title: Novel age related alterations revealed by a comparative kinetic transcriptome analysis of naïve CD4+ and CD8+ T cells from young and old animals.

status: Public on Mar 25 2011

city: Scottsdale

first: Cheryl

last: Myers

state: AZ

address: 13400 E Shea Blvd

department: Immunology

institute: Mayo Clinic College of Medicine

summary: Define,(a) intrinsic differences and (b) changes occuring upon TCR activation in genetic profiles of naive CD4+ and CD8+ T cells from young and old animals, to identify candidate genes altered in old T cells involved in impairement of immune response in order to restore immune function in the old.

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE28nnn/GSE28165/suppl/GSE28165_Table S1 cd8n 2fc t=0.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE28nnn/GSE28165/suppl/GSE28165_Table S10 cd4n 2fc 3of4 & not t=0.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE28nnn/GSE28165/suppl/GSE28165_Table S11 cd8n k-means cluster analysis.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE28nnn/GSE28165/suppl/GSE28165_Table S12 cd4n k-means cluster analysis.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE28nnn/GSE28165/suppl/GSE28165_Table S13 cd8n 2fc each time point immune system process.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE28nnn/GSE28165/suppl/GSE28165_Table S14 cd4n 2fc each time point immune system process.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE28nnn/GSE28165/suppl/GSE28165_Table S15 cd8n 2fc t=0 only.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE28nnn/GSE28165/suppl/GSE28165_Table S16 cd4n 2fc t=0 only.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE28nnn/GSE28165/suppl/GSE28165_Table S17 cd8n 2fc 4of4 only.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE28nnn/GSE28165/suppl/GSE28165_Table S18 cd4n 2fc 4of4 only.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE28nnn/GSE28165/suppl/GSE28165_Table S2 cd8n 2fc 2of4.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE28nnn/GSE28165/suppl/GSE28165_Table S3 cd8n 2fc t=0 & 2of4.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE28nnn/GSE28165/suppl/GSE28165_Table S4 cd8n 2fc 3of4.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE28nnn/GSE28165/suppl/GSE28165_Table S5 cd8n 2fc 3of4 & not t=0.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE28nnn/GSE28165/suppl/GSE28165_Table S6 cd4n 2fc t=0.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE28nnn/GSE28165/suppl/GSE28165_Table S7 cd4n 2fc 2of4.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE28nnn/GSE28165/suppl/GSE28165_Table S8 cd4n 2fc t=0 & 2of4.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE28nnn/GSE28165/suppl/GSE28165_Table S9 cd4n 2fc 3of4.txt.gz

overall_design: Activation dependant time series on sorted naive (CD62Lhi/CD44lo) CD4 and CD8 T cells from young and old animals-Each time point contains RNA pooled from 4 independent sortings

first: Joseph

last: Lustgarten

last: Pollock

first: Noweeda

last: Mirza

first: Dominique

last: Hoelzinger


title: Gene expression profile of Foxp3 expressing naturally ocurring regulatory macrophages from mice

status: Public on Apr 01 2011

middle: E

country: USA

summary: Define the genetic profile of naturally occurring regulatory macrophages that express Foxp3 (MacRegs) compared to Foxp3 neg macrophages, to determine candidate genes responsible for their regulatory function. Compare this new cellular population with T regulatory cells.

overall_design: Two conditions were compared: Fresh CD11b+ F4/80+ FOXP3+ cells (3 independent isolates) and CD11b+ F4/80+ FOXP3- cells (3 independent isolates). MacRegs were also compared to CD4+Foxp3+ Tregs .

first: Soraya

last: Zorro


title: The effect of trichloroethylene on gene expression in mouse liver

status: Public on Feb 01 2011

city: Chapel Hill

first: Blair

middle: Urquhart

last: Bradford

state: NC

address: 135 Dauer Dr.  CB 7431

department: Environmental Sciences and Engineering

institute: University of North Carolina

summary: Trichloroethylene (TCE) is a widely used industrial chemical, and a common environmental contaminant. It is a well-known carcinogen in rodents and a probable carcinogen in humans.   Studies utilizing panels of mouse inbred strains afford a unique opportunity to understand both metabolic and genetic basis for differences in responses to TCE. We tested the hypothesis that individual and liver-specific toxic effects of TCE are genetically controlled and that the mechanisms of toxicity and susceptibility can be uncovered by exploring responses to TCE using a diverse panel of inbred mouse strains. TCE (2100 mg/kg) or corn oil vehicle were administered by gavage to 6-8 wk old male mice of 15 mouse strains. Serum and liver were collected at 2, 8, and 24 hr post dosing and were analyzed for TCE metabolites, hepatocellular injury and gene expression of liver. TCE metabolism, as evident from the levels of individual oxidative and conjugative metabolites, varied considerably between strains. TCE treatment-specific effect on the liver transcriptome was strongly dependent on the individual’s genetic background. PPAR-mediated molecular networks, consisting of the metabolism genes known to be induced by TCE, represent some of the most pronounced molecular effects of TCE treatment in mouse liver that are dependent on the individual’s genetic background. Conversely, cell death, liver necrosis, and immune mediated response pathways which are affected by TCE treatment in liver are largely genetic background-independent. These studies provide better understanding of the mechanisms of TCE-induced toxicity anchored on metabolism and genotype-phenotype correlations that may define susceptibility or resistance.

overall_design: 16 mouse strains were studied, vehicle control and mice treated by gavage with 2100 mg/kg Trichloroethylene and sacrificed 24 hrs after dosing

middle: U

first: Eric

last: Lock

first: Oksana

last: Kosyk

first: Sungkyoon

last: Kim

first: Takeki

last: Uehara

first: David

last: Harbourt

first: Michelle

last: DeSimone

middle: W

last: Threadgill

first: Igor

middle: P

last: Progribny

first: Lisa

last: Bleyle

first: Dennis

middle: R

last: Koop

first: Ivan

last: Rusyn


title: Gene expression in Tcf4Het ApcHet mouse colon tumors compared to normal colon

status: Public on Mar 15 2011

city: Salt Lake City

first: Mario

middle: R.

last: Capecchi

state: UT

address: 15 North 2030 East

institute: University of Utah

summary: The Wnt/β-catenin pathway plays multiple/diverse roles in development by regulating gene expression via Tcf/Lef DNA binding factors. Misregulation of this pathway is thought to initiate colon adenoma formation. It is controversial whether Tcf4 (Tcf7L2) functions as an oncogene or tumor suppressor gene in colon carcinogenesis. We show here that Tcf4 haploinsufficiency results in colon tumor formation in a mouse tumor model that normally only develops small intestinal tumors. Further, we show that loss of Tcf4 early in development and in adult colon results in increased cell proliferation. These findings strongly suggest that Tcf4 normally modulates proliferation of the colonic epithelium and that disruption of Tcf4 activity increases proliferation leading to colon tumorigenesis. Taken together our in vivo studies favor a tumor suppressor function for Tcf4.

overall_design: 4 Normal Colon and 4 colon tumor from independent mouse tissue samples

first: Melinda

middle: L

last: Angus-Hill


title: The codon 72 polymorphism of p53 regulates interactions with NF-κB and transactivation of genes involoved in immunity and inflamation

status: Public on Jan 25 2011

city: 3601 Spruce Street

first: Yan

last: Zhou

state: PA

address: 333 Cottman Ave

department: Bioinformatics

institute: Fox Chase Cancer Center

summary: A common polymorphism at codon 72 in the p53 tumor suppressor gene encodes either proline(P72) or arginine(R72). These two variants might possess altered biological function which influences p53’s transcriptional, senescence and apoptotic functions. We found that P72 has increased apoptosis when compare to R72. To further identify unknown p53 target genes which might play a role in the increased apoptosis in P72 thymocytes, we have employed whole genome microarray expression profiling as a discovery platform. Mouse thymocytes were isolated from the thymuses of mice that were untreated (0 hour) or following 2 or 4 hours of exposure to 5 Gray of gamma radiation.

overall_design: Mouse thymocytes were isolated from the thymuses of mice that were untreated (0 hour) or following 2 or 4 hours of exposure to 5 Gray of gamma radiation. Four independent experiments were performed at each time point (P72 and R72) and at each timepoint 2 mice of each genotype were used, and their thymocytes were pooled together.

first: Amanda

middle: K

last: Frank

first: Julia

last: Leu

first: Karthik

last: Devarajan

first: Tatiana

last: Nedelko

first: Andres

last: Klein-Szanto

first: Monica

last: Hollstein

first: Maureen

last: Murphy


title: Gene expression in the liver of ethanol-treated mice via gastric tube in multiple strains

status: Public on Jan 23 2011

address: 0031 Michael Hooker Research Center

department: Gillings School of Global Public Health

summary: This study tested a hypothesis that a population-based approach may identify genetic background-dependent and -independent genes/pathways that modulate alcohol-induced liver injury. A sub-chronic (4 weeks) intra-gastric alcohol infusion (up to 27 g/kg/day) model was used to control for alcohol intake in 15 genetically diverse inbred mouse strains. Urine, serum and liver markers of alcoholic steato-hepatitis were assessed and a wide range of liver damage was observed across the panel. Gene expression profiling was performed on liver tissue collected at the end of the study and statistical models, with strain, degree of liver injury, treatment, and their interaction terms as factors, were used to select transcripts associated with strain-dependent and -independent effects of alcohol on the liver. Translational control of hepatic protein synthesis, related to eukaryotic initiation factors (eiFs) and accessory proteins, was identified as genetic background-independent mode of alcohol-induced liver injury. Interestingly, immune response-related transcription factors signal transducer and activator of transcription 1 (Stat1) and nuclear factor, interleukin 3 regulated (Nfil3/E4bp4) are likely determinants of genetic background-dependent responses to liver injury and alcohol treatment, respectively. Our data demonstrate that a multistrain approach provides critical mechanistic information for understanding genetic factors influencing alcohol toxicity and facilitate identification of novel targets of therapeutic intervention.

overall_design:
A high-fat diet or EtOH-containing high-fat diet was administered to 15 strains of mice via gastric tube for 28 days. 3 replicates per strain/diet.
Inter-batch normalization was carried out using the ComBat procedure.

