-existing enhancer landscape.  Analysis of the chromatin accessibility of Foxp3-bound enhancers in Treg and Foxp3-negative T cells showed that Foxp3 was bound overwhelmingly to pre-accessible enhancers occupied by its cofactors in precursor cells or a structurally related predecessor. Furthermore, the bulk of Foxp3-bound Treg cell enhancers inaccessible in Foxp3- CD4+ cells became accessible upon T cell receptor activation prior to Foxp3 expression with only a small subset associated with several functionally important genes being exclusively Treg cell-specific.  Thus, in a late cellular differentiation process Foxp3 defines Treg cell functionality in an “opportunistic” manner by largely exploiting the preformed enhancer network instead of establishing a new enhancer landscape.

overall_design: Array expression. Three cell types with 3-5 replicates each.

first: Robert

middle: M

last: Samstein

first: Alexander

last: Rudensky


title: Gene expression profiling of ovaries collected from wild type (WT) mice and progesterone receptor (PR) knock out mice

status: Public on Oct 04 2012

city: Urbana

first: Shanmugasundaram

last: Nallasamy

state: IL

address: 2001 S Lincoln Ave

department: Comparative Biosciences

institute: University of illinois at Urbana-Champaign

summary: Previous studies have shown that PR is a critical regulator of ovulation. The PR-null mice (PRKO) failed to ovulate due to a failure in the rupture of the preovulatory follicles.

overall_design: To experimentally induce ovulation, the wild type and PR null mice (C57BL/6, 24–28 d old) were injected ip with 5 IU of PMSG and 48 h later by 5 IU of hCG.  Ovaries were collected at 11 h and total RNA was analyzed using Affymetrix mouse arrays

first: J

last: Kim

first: Indrani

middle: C

last: Bagchi

first: Milan

middle: K


title: Maternal diabetes alters transcriptional programs in the developing embryo.

status: Public on Sep 25 2012

city: Baton Rouge

first: Claudia

last: Kappen

state: LA

address: 6400 Perkins Road

department: Developmental Biology

institute: Pennington Biomedical Research Center

summary:
Exposure to maternal diabetes during pregnancy alters transcriptional profiles in the developing embryo.  The enrichment, within the set of de-regulated genes, of those encoding transcriptional regulatory molecules provides support for the hypothesis that maternal diabetes affects specific developmental programs.
We compared E10.5 cntrol embryos to E10.5 embryos from diabetic pregnancies in the FVB mouse strain.

overall_design: Diabetes was induced in 7-9 week old female FVB mice by streptozotocin. Dams whose blood glucose levels exceeded 250 mg/dl were set up for mating. Embryos were dissected at E10.5 and total RNA was isolated. Equal amounts of RNA prepared from 3 individual embryos were pooled into one sample; each embryo was from a different pregnancy. Three pools were constructed for a total of nine embryos from diabetic pregnancies, and independently three pools for control embryos.

first: Gabriela

last: Pavlinkova

first: Michael

last: Salbaum


title: Transcriptomic analysis of the cerebellum of daDREAM mice

status: Public on Sep 30 2012

city: Cantoblanco

first: Juan

middle: Carlos

last: Oliveros

state: Madrid

address: Darwin 3

country: Spain

institute: CNB, CSIC

summary: DREAM (downstream regulatory element antagonist modulator) is a Ca2+-binding protein that binds DNA and represses transcription in a Ca2+-dependent manner. Previous studies have shown a role for DREAM in cerebellar function regulating the expression of the sodium/calcium exchanger3 (NCX3) in cerebellar granules to control Ca2+ homeostasis and survival of these neurons. To achieve a more global view of the genes regulated by DREAM in the cerebellum, we performed a genome-wide analysis in transgenic cerebellum expressing a Ca2+-insensitive/CREB-independent dominant active mutant DREAM (daDREAM). Our results indicate that DREAM is a major transcription factor in the cerebellum that regulates genes important for cerebellar development.

overall_design: We used Affymetrix microarrays (GeneChip Mouse Genome 430 2.0) to compare global gene expression in wild type (WT) versus transgenic cerebellum cells. For ech type of sample three hybridizations were carried-out (independent biological replicates).

first: Mara

last: Dierssen

last: Fedrizzi

first: María

last: Martínez de Lagran

first: Ignasi

last: Sahún

first: Rosa

last: Gómez-Villafuerte

first: Alfonso

last: Gutierrez-Adán

first: Belén

last: Pintado

first: Xose

last: Dopazo

first: Paz

last: González

first: Marisa

last: Brini

first: Britt

last: Mellström

first: Ernesto

last: Carafoli

first: José

middle: R

last: Naranjo


title: Conditional deletion of Bcl6 in naive B cells

status: Public on Sep 21 2012

city: Yokohama

first: Kaji

last: Tomohiro

state: Kanagawa

address: 1-7-22, Suehiro-cho, Tsurumi-ku

department: Research center for allergy and immunology

country: Japan

institute: RIKEN

summary: Bcl6 germline deletion causes a prominent inflammatory disease, owing to over-expression of Th2 cytokines, and affects the properties of B cells prior to immunization. Therefore we established the B cell-specific Bcl6 deletion mice and analyze the gene expression of naive B cells under physiological conditions.

overall_design: Total RNAs of splenic follicular and marginal zone B cells from Bcl6(flox/flox), Bcl6(+/flox) or Bcl6(+/+) mice heterozygous for mb1-cre were extracted and analysed on Affymetrix microarrays.

first: Akiko

last: Sugimoto

first: Masaki

last: Hikida

first: Atsushi

last: Hijikata

first: Toshitada

last: Takemori


title: Butyrophilin 3A1 binds phosphorylated antigens and stimulates human TCR γδ cells.

status: Public on Oct 01 2012

city: Singapore

first: jinmiao

last: chen

address: Biopolis

country: Singapore

institute: Singapore Immunology Network

summary:
We used genetic approaches to identify butyrophilin 3A1 (BTN3A1) as the molecule that binds and presents phosphorylated antigens to Vγ9Vδ2 TCR–expressing cells.
BTN3A1 represents a novel antigen–presenting molecule for the activation of Vγ9Vδ2 TCR–expressing cells which play important roles in human tumor immunity and host defense.

overall_design: 3 replicates of 4 cell lines (12 samples total) were analysed.  Data was RMA normalized, and genes that expressed above the negative control in all 4 cell lines from chromosome 6 considered for further analysis

first: Lucia

last: Mori

first: Gennaro

last: De Libero


title: Gene Expression Profiles of MYC+ and MYC- mouse Germinal Center B cells

status: Public on Sep 24 2012

first: David

last: Dominguez-Sola

address: 1130 Saint Nicholas Ave, ICRC Room 507

department: Institute for Cancer Genetics

institute: Columbia University

summary:
Germinal centers (GC) arise within B cell follicles upon antigenic challenge. In the dark zones (DZ) of GCs, B cells proliferate and hypermutate their immunoglobulin genes, and mutants with increased affinity are positively selected in the light zone (LZ) to either differentiate into plasma and memory cells, or re-enter the DZ for further refinement. However, the molecular circuits governing GC positive selection are not known. Here, we show that the GC reaction requires the biphasic regulation of c-MYC expression, involving its transient induction during early GC commitment, its repression by BCL6 in DZ B cells, and its re-induction in a subpopulation of positively selected LZ B cells destined to DZ re-entry. Accordingly, acute disruption of MYC function in vivo leads to GC collapse, indicating an essential role in GC physiology. These results have implications for our understanding of GC selection and the role of MYC deregulation in B cell lymphomas.
We used microarrays to determine the global gene expression programs that distinguish MYC+ GC B cells from their MYC- negative counterparts.

overall_design: GFPMYC+ and GFPMYC- GC B cell subpopulations were collected by Fluorescence Activated Cell Sorting (FACS) from B cell enriched fractions of splenic mononuclear cell pools of GFPMYC knock-in mice (12 days after SRBC immunization).  5-20ng of total RNA (RIN>9) for each sample was used as a template for linear cDNA amplification (Ovation RNA amplification Kit, NuGen). cDNA was labeled using the Encore Biotin Labeling Kit (NuGen) and hybridized to Affymetrix Mouse 430.2 gene expression arrays.

first: Riccardo

last: Dalla-Favera


title: Microarray analysis of WT and Batf3-/- CD8alpha dendritic cells from C57BL/6 spleen

city: St. Louis

first: Kenneth

last: Murphy

address: 660 S. Euclid

department: Pathology and Immunology

institute: Wustl/HHMI

summary: Batf3 regulates key CD8alpha DC-specific genes.

overall_design: WT and KO cells were isolated from pooled spleens of C57BL/6 genetic background mice, that were either untreated, or injected with recombinant murine IL-12 in pyrogen-free saline at 2.5 ug/mL. Mice were injected i.p. with 0.5 ug of IL-12 once and sorted after 3 days.  CD8alpha+ dendritic cells were sorted as B220- NK1.1- CD172a- CD11c+ MHCII+ CD24+ DEC205+ CD8alpha+ cells.

first: K

last: Wumesh


title: Gene-expression changes resulting from loss of the mTORC1 component Raptor in murine hematopoietic stem and progenitor cell-enriched populations (HSPC)

status: Public on Sep 19 2012

city: Boston

first: Amit

last: Sinha

state: MA

address: 44 Binney St

department: Pediatric Oncology

institute: Dana-Farber Cancer Institute

summary: We investigated the role of mTORC1 in murine hematopoiesis by conditionally deleting the Raptor gene in murine hematopoietic stem cells. We observed mutliple alterations evoked by Raptor loss in hematopoiesis and profiled gene-expression alterations induced by raptor loss in Flt3-Lin-Sca1+cKit+ hematopoietic stem and progenitor enriched cell populations, 5 weeks post Raptor deletion.

overall_design: Flt3-Lin-Sca1+cKit+ cells were flow sorted from mice containing homozygous floxed alleles for exon 6 of the Raptor gene in the presence (MT group) or absence (WT group) of the MxCre transgene, which was induced with injections of mice with pIpC 5 weeks before cell isolation.

first: D

last: Kalaitzidis

first: S

middle: A

last: Armstrong


title: Gene Expression Profile of Epiretinal Fibrous Membrane Associated with Proliferative Vitreoretinopathy

city: Fukuoka

first: Keijiro

last: Ishikawa

address: 3-1-1  Maidashi, Higashi-ku

department: Ophthalmology

institute: Kyushu University

summary: Proliferative vitreoretinopathy (PVR) is a severe vision-threatening disorder characterized by the formation of cicatricial fibrous membranes leading to traction retinal detachment. As the pathophysiology remains unclear, there has been no effective therapeutic approach to date other than vitreoretinal surgery.

overall_design:
In order to identify genes associated with the pathogenesis of PVR, we performed gene expression analyses in fibrous membrane in patients with PVR using DNA microarray technology.
This study was approved by the Ethics Committee of the Kyushu University Hospital and Fukuoka University Chikushi Hospital, and the surgical specimens were handled in accordance with the ethical standards of the 1989 Declaration of Helsinki. All patients gave informed consent before inclusion in the study. Fibrousl membranes were surgically dissected from the retinal surface with horizontal scissors of patients with PVR undergoing pars plana vitrectomy. Total RNA were extracted from the fibrous membranes with three different PVR patients. RNA from human retina was obtained from Clontech (Palo Alto, CA).

first: Shigeo

last: Yoshida


title: Tissue-specific differences in PPARγ control of macrophage function.

status: Public on Oct 03 2012

first: Emmanuel

last: GAUTIER

address: 1425 Madison ave

institute: Mount Sinai School of Medecine

summary: PPARγ is known for its anti-inflammatory actions in macrophages. However, which macrophage populations express PPARγ in vivo and how it regulates tissue homeostasis in the steady state and during inflammation is not completely understood. We show that lung and spleen macrophages constitutively expressed PPARγ, while other macrophage populations did not. Recruitment of monocytes to sites of inflammation was associated with induction of PPARγ as they differentiated to macrophages. Its absence in these macrophages led to failed resolution of inflammation, characterized by persistent, low-level recruitment of leukocytes. Conversely, PPARγ agonists supported an earlier cessation in leukocyte recruitment during resolution of acute inflammation and likewise suppressed monocyte recruitment to chronically inflamed atherosclerotic vessels. In the steady state, PPARγ deficiency in macrophages had no obvious impact in the spleen but profoundly altered cellular lipid homeostasis in lung macrophages. Reminiscent of pulmonary alveolar proteinosis, LysM-Cre x PPARγflox/flox mice displayed mild leukocytic inflammation in the steady-state lung and succumbed faster to mortality upon infection with S. pneumoniae. Surprisingly, this mortality was not due to overly exuberant inflammation, but instead to impaired bacterial clearance. Thus, in addition to its anti-inflammatory role in promoting resolution of inflammation, PPARγ sustains functionality in lung macrophages and thereby has a pivotal role in supporting pulmonary host defense.

overall_design: The two major subsets of monocytes (Ly-6C+ and Ly-6Clo) from 12-week old C57Bl/6 mice were sorted and the RNA extracted and hybridized to Affymetrix GeneChip® 430 2.0 arrays. We pooled leukocytes from 5 mice for each sort and sorted 3 to 4 separate times for 3 to 4 biological replicates.

middle: L

last: Gautier

first: Andrew

last: Chow

first: Rainer

last: Spanbroek

first: Susan

middle: B

last: Hutchison

first: Stephane

last: Potteaux

first: Melanie

last: Greter

first: Marylène

last: Leboeuf

first: Claudia

last: Jakubzick

first: Milena

last: Bogunovic

first: Nico

last: van Rooijen

first: Andreas

middle: J

last: Habenicht

first: Miriam

last: Merad

first: Gwendalyn

last: Randolph


title: Expression data from small intestinal Lin-c-Kit+Sca-1- cells and Lin-c-Kit-Sca-1- cells.

status: Public on Sep 15 2012

city: Osaka

first: Youngae

last: Lee

address: 3-1 Yamadaoka, Suita

institute: Osaka University

summary:
Small intestinal innate lymphoid cells (ILCs) are known to regulate intestinal epithelial cell homeostasis and to help prevent pathogenic bacterial infections, by producing IL-22. However, other functions of these cells and the lineal relationship between ILCs and lymphoid or myeloid cells have not been clear.
We performed a global gene expression analysis to examine which genes are highly expressed by small intestinal ILCs (Lin-c-Kit+Sca-1- cells) compared with non-ILCs (Lin-c-Kit-Sca-1- cells).

overall_design: To examine the gene expression profiles of ILCs within the small intestinal lamina propria (LP), we isolated Lingeage (Lin)-c-Kit+Sca-1- cells [consisting of NKp46+ ILC22 (Lin-c-Kit+Sca-1-NKp46+ cells) and LTi-like ILC (Lin-c-Kit+Sca-1-CD4+ cells)] as the ILC population, and Lin-c-Kit-Sca-1- cells as the non-ILC population, from the small intestinal LP of 8 week-old mice by FACS, then compared the gene expression profiles between these two populations by microarray analysis.

first: Myoung

middle: H

last: Jang


title: HSF1 mediated Gene regulation in T cells at normal (37C) and febrile (40C) temperatures

status: Public on Sep 20 2012

city: Lexington

first: Jerold

middle: G

last: Woodward

state: ky

address: 800 Rose St. MS-415

department: Microbiology, Immunology & Molecular Genetics

institute: University of Kentucky

summary:
HSF1 is a major transcriptional regulator of heat shock responses. Many cells activate HSF1 in response to heat shock temperatures (>42oC) and other cellular stress causing agents. Unlike other cell types, T cells activate HSF1 in response to T cell activation or when exposed to febrile (40oC) temperatures, suggesting a role for HSF1 beyond the heat-shock response.
We used microarray analysis and HSF1 knock-out mice to study the HSF1 mediated gene regulation in activated T cells under normal and fever temperatures.

overall_design: T cells were purifed from spleen and lymphnodes using miltenyi anti-CD3 magnetic beads and were activated for 5 hr with plate bound anti-CD3 at  normal (37oC) and febrile( 40oC) temperatures in triplicate cultures. Total RNA from triplicate cultures were extracted, pooled and processed for hybridization on to whole mouse genome 430 2.0 affymetrix microarray chips.


title: KSP-positive or -negative cells derived from mouse embryonic stem cells

status: Public on Sep 07 2012

city: Tokyo

first: Ryuji

last: Morizane

address: 35 shinanomachi, shinjukuku

department: Internal Medicine

institute: Keio University School of Medicine

summary: The goals and objectives of this study was to characterize KSP-positive cells derived from mouse embryonic stem cells. KSP is a specific cadherin expressed in renal tubular cells, so it was predicted that KSP-positive cells have characteristics of renal tubular cells.

overall_design:
To purify renal lineage cells from differentiated mouse embryonic stem cells, KSP-positive cells were sorted out by use of anti-KSP antibody.
Mouse embryonic stem cells were differentiated with Activin 10ng/ml for 18 days through embryoid body formation.
2 independent experiments were carried out. KSP-negative cells were also purified as negative control.

first: Toshiaki

last: Monkawa


title: Transcriptional response of cap mesenchyme (undifferentiated nephron progenitors) to Wnt activation

status: Public on Sep 11 2012

city: Cincinnati

first: Joo-Seop

last: Park

address: 3333 Burnet Avenue

institute: Cincinnati Children's Hospital Medical Center

summary: During mammalian kidney development, mesenchymal nephron progenitors (cap mesenchyme) differentiate into the epithelial cells that go on to form the nephron. Although differentiation of nephron progenitors is triggered by activation of Wnt/b-catenin signaling, constitutive activation of Wnt/b-catenin signaling blocks epithelialization of nephron progenitors. Full epithelialization of nephron progenitors requires transient activation of Wnt/b-catenin signaling. We performed transcriptional profiling of nephron progenitors responding to constitutive or transient activation of Wnt/b-catenin signaling.

overall_design: Nephron progenitors were FACS-isolated from BAC transgenic Six2GFPcre-positive embryonic kidneys at E16.5. Cells were aggregated by centrifugation at 850g for 5min and incubated in 10%FBS/DMEM containing either 4uM BIO or the equal volume of DMSO for 24hrs or 48hrs.

first: Wenxiu

last: Ma

first: Wing

last: Wong

first: Andrew

middle: P

last: McMahon


title: IL-2 regulated genes in scurfy CD4+ T-cells

status: Public on Sep 18 2012

city: Charlottesville

first: Rahul

last: Sharma

state: VA

address: Room 5768, Old Medical School Building, 21 Hospital Drive

department: Center for Immunity, Inflammation and Regenerative Medicine

institute: University of Virginia

summary:
The goal of the study was to identify the genes which are regulated by Interleukin-2 in the CD4+ T cells of the scurfy mice during regulatory T-cell deficiency. Scurfy (Sf) mice bear a mutation in the forkhead box P3 (Foxp3) transcription factor, lack regulatory T-cells (Treg), develop multi-organ inflammation, and die prematurely. The major target organs affected are skin, lungs, and liver. Sf mice lacking the Il2 gene (Sf.Il2-/-), despite devoid of Treg, did not develop skin and lung inflammation, but the inflammation in liver, pancreas, submandibular gland and colon remained. Genome-wide microarray analysis revealed hundreds of genes were differentially regulated among Sf, Sf.Il2-/-, and B6 CD4+ T-cells but the most changes were those encoding receptors for trafficking/chemotaxis/retention and lymphokines. Our study suggests that IL-2 controls the skin and lung inflammation in Sf mice in an apparent "organ-specific" manner through two novel mechanisms: by regulating the expression of genes encoding receptors for T-cell trafficking/chemotaxis/retention and by regulating Th2 cell expansion and lymphokine production. Thus, IL-2 is a master regulator for multi-organ inflammation and an underlying etiological factor for various diseases associated with skin and lung inflammation.
Methods: CD4+ T cells were purified by Fluorescence Assisted Cell Sorting from the peripheral lymph nodes of (A) three individual Scurfy (Sf; B6.Cg-Foxp3sf/J) male mice, (B) three individual Sf.Il2-/- male mice (Scurfy mice carrying a null Interleukin (IL)-2 gene (B6.129P2-Il2tm1Hor/J)) and (C) a pooled sample of lymph nodes from two B6 (C57BL/6J) mice. All the mice were 3 weeks old. Total RNA was prepared using RNeasy mini kit (Qiagen). RNA samples were converted to cRNA, labeled and hybridized to Affymetrix Mouse 430_2 chips (Mouse Genome 430 2.0 Array, Affymetrix, Santa Clara, CA) at the University of Virginia DNA Sciences Core Facility.

overall_design:
1. RNA from CD4+ T cells purified from pooled peripheral lymph nodes of two 3-week old B6 mice) - 1 biological replicate
2. RNA from CD4+ T-cells purified from peripheral lymph nodes of 3-week old scurfy (Sf) mice - 3 biological replicates.
3. RNA from CD4+ T cells purified from peripheral lymph nodes of Sf.Il2-/- mice - 3 biological replicates.

first: Shyr

middle: T

last: Ju


title: Gene expression profiling of N-acetylglucosaminidase (NAGLU)-depleted HeLa cells versus non-depleted cells

status: Public on Sep 13 2012

city: Paris

first: Pierre

last: de la Grange

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

country: France

institute: GenoSplice technology

summary:
We generated a HeLa cell model of mucopolysaccharidosis IIIB (MPSIIIB) by depleting NAGLU. MPSIIIB-associated cell defects were prominent in NAGLU-depleted cells.
We explored alterations of metabolic pathways in NAGLU-depleted cells versus non-depleted control cells by performing gene expression profiling. Exon array transcriptome analysis showed 96 transcripts with increased expression level and 38 transcripts with decreased expression level in NAGLU-depleted versus non-depleted cells.

overall_design: Total RNA was extracted from two independent cultures of non-depleted cells and NAGLU-depleted cells. We considered a minimal fold change of 1.5 fold and a corrected P value lower than 0.05.