The supplementary file 'GSE20052_Readme.txt' contains a description of the replicates used for normalization. The 'GSE20052_US14702406_25148681*' files linked to the GSE20052 record are the raw data files for the replicates.

first: Masato

last: Tsuchiya

first: Daniel

last: Gatti

first: Atsushi

last: Kawaguchi

first: Fred

last: Wright

first: Hiroshi

last: Kono

first: Takeki

last: Uehara

first: Patrick

last: Craig

first: Oksana

last: Kosik

first: Svitlana

last: Shymoniak

first: Stepan

last: Melnyk


title: Gestational high salt stressed Embryonic Day 14.5 BdkrB2 Null Mouse Kidney vs. BdkrB2 Wild Type Mouse Kidney

status: Public on Jan 19 2011

city: NEW ORLEANS

first: Lei

last: Yan

state: LA

address: 1430 Tulane Ave #SL37

department: Pediatrics

institute: Tulane University

summary: Transcriptional profiling of Embryonic Day 14.5 mouse kidneys comparing the infuence of gestational high salt stress on gene expression remolding of BdkrB2 receptor null mice with that of BdkrB2 receptor wild type mice. The BdkrB2 receptor has been shown to be playing a role in renal vascular tone, kidney secretion and reabsorption function, normal kidney development, while impaired BdkrB2 receptor in kidney shown being associated with renal agenesis and renal dysplasia. Goal was to determine the effects of BdkrB2 receptor knockout together with gestational high salt stress on renal gene expression pattern.

overall_design: Two-condition experiment, BdkrB2 null mouse kidney vs. BdkrB2 WT mosue kidney with both on gestational high salt stress . Biological replicates: 3 BdkrB2 null/WT replicates, 3 BdkrB2 WT/null replicates, all 6 replicates were duplicated.

first: Dimcho

last: Bachvarov

first: Nathaniel

middle: J

last: McLaughlin

first: Zubaida

last: Saifudeen

first: Samir

middle: S

last: El-Dahr


title: Mechanisms Establishing TLR4-Responsive Activation States of Inflammatory Response Genes (Agilent expression data)

status: Public on Jan 01 2011

city: La Jolla

first: Christopher

last: Benner

state: California

address: 9500 Gilman Dr. MC 0640

department: Medicine

institute: University of California, San Diego (UCSD)

summary: Precise control of the innate immune response is required for resistance to microbial infections and maintenance of normal tissue homeostasis. Because this response involves coordinate regulation of hundreds of genes, it provides a powerful biological system to elucidate the molecular strategies that underlie signal- and time-dependent transitions of gene expression. Using a combination of genome-wide and gene-specific approaches, we provide evidence that rather than representing off/on transitions, Toll-like receptor 4 (TLR4)-dependent activation of nearly all immediate/early (I/E) and late response genes results from a sequential process in which signal-independent factors, exemplified by Gabpa, initially establish basal levels of gene expression that are then amplified by signal-dependent transcription factors. Promoters of I/E genes are distinguished from those of late genes by the use of distinct sets of signal-dependent transcription factors, preferential binding of TBP and basal enrichment for RNA Pol II immediately downstream of transcriptional start sites. Global nuclear run-on (GRO) sequencing and total RNA sequencing further indicates that TLR4 signaling markedly increases efficiency of transcriptional elongation of nearly all I/E genes, while RNA splicing is largely unaffected. NCoR/SMRT co-repressor complexes are unexpectedly found to be associated with H3K4me3-positive promoters of TLR4-responsive genes that exhibit a broad range of basal expression levels, implying a dynamic, rather than static role in regulation of gene expression. Collectively, these findings reveal mechanisms underlying temporally distinct patterns of TLR4-dependent gene activation required for homeostasis and effective immune responses.

overall_design: ChIP-Seq, Total RNA-Seq, Gro-Seq, and gene expression profiling was performed in macrophages treated with Kdo2 Lipid A. Control samples for H3K4me3 and Input in Macrophages and B cells, in addition to control microarray data are included in GEO accession# GSE21512

first: Laure

last: Escoubet-Lozach

first: Minna

last: Kaikkonen

first: Jean

last: Lozach

first: Sven

last: Heinz

first: Nathanael

last: Spann

first: Andrea

last: Crotti

first: Josh

last: Stender

first: Serena

last: Ghisletti

last: Glass


title: The expression programme of  ERR-alphain human mammary epithelial cells

status: Public on Nov 01 2010

city: Palo Alto

first: Dmitri

middle: A

last: Kazmin

state: CA

address: 240 Pasteur Dr

department: Institute for Immunity, Transplantation and Infection

institute: Stanford University

summary: This dataset is part of the manuscript titled "The metabolic regulator ERRalpha, a downstream target of HER2/IGF1, as a therapeutic target in breast cancer" (in review). The expression data obtained in human mammary epithelial cells were used to generate a list of ERRalpha-regulated genes that was later refined in clinical breast cancer datasets to generate a clinically relevant signature of ERalpha activity (referred to as Cluster 3 signature). Using this signature of the estrogen-related receptor alpha (ERRa) to profile more than eight-hundred breast tumors, we found that patients with tumors exhibiting higher ERRa activity were predicted to have shorter disease free survival.  Further, the ability of an ERRa antagonist, XCT790, to inhibit breast cancer cell proliferation correlates with the cell’s intrinsic ERRa activity.  These findings highlight the potential of using the ERRa signature and antagonists in targeted therapy for breast cancer.  Using a chemical genomic approach we determined that activation of the HER2/IGF1 signaling pathways upregulates the expression of PGC-1b, an obligate cofactor for ERRa activity.  Knockdown of PGC-1b in HER2 positive breast cancer cells impaired ERRa signaling and reduced cell proliferation, implicating a functional role of PGC1b/ERRa in the pathogenesis HER2 positive breast cancer.

overall_design: Primary human mammary epithelial cells were a gift from Dr. J. Marks (Duke University, Durham, NC) and cultured in MEBM (Cambrex, East Rutherford, NJ) with MEGM bullet kit and supplemented with 5mg/ml transferrin and 10-5M isoproterenol.  To generate ERR-alpha signature, hMECs were serum starved for 36h followed by infection with MOI=150 of adenoviruses expressing two variants of PGC1alpha, a protein ligand for ERRalpha: PGC-1alpha2x9 or PGC-1alpha L2L3M.  PGC-1-2x9 is specific to ERRalpha, while PGC-1-L2L3M lacks the NR box and does not interact with ERRalpha or other nuclear receptors. The generation and purification of variant PGC-1alpha viruses were described previously (Gaillard et al., Molecular Cell 24:5, 2006).  Comparable expression levels of the two PGC-1alpha variants were verified by Western immonoblot analysis (data not shown).   RNA was collect 16h after infection and purified using RNeasy mini kit (Qiagen, Valencia, CA).  Ten independent biological replicates from each virus infection were collected.

first: Ching-Yi

last: Chang

first: Donald

last: McDonnell


title: The gene expression in the skeletal muscle affected by TBP-2/Txnip deficiency

status: Public on Oct 22 2010

city: Kyoto

first: Hiroshi

last: Masutani

address: 53, Kawaharacho, Shogoin, Sakyo

country: Japan

institute: Institute for Virus Research, Kyoto University

summary: To investigate how TBP-2/Txnip regulates insulin sensitivity in the skeletal muscle, we performed microarray analyses.

overall_design: The gene expression in the skeletal muscle from WT, TBP-2-/-, ob/ob, ob/ob TBP-2-/-  at 10 weeks age were performed.

first: Eiji

last: Yoshihara


title: Gene expression under normoxia and hypoxia in mouse embryonic fibroblasts

status: Public on Jan 15 2011

first: Shinya

last: Yamanaka

address: 53 Kawahara-machi, Shogoin, Sakyo-ku

institute: Center for iPS Cell Research and Applicaton (CiRA), Kyoto University

summary: Mouse and human somatic cells can be reprogrammed to induced pluripotent stem cells (iPSCs) by the transduction of four transcription factors, Oct 3/4, Sox2, Klf4, and c-Myc. Conducting reprogramming in hypoxic conditions was shown to result in improved efficiency for both mouse and human cells. To examine the effect of hypoxic cultivation, we performed microarray analyses using mouse embryonic fibroblasts cultivated under normoxia and hypoxia.

overall_design: Mouse embryonic fibroblasts and four factor-transduced reprogramming fibroblasts were grown under normoxia and hypoxia. These cells were used for microarray analyses.

first: Yoshinori

last: Yoshida

first: Kazutoshi

last: Takahashi

first: Keisuke

last: Okita

first: Tomoko

last: Ichisaka


title: Comparison of gene expression profiles of HIV-specific CD8 T cells from controllers and progressors and Jurkat cells with or without PD-1 ligation

status: Public on Oct 03 2010

city: Boston

first: W.

middle: Nicholas

last: Haining

state: MA

address: 44 Binney Street

department: Pediatric Oncology

institute: Dana-Farber Cancer Institute

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

overall_design: Refer to individual Series


title: Comparison of gene expression profiles of HIV-specific CD8 T cells from controllers  and progressors

summary: CD8+ T cells in chronic viral infections like HIV develop functional defects such as loss of IL-2 secretion and decreased proliferative potential that are collectively termed exhaustion1.   Exhausted T cells express increased levels of multiple inhibitory receptors, such as Programmed Death 1 (PD-1). PD-1 inhibition contributes to impaired virus-specific T cell function in chronic infection because antibody-mediated blockade of its ligand, Programmed Death Ligand 1 (PD-L1) is sufficient to improve T cell function and reduce viral replication in animal models.  Reversing PD-1 inhibition is therefore an attractive therapeutic target, but the cellular mechanisms by which PD-1 ligation results in T cell inhibition are not fully understood. PD-1 is thought to limit T cell activation by attenuating T cell receptor (TCR) signaling.  It is not known whether PD-1 ligation also acts by upregulating genes in exhausted T cells that impair their function.  Here, we analyzed gene-expression profiles from HIV-specific CD8+ T cells in patients with HIV and show that PD-1 coordinately upregulates a program of genes in exhausted CD8+ T cells from humans and mice.  This program includes upregulation of basic leucine transcription factor, ATF-like (BATF), a transcription factor in the AP-1 family.  Enforced expression of BATF was sufficient to impair T cell proliferation and cytokine secretion, while BATF knockdown reduced PD-1 inhibition.  Silencing BATF in CD4+ and CD8+ T cells from chronic viremic patients rescued HIV-specific T cell function.  Thus inhibitory receptors can cause T cell exhaustion by upregulating genes  – such as BATF – that inhibit T cell function.

overall_design: We sorted HIV-specific CD8+ T cells from 18 progressors and 24 controllers, cohorts with a two-log difference in mean viral load

first: W

middle: N

first: Bjorn

last: Nilsson


title: Microarray skeletal muscle PGC-1alpha-/- - beta f/f/Mlc1fCre mice

status: Public on Dec 01 2010

city: Orlando

first: Christoph

last: Zechner

state: FL

address: 6400 Sanger Road

institute: Sanford-Burnham Medical Research Institute at Lake Nona

summary:
Title: Total Skeletal Muscle PGC-1 Deficiency Uncouples Mitochondrial Derangements from Fiber Type Determination and Insulin Sensitivity
Abstract: Evidence is emerging that the PGC-1 coactivators serve a critical role in skeletal muscle  metabolism, function, and disease. Mice with total PGC-1 deficiency in skeletal muscle (PGC-1α-/-  βf/f/MLC-Cre mice) were generated and characterized. PGC-1α-/-βf/f/MLC-Cre mice exhibit a  dramatic reduction in exercise performance compared to single PGC-1α- or PGC-1β-deficient mice and  wild-type controls. The exercise phenotype of the PGC-1α-/-βf/f/MLC-Cre mice was associated with a  marked diminution in muscle oxidative capacity and mitochondrial structural derangements  consistent with fusion/fission and biogenic defects together with rapid depletion of muscle glycogen  stores during exercise. Surprisingly, the skeletal muscle fiber type profile of the PGC-1α-/-βf/f/MLCCre  mice was not significantly different than the wild-type mice. Moreover, insulin sensitivity and  glucose tolerance were also not altered in the PGC-1α-/-βf/f/MLC-Cre mice. Taken together, we  conclude that PGC-1 coactivators are necessary for the oxidative and mitochondrial programs of  skeletal muscle but are dispensable for fundamental fiber type determination and insulin sensitivity.

overall_design:
RNA from PGC-1alpha-/- beta f/f/Mlc1fcre was obtained and gene expression pattern compared with PGC-1alpha -/-, PGC-1beta f/f, and PGC-1beta f/f/Mlc1fCre controls.

Results file descriptions:

1. GSE23365_skfloxAKO_PPexcl_genesup_GEO-8-16-2010:

This table contains genes that were upregulated ≥2.0 fold in gastrocnemius muscle from PGC-1alpha-/- - mice, PGC-1beta f/f/Mlc1fCre mice and PGC-1alpha-/- - beta f/f/Mlc1fCre mice. All groups are normalized to PGC-1beta f/f mice and values are expressed as mean±SEM. The column “description’ contains the gene name, and the column “ID” contains Agilent probe names.

2. GSE23365_skfloxAKO_PPexcl_genesdown_GEO-8-16-2010

This table contains genes that were downregulated ≤0.7 fold in gastrocnemius muscle from PGC-1alpha-/- - mice, PGC-1beta f/f/Mlc1fCre mice and PGC-1alpha-/- - beta f/f/Mlc1fCre mice. All groups are normalized to PGC-1beta f/f mice and values are expressed as mean±SEM. The column “description’ contains the gene name, and the column “ID” contains Agilent probe names.

first: Daniel

last: Kelly


title: Analysis of TLR4 induced transcriptional responses in interleukin 4 primed mouse macrophages

status: Public on Oct 01 2010

city: Regensburg

first: Michael

last: Rehli

address: F.-J.-Strauss-Allee 11

department: Internal Med III

country: Germany

institute: University Hospital Regensburg

summary:
Interferon (IFN)γ and interleukin (IL)-4 are central regulators of T helper 1 (Th1) and T helper 2 (Th2) immune responses, respectively. Both cytokines have a major impact on macrophage phenotypes: IFNγ–priming and subsequent TLR4 activation induces so called classically activated macrophages that are characterized by pronounced pro-inflammatory responses, whereas IL-4–treated macrophages, commonly called alternatively activated, are known to develop enhanced capacity for endocytosis, antigen presentation, and tissue repair and are generally considered anti-inflammatory. Considering IL-4 as priming rather than activating stimulus, we now compared the TLR4–dependent global gene activation program in IFNγ– versus IL-4–pretreated mouse macrophages, which has rarely been studied so far. Although both cytokines frequently induced opposing effects on gene transcription, the subsequent activation of bone marrow-derived macrophages by lipopolysaccharide (LPS) produced a strong, priming dependent pro-inflammatory response in both macrophage types. For example, the production of key pro-inflammatory cytokines IL-6 and IL-12 was significantly higher in IL-4– versus IFNγ–primed macrophages and several cytokine genes, including Il19, Ccl17, Ccl22, Ccl24 and Cxcl5, were preferentially induced in alternatively primed and LPS activated mouse macrophages. In a subset of genes, including IL12a, IFNγ priming was actually found to suppress LPS–induced gene expression in a Stat1–dependent manner. Our data suggest that IL-4–priming is not per se anti-inflammatory but generates a macrophage that is “tissue protective” but still capable of mounting a strong inflammatory response after TLR4–dependent activation.