first: E

last: Roy

first: P

last: Flamant

first: J

last: Heard


title: c-Myc is a universal amplifier of gene expression [Microarray]

status: Public on Sep 27 2012

city: Morgantown

first: Gangqing

last: Hu

state: West Virginia

address: 64 Medical Center Drive

department: MicroBiology, Immunology, and Cell Biology

institute: West Virginia University

summary: The c-Myc HLH-bZIP protein has been implicated in physiological or pathological growth, proliferation, apoptosis, metabolism and differentiation at the cellular, tissue or organismal levels via regulation of numerous target genes. In part due to the incomplete inventory and functional accounting of Myc’s targets, no principle unifies Myc action. To relate the dynamics of Myc-binding with target expression and function in a system where Myc-levels are temporally and physiologically regulated, the transcriptomes and the genome-wide distributions of Myc, RNA polymerase II and chromatin modifications were compared during lymphocyte activation and in ES cells. A remarkably simple rule emerged from this quantitative analysis: Myc is not an on-off switch, but is a non-linear amplifier of expression, acting universally at active genes, except for immediate early genes that are strongly induced before Myc. This rule of Myc action explains the vast majority of Myc biology observed in literature.

overall_design: Quiescent B-cells (B0) were treated with lipopolysaccharide (LPS) for 4 hrs (B4), and resting T-cells (T0) were activated with conA for 4 hrs (T4) and for 14 hrs (T14). Following treatments,  RNA was harvested and chromatin was prepared at these time points. The RNA was analyzed by hybridization with Affymetrix microarrays.

first: Zuqin

last: Nie

first: Gang

last: Wei

first: Kairong

last: Cui

first: Arito

last: Yamane

first: Wolfgang

last: Resch

first: Lino

last: Tessarollo

first: Rafael

last: Casellas

first: Keji

last: Zhao

first: David

last: Levens


title: An Integrated Analysis of miRNA and mRNA Expressions of Non-small Cell Lung Cancer

status: Public on Sep 16 2012

city: Zhoushan

first: lina

last: ma

address: Renmin North Road No.238

country: China

institute: Zhoushan Hospital

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

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

overall_design: Refer to individual Series


title: A gene expression signature of emphysema-related lung destruction and its reversal by the tripeptide GHK.

first: Joshua

middle: David

last: Campbell

address: 72 East Concord St.

institute: Boston University

summary: BACKGROUND: Chronic obstructive pulmonary disease (COPD) is a heterogeneous disease consisting of emphysema, small airway obstruction, and/or chronic bronchitis that results in significant loss of lung function over time. METHODS: In order to gain insights into the molecular pathways underlying progression of emphysema and explore computational strategies for identifying COPD therapeutics, we profiled gene expression in lung tissue samples obtained from regions within the same lung with varying amounts of emphysematous destruction from smokers with COPD (8 regions x 8 lungs = 64 samples). Regional emphysema severity was quantified in each tissue sample using the mean linear intercept (Lm) between alveolar walls from micro-CT scans. RESULTS: We identified 127 genes whose expression levels were significantly associated with regional emphysema severity while controlling for gene expression differences between individuals. Genes increasing in expression with increasing emphysematous destruction included those involved in inflammation, such as the B-cell receptor signaling pathway, while genes decreasing in expression were enriched in tissue repair processes, including the transforming growth factor beta (TGF beta) pathway, actin organization, and integrin signaling. We found concordant differential expression of these emphysema severity-associated genes in four cross-sectional studies of COPD. Using the Connectivity Map, we identified GHK as a compound that can reverse the gene-expression signature associated with emphysematous destruction and induce expression patterns consistent with TGF beta pathway activation. Treatment of human fibroblasts with GHK recapitulated TGF beta-induced gene-expression patterns, led to the organization of the actin cytoskeleton, and elevated the expression of integrin beta1. Furthermore, addition of GHK or TGF beta restored collagen I contraction and remodeling by fibroblasts derived from COPD lungs compared to fibroblasts from former smokers without COPD. CONCLUSIONS: These results demonstrate that gene-expression changes associated with regional emphysema severity within an individual¿s lung can provide insights into emphysema pathogenesis and identify novel therapeutic opportunities for this deadly disease. They also suggest the need for additional studies to examine the mechanisms by which TGF beta and GHK each reverse the gene-expression signature of emphysematous destruction and the effects of this reversal on disease progression.

overall_design: Paired samples were obtained from 8 regions at regular intervals between the apex and base of each explanted lung from six patients with severe COPD and two donors.   The degree of emphysematous destruction was quantified in one sample from each region by mean linear intercept (Lm), while gene expression was profiled in the adjacent sample from the same region using the Affymetrix Human Exon 1.0 ST GeneChip.  Human fibroblast cell lines (HLF-1) were treated with GHK or TGF-Beta1 for 48 hours and profiled using the Affymetrix Human Gene 1.0 ST GeneChip.

middle: D

first: John

middle: E

last: McDonough

first: Julie

last: Zeskind

first: Tillie

last: Hackett

first: Dmitri

middle: V

last: Pechkovsky

first: Corry

last: Brandsma

first: Masaru

last: Suzuki

last: Gosselink

last: Liu

first: Yuriy

last: Alekseyev

first: Ji

last: Xiao

first: Xiaohui

last: Zhang

first: Shizu

last: Hayashi

first: Joel

last: Cooper

first: Wim

last: Timens

first: Dirkje

middle: S

last: Postma

first: Darryl

last: Knight

first: Marc

last: Lenburg

first: James

last: Hogg

first: Avrum

last: Spira


title: Cigarette smoking alters mRNA expression in human alveolar macrophages

status: Public on Oct 02 2012

city: Iowa City

first: Thomas

last: Bair

state: IA

address: 335 EMRB

institute: University of Iowa

summary: Alveolar macrophages from never smokers and active smokers were isolated by bronchoalveolar lavage and gene expression was measured. Chronic cigarette smoke exposure, as occurs in smoker's lungs, leads to significant changes in gene expression.  Of note, RNA was isolated immediately following bronchoscopy. Alveolar macrophage levels were >95%.

overall_design: 4 never smokers and 4 active smokers were recruited for the study. After bronchoalveolar lavage and RNA isolation, gene expression was measured using Affymetrix Human Exon 1.0 ST arrays.

first: Martha

middle: M

last: Monick


title: Genome-wide analysis of  microRNA expression in Non-small Cell Lung Cancer

first: lina

last: ma

summary:
Analysis of NSCLC development at microRNA expression level.  Results shows that has-miR-96 is significant up-regulated in the cancer tissue compared with the adjacent normal tissue.
Illumina Human v2 MicroRNA expression beadchip

overall_design: Total microRNA obtained from 6 paired NSCLC cancer tissue and the adjacent normal tissue.

first: Lina

last: Ma

first: Xiaoguang


title: Inducible Astrocytomas in Genetically Engineered Mice: Affymetrix

city: Seattle

first: Burak

last: Kutlu

state: WA

address: 1441 North 34th Street

institute: Institute for Systems Biology

summary:
To determine the regulatory pathways necessary for astrocytoma formation within complex adult brain microenvironments, we engineered mice for adult astrocyte-specific disruption of key regulators (pRb, Kras and Pten). Drivers of all astrocytoma grades were identified using CreERTM-inducible alleles. Inactivation of pRb was necessary to initiate grade II disease, and was the only lesion to do so.  Additional activation of Kras progressed disease to grade III, while further Pten inactivation facilitated grade IV (glioblastoma) progression. These outcomes were elicited whether somatic events were induced broadly or focally. In vivo inactivation of pRb, which induced astrocyte proliferation and apoptosis, activated the MAPK pathway, while Kras activation and Pten loss triggered PI3K pathways.
TRPhet denotes mice with Inhibition of Rb, Over-expression of Kras and Deletion of one Copy of PTEN; TRPnull denotes mice with Inhibition of Rb, Over-expression of Kras and Deletion of both copies of PTEN; TR denotes mice with Inhibition of Rb, Over-expression of Kras.

overall_design: high grade astrocytoma tumors were obtained from tamoxifen induced mice

first: Yurong

last: Song


title: Gene expressions of memory B cells and other type of B cells

first: Kaji

last: Tomohiro

address: 1-7-22, Suehiro-cho, Tsurumi-ku

institute: RIKEN

summary: To obtain insight into the genetic basis of the increase of functional activity of memory B cells over time, we compared the gene expression profiles of day 7 and day 40 NP-specific/IgG1 memory B cells, GC B cells and plasma cells in immunized WT mice and naïve B cells, before and after activation in vitro.

overall_design: Total RNAs in three replicates of NP-specific/IgG1 memory B cells, GC B cells and plasma cells in immunized WT mice at day 7 and 40 postimmunization and naïve follicular and marginal zone B cells, before and after activation in vitro, were amplified and labeled according to the Affymetrix's instructions. cRNA was hybridized to Mouse Genome 430 2.0 GeneChips (Affymetrix).

first: Akiko

last: Sugimoto

first: Atushi

last: Hijikata

first: Takeshi

last: Nagashima

first: Osamu

last: Ohara

first: Mariko

last: Okada

first: Toshitada

last: Takemori


title: Transcriptional profiling of SmoM2 expressing IFE cells at different stages of basal cell carcinoma formation

status: Public on Sep 06 2012

city: Brussels

first: KHALIL

last: KASS YOUSSEF

address: 808, Route de Lennick

country: Belgium

institute: ULB-IRIBHM

summary:
Basal cell carcinoma initiating cells undergo profound and rapid reprogramming into embryonic hair follicle progenitor like fate upon SmoM2 expression. Activation of Wnt/β-catenin signaling pathways is required in a cell autonomous manner for the reprogramming of adult IFE progenitors into EHFP-like fate as well as for tumor initiation.
We used MA to define the molecular changes that occur in basal cell carcinoma initiating cells form the first oncogenic hit to the development of invasive tumor and further on to investigate the role of Wnt/β-catenin signaling activation in molecular changes occurring early during BCC development.

overall_design: Basal interfollicular cells expressing SmoM2 were FACS isolated at different stages of tumor development and in β-catenin LOF condition for RNA extraction and hybridization on Affymetrix microarrays. By comparing the transcriptional profile of SmoM2 expressing cells with FACS-isolated cells from littermate control mice, we determined a list of genes differentially regulated by SmoM2 expression as specific SmoM2 signature.

first: Khalil

middle: K

last: Youssef

first: Cédric

last: Blanpain


title: Phf19 knockdown effect on F9 embryonal carcinoma cells

status: Public on Dec 20 2012

city: Birmingham

first: Rui

last: Lu

state: AL

address: 1824 6th Ave S

institute: Univ of Alabama at Birmingham

summary:
PCL family protein Phf19/Pcl3 is one of the accessory components of the PRC2 core complex, and Phf19 is highly expressed in murine ES cells and an ES cell-like embryonic carcinoma cell line, F9 cells.
Here we performed microarray analysis of embryonal carcinoma cell line F9 following Phf19 knockdown by shRNA. Knocking down Phf19/Pcl3 in F9 embryonic cells led to derepression of numerous PRC2 direct target genes.

overall_design: 4 sampels including 2 shRNA vector control cell lines and 2 shPhf19 cell lines were used for RNA extraction and Affymetrix mouse 430 2.0 arrays.