Keywords: Gene expression profiling

overall_design: Gene expression was investigated in mouse bone marrow-derived macrophages (BMM). On day 7, BMM were stimulated with either IL-4 or IFNγ overnight (18h in total). LPS treatment was performed in primed and unprimed macrophages 4 h prior to harvesting. At least three independent experiments were performed for each condition.

first: Carol

last: El Chartouni


title: Purified mesenchymal stem cells are an efficient source for iPS cell induction

status: Public on Aug 21 2010

city: Shinjuku

first: Yumi

last: Matsuzaki

state: Tokyo

address: 35 Shinanomachi

department: Physiology

institute: Keio University, School of Medicine

summary: The ectopic expression of a defined set of transcription factors, Oct4, Klf4, Sox2, and c-Myc, reprograms mouse embryonic fibroblasts (MEFs) and adult tail-tip fibroblasts (TTFs) into embryonic stem (ES)-like cells called induced pluripotent stem (iPS) cells.  iPS cells have been generated from a variety of somatic cells, including embryonic and adult dermal fibroblasts, epithelial cells of the liver and stomach, pancreatic b cells, mature B lymphocytes, and adult neural stem cells (NSCs).  While these studies demonstrated that most somatic cells are capable of acquiring pluripotency with minimal gene transduction, the poor efficiency of cell reprogramming and the uneven quality of iPS cells are still important problems.  In particular, the choice of cell type most suitable for inducing high-quality iPS cells remains unclear.  Here, we generated iPS cells from PDGFRa+ Sca-1+ (PaS) cells that represent highly enriched adult mouse mesenchymal stem cells (MSCs) and PDGFRa- Sca-1- osteo-progenitor (OP) cells. When we compared the induction efficiency and quality of individual iPS clones, MSCs had a higher reprogramming efficiency compared with OP cells and TTFs.  The iPS cells induced from MSCs by Oct3/4, Sox2, and Klf4 appeared to be the closest equivalent to ES cells by DNA microarray gene profile and germline-transmission efficiency.  We conclude that prospectively isolated MSCs are a promising candidate for the efficient and stable generation of high-quality iPS cells.

overall_design: Previously report that iPS cell raise two possibilities: 1) embryonic tissue is a better source for iPS cells than adult tissue, and 2) tissue stem cells are more suitable for reprogramming than differentiated cells.  To test our hypothesis that stem cells are more efficiently reprogrammed into iPS cells than mature cells, we needed to compare cells from the same cell lineage but from distinct developmental stages. we compared three cell sources including PaS (MSCs), OP (Osteo progenitor cells), TTF, ES cell, and thirty iPS lines.

first: Kunimichi

last: Niibe

first: Yoshimi

last: Kawamura

first: Daisuke

last: Araki

first: Satoru

last: Morikawa

first: Kyoko

last: Miura

first: Sadafumi

last: Suzuki

first: Shigeto

last: Shimmura

first: Takehiko

last: Sunabori

first: Yo

last: Mabuchi

first: Yasuo

last: Nagai

first: Taneaki

last: Nakagawa

first: Hideyuki

last: Okano


title: Expression data from genetically modified HMLE human mammary epithelial cells

status: Public on Sep 20 2010

city: Cambridge

first: Piyush

middle: B.

last: Gupta

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research/MIT

summary: Microarrays were used to determine relative global gene expression changes upon introduction of EMT-inducing or control vectors.

overall_design: Experimentally immortalized HMLE breast epithelial cells were retrovirally transduced in culture with  vectors encoding EMT-inducing genes or control vectors. There were three biologic replicates for each genetic perturbation condition. After treatment, the cells  were selected and expanded, after which total RNA was isolated and subjected to microarray analysis.

middle: B

first: Sendurai

last: Mani

first: Tamer

middle: T

last: Onder

first: Supriya

first: Eric

last: Lander

first: Robert

last: Weinberg


title: The Role of Nogo in asthma pathogenesis

status: Public on Oct 20 2010

city: New Haven

first: Paulette

middle: Lee

last: Wright

state: CT

address: 10 Amistad St.

department: Pharmacology

institute: Yale University

summary: In order to determine if there are any genetic differences among lungs of Nogo-A/B knockout mice which may explain their enhanced asthmatic-like responses, we have employed whole genome microarray expression profiling as a discovery platform to identify any genes that may be altered in the lung of Nogo-A/B knockout mice.  RNA was isolated from three biological replicates of mouse lungs from naive WT and Nogo-A/B Knockout mice and run on agilent array.  Two genes was significantly altered in Nogo-A/B Knockout lungs, SPLUNC1 and RTN4 (Nogo) which was significantly decreased and confirmed by real-time PCR.

overall_design: Gene expression in naïve mouse lungs of WT and Nogo-A/B knockout mice was measured in three individual biological replicates from each group.

first: William

middle: C

last: Sessa


title: FGF2-regulated gene expression in cultured mouse spermatogonial stem cells

status: Public on Aug 01 2010

city: Beijing

first: Chunsheng

last: Han

address: 1 Beichen West Road, Chaoyang District

country: China

institute: Institute of Zoology, CAS

summary: Transcriptional profiling of mouse spermatogonial stem cells (SSCs) comparing control untreated SSCs with SSCs with exogenous FGF2 withdrawn and FGFR inhibitor SU5402 supplemented (-F+S). Results provide insight into the mechanisms of FGF2-supported in vitro self-renewal of SSCs.

overall_design: Two-condition experiment, SSCs-F+S vs. SSCs. Biological replicates: 4 control replicates, 4 -F+S replicates.

first: Yan

last: Zhang

first: Shangying

last: Liao


title: Impeding Xist expression from the active X chromosome improves mouse somatic cell cloning

status: Public on Sep 16 2010

city: Tsukuba

first: Kimiko

last: Inoue

state: Ibaraki

address: 3-1-1 Koyadai

department: Bioresource Engineering Division

institute: BRC, RIKEN

summary: Cloning mammals by somatic cell nuclear transfer (SCNT) is highly inefficient because of aberrant genomic reprogramming. In addition to random reprogramming errors, we hypothesized the presence of specific errors as evidenced by common anomalies among clones. We found that Xist, which normally inactivates one of the two X chromosomes in females, was ectopically expressed from the active X (Xa) chromosome in cloned mouse embryos of both sexes. Deletion of Xist on Xa normalized global gene expression and produced about a 10-fold increase in cloning efficiency. We also identified an Xist-independent mechanism that specifically downregulated a subset of X-linked genes through somatic-type repressive histone blocks. Thus, we have identified nonrandom reprogramming errors in mouse cloning, which provide promising targets for breakthroughs in SCNT cloning technology.

overall_design: Gene expression were measured in mouse in vitro fertilized and somatic cell cloned blastocysts. More than three biological replicates were performed in each group using defferent nuclear donor cells.

first: Takashi

last: Kohda

first: Michihiko

last: Sugimoto

last: Sado

first: Narumi

last: Ogonuki

first: Shogo

last: Matoba

first: Hirosuke

last: Shiura

first: Rieko

last: Ikeda

first: Keiji

last: Mochida

last: Fujii

first: Ken

last: Sawai

first: Arie

last: Otte

first: Cindy

last: Tian

first: Xiangzhong

last: Yang

first: Fumitoshi

last: Ishino

first: Kuniya

last: Abe

first: Atsuo

last: Ogura


title: Integrated array-CGH and expression microarray analyses on medulloblastomas in heterozygous Ptch1 mice

status: Public on Jul 14 2010

city: Chiba

last: Takabatake

state: Chiba

address: Anagawa 4-9-1, Inage-ku

institute: National Institute of Radiological Sciences

type: Genome variation profiling by genome tiling array


title: The intracellular domain of amyloid precursor protein induces the dynamic change of the gene expression profile in P19 cells.

city: Matsumoto

first: Kohzo

last: Nakayama

address: Asahi

department: Anatomy

institute: Shinshu University

summary: As previously reported (Neuroscience letters 444(2008)127-131), we established embryonic carcinoma P19 cell line expressing the intracellular domain of APP (AICD). Although neurons could be differentiated from these cell lines with RA treatment, expression of AICD gave rise to neuron-specific apoptosis. To identify the genes that are involved in this cell death, we evaluated changes of gene expressions that was induced by AICD through this process of cell death. The expression profiles of almost forty thousands transcripts were monitored by DNA microarrays.

overall_design: AICD-expressing P19 cell lines (AICD/P19) and control P19 cell lines (pCDNA/P19) that carry vector alone were used and cultured. To induce neural differentiation of these P19 cell lines, cells were allowed to aggregate in culture medium with 5×10-7 M all-trans-retinoic acid (RA) for 4 days (aggregated state). After aggregation, cells were replated onto cell culture grade dishes or poly-L-Lysine coated cell-disks for two days (differentiated state). RNAs were isolated at each states.

first: Takeshi

last: Ohkawara


title: Roles of mammalian Rap1 in TERT recruitment to chromatin, subtelomeric gene silencing and transcriptional regulation

status: Public on Jul 10 2010

city: Madrid

first: Paula

last: Martinez

state: Madrid

address: Melchor Fernandez Almagro 3

country: Spain

institute: CNIO

summary: Repressor-activator protein 1 (scRap1) is the major binding activity at Saccharomyces cerevisiae telomeres, with roles in telomere length regulation and establishment of subtelomeric silencing by recruiting the Sir proteins. scRap1 also acts as a transcription factor controlling the expression of ribosomal proteins and glycolytic enzymes. A homolog of scRap1 exist in mammals, Rap1 (also known as Terf2ip), however, its roles in telomere biology and transcriptional regulation are largely unknown. We have employed microarrays to obtain gene expression signatures related to Rap1-deleted mice when compared to the wild-type.

overall_design:
Construction of the Rap1 targeting vector:

The strategy for disrupting the Rap1 locus was designed to conditionallty delete exon 3 (E3) through a Cre-mediated excision. Deletion of E3 leads to the removal of coding sequences encoding for the RCT domain and the NLS sequence, as well as the whole 3’UTR region and poly-adenylation signal (Fig.1A,B). Deletion of E3 was expected to destabilize the Rap1 transcript and thereby to prevent translation of any truncated RAP1 protein. The targeting vector contains homology regions isogenic with the ES cell line used (129Sv/Pas). The short homology region (SA) harbors a 2.4 kb DNA fragment encompassing exon 2 (E2) and intron 2 (Fig. 1A). The long homology region (LA) is a 5.6 kb DNA fragment downstream the end of E3 (Fig. 1A). The central part contains E3 flanked by two loxP sites and a positive selection neomycin gene (PGK-Neo) flanked by two Frt sites (Fig. 1A). At the 3’-end of the LA a Diphteria Toxin (DTA) selection marker was cloned (Fig. 1A). The vector contains a unique NruI linearization site. The targeting vector was quality controlled by sequencing of the coding exons, the junctions between the homology arms and the selection cassettes, the selection cassettes and the junctions between the homology arms and the plasmid backbone. The analysis of the sequencing results showed no polymorphis between the C57BL/6 and 129Sv/Pas genetic background within the isolated Rap1 sequences. The sequence of the primers used for the PCR amplification of the different targeting vector parts and the details of the cloning steps are available upon request. The construction of the targeting vector was performed by genOway (www.genoway.com; Lyon, France).

Generation of conditional Rap1 knockout mice

129Sv/Pas ES cells were transfected with 40 µg of linearized plasmid. Positive selection was started 48 hours after electroporation by addition of 200 µg/ML G418. Approximately 230 positive resistant clones were isolated and amplified. They were PCR screened for homologous recombination first at the 5’ end of the Rap1 locus. The 6 positive identified 5’ targeted ES cells were further investigated by PCR amplification over the 3’ long homology arm to amplify the region of the targeted locus containing the distal loxP site. The direct sequencing of the PCR products amplified from the 6 ES clones revealed that 3 of them contained the distal loxP site. The recombinant clones identified by PCR were further verified by Southern blot analysis of AflII and PciI restricted genomic DNA using a 5’-internal and a 3’-external probes, respectively (data not shown). The Southern blots confirmed the correct homologous integration over the 5’ and the 3’ homology arm and the absence of any additional randomly integrated copies of the targeting vector. Chimeric mice were generated by microinjection of three independently targeted ES clones into C57BL/6J host blastocyst. The resulting offspring showed a high level of chimerism as shown by coat color, and were mated to C57BL/6J mice to assess germ line transmission. The resulting heterozygous Rap1+/flox-Neo mice were then bred to transgenic mice expressing the Flpe recombinase (Rodriguez et al., 2000) to induce excision of the Neo marker. The Rap1+/flox heterozygous mice were then intercrossed to generate Rap1flox/flox, and Rap1+/flox mice. Homozygous Rap1flox/flox mice were crossed with transgenic mice expressing the Cre recombinase under the control of the keratine 5 promoter (Tarutani et al., 1997) (Fig. 5A). Heterozygous Rap1+/D K5-Cre were crossed either to Rap1flox/flox or Rap1+/flox to generate Rap1Δ/Δ K5-Cre. The removal of exon 3 by Cre-mediated recombination was confirmed by PCR analysis using primers F and R (Fig. 1A,C and Fig. 5A). Amplification of the wild type, flox and knockout alleles renders a 3.2 kb, 3.3 kb and 0.5 kb fragments, respectively.

The breeding to the F1 generation and characterization of heterozygous Rap1+/flox-Neo F1 animals was performed by geneOway (www.genoway.com; Lyon, France). All mice were generated and maintained at the Spanish National Cancer Centre (CNIO) under specific pathogen-free conditions in accordance with the recommendation of the Federation of European Laboratory Animal Science Associations.

first: Maria

last: Thanasoula

first: Chunyan

last: Liao

first: Gonzalo

last: Gómez-López

first: Agueda

middle: M

last: Tejera

first: David

middle: G

last: Pisano

first: Stefan

last: Schoeftner

first: Orlando

last: Dominguez

first: Alfonso

last: Valencia

first: Anais

last: Baudot

first: Madalena

last: Tarsounas

last: Blasco


title: Comparison of gene expression profiles of Jurkat cells with or without PD-1 ligation

first: W.

last: Haining

overall_design: PD-1 expressing Jurkat cells were cultured for 18 hours with beads coated with antibodies to CD3 and CD28, with our without an antibody to PD-1.

first: Nicholas

first: Björn

last: Nilsson


title: Mycobacterium bovis-BCG vaccination induces a specific pulmonary transcriptome biosignature in mice

status: Public on Jun 28 2010

city: ADDLESTON

first: ELIHU

last: Aranday-Cortes

state: SURREY

address: Woodham Lane, New Haw

department: SEB 4

country: United Kingdom

institute: Central Veterinary Laboratories Agency-Weybridge

summary: In the present study, we applied microarray technology to define a biosignature from the whole genome expression in lung and spleen samples after BCG vaccination and M. bovis infection of BALB/c mice. The aims were two-fold, namely to define biosignatures that could predict vaccine success before challenge, and biomarker patterns that correlated with anamnestic protective responses following exposure to virulent M. bovis. Further, Our aim was to define these markers to be detectable without in vitro antigenic challenge. After BCG vaccination, we defined a specific pulmonary gene expression signature related to the connective tissue development and function network that predicted vaccine success before M. bovis challenge. In addition, a Th17-related cytokine profile was found that correlated with vaccine-induced protective immunity following infection with virulent M. bovis in the lung as well as additional genes that were up-regulated in the spleens of vaccinated animals post-infection that was related to neutrophil biology and inflammation. This study has therefore prioritized both biomarkers predicting vaccination success before challenge and bio-signatures that are associated with protective immune responses that will be useful to evaluate future vaccine candidates.

overall_design: Two groups of 20 mice each were immunised by a single intradermal injection of 2 x 10 to 5 CFU of M. bovis BCG (Vaccinated), or Hanks buffered salt solution (HBSS) (Unvaccinated). Six weeks later 5 mice from each group were euthanized for immunological analyses and the remaining mice from each group were challenged with approx 600 CFU M. bovis via the intranasal route. At days 3 and 14 post challenge five mice per group were euthanized and spleens and lungs harvested.

first: Elihu

first: Daryan

last: Kaveh

first: Javier

last: Nunez-Garcia

first: Philip

last: Hogarth

first: Martin

last: Vordermeier


title: Bone Marrow Derived Mesenchymal Stem Cells Incorporate Into the Prostate During Regrowth

status: Public on Jun 05 2010

city: Nashville

first: Neil

last: Bhowmick

state: TN

address: A1302 Medical Center North

department: Urologic Surgery

institute: Vanderbilt University

summary: Transcriptional profiling of mouse prostate stromal cells knocked out for Tgfbr2 were compared to that of the Tgfbr2-flox control.   Elevated chemokine expression in the prostate stroma of a castrate resistant mouse model, Tgfbr2-fspKO, prompted us to determine the role of bone marrow derived cell recruitment to the prostate during regrowth.

overall_design: Tgfbr2-flox prostate epithelia vs. Tgfbr2-fspKO prostae epithelia. Biological replicates: 3 Tgfbr2-flox mouse prostates pooled, 3 Tgfbr2-fspKO mouse prostate replicates.


title: Primary human erythroid progenitor cells HDAC1 and HDAC2 shRNA knockdown samples

first: Benjamin

last: Ebert

address: Harvard Medical School

summary:
Gene expression profiling was performed on primary human erythroid progenitor cells expressing a control shRNA (luciferase), two different HDAC1 shRNAs, and two different HDAC2 shRNAs.
The worldwide burden of sickle cell disease is enormous, with over 200,000 infants born with the disease each year in Africa alone. Induction of fetal hemoglobin is a validated strategy to improve symptoms and complications of this disease. The development of targeted therapies has been limited by the absence of discrete druggable targets. We developed a novel bead-based strategy for the identification of inducers of fetal hemoglobin transcripts in primary human erythroid cells. A small-molecule screen of bioactive compounds identified remarkable class-associated activity among histone deacetylase (HDAC) inhibitors. Using a chemical genetic strategy combining focused libraries of biased chemical probes and reverse genetics by RNA interference, we have identified HDAC1 and HDAC2 as molecular targets mediating fetal hemoglobin induction. Our findings suggest the potential of isoform-selective inhibitors of HDAC1 and HDAC2 for the treatment of sickle cell disease.

overall_design: Gene expression profiling was performed on primary human erythroid progenitor cells expressing a control shRNA (luciferase, n=3), two different HDAC1 shRNAs (n=2 and n=3), and two different HDAC2 shRNAs (n=3 for each).