first: Ling

last: Cai

first: Greg

last: Wang


title: Expression data for inbred mouse brains

status: Public on Sep 04 2012

city: London

first: Sarah

last: Lloyd

address: Queen Square

department: Neurodegenerative Disease

institute: MRC Prion Unit, UCL Institute of Neurology

summary: Prion diseases are fatal neurodegenerative disorders that include bovine spongiform encephalopathy (BSE) and scrapie in animals and Creutzfeldt-Jakob disease (CJD) in humans. They are characterized by long incubation periods, variation in which is determined by many factors including genetic background. In some cases it is possible that incubation time may be directly correlated to the level of gene expression. In order to test this hypothesis we combined incubation time data from five different inbred lines of mice with quantitative gene expression profiling in normal brains and identified five genes with expression levels that correlate with incubation time. One of these genes, Hspa13 (Stch), is a member of the Hsp70 family of ATPase heat shock proteins which have been previously implicated in prion propagation. To test whether Hspa13 plays a causal role in determining the incubation period we tested two over-expressing mouse models. The Tc1 human chromosome 21 (Hsa21) transchromosomic mouse model of Down syndrome is trisomic for many Hsa21 genes including Hspa13 and following Chandler/RML prion inoculation shows a 4% reduction in incubation time. Furthermore, a transgenic model with eight fold over-expression of mouse Hspa13 exhibited highly significant reductions in incubation time of 16%, 15% and 7% following infection with Chandler/RML, ME7 and MRC2 prion strains respectively. These data further implicate Hsp70-like molecular chaperones in protein misfolding disorders such as prion disease.

overall_design: 5 inbred lines of mice, 5 samples for each line


title: Inducible Astrocytomas in Genetically Engineered Mice


title: In vivo gene expression data from wild type and CTLA-4 KO 5C.C7 T cells

status: Public on Sep 05 2012

city: New York

first: Jeffrey

last: Zhao

address: 1275 York Avenue

department: Genomics Core

institute: Memorial Sloan Kettering Cancer Center

summary: CTLA-4 is thought to inhibit effector T cells both intrinsically, by competing with CD28 for B7 ligands, and extrinsically, through the action of regulatory T cells. We studied in vivo responses of normal and CTLA-4-deficient antigen-specific murine effector CD4+ T cells. In order to do these studies in a physiological model of immunity to foreign antigen, we transferred small numbers of congenically marked RAG2-deficient 5C.C7 T cells with either a normal or knockout allele of CTLA-4 into normal syngeneic B10.A recipient mice. The T cells were then activated by immunization with MCC peptide and LPS. To look for transcriptional signatures of negative regulation of T cell responses by CTLA-4, we used microarray analysis to compare transcripts in wild type and CTLA-4 KO 5C.C7 T cells four days after immunization. This is the first instance in which differences are observed in extent of accumulation of wild type and CTLA-4 KO 5C.C7 T cells.

overall_design: To compare the gene expression profile between wild type and CTLA-4 KO adoptively transferred T cells 4 days after immunization.

first: Emily

last: Corse

first: James

last: Allison


title: Transcript profiling of Lin-Sca-1+c-Kit+ (LSK) cells from mice reconstituted with wild type and necdin null fetal liver cells following a sublethal dose of irradiation (6,5 Gy)

summary:
compare the gene expression profile between irradiated Lin-Sca-1+c-Kit+ (LSK) cells from mouse bone marrow reconstituted with wild type and necdin null fetal liver cells
The Affymetrix oligonucleotide array was used for this analysis

overall_design: compare the gene expression profile betweenirradiated Lin-Sca-1+c-Kit+ (LSK) cells from mouse bone marrow reconstituted with wild type and necdin null fetal liver cells

first: Stephen

last: Nimer

first: Takashi

last: Asai


title: Novel Foxo1-dependent Transcriptional Programs Control Treg Cell Function [Affymetrix gene expression data]

first: Willey

last: Liao

address: 101 Avenue of the Americas

department: Bioinformatics

institute: New York Genome Center

summary: Regulatory T (Treg) cells characterized by expression of the transcription factor forkhead box P3 (Foxp3) maintain immune homeostasis by suppressing self-destructive immune responses1-4.  Foxp3 operates as a late acting differentiation factor controlling Treg cell homeostasis and function5, whereas the early Treg cell lineage commitment is regulated by the Akt kinase and the forkhead box O (Foxo) family of transcription factors6-10. However, whether Foxo proteins act beyond the Treg cell commitment stage to control Treg cell homeostasis and function remains largely unexplored.  Here we show that Foxo1 is a pivotal regulator of Treg cell function.  Treg cells express high amounts of Foxo1, and display reduced T-cell receptor-induced Akt activation, Foxo1 phosphorylation, and Foxo1 nuclear exclusion.  Mice with Treg cell-specific deletion of Foxo1 develop a fatal inflammatory disorder similar in severity to Foxp3-deficient mice, but without the loss of Treg cells.  Genome-wide analysis of Foxo1 binding sites reveals ~300 Foxo1-bound target genes, including the proinflammatory cytokine Ifng, that do not appear to be directly regulated by Foxp3.  These findings demonstrate that the evolutionarily ancient Akt-Foxo1 signaling module controls a novel genetic program indispensable for Treg cell function.

overall_design: Regulatory T cells were FACS sorted in WT mice (2 reps), Foxo1 KO mice (2 reps), mice expressing a constitutively active form of Foxo1 (1 rep), and Foxo1 KO mice expressing constitutively active Foxo1. We identified genes differentially expressed in WT vs. KO mice and assessed whether expression was recovered in the KO in presence of constitutively active Foxo1

first: Weiming

last: Ouyang

first: Will

first: Chong

last: Luo

last: Yin

first: Morgan

last: Huse

first: Myoungjoo

last: Kim

first: Min

last: Peng

first: Pamela

last: Chan

first: Qian

last: Ma

first: Yifan

last: Mo

first: Dies

last: Meijer

first: Keji

first: Alexander

middle: Y

last: Rudensky

first: Gurinder

last: Atwal

first: Michael

middle: Q

last: Zhang

first: Ming

middle: O

last: Li


title: Genome-wide Profiling of Progesterone Receptor and GATA2 Binding in the Mouse Uterus [Affymetrix]

city: Research Triangle Park

first: Franco

last: DeMayo

state: NC

address: Building 101, Room F191 111 T.W. Alexander Drive

department: Reproductive and Developmental Biology Laboratory

institute: National Institute of Environmental Health Sciences

summary: Progesterone (P4) signaling through its nuclear transcription factor, the progesterone receptor (PR), is essential for normal uterine function.  Although deregulation of PR mediated signaling is known to underscore uterine dysfunction and a number of endometrial pathologies, the early molecular mechanisms of this deregulation are unclear. To address this issue, we have defined the genome-wide PR and GATA2 cistrome in the murine uterus using chromatin immunoprecipitation followed by massively parallel sequencing (ChIP-seq). In uteri of ovariectomized mice, we identified 6367 PR binding sites in the absence of P4 ligand; however, this number increased at nearly three fold (18,432) following acute P4 exposure. Sequence analysis revealed that approximately 73% of these binding sites contain a progesterone response element (PRE) or a half-site motif recognized by the PR. Many previously identified P4 target genes known to regulate uterine function were found to contain PR binding sites, confirming the validity of our methodology.  In addition we identified 46,183 GATA2 binding sites in P4 treatment conditions with 7,954 binding sites overlapping that of the PR.

overall_design: Gene expression data from ovariectomized Oil and P4 treated Gata2 f/f uterus horn

first: Cory

middle: A

last: Rubel

first: Rainer

last: Lanz

first: Heather

middle: L

last: Franco

first: Ertug

last: Kovanci

first: Sally

last: Camper

first: Qiang

last: Tong

first: Jae-Wook

last: Jeong

first: John

last: Lydon

first: Francesco


title: UTX regulated genes in mouse embryonic stem cells

city: Bethesda

first: Chaochen

last: Wang

state: MD

address: 9000 Rockville Pike

department: LGP

institute: NIDDK

summary: UTX gene is localized on the X chromosome, identified as a demethylase on histone H3 lysine 27.

overall_design: Two independent UTX conditional knockout (cKO) embryonic stem cell lines and two UTX knockout (KO) cell lines were cultured on 0.1% gelatin-coated dishes without feeder cells at desity of 1 million cells/10 cm dish. Cells were cultured overnight and collected. Total RNAs were sequentially purified with Trizol (Invitrogen) and RNeasy kit (Qiagen) and analyzed on Mouse Genome 430 2.0 Array (Affymetrix) at NIDDK Microarray Core Facility following standard protocols.

first: Kai

last: Ge


title: Expression data from primary mouse keratinocytes derived from keratinocyte-specific MED1 null mouse and control littermate

status: Public on Sep 02 2012

city: Suita

first: Takeshi

last: Nakajima

address: 2-2 Yamadaoka

institute: Osaka University

summary:
MED1 (Mediator complex subunit 1) is expressed by human epidermal keratinocytes and functions as a coactivator of several transcription factors. To elucidate the role of MED1 in keratinocytes, we established keratinocyte-specific MED1-null (MED1epi-/-) mice using the K5Cre-LoxP system.
To elucidate the mechanism(s) underlying abnormalities of keratinocytes derived from MED1epi-/- mice, we compared the gene expression patterns of MED1epi-/--derived keratinocytes with their wild type counterparts by microarray analysis.

overall_design:
Generation of the MED1 conditional null mutation in epidermal keratinocytes and cell culture:
MED1flox/flox mice (Jia et al, J Biol Chem 279:24427. 2004) were mated with K5Cre mice (Tarutani et al, Proc Natl Acad Sci U S A 94:7400. 1997) to generate F1 K5Cre+;MED1flox/+ mice. The K5Cre+;MED1flox/+ mice were then mated with MED1flox/flox mice to generate K5Cre+;MED1flox/flox mice (MED1epi-/-). Mice were screened for presence of the transgene by PCR using specific primers for the floxed MED1 gene and the human K5 gene according to the previous reports. Skin of newborn mice was excised after the mice were sacrificed with excessive anesthetic and were treated with dispase followed by trypsin to separate the epidermis from the dermis. Keratinocytes were seeded on type I collagen coated dishes, and were cultured in CnT07 conditioned culture medium (CELLnTEC, Bern, Switzerland). Keratinocytes were used for the experiment as a primary culture. All animal studies were conducted according to protocols approved by the Institutional Animal Care and Use Committee at Osaka University.
Microarray analysis:
For comprehensive comparison of gene expression patterns between keratinocytes derived from MED1epi-/- and from WT mice, microarray analysis was used. Total RNAs were extracted using an RNeasy kit (Qiagen, San Diego, CA). Then, 2μg total RNA was reverse transcribed to cDNA with T7 oligo d(T) primer (Affymetrix, Santa Clara, CA). The cDNA synthesis products were used for in vitro transcription reactions containing T7 RNA polymerase and biotinylated nucleotide analogue (pheudouridine base) cRNAs. The labeled cRNA products were then fragmented and loaded onto GeneChip(R) Mouse Genome 430 2.0 arrays (Affymetrix), and were hybridized according to the manufacturer’s protocol. Streptavidin-Phycoerythrin (Molecular Probes) was used as the fluorescent conjugate to detect hybridized target sequences. Raw intensity data from the GeneChip array were analyzed by GeneChip Operating Software (Affymetrix).

first: Shigeki

last: Inui

first: Satoshi

last: Itami


title: Anti-proliferative tumor suppressor-like activity of mir-9 overexpression and identification of novel mir-9 targets by trancription profiling in breast cancer cells

city: Galway

first: Charles

last: Spillane

state: Galway

address: University Road

department: Botany and Plant Science

country: Ireland

institute: National University of Ireland, Galway

summary: Investigation of genome-wide effects (transcriptome profiling) and direct targets of mir-9 in MCF-7 cells transfected with mir-9 in two dosages (1X and 2X)

overall_design: Following transfections of mir-9 or control miRNA mimics, total RNA was isolated and microarray profiling was performed.