first: James

middle: E

last: Bradner

first: Kenneth

last: Ross


title: Primary human erythroid progenitor cells SAHA treatment samples

summary:
Gene expression profiling was performed on primary human erythroid progenitor cells left untreated or treated with 0.5uM SAHA.
The worldwide burden of sickle cell disease is enormous, with over 200,000 infants born with the disease each year in Africa alone. Induction of fetal hemoglobin is a validated strategy to improve symptoms and complications of this disease. The development of targeted therapies has been limited by the absence of discrete druggable targets. We developed a novel bead-based strategy for the identification of inducers of fetal hemoglobin transcripts in primary human erythroid cells. A small-molecule screen of bioactive compounds identified remarkable class-associated activity among histone deacetylase (HDAC) inhibitors. Using a chemical genetic strategy combining focused libraries of biased chemical probes and reverse genetics by RNA interference, we have identified HDAC1 and HDAC2 as molecular targets mediating fetal hemoglobin induction. Our findings suggest the potential of isoform-selective inhibitors of HDAC1 and HDAC2 for the treatment of sickle cell disease.

overall_design: Gene expression profiling was performed on primary human erythroid progenitor cells left untreated (n=3) or treated with 0.5uM SAHA (n=3).


title: A Pathobiont of the Microbiota Balances Host Colonization and Intestinal Inflammation

status: Public on Jun 01 2010

city: Pasadena

first: Janet

last: Chow

address: 1200 E. California Blvd

institute: Caltech

summary: The mammalian gastrointestinal tract harbors a diverse microbiota residing in intimate contact with the host immune system. Though most associations are symbiotic or commensal, some resident bacteria (termed pathobionts) have the potential to induce disease in immunocompromised hosts. Type VI secretion systems (T6SSs) have recently emerged as a novel mechanism for forging microbial-host interactions during infection. We reveal here a unique protective role for the T6SS of Helicobacter hepaticus, a Gram-negative bacterium of the murine intestinal microbiota. The T6SS of H. hepaticus targets effector substrates to intestinal epithelial cells (IECs). Mutants in T6SSs display higher intracellular and cell-associated numbers upon incubation with IECs, and exhibit increased bacterial colonization of the gastrointestinal tract compared to wild-type bacteria. The T6SS accordingly directs an anti-inflammatory gene expression profile in IECs co-cultured with H. hepaticus. Remarkably, T6SS mutants induce an exacerbated pro-inflammatory response in an experimental model of colitis. CD4+ T cells isolated from T6SS mutant-colonized animals produce increased T-helper 17 (Th17) cytokines in response to IECs presenting H. hepaticus antigens. These data demonstrate that H. hepaticus intimately interacts with IECs and employs type VI secretion to establish a balanced host relationship by limiting microbial colonization and intestinal inflammation. We propose that altering host-bacterial equilibriums that lead to dysbiosis of the microbiota contributes to human disorders such as inflammatory bowel disease and colon cancer.

overall_design: RNA was harvested from MODE-K intestinal epithelial cells incubated for 6hr with either wild-type H. hepaticus, ΔIcmF mutant, or no bacteria. RNA was prepared using TRIzol. RNA was labeled and hybridized to Agilent microarrays (Whole Mouse Genome Microarray) following manufacturer's instructions. Microarrays were scanned using an Agilent DNA Microarray Scanner G2565CA, and data were acquired using Agilent's Feature Extraction Software version 10.1.1.1. Significant genes were selected based on p<0.05 and fold change >1.5.

first: Sarkis

last: Mazmanian


title: Integrated array-CGH and expression microarray analyses on medulloblastomas in heterozygous Ptch1 mice, expression

first: Takashi

last: Takabatake

summary:
Genomic radiation signature illuminates low-dose effects with sharply reflected transcriptome in Ptch1-deficient medulloblastomas.
Cancer risks of low-dose radiation are of great concern especially in relation to rapidly increasing medical exposures; however, their accurate assessments cope with many challenges and difficulties, partly due to the inability to distinguish radiation-induced tumors from spontaneous ones.  Here, we analyzed the dose-dependent effect of radiation on medulloblastoma development in Ptch1 heterozygous mice on C3B6F1 background.  The incidence and latency of medulloblastoma increased and shortened with increasing radiation dose, respectively.  Amazingly, radiation contributed to tumorigenesis even at 50 mGy and 100% of mice got medulloblastoma with 1.5 Gy.  Loss of heterozygosity (LOH) analysis on a total of 164 tumors indicated that spontaneous tumors showed LOH in broad regions on chromosome 13, including Ptch1 and distally-extending telomeric portion (S-type).  In contrast, tumors developed after 3 Gy irradiation exhibited interstitial losses around Ptch1 (R-type).  A clear dose-dependent increase in the proportion of R-type tumor at intermediate doses suggested R-type to be a reliable radiation signature.  Array-CGH analysis indicated the R-type-specific copy-number reduction around Ptch1 and LOH-type-independent frequent gains of whole chromosome 6. Integrated expression microarray analysis indicated that expression levels of many genes within the altered genomic regions faithfully reflected the genomic copy-number changes.  Furthermore, it was also suggested that these expression changes in turn influenced on many other genes, such as Tgfb2 and Tgfb3, on widespread genomic regions.  This is the first demonstration that radiation-induced tumors developed after low-dose irradiation can be characterized quite precisely by interstitial deletion of Ptch1 and by associated gene expression profile.

overall_design: Gene expression in 3 normal cerebellum tissues and 12 medulloblastomas was measured.

first: Yuka

last: Ishida

first: Shizuko

last: Kakinuma

first: Kazutaka

last: Doi

first: Kazumi

last: Yamauchi

first: Mutsumi

last: Kaminishi

first: Seiji

last: Kito

first: Yuki

last: Ohta

first: Toshiko

last: Amasaki

first: Hiroyuki

last: Moritake

first: Toshiaki

last: Kokubo

first: Mayumi

last: Nishimura

first: Tetsu

last: Nishikawa

first: Okio

last: Hino

first: Yoshiya

last: Shimada


title: Transcript profiling of individual twin blastomeres derived by splitting 2-cell stage murine embryos

status: Public on May 15 2010

city: Northbrook

first: Michael

last: Falduto

state: IL

address: 1808 Janke, Unit M

institute: GenUs BioSystems, Inc.

summary: We have examined whether twin blastomeres from 2-cell stage mouse embryos differ in mRNA content. Amplified mRNA from 12 blastomeres derived from six embryos approximately mid-way through their second cell cycle was analyzed. Probes displaying normalized values greater than 0.25 were selected and examined for consistent bias in expression within blastomere pairs. Although transcript content varied both between individual embryos and twin blastomeres, no consistent asymmetries were observed for the majority of genes. On the other hand, 769 genes displayed a greater than 1.4-fold difference in expression across 5 of 6 pairs of blastomeres and 178 genes differed across all 6 pairs. These genes separated into two groups by class discovery clustering. Of the 769 differentially expressed genes, 163 were significantly up- or down-regulated in one sister blastomere compared to the other.  Transcripts encoding proteins implicated in RNA processing and cytoskeletal organization were highly represented among the most abundant, differentially distributed mRNA. We conclude that there are many differences that distinguish twin blastomeres derived from a single 2-cell stage embryo but that only a few of these differences are consistent across multiple pairs of embryos. We hypothesize that a stochastically-based lack of synchrony in cell cycle progression between the two cells might explain some or all of the asymmetries in transcript composition.

overall_design: 6 pairs of blastomeres were analyzed for a total of 12 samples.

first: R

last: Roberts

first: Mika

last: Katayama

first: Scott

last: Magnuson

first: Karen

last: Torres


title: Coordination of frontline defense mechanisms under severe oxidative stress.

status: Public on May 26 2010

city: Seattle

first: Dan

last: Tenenbaum

state: WA

institute: Institute for Systems Biology

summary: Oxidative stress (OS) results from genetic defects or stressful environmental challenges that cause unchecked production of reactive oxygen species (ROS).  OS has been implicated in many diseases due to its wide ranging damage to nucleic acids, proteins and lipids.  Using Halobacterium salinarum NRC-1, an extremophile that thrives under conditions of excessive OS, we have constructed a systems model for oxidative stress response (OSR) by integrating transcriptional changes induced by treatments with H2O2 and paraquat, functional associations inferred through comparative genomics, and de novo discovered cis-regulatory motifs.  Together with phenotypic analysis of mutant strains this has revealed a multi-tiered OS management program to transcriptionally coordinate three peroxidase/catalase enzymes, two superoxide dismutases, production of rhodopsins, carotenoids, and gas vesicles, metal trafficking, and various other aspects of metabolism.  Remarkably, a significant fraction of this OSR was accurately recapitulated by a model that was previously constructed from cellular responses to diverse environmental perturbations –this constitutes the general stress response component.  Notwithstanding this observation, comparison of the two models has identified the coordination of frontline defense and repair systems by regulatory mechanisms that are triggered uniquely by severe OS and not by other environmental stressors, including sub-inhibitory levels of redox-active metals, extreme changes in oxygen tension, and a sub-lethal dose of g rays.