first: S

last: Selcuklu

first: Mark

last: Donoghue

first: Matheus

last: Gomes

first: Prasad

last: Kovvuru

first: Antoine

last: Fort

first: Mohan

last: Muniyappa

first: Michael

middle: J

last: Kerin

first: Anton

last: Enright


title: Expression data from sorted interfollicular basal cells (alpha6 integrin-high/CD34-neg) from K14CREER and InvCREER/RosaYFP induced mice

city: Bruxelles

first: Cédric

last: Blanpain

address: route de Lennik 808

institute: IRIBHM

summary: The skin interfollicular epidermis (IFE) is the first barrier against the external environment and its maintenance is critical for survival. Two seemingly opposite theories have been proposed to explain IFE homeostasis. One posits that IFE is maintained by a long-lived slow-cycling stem cell (SC) population that give rise to short-lived transit-amplifying (TA) cell progeny, while the other suggests that homeostasis is achieved by a single committed progenitor (CP) that balances stochastic fate. Here, we probed the cellular heterogeneity within the IFE using two different inducible CREER targeting IFE progenitors. Quantitative analysis of clonal fate data and proliferation dynamics demonstrate the existence of two distinct proliferative cell compartments composed of slow-cycling SC and CP, both of which undergo population asymmetric self-renewal. However, following wounding, only SCs contribute substantially to the repair and long-term regeneration of the tissue, while CP cells make a minimal and transient contribution.

overall_design:
Transcriptional profile of InvCREER/RosaYFP and K14CREER/RosaYFP targeted FACS-isolated alpha6 integrin-high CD34-neg basal cells from mouse tail epidermis.

Skin epidermis was removed from tail bone and incubated overnight in HBSS (Gibco) 0.25% trypsin (Gibco) at 4°C. Epidermis was separated from the dermis and incubated on a rocking plate (100 rpm) at room temperature for 5 min. Basal cells were mechanically separated from the epidermis by flushing 10 times under the epidermis. Tissues were then cut in pieces of 1 mm2 with scalpel, and trypsin was neutralized by adding DMEM medium (Gibco) supplemented with 2% Chelex Fetal Calf Serum (FCS). Samples were filtrated on 70 and 40µm filter (Falcon). Immunostaining was performed using biotin-conjugated anti-CD34 (clone RAM34; BD Biosciences) PE-conjugated anti-α6-integrin (clone GoH3; BD biosciences). Primary antibodies were washed with 2% FCS/PBS and cells were incubated for 30 min in APC conjugated streptavidin (BD Biosciences) secondary antibodies, on ice, with shaking every 10 min. Living K14- and involucrin-expressing epidermal cells were gated by forward scatter, side scatter, negative staining for Hoechst dye and by following the YFP signal. Basal cells from the interfollicular epidermis were targeted using CD34 negative alpha 6 high gating. Fluorescence-activated cell sorting analysis was performed using FACSAria I at high pressure (70 psi) and FACSDiva software (BD Biosciences). Sorted cells were harvested directly in the lysis buffer provided by the RNeasy microkit (QIAGEN) supplemented with 1µl of beta-mercaptoethanol for every 100µl of lysis buffer. RNA extraction was performed on freshly sorted cells according to the manufacturer’s protocol.

first: Guilhem

last: Mascré

first: Sophie

last: Dekoninck

first: Panagiotta

last: Sotiropoulou

first: Benjamin

last: Drogat

first: Cedric


title: Expression profiling of primary leukemia initiating cell-enriched population induced by AML1-ETO9a

city: La Jolla

first: Dong-Er

last: Zhang

state: CA

address: 3855 Health Sciences Drive, Mail Stop 0815

department: Cancer Center

institute: University of California San Diego

summary:
Combined gene expression and DNA occupancy profiling identifies JAK/STAT signaling as a valid therapeutic target of t(8;21) AML

t(8;21) is commonly associated with acute myeloid leukemia (AML). The resulting AML1-ETO fusion proteins are involved in the pathogenesis of AML. To identify novel molecular and therapeutic targets, we performed combined gene expression and promoter occupancy profiling using a primary leukemia initiating cell-enriched population induced by AML1-ETO9a (AE9a). CD45, a negative regulator of cytokine/growth factor receptor and JAK/STAT signaling, is greatly downregulated; furthermore JAK1 and JAK2 are upregulated in these leukemia cells. Consequently, JAK/STAT signaling is enhanced in the AE9a leukemia cells. Importantly, AE9a leukemia cells are highly susceptible to perturbation of JAK/STAT signaling, and a JAK2-selective inhibitor, TG101209, effectively targets these leukemia cells in vivo, suggesting the potential efficacy of JAK2 inhibitors in treating t(8;21) AML.

overall_design: Wild-type or AE9a leukemic samples in triplicate.

first: Miao-Chia

last: Lo

first: Luke

middle: F

last: Peterson

first: Ming

last: Yan

first: Eun-Young

last: Ahn

first: Hans

middle: B

last: Ommen

first: I-Ming

last: Chen

first: Peter

last: Hokland

first: Cheryl

last: Willman


title: Gene expression profiling of CA10 and NHD13 murine AML

status: Public on Sep 01 2012

first: Rachel

middle: Lynn

last: Novak

state: Maryland

address: 41 Center Drive

institute: NCI

summary: We have compared the gene expression profiles of leukemic tissues in two different mouse models of AML, CALM-AF10 and NHD13, to clincally healthy transgenic and wildtype hematopoetic tissue to identify genes and pathways that can collaborate with these oncogenic fusion proteins to promote leukemic transformation.

overall_design: CA10 and NHD13 transgenic mice were sacrificed when clinical signs of leukemia manifested (mice were hunched, skinny, or had an abnormal complete blood count). For comparsion, we harvested age matched bone marrow, thymi, and spleen from wildtype and clinically healthy trangenic tissues. Transgenic animals were considered clinically healthy if no evident signs of leukemia were present.

first: David

middle: P

last: Harper

last: Caudell

first: Christopher

last: Slape

first: Sarah

middle: H

last: Beachy

last: Aplan


title: Comparing gene expression between PICs and satellite cells from 1 week old muscle

city: PARIS

first: Alice

last: Pannérec

address: 105 boulevard de l'hopital

institute: INSERM 787

summary: The satellite cell is considered the major tissue-resident stem cell underlying muscle regeneration, however, multiple non-satellite cell myogenic progenitors have been identified. PW1/Peg3 is expressed in satellite cells as well as a subset of interstitial cells with myogenic potential termed PICs (PW1+ Interstitial Cells). PICs differ from satellite cells by their anatomical location (satellite cells are sublaminal and PICs are interstitial), they do not express any myogenic marker and arise from a Pax3-independent lineage. Upon isolation from juvenile muscle (1 to 3 weeks old), PICs are capable to form both skeletal and smooth muscle suggesting they constitute a more plastic population compared to satellite cells. We used microarrays to gain insight into the relantionship between PICs and satellite cells.

overall_design: PICs and satellite cells were isolated from 1-week old mouse muscle and subsequent RNA extraction was performed.

last: Sassoon


title: Induction and molecular signature of pathogenic Th17 cells

city: Boston

first: Youjin

last: Lee

address: 4 Blackfan Circle, HIM#730

institute: Harvard Medical School/ Brigham Women's Hospital

summary: TGF-beta3 produced by developing Th17 cells induces highly pathogenic T cells that are functionally and molecularly distinct from TGF-beta1-induced Th17 cells. The microarray data represent a distinct molecular signature for pathogenic versus non-pathogenic Th17 cells.

overall_design:
Total of seven groups with two to four samples per group from two independent experiments. The no cytokines group (Th0) was used as a control to normalize the data.

7 groups:
B6: (IL-1beta, IL-6)
B623: (IL-1beta, IL-6, IL-23)
T16: (TGF-beta1, IL-6)
T1623: (TGF-beta1, IL-6, IL-23)
T36: (TGF-beta3, IL-6)
T3623: (TGF-beta3, IL-6, IL-23)
NOCYTO: no cytokines

first: Amit

last: Awasthi

first: Nir

last: Yosef

first: Francisco

last: Quintana

first: Anneli

last: Peters

first: Chuan

last: Wu

first: Markus

last: Kleinewietfeld

first: Sharon

last: Kunder

last: Hafler

first: Raymond

last: Sobel

first: Vijay

last: Kuchroo


title: Expression data from untreated and DSS-treated Adamts12 WT and KO mice

city: OVIEDO

first: ANGELA

last: MONCADA PAZOS

address: FERNANDO BONGERA

institute: UNIVERSIDAD DE OVIEDO

summary:
Adamts12-deficient mice undergo more severe colitis than WT mice after induction with DSS.
We used microarrays to determine the gene expression differences between Adamts12-deficient and WT mice during ulcerative colitis induced with DSS (dextran sodium sulfate)

overall_design: Fragments of distal colon from DSS-treated (2% DSS during 7 days and 1 day of recovery) and untreated Adamts12-deficient and WT mice were obtained for RNA extraction and hybridiztion with Affymetrix microarrays

first: Angela

last: Moncada-Pazos

first: Carlos

last: Lopez-Otin

first: Santiago

last: Cal

first: Alvaro

last: Obaya


title: Ewing Sarcoma

city: Nashville

first: Scott

last: Borinstein

address: 2200 Pierce Ave

institute: Vanderbilt University

type:
Expression profiling by array
Methylation profiling by array

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

overall_design: Refer to individual Series


title: Microarray analysis of gene expression of microdissected epidermis and dermis in mycosis fungoides and adult T-cell leukemia/lymphoma

city: Kurume

first: Keiko

last: Hashikawa

state: Fukuoka

department: Department of Dermatology

institute: Kurume University School of Medicine

summary: In the epidermis, CCR4, CCR6, CCL20 and CCL27 were higher in ATLL than in MF.

overall_design:
We obtained the epidermal samples from MF (n=5) and ATLL (n=5) with the aid of laser microdissection. Complementary RNA  amplification were used for gene expression profiling by microarray analysis. We compaired MF with ATLL in epidermis.
We obtained the epidermal dermal samples from MF (n=3) and ATLL (n=3) with the aid of laser microdissection. Complementary RNA  amplification were used for gene expression profiling by microarray analysis. We compaired MF with ATLL in dermis.

first: Fumiko

last: Arakawa


title: MicroRNA Profiling of Surgical Myectomy Tissue from Patients with Hypertrophic Cardiomyopathy

city: Rochester

first: Virginia

middle: Bartleson

last: Hebl

state: MN

address: 200 1st St. SW

institute: Mayo Clinic

summary: Using a high-throughput gene expression profiling technology, we have illuminated novel potential microRNA (miRNA) components of the molecular disease process underlying human hypertrophic cardiomyopathy (HCM).  It is hoped that this will fuel future research endeavors that will eventually uncover the role miRNAs may play in the phenotypic heterogeneity of the disease, and thus, provide potential tools for identifying patients with benign versus malignant forms of the disease.

overall_design: Case (n = 107)-Control (n=20) study comparing the microRNA transcriptome of cardiac tissues from patients with hypertrophic cardiomyopathy to the microRNA transcriptome of control donor cardiac tissues.

first: J

last: Bos

first: Ann

last: Oberg

first: Zhifu

last: Sun

first: Daniel

last: Herman

first: Polakit

last: Teekakirikul

middle: G

last: Seidman

first: Christine

first: Cristobal

last: dos Remedios

first: Hartzell

last: Schaff

first: Joseph

last: Dearani

first: Steve

middle: R

last: Ommen

first: Frank

last: Brozovich

first: Michael

last: Ackerman


title: 5- AZA treatment of EWS cell lines

summary: The Ewing Sarcoma cell lines A673, SK-ES-1, and SK-N-MC were treated with without 5-AZA to identify upregulated genes

overall_design: A673, SK-ES-1, and SK-N-MC were treated with 5-AZA

middle: C


title: Expression data from  E2f7/E2f8 and E2f1/E2f2/E2f3 null liver (Affymetrix)

status: Public on Aug 31 2012

city: Columbus

first: Madhu

last: Ouseph

state: Ohio

address: 460w 12th Ave

institute: The Ohio State University

summary: To understand the underlying cause and mechanisms of changes in hepatocyte ploidy upon Albumin-Cre mediated deletion of E2f7&8 and Mx1-Cre mediated deletion of E2f1,2&3, we analysed global gene expression of 6 weeks and 2 months liver tissues.

overall_design: RNA was extracted from liver tissues. Gene deletion in samples confirmed by PCR genotyping of DNA isolated from each sample.

first: M

first: H

last: Chen

first: T

last: Pecot


title: Polysome profiling in liver identifies dynamic regulation of endoplasmic reticulum translatome by obesity and fasting

city: Bostn

first: Suneng

last: Fu

address: 665 Huntington Ave

department: Genetics and Complex Diseases

institute: Harvard School of Public Health

type:
Expression profiling by array
Other

summary: Obesity-associated metabolic complications are generally considered to emerge from abnormalities in carbohydrate and lipid metabolism, whereas the status of protein metabolism is not well studied. Here, we performed comparative polysome and associated transcriptional profiling analyses to study the dynamics and functional implications of endoplasmic reticulum (ER)-associated protein synthesis in the mouse liver under conditions of obesity and nutrient deprivation.

overall_design: lean wild type and genetically obese (ob/ob) mice with or without overnight fasting were sacrificed with their liver tissues removed.  ER-associated polysomes were purified and analyzed by microarray.

first: Gokhan

middle: S

last: Hotamisligil


title: Expression data from  E2f7/E2f8/E2f3a null placentas and embryos

summary: To understand the underlying cause and mechanisms of embryonic lethality observed in combined loss of E2f7 and E2f8, we compared global gene expression profiles of wild type, germline deleted and sox2-Cre/Cyp19-Cre deleted embryos and placentas.

overall_design: RNA was extracted from E10.5 embryos and placentas. Gene deletion in samples confirmed by PCR genotyping of DNA isolated from each sample.

first: J

last: Li


title: Transcriptomics-based characterization of smoking and cessation effects in mouse muscle

city: King of Prussia

first: Guanghui

last: Hu

state: PA

address: 709 Swedeland Road

institute: GlaxoSmithKline

summary:
COPD is a disorder characterized by the progressive development of airflow limitation that is not fully reversible. Cigarette smoke has been generally accepted as the most important of many risk factors for the development of COPD.
We used microarray technology to perform comprehensive gene expression profiling of smoke exposure and cessation effects in mouse muscle tissue.

overall_design: Mice received nose-only exposure of 4% mainstream cigarette smoke or air (sham exposure) for 2 hours/day, 5 days/week for 2, 12 or 24 weeks.  Mice undergoing smoke cessation received cigarette smoke exposure for 12 weeks, and then sham exposure for 12 weeks.

first: Patricia

last: Podolin


title: Expression data from sleep deprivation experiment in mouse hippocampus

city: Spokane

first: Lucia

last: Peixoto

address: PO Box 1495

department: College of Medicine

institute: Washington State University, Spokane

summary: We used microarrays to detail the global programme of gene expression underlying the effect of sleep deprivation in the mouse hippocampus and identified distinct classes of regulated genes during this process.

overall_design: Hippocampal tissue was taken from sleep deprived mice and time-matched non-sleep-deprived control animals that were left undisturbed in their home cages during the sleep deprivation period for a total of 8 and 9 replicates per group. RNA was isolated and cDNA was synthesized from hippocampal tissue, and the sample from each animal was hybridized to a separate Affymetrix Mouse 430_2 microarray

first: Chris

last: Vecsey

first: Ted

last: Abel


title: Murine PDAC cell lines

city: München

first: Günter

last: Schneider

address: Ismaninger Str. 22

department: II. Medizinische Klinik

country: Germany

institute: Technische Universität München

summary: Expression profiles of 28 murine pancreatic cancer cell lines isolated from a KrasG12D-based mouse model of pancreatic cancer

overall_design: mRNA of 28 low passaged murine pancreatic cancer cell lines was extracted and hybridized to Affymetrix microarrays

first: Dieter

last: Saur

first: Mariel

last: Paul

first: Annegret

last: Gohlke


title: Androgenetic haploid embryonic stem cells

status: Public on Aug 30 2012

city: Beijing

first: Wei

address: Beichen West Road

department: State key lab of Reproductive Biology

institute: Institute of Zoology, Chinese Academy of Sciences

type: Genome variation profiling by genome tiling array


title: Gene expression data from ahES cells, ES cells, MEF cells and round sperm

summary:
Haploid stem cells offer an easy-to-manipulate genetic system and therefore have great values for studies of recessive phenotypes. Here, we show that mouse androgenetic haploid ES (ahES) cell lines can be established by transferring sperm into enucleated oocyte. The ahES cells maintain haploidy and stable growth over 30 passages, express pluripotent markers, possess the ability to differentiate into all three germ-layers in vitro and in vivo, and contribute to germline of chimeras when injected into blastocysts. Although epigenetically distinct from sperm cells, the ahES cells can produce viable and fertile progenies after intracytoplasmic injection into mature oocytes. The oocyte injection procedure can also produce viable transgenic mice from genetically engineered ahES cells.
We used microarrays to compare the global programme of gene expression among ahES cells, normal diploid ES cells, MEF cells and round sperm cells and found that gene expression pattern of ahES cells was highly similar with ES cells but was distinct from MEF cells and round sperms.

overall_design: Androgenetic haploid ES cells were FACS sorted to harvest the G0/G1 phase haploid cells. Total RNA were extracted from three ahES cell lines (AH129-5, AH129-N1, AH129-NC1, all 129Sv genetic background), two ES cell lines ( CS1-1, R1, 129Sv background), MEF cells and round sperm and hybridized with Affymetrix GeneChip 430 2.0 array. Data were collected and analyzed to compare their gene expression pattern.

first: Qi

last: Zhou

first: Xiaoyang

last: Zhao


title: Expression data from mice mammary glands from Elf5 knockout (KO) and wildtype controls

city: BUFFALO

first: SATRAJIT

last: SINHA

address: 701 ELLICOTT STREET

institute: SUNY AT BUFFALO

summary: We developed conditional knockout mice where the transcription factor Elf5 (also called ESE-2) is deleted in the mammary glands. Loss of Elf5 results in block in alveologenesis and epithelial differentiation defects. Mammary gland samples from Elf5 knockout and wild type animals were analyzed for global transcriptome changes.

overall_design: We used microarrays to performing transcriptional profiling of Elf5KO and control mammary glands at Lac1 (Lactation day 1)

first: Rumela

last: Chakrabarti

first: Yong

last: Wei

first: Mario

last: Blanco

first: Rose-Anne

last: Romano

first: Kirsten

last: Smalley

first: Song

last: Liu

first: Yibing

last: Kang

first: Satrajit

last: Sinha


title: iTreg cells compared to WT Total Treg

city: New York

first: Jonathan

last: Weiss

address: 550 First Ave

institute: NYU Medical Center

summary: iTreg cells from Tbmc mLN mice treated with one week of 1% Oral Ova were compared to Total Treg from WT mice.

overall_design:
Tbmc mice were treated with 1% Oral Ova and Foxp3 GFP+ CD4+ cells were sorted from mLN.
CD4+ Foxp3+ cells were also sorted from WT Foxp3 GFP Balb/c mice.

middle: M

first: Juan

last: Lafaille


title: Comparison of Splenic Nrp1- and Nrp1+ Treg Populations

summary: To compare subpopulations of Treg cells in wild type mice based upon Nrp1 Expression, differentiating  nTreg and iTreg

overall_design: Cells were FACS sorted based upon expression of CD4, Foxp3 and expression of Nrp1.


title: Expression data from primary and secondary CD4 T cell effectors responding towards influenza A virus infection

status: Public on Aug 27 2012

city: Worcester

first: Susan

last: Swain

address: 55 Lake Avenue North

department: Pathology

institute: University of Massachusetts Medical School

summary:
How secondary CD4 T cell effectors, derived from resting memory cells, differ from primary cells, derived from naïve precursors, and how such differences impact recall responses to pathogens is unknown.
We used microarrays to detail the global programme of gene expression underlying differences between primary and secondary CD4 T cell effectors purified from the spleen, dLN, and lung on day 7 following A/PR8/34 influenza infection.

overall_design: Congenic naïve or in vivo influenza primed memory HNT TCR trangenic CD4 T cells were sort purifed from the spleens, dLNs, and lungs of infected mice on day 7 post infection for RNA extraction and hybridization on Affymetrix microarrays. We sought to obtain only CD4 T cell populations that had entered into the immune response by also sorting and collecting only those cells that had divided at least 5 times by CFSE analysis.

first: Tara

last: Strutt

first: Karl

middle: K

last: McKinstry


title: Scaling proprioceptor gene transcription by retrograde NT3 signaling

status: Public on Aug 23 2012

city: Basel

first: Tim

last: Roloff

address: Maulbeerstrasse 66

department: Functional Genomics

country: Switzerland

institute: FMI

summary:
Transcriptional analysis of identified DRG subpopulations.
Cell-type specific intrinsic programs instruct neuronal subpopulations before target-derived factors influence later neuronal maturation. Retrograde neurotrophin signaling controls neuronal survival and maturation of dorsal root ganglion (DRG) sensory neurons, but how these potent signaling pathways intersect with transcriptional programs established at earlier developmental stages remains poorly understood. Here we determine the consequences of genetic alternation of NT3 signaling on genome-wide transcription programs in proprioceptors, an important sensory neuron subpopulation involved in motor reflex behavior. We find that the expression of many proprioceptor-enriched genes is dramatically altered by genetic NT3 elimination, independent of survival-related activities. Combinatorial analysis of gene expression profiles with proprioceptors isolated from mice expressing surplus muscular NT3 identifies an anticorrelated gene set with transcriptional levels scaled in opposite directions. Voluntary running experiments in adult mice further demonstrate the maintenance of transcriptional adjustability of genes expressed by DRG neurons, pointing to life-long gene expression plasticity in sensory neurons.