overall_design: Mid-log phase cultures of H. salinarum NRC-1 (2 biological replicates) grown in flasks were treated with either sub-lethal concentrations of 25mM H2O2 or 4mM PQ and incubated with shaking for up to 240 min. For each treatment, two time courses were run to determine the transcriptional responses to (1) constant stress and (2) recovery of H. salinarum NRC-1 to H2O2 and PQ. During constant stress, culture aliquots (~4ml) were collected over a time course (-1, 5, 10, 20, 40, 80 and 160 minutes), centrifuged (16000g, 90 seconds) and flash frozen. For recovery, cells were first treated for 2-hours with either 25 mM H2O2 or 4mM PQ, recovered by centrifugation, washed and re-suspended in CM.  Cultures were returned to the incubator with shaking and samples were taken at 0, 10, 20, 30, 40, 50, 60, 120, and 240 minutes and processed as described previously. Analysis of temporal transcriptional changes (-1, 0, 5, 10, 20, 40, 80, 160 and 320m) to sub-inhibitory concentrations of PQ (0.25mM) was also characterized. Total RNA was prepared and labeled with Alexa547 and Alexa647 dyes. Intensities were normalized between the Alexa 546 and Alexa 647 channels by scaling all intensities in one channel such that the 75th percentile in each channel was made equal.

first: Amardeep

last: Kaur

first: Phu

last: Van

first: Courtney

middle: R

last: Busch

last: Robinson

first: Min

last: Pan

first: Wyming

last: Pang

first: David

last: Reiss

first: Jocelyne

last: DiRuggiero

first: Nitin

last: Baliga


title: Gene expression changes induced by the human aristolochic acid I in renal and hepatic tissue of mice

status: Public on Jun 09 2010

city: Sutton

first: Ian

last: Giddings

state: Surrey

address: 15 Cotswold Road

department: Section of Molecular Carcinogenesis

institute: Institute of Cancer Research

summary:
Aristolochic acid (AA) is the causative agent of urothelial tumours associated with aristolochic acid nephropathy and is also implicated in the development of Balkan endemic nephropathy-associated urothelial tumours. These tumours contain AA-characteristic TP53 mutations. We examined gene expression changes in Hupki (human TP53 knock-in) mice after treatment with aristolochic acid I (AAI) by gavage (5 mg/kg body weight). After 3, 12 and 21 days of treatment gene expression profiles were investigated using Agilent Whole Mouse 44K Genome Oligo Array. Expression profiles were significantly altered by AAI treatment in both target (kidney) and non-target (liver) tissue. Renal pathology and DNA adduct analysis confirmed kidney as the target tissue of AAI-induced toxicity. Gene ontology for functional analysis revealed that processes related to apoptosis, cell cycle, stress response, immune system, inflammatory response and kidney development were altered in kidney. Canonical pathway analysis indicated Nfkb, aryl hydrocarbon receptor, Tp53 and cell cycle signalling as the most important pathways modulated in kidney. Expression of Nfkb1 and other Nfkb-target genes was confirmed by quantitative real-time PCR (qRT-PCR) and was consistent with the induction of Nfkb1 protein. Myc oncogene, frequently over-expressed in urothelial tumours, was up-regulated by AAI on the microarrays and confirmed by qRT-PCR and protein induction. Collectively we found that microarray gene expression analysis is a useful tool to define tissue-specific responses in AAI-induced toxicity. Several genes identified such as TP53, Rb1, Mdm2, Cdkn2a and Myc are frequently affected in human urothelial cancer, and may be valuable prognostic markers in future clinical studies.

Keywords: Carcinogen treatment

overall_design: Two-color Agilent array. A reference design was chosen that all samples were hybridised to universal mouse reference RNA (UMRR). 12-condition experiment (2 mouse organs: kidney and liver; 2 treatments: AAI and water; 3 time points: 3, 12 and 21 days). Three biological replicates for each condition. One replicate per array.

first: Volker

last: Arlt

first: Jie

last: Zuo

first: Kristina

last: Trenz

first: Candice

last: Roufosse

first: Graham

last: Lord

first: Joelle

last: Nortier

first: Heinz

middle: H

last: Schmeiser

first: Monica

last: Hollstein

last: Phillips


title: miRNA signatures of intracellular and extracellular fractions from cancer cell lines

status: Public on Apr 16 2010

city: Nagaizumi-cho

first: Keiichi

last: HATAKEYAMA

state: Sunto-gun, Shizuoka

address: 1007 Shimonagakubo

institute: Shizuoka Cancer Center Research Institute

summary: For the purpose of finding a novel tumor marker, we conducted microRNA profiling analysis in fractions of cells, exosomes, and culture medium from seven cancer cell lines. Ranking data of the intracellular and extracellular microRNAs obtained by microarray analysis, we found that let-7 microRNA family are rich in all fractions from AZ-P7a cells, a metastatic gastric cancer cell line.

overall_design: miRNA profiling in fractions of cells, exosomes, and culture medium were conducted by miRNA microarray analysis. Two replicates of intra-samples were performed.

last: Ohshima

last: Hatakeyama


title: TGFb dependent Treg conversion and the inhibition of conversion by IL6

status: Public on Mar 25 2010

city: Scottsdale

first: Cheryl

last: Myers

state: AZ

address: 13400 E Shea Blvd

institute: Mayo Clinic College of Medicine

summary: Analysis of CD4+ cells activated with anti-CD3 and cultured in the presence of IL2. The effects of TGFb and IL6 on Treg conversion were analyzed to discover methods of inhibiting Treg conversion and/or Treg functional inhibition. CD4+ T-cells were enriched from lymph nodes of Foxp3-GFP mice and cultured under the under the following conditions: 1) anti-CD3+IL2; 2) anti-CD3+IL2+TGFβ; 3) anti-CD3+IL2+TGFβ+IL6; and 4) anti-CD3+IL2+IL6. On day 4 cells were collected, stained with anti-CD4-PE, and sorted into CD4+FOXP3- and CD4+FOXP3+ populations (>95% purity). For each treatment condition T-effector cells and Tregs were labeled independently  (either cy3 or cy5) and hybridized together for a two-color array experiment. Each treatment condition had dye swapped replicates, and a minimum of 3 replicate in total.

overall_design: Two color experiment. Four conditions : 1) anti-CD3+IL2, 3 samples  2) anti-CD3+IL2+TGFβ, 3 samples   3) anti-CD3+IL2+TGFβ+IL6, 4 samples   4) anti-CD3+IL2+IL6, 3 samples

first: Dominique

last: Hoelzinger

first: Joseph

last: Lustgarten


title: The apoA-I induced transcriptome and dependence on MyD88

status: Public on Jun 15 2010

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

summary: Apolipoprotein A-I is well known to play a role in cholesterol efflux, but our studies suggest that apoA-I may also induce proinflammatory signaling.  The molecular mechanisms behind apoA-I-mediated proinflammatory signaling have not yet been explored, nor has the link between this signaling and cholesterol efflux. We hypothesize that apoA-I is a novel TLR agonist, signaling through the MyD88 proinflammatory signaling adaptor to induce cytokines.  Microarray analysis confirmed that a suite of pro-inflammatory genes are induced by apoA-I with varying dependence upon MyD88, and that MyD88 regulates >6% of the apoA-I-induced transcriptome.

overall_design: Three replicate experiments were analyzed.  Each experiment consisted of a control sample and an apoA-I treated sample of RNA extracted from peritoneal macrophages isolated from both MyD88 +/+ and MyD88-/- mice, totaling four samples per experiment; 12 samples together.

first: Kathleen

last: Smoak

first: Michael

last: Fessler

first: Jennifer

last: Collins

first: Kevin

last: Gerrish

first: Laura

last: Wharey


title: Gene Expression Profiling of the Calvaria from Conditional Hdac3 Defecient and Wild-type Mice

status: Public on Mar 27 2010

city: Jacksonville

first: Yan

middle: W.

last: Asmann

address: 4500 San Pablo Road South

institute: Mayo Clinic

summary: We utilized the Illumina MouseRef-8 gene expression technology to quantify differential gene expression between wildtype mice and mice with Osterix driven Cre conditional knockout of Hdac3 (Hdac3-CKO).  We compared the RNA extracted from calvaria from 8 wildtype and 8 conditional knockout litter matched mice using two separate Illumina MouseRef-8 chips.

overall_design: Mice with exon 7 of Hdac3 flanked by loxP sites were crossed with mice expressing Cre driven by the Osterix promoter.  RNA from 5 day old mouse calvarial explants (digested for 20 minutes with collagenase) was purified using TRIzol according to the manufacturer’s protocol (Invitrogen) and reverse transcribed using Qiagen’s Quantitect Reverse Transcription Kit.  Two independent microarray experiments were performed; each experiment used RNA from four wildtype and four conditional knockout litter matched mouse calvaria.