overall_design: We combined a mouse line expressing GFP under the control of the TrkC promoter (BAC transgene approach) with various NT3 signaling  mutants in order to identify the transcriptional changes in identified subpopulations of dorsal root ganglia (DRG) neurons. Sorted cells were processed for RNA extraction and hybridization on Affymetrix microarrays. Analysis was performed a postnatal (p) day p0. Subsequent analysis focused on the transcriptional profile of DRG neuron subpopulations at specific lumbar levels. Additional work addressed the transcriptional changes in whole DRG in adult mice with and without physical exercise.

first: Jun

last: Lee

first: Silvia

last: Arber

first: Erik

last: Cabuy

first: Stephane

last: Thiry


title: Ayu macrophages at 3.5 hours, 0, 0.5 or 5 ug/ml Leukocyte cell-derived chemotaxin 2 (LECT2), gene expression array, three independent biological replicates

status: Public on Aug 21 2012

first: wang

last: liang

address: 7A North Yongchang Road BDA

institute: BioChainBJ

summary: Ayu, Plecoglossus altivelis, is an economically important amphidromous fish species cultured in East Asia. LECT2 is a liver derived cytokine and involved in many pathologic conditions, especially in immune regulation. To understand cellular and molecular mechanisms of LECT2 in immune response of ayu, macrophages were isolated from ayu head kidney. After treatment with 0, 0.5 or 5 μg/ml of LECT2 for 3.5 hour, gene expression profile in ayu macrophages was measured using gene expression array. Results showed that LECT2 treatment led to the altered expression of immune related genes in ayu macrophages.

overall_design: Gene expression in ayu macrophages isolated from head kidney were measured after exposure to 0, 0.5 or 5 μg/ml LECT2 for 3.5 hours using gene expression array. Three independent experiments were performed using different ayu for each experiment for gene expression array analysis.

first: Jiong

last: Chen

first: Xinjiang

last: Lu

first: Yuhong

last: Shi


title: Expression profiling of pancreatic beta-cells harboring a pancreatic-specific deletion of PPAR-beta

city: Lausanne

first: Sylvain

last: Pradervand

address: Genopode

department: CIG

institute: UNI Lausanne

summary: Peroxisome proliferator-activated receptor beta/delta protects against obesity by reducing dyslipidemia and insulin resistance via effects in various organs, including muscle, adipose tissue, liver, and heart.  However, nothing is known about the function of PPAR-beta in pancreas, a prime organ in the control of glucose metabolism. To gain insight into so far hypothetical functions of this PPAR isotype in insulin production, we specifically ablated Ppar-beta in pancreas.  The mutated mice developed a chronic hyperinsulinemia, due to an increase in both beta-cell mass and insulin secretion. Gene expression profiling indicated a broad repressive function of PPAR-beta impacting the vesicular compartment, actin cytoskeleton, and metabolism of glucose and fatty acids. Analyses of insulin release from the islets revealed an increased second-phase glucose-stimulated insulin secretion. Higher levels of PKD, PKC-delta and diacyglycerol in mutated animals lead to an enhanced formation of trans-Golgi network (TGN)-to-plasma-membrane transport carriers in concert with F-actin disassembly, which resulted in increased insulin secretion and its associated systemic effects. Taken together, these results provide evidence for PPAR-beta playing a repressive role on beta-cell growth and insulin exocytosis, which shed new light on its anti-obesity action.

overall_design: Pancreas-specific knock-out animals were generated by breeding mice harbouring a floxed Ppar-beta (PPARbetafl/fl) to mice expressing the Cre transgene under the control of the Pdx1 promoter (Pdx1Cre). Islets from 3 different animals from the knock-out group Pdx1Cre;PPARbetafl/fl and the control littermates group PPARbetafl/fl were compared.

first: José

last: Iglesias

first: Walter

last: Wahli


title: Essential roles of the histone methyltransferase ESET in the epigenetic control of neural progenitor cells during development

city: Kyoto

first: Siok Lay

last: Tan

address: Sakyo-Ku, Shogoin Kawahara

institute: Kyoto University

summary:
In the developing brain, neural progenitor cells (NPCs) switch the differentiation competency via changing gene expression profiles that are governed partly by epigenetic control such as histone modification, although the precise mechanism is unknown. Here we found that ESET/Setdb1/KMT1E, a histone H3 Lys-9 (H3K9) methyltransferase, was highly expressed at early stages of brain development but down-regulated over time, and that ablation of ESET led to decreased H3K9 trimethylation and misregulation of genes, resulting in severe brain defects and early lethality. In the mutant brain, endogenous retrotransposons were derepressed, and non-neural gene expression was activated. Furthermore, early neurogenesis was most severely impaired, while astrocyte formation was enhanced. We conclude that there is an epigenetic role of ESET in temporal and tissue-specific gene regulation in the developing brain.
We used microarrays to identify genes up- or down- regulated when ESET is ablated in the dorsal telencephalon.

overall_design: We used 3 WT and 3 cKO male E14.5 embryo for each analysis

first: Siok

first: Ryoichiro

last: Kageyama


title: Chondrogenic differentiation of human bone marrow-derived mesenchymal stem cells in self-gelling alginate discs reveals novel chondrogenic signature gene clusters

status: Public on Aug 17 2012

city: Oslo

first: Sarah

last: Herlofsen

address: Sognsvannveien 9

country: Norway

institute: Norwegian Centre for Stem Cell Research

summary: We have used a disc-shaped self-gelling alginate hydrogel as a scaffold for in vitro chondrogenic differentiation of human bone marrow-derived mesenchymal stem cells. The comparison of monolayer cells and alginate embedded cells with or without differentiation medium allowed us to perform a detailed kinetic study of the expression of a range of genes and proteins known to be involved in chondrogenesis, using real-time polymerase chain reaction, fluorescence immunohistochemistry, and glycosaminoglycan measurement in the supernatant. mRNA encoding type II collagen (COL2), COL10, aggrecan, and SOX5, 6, and 9 were greatly elevated already at day 7, whereas COL1 and versican mRNA were gradually reduced. COL2 and aggrecan were dispersed throughout the extracellular matrix at day 21, whereas COL10 distribution was mainly intra/pericellular. COL1 seemed to be produced by only some of the cells. SOX proteins were predominantly localized in the nuclei. Then, using microarray analysis, we identified a signature cluster of extracellular matrix and transcription factor genes upregulated during chondrogenesis similar to COL2A1, and clusters of genes involved in immune responses, blood vessel development, and cell adhesion downregulated similar to the chemokine CXCL12. Analysis of the signature chondrogenic clusters, including novel potential marker genes identified here, may provide a better understanding of how the stem cell fate could be directed to produce perfect hyaline cartilage implants

overall_design: Comparison of gene expression patterns in 4 BM-MSC donors, before and after chondrogenic differentiation in alginate (BM-MSCs and DIF)

first: Axel

last: Kuchler

first: Jan

middle: E

last: Melvik

last: Brinchmann


title: Hepatic gene expression changes following antisense oligonucleotide-based inhibition of miR-29a

status: Public on Aug 22 2012

city: Philadelphia

first: Joshua

last: Friedman

address: ARC 1007B, 3615 Civic Center Blvd.

department: Pediatrics

institute: University of Pennsylvania School of Medicine

summary: Adult BALB/c female mice were injected intraperitoneally with a single dose at 20 mg per kg of antisense oligonucleotide either against miR-29a (5’-TAACCGATTTCAGATGGTGCTA-3’) or against a scrambled sequence (5’-TCATTGGCATGTACCATGCAGCT-3’ Antisense oligonucleotides contained 2’-O-methoxyethyl (2’-MOE), 2’-flouro (2’-F) 2'-alpha-flouro units with a phosphorothioate backbone (Regulus Therapeutics). Six days following the injection, liver was isolated, total RNA was prepared as described above, and the RNA was amplified and biotinylated using the MessageAmp Premier kit (Ambion). Samples (n=4 each experimental and control) were hybridized to Affymetrix GeneChip Mouse Genome 430 2.0 Arrays in the Children’s Hospital of Philadelphia Nucleic Acids Core Facility and analyzed with the assistance of the Penn Bioinformatics Core. Probe intensities were normalized using the GCRMA method and the significance of the log2-transformed, GCRMA-normalized signal intensities was determined using SAM

overall_design: Adult mice injected with anti-miR-29a or scrambled control ASO, n=4 per group


title: Microarray profiling of WT or PDE10A KO mice treated with vehicle or a PDE10 inhibitor

status: Public on Aug 25 2012

city: Groton

first: Thomas

last: Lanz

state: CT

address: Eastern Point Rd

department: Multi-Omics & Biomarkers

institute: Pfizer

summary: Inhibition of phosphodiesterase 10A (PDE10A) promotes cyclic nucleotide signaling, increases striatal activation, and decreases behavioral activity. Enhanced cyclic nucleotide signaling is a well established route to producing changes in gene expression. We hypothesized that chronic suppression of PDE10A activity would have significant effects on gene expression in the striatum. A comparison of the expression profile of PDE10A knockout (KO) mice and wild-type mice after chronic PDE10A inhibition revealed altered expression of 19 overlapping genes with few significant changes outside the striatum or after administration of a PDE10A inhibitor to KO animals. Chronic inhibition of PDE10A produced up-regulation of mRNAs encoding genes that included prodynorphin, synaptotagmin10, phosphodiesterase 1C, glutamate decarboxylase 1, and diacylglycerol O-acyltransferase and a down-regulation of mRNAs encoding choline acetyltransferase and Kv1.6, suggesting long-term suppression of the PDE10A enzyme is consistent with altered striatal excitability and potential utility as a antipsychotic therapy. In addition, up-regulation of mRNAs encoding histone 3 (H3) and down-regulation of histone deacetylase 4, follistatin, and claspin mRNAs suggests activation of molecular cascades capable of neuroprotection. We used lentiviral delivery of cAMP response element (CRE)-luciferase reporter constructs into the striatum and live animal imaging of 2-{4-[-pyridin-4-yl-1-(2,2,2-trifluoro-ethyl)-1H-pyrazol-3-yl]-phenoxymethyl}-quinoline succinic acid (TP-10)-induced luciferase activity to further demonstrate PDE10 inhibition results in CRE-mediated transcription. Consistent with potential neuroprotective cascades, we also demonstrate phosphorylation of mitogen- and stress-activated kinase 1 and H3 in vivo after TP-10 treatment. The observed changes in signaling and gene expression are predicted to provide neuroprotective effects in models of Huntington's disease.

overall_design: n=4-6 per group.  WT mice used as a control for PDE10A KO mice, vehicle control for PDE10A inhibitor treatment.

first: Robin

last: Kleiman


title: Gene expression profile on ischemic kidneys from wildtype C57BL/10 and TLR4 null C57BL/10ScNJ mice

status: Public on Aug 15 2012

city: DALLAS

first: JIANLIN

last: CHEN

state: TEXAS

address: 5323 HARY HINES BLVD.

department: Nephrology/Internal Medicine

institute: University of Texas Southwestern Medical Center at Dallas

summary: TLR4 deficiency attenuates kidney injury after ischemic reperfusion as measured by both renal function and morphology. To better understand the role of TLR4 during the acute kidney injury, we used DNA microarray to identify genes that were differentially expressed on kidneys in wildtype B10 mice and TLR4 null mice during the early stage of injury.

overall_design: A murine ischemic reperfusion injury model was established. After right nephrectomy, the left pedicle was clamped for 23min followed by 4hr reperfusion. Sham mice were used as controls. 6  WT males and 6 TLR4 null males were included with 3 ischemic and 3 shams in each group.

first: Jianlin

first: Christopher


title: E2f7/E2f8 and E2f1/E2f2/E2f3 null and wild type liver along with E2f7/E2f8 null and wild type trophoblast giant cells

first: Madhu

last: Ouseph

address: 460w 12th Ave

institute: The Ohio State University

type:
Other
Expression profiling by array

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

overall_design: Refer to individual Series


title: Blockade of TNFα after ischemia reperfusion injury ameliorates renal prognosis

status: Public on Aug 10 2012

first: Takaomi

last: Adachi

address: Kajiicho 465

department: Nephrology

institute: kyoto prefectural university of medicine

summary: Recently, acute kidney injury (AKI) is thought to develop a predisposition toward chronic kidney disease. But the detailed mechanism of the disease progression after AKI is unknown. We made two ischemia-reperfusion injury (IRI) mice models, repaired kidney model and atrophic kidney model, and studied the mechanism that kidney after IRI became atrophy. We found that the atrophy kidney model had two peaks of apoptosis 3 and 14 days after IRI, whereas the repaired kidney model had only one apoptosis peak 3 days after IRI. We showed that the second apoptosis is responsible for the kidney atrophy. Moreover, apoptotic ligands, TNFα and FasL were upregulated at the same time of two apoptosis peaks on the atrophic kidney, and blockade of them before IRI prevented kidney from falling into atrophy. Surprisingly, inhibition of the second apoptosis by anti-TNFα antibody protected from renal atrophy. We propose that apoptosis might play a major role in AKI progression and blockade of TNFα after IRI will be a new therapeutic approach for AKI.

overall_design: Mice were subjected for 0, 45, and 60 min of unilateral IRI. Mice kidneys were collected at day 1 and 3 after IRI for RNA extraction and hybridization on Affymetrix microarrays. There are 6 samples, 1day IRI45(1), 1day IRI60(2), 1day IRI0(3), 3day IRI45(4), 3day IRI60(5), 3day IRI0(6).

first: Noriyuki

last: Sugiyama


title: Treg cells

first: Jonathan

last: Weiss


title: Effect of CDK8/19 inhibitor Senexin A on p21-regulated gene expression in human HT1080 p21-9 cells with IPTG-inducible p21

status: Public on Aug 13 2012

city: Columbia

first: Igor

last: Roninson

state: SC

address: 715 Sumter St

department: Pharmaceutical and Biomedical Sciences

institute: SC College of Pharmacy

summary:
p21 (CDKN1A) expression from an IPTG-inducible promoter in HT1080 p21-9 cells was previously shown to inhibit a set of genes, many of which are involved in cell cycle progression, and to upregulate another set of genes, some of which have been implicated in cancer and age-related diseases. We have now developed Senexin A, a small-molecule inhibitor of p21-induced transcription, which we found to be a selective inhibitor of CDK8 and CDK19. Here we tested the effect of Senexin A on the induction and inhibition of transcription by p21.
In this dataset, we include microarray gene expression data from samples of HT1080 p21-9 cells that were either untreated, treated with p21-inducing IPTG alone, with Senexin A alone, or with IPTG and Senexin A. This experiment shows that Senexin A inhibits primarily the induction but not the inhibition of gene expression by p21.

overall_design: The data for each of the four samples were normalized to the sample from untreated cells, using GeneSpring GX. Fold changes in gene expression upon the addition of IPTG with or without Senexin A were compared using Microsft Excel. Changes in the expression of specific GO categories of genes were compared using GeneSpring.


title: Expression data of Rag2-deficient Ets1++ and Rag2-deficient Ets1-- mature NK cells and WT bone marrow progenitors

city: Chicago

first: Barbara

last: Kee

state: IL

address: 924 East 57th Street

institute: University of Chicago

summary: Expression profiling of Rag2-deficient Ets1++ and Rag2-deficient Ets1-- mature NK cells and WT bone marrow progenitors, WT T cells, and WT Pro B cells

overall_design: WT Hematopoietic progenitors, CD4 T cells, Pro B cells, and WT and Ets1-deficient NK cells were FACs sorted. RNA was subsequently extracted, labelled, and hybridized to Affymetrix microarrays. The goal if this experiment was to identify Ets1 dependent genes in NK cells

first: Mikael

last: Sivardsson


title: Regulation of epidermal growth factor receptor signaling and erlotinib sensitivity in head and neck cancer cells by miR-7

status: Public on Aug 16 2012

city: Nedlands

first: Patrick

middle: Aaron

last: Candy

state: Western Australia

address: 6 Verdun St

department: Cancer Medicine

country: Australia

institute: Perkins Institute

summary: Elevated expression and activity of the epidermal growth factor receptor (EGFR)/protein kinase B (Akt) signaling pathway is associated with development, progression and treatment resistance of head and neck cancer (HNC). Several studies have demonstrated that microRNA-7 (miR-7) regulates EGFR expression and Akt activity in a range of cancer cell types via its specific interaction with the EGFR mRNA 3′ untranslated region (3′-UTR). In the present study, we found that miR-7 regulated EGFR expression and Akt activity in HNC cell lines, and that this was associated with reduced growth in vitro and in vivo of cells (HN5) that were sensitive to the EGFR tyrosine kinase inhibitor (TKI) erlotinib (Tarceva). miR-7 acted synergistically with erlotinib to inhibit growth of erlotinib-resistant FaDu cells, an effect associated with increased inhibition of Akt activity. Microarray analysis of HN5 and FaDu cell lines transfected with miR-7 identified a common set of downregulated miR-7 target genes, providing insight into the tumor suppressor function of miR-7. Furthermore, we identified several target miR-7 mRNAs with a putative role in the sensitization of FaDu cells to erlotinib. Together, these data support the coordinate regulation of Akt signaling by miR-7 in HNC cells and suggest the therapeutic potential of miR-7 alone or in combination with EGFR TKIs in this disease.

overall_design: Differential gene expression in head and neck cancer cell lines HN5 and FaDu under conditions of 24 h miR-NC (negative control) vs. miR-7 treatment.

first: Felicity

last: Kalinowski

first: Peter

last: Leedman

first: Keith

last: Giles

first: Clarissa

last: Ganda

first: Mike

last: Epis


title: Synergy between PI3K Signaling and MYC in Burkitt Lymphomagenesis

status: Public on Aug 14 2012

city: Berlin

first: Lars

last: Bullinger

address: Augustenburger Platz 1

department: Hematology, Oncology and Tumorimmunology

institute: Charité

type:
Expression profiling by array
Genome variation profiling by SNP array

summary: In Burkitt lymphoma (BL), an aggressive germinal-center (GC) derived non-Hodgkin B-cell lymphoma characterized by MYC translocations as early transforming event, the apoptotic properties of MYC must have been overcome by pro-survival signals. Whereas activation of the pro-survival factor NFkappaB is not eminent in BL, PI3K signalling, which mediates B cell receptor associated survival signals in mature B cells, might be the cooperating event. Here we prove this hypothesis by the generation of BL in mice upon concordant expression of MYC and activation of PI3K in GC B cells. Unlike existing murine BL-like models, our tumour model fully phenocopies primary human BL and reflects the complexity of the disease with regard to histological appearance, surface marker expression, and characteristic gene expression profiles. Like in human BL, tumour monoclonality indicated a multistep pathogenesis underlining MYC and PI3K as predisposing events that invariably lead to GC-derived BL formation. In accordance, copy number alteration analysis revealed genomic regions involved in BL pathogenesis.

overall_design: All samples were obtained from murine lymphomas (Cgamma1-cre; R26StopFLMYC;R26StopFLP110* animals). Cells used for microarray analysis were sorted reporter positive cells. Tumour cells were compared to a matched germline DANN sample to identify acquired aberrations.

first: Sandrine

last: Sander

first: Klaus

last: Rajewsky


title: Hypoxia effect on human umbilical vein endothelial cells - gene and exon expression

city: Marburg

first: Julia

middle: E.

last: Weigand

address: Marbacher Weg 6

department: Pharmacy

institute: University of Marburg

summary:
Human umbilical vein endothelial cells (HUVECs) were incubated for 48 h under normoxic or hypoxic (1% oxygen) conditions.
Changes in transcript and exon levels were analyzed.

overall_design: 6 samples; 2 conditions: normoxia vs. hypoxia (1% oxygen); 3 replicates per condition

first: J

middle: N

last: Boeckel

first: S

last: Dimmeler


title: Affymetrix Human Exon 1.0 ST array assay of 15 human MLL-associated samples and 9 human normal bone marrow   [HuEx-1_0-st]

city: chicago

first: chunjiang

last: he

state: il

address: 900 east 57th st

institute: university of chicago

summary: To identify potential target genes of leukemia-related miRNAs such as miR-196b and miR-150 in human MLL-associated leukemia, we performed Affymetrix Human Exon 1.0 ST array assay of 15 human MLL-associated samples and 9 human normal bone marrow (including 3 each of CD34+, CD33+, and MNC) cell samples.

overall_design: A total of 15 MLL-associated (9 primary untreated leukemia and 6 leukemia cell line) samples and 9 human normal bone marrow samples (including 3 each of CD34+ hematopoietic stem/progenitor, CD33+ myeloid, and mononuclear cell (MNC) samples) were analyzed by use of Affymetrix Human Exon 1.0 ST arrays (Affymetirx, Santa Clara, CA).

first: Zejuan

last: Li

first: Ping

last: Chen

first: Jianjun


title: Sirt1, p53 and p38MAPK are crucial regulators of detrimental phenotypes of ESCs with Max expression ablation

status: Public on Aug 28 2012

city: Hidaka

first: Akihiko

last: Okuda

state: Saitama

address: 1397-1 Yamane

department: Research Center for Genomic Medicine

institute: Saitama Medical University

summary: Ablation of expression of the Max gene encoding a Myc protein partner in ES cells provoked two major phenomena, i.e. loss of pluripotency and apoptotic cell death. We found that nicotinamide (Nam) significantly alleviates these Max expression ablation-coupled phenotypes in ES cells. To see the alleviation effect of Nam on the overall expression profile of Max-null ES cells whose Max expression is controlled by the tet-off system, we eliminated Max expression by adding doxycycline (Dox) in the presence of Nam.

overall_design: DNA microarray analyses were performed using total RNAs from Nam (4 mM)-treated Max-null ES cells that were cultured in the presence or absence of doxycycline for 6 days.

first: Tomoaki

last: Hishida

first: Yutaka

last: Nakachi

first: Yosuke

last: Mizuno

first: Yasushi

last: Okazaki


title: Transcriptomic analysis of the effect of CT16 (PAGE5) expression in WM-266-4 melanoma cells

city: Turku

first: Jyrki

last: Heino

address: Vatselankatu 2

department: Biochemistry

country: Finland

institute: University of Turku

summary: The cellular gene expression profiles were investigated in CT16 (PAGE5) negative WM-266-4 melanoma cells as well as in the WM-266-4 cells expressing transfected CT16 cDNA.

overall_design: Total RNA obtained from three individual cultures of WM-266-4 cells stably transfected with CT16 cDNA- containing plasmid and from three individual cultures of WM-266-4 cells stably transfected with intact vector.

first: Camilla

last: Nylund


title: Transcriptomic analysis of CT16 (PAGE5) function in A2058 and WM-266-4 melanoma cells