last: Westendorf

first: David

middle: F

last: Razidlo

first: Tiffany

last: Whitney

first: Michelle

last: Casper

first: Bridget

last: Stensgard

first: Frank

last: Secreto

first: Sarah

last: Knutson

first: Scott

middle: W

last: Heibert


title: Expression of human aortic endothelial cells treated with or without oxidized phospholipids

status: Public on Mar 03 2010

city: La Jolla

first: Casey

last: Romanoski

address: 9500 Gliman Dr.

institute: UCSD

summary: Oxidized phospoholipids are a pro-inflammatory component of minimally modified lipoproteins that get trapped in the subendothelial space of atherosclerotic plaques of large arteries. To model the response of endothelial cells in a pro-atherosclerotic enviroment we measured the expression in primary endothelial cells with and without treatment with oxidized phsopolipids from 96 genetically identical donors of anonymous origin.

overall_design:
Primary human aortic endothelial cells were collected from aortic heart explants of heart transplant donors and cultured in standard cell culture conditions. At confluence, cells were treated with or without  40 ug/ml oxidized 1-palmitoyl-2-arachidonoyl-sn-glycero-3-phosphatidylcholine (Ox-PAPC) for 4 hours in media 199 containing 1% fetal bovine serum. After 4 hours, the cells were collected for RNA extraction and quantification of transcripts via microarrays.
Application of electronic probe mask (HT_U133Amsk.cdf) on raw data.

first: A

middle: J

last: Lusis


title: Distinctions between the stasis and telomere attrition senescence barriers in cultured human mammary epithelial cells

status: Public on May 12 2010

city: Berkely

first: Sanchita

last: Bhattacharya

address: 1 Cyclotron Rd

institute: MIT

summary:
Molecular distinctions between the stasis and telomere attrition senescence barriers in cultured human mammary epithelial cells

Normal human epithelial cells in culture have generally shown a limited proliferative potential of ~10-40 population doublings before encountering a stress-associated senescence barrier (stasis) associated with elevated levels of cyclin-dependent kinase inhibitors p16 and/or p21. We now show that simple changes in media composition can expand the proliferative potential of human mammary epithelial cells (HMEC) initiated as primary cultures to 50-60 population doublings, followed by p16(+), senescence-associated b-galactosidase(+) stasis. We compared the properties of growing and senescent pre-stasis HMEC with growing and senescent post-selection HMEC, i.e., cells grown in a serum-free medium that overcame stasis via silencing of p16 expression and that display senescence associated with telomere dysfunction. Cultured pre-stasis populations contained cells expressing markers associated with luminal and myoepithelial HMEC lineages in vivo, in contrast to the basal-like phenotype of the post-selection HMEC. Gene transcript and protein expression, DNA damage-associated markers, mean TRF length, and genomic stability, differed significantly between HMEC populations at the stasis vs. telomere attrition senescence barriers. Senescent isogenic fibroblasts showed greater similarity to HMEC at stasis than at telomere attrition, although their gene transcript profile was distinct from HMEC at both senescence barriers. These studies support our model of the senescence barriers encountered by cultured HMEC in which the first barrier, stasis, is Rb-mediated and independent of telomere length, while a second barrier (agonescence or crisis) results from telomere attrition leading to telomere dysfunction. Additionally, the ability to maintain long-term growth of genomically stable multi-lineage pre-stasis HMEC populations can greatly enhance experimentation with normal HMEC.

overall_design: 48 samples from Human Mammary Epithelial cells which includes samples from four different individuals at different passage levels which includes prestasis,intermediate,post selection and agonesence stages of cell cycle.

first: James

last: Garbe


title: Halobacterium growth

status: Public on Feb 11 2010

first: Dan

last: Tenenbaum

summary:
We report detailed characterization of physiological changes encoded by 63% of all genes within the archaeon Halobacterium salinarum subsp. NRC-1 during routine laboratory growth.  While the majority of these changes occur during the transition from rapid exponential growth to the stationary phase, we were also able to detect transient changes in gene expression.   This demonstrated the presence of several additional albeit subtle physiological states that exist beyond what might be anticipated from a direct interpretation of the growth profile.  Changes in the abundance of several key intracellular metabolites over the growth curve corroborated observations of changes in gene expression of enzymes that catalyze their synthesis.  Next, we investigated the roles of general transcription factors (GTFs) in mediating these global growth-associated gene expression changes.  This revealed numerous phenotypic perturbations including slowed growth, gas vesicle biogenesis deficiency and morphologic abnormalities upon the overexpression of a single GTF - TBPd.  These phenotypes were quantified and were attributed to a perturbation in the regulation of aconitase.  Importantly, our results demonstrate why an experiment design as simple as a simple batch culture can be enormously informative of activities and interrelationships of a large fraction of all genes in a microbe.

This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series

first: Marc

last: Facciotti

first: Wyming

middle: L

last: Pang

first: Fangyin

last: Lo

first: Kenia

last: Whitehead

first: Tie

last: Koide

first: Ken-ichi

last: Masumura

first: Min

last: Pan

first: Amardeep

last: Kaur

last: Larsen

last: Reiss

first: Linh

last: Hoang

first: Ewa

last: Kalisiak

first: Trent

last: Northern

first: Sunia

middle: A

last: Trauger

first: Gary

last: Siuzdak

first: Nitin

middle: S

last: Baliga


title: Diabetic db/db mice treated with three doses of rosiglitazone and S compound

status: Public on Jan 16 2010

city: Croissy-sur-Seine

first: Aurélie

last: Cotillard

address: 125 chemin de ronde

country: France

institute: Institut de Recherches Servier

summary: A reference PPARg agonist, rosiglitazone, is compared to a newly synthesised selective PPARg modulator in db/db mice through transcriptomic analysis using microarray technology. Two tissues and three doses are available. These data were used to develop a new methodology of gene selection. Data of a technical variability study are also available for two liver samples.

overall_design: Two tissues, two compounds and three doses (24 conditions). 6 biological replicates per condition (with a dye-swap design). 6 technical replicates for two of the liver samples.

first: Sabrina

last: Le Bouter

first: Nolwen

last: Guigal-Stéphan

first: Sophie

last: Courtade-Gaïani

first: Catherine

last: Dacquet

first: Michel

last: Lonchampt

first: Alain

last: Ktorza

first: Françoise

last: Xavier

first: Brian

last: Lockhart

first: Jean-Pierre

last: Galizzi


title: Halobacterium growth in standard growth media: time course

first: Dan

last: Tenenbaum

summary: We report detailed characterization of physiological changes encoded by 63% of all genes within the archaeon Halobacterium salinarum subsp. NRC-1 during routine laboratory growth.  While the majority of these changes occur during the transition from rapid exponential growth to the stationary phase, we were also able to detect transient changes in gene expression.   This demonstrated the presence of several additional albeit subtle physiological states that exist beyond what might be anticipated from a direct interpretation of the growth profile.  Changes in the abundance of several key intracellular metabolites over the growth curve corroborated observations of changes in gene expression of enzymes that catalyze their synthesis.  Next, we investigated the roles of general transcription factors (GTFs) in mediating these global growth-associated gene expression changes.  This revealed numerous phenotypic perturbations including slowed growth, gas vesicle biogenesis deficiency and morphologic abnormalities upon the overexpression of a single GTF - TBPd.  These phenotypes were quantified and were attributed to a perturbation in the regulation of aconitase.  Importantly, our results demonstrate why an experiment design as simple as a simple batch culture can be enormously informative of activities and interrelationships of a large fraction of all genes in a microbe.

overall_design:
Halobacterium NRC-1 was grown in shaken (220RPM) complete medium liquid culture at 37°C in duplicate flasks.  Samples were selected at 7 timepoints during the growth of this organism representing different phases of growth (e.g. early exponential, logrithmic, stationary etc.).

RNA extractions were performed using the Stratagene Absolutely RNA Miniprep Kit and RNA quality checked with the Agilent Bioanalyzer and with Oligo Microarrays were fabricated at the Institute for Systems Biology Microarray Facility. The arrays contain 4 spots per unique 70-mer oligonucleotides for each of 2400 non-redundant genes in Halobacterium NRC-1 Labeling, hybridization and washing have been previously described (Baliga et al. 2002) with 10 μg of RNA from the sample and reference. RNA from the final time point of a replicate experiment was used as the reference. Bias in dye incorporation was accounted for by reversing the labeling dyes (dye-flip). Raw data was processed and converted into log10 ratios with lambda (λ) values determined by a maximum likelihood method.Baliga, N. S., Pan, M., Goo, Y. A., Yi, E. C., Goodlett, D. R., Dimitrov, K., Shannon, P., Aebersold, R., Ng, W. V. & Hood, L. (2002) Proc Natl Acad Sci U S A 99:14913-84.

first: Marc

last: Facciotti

first: Wyming

last: Pang

first: Fangyin

last: Lo

first: Kenia

last: Whitehead

first: Tie

last: Koide

first: Ken-ichi

last: Masumura

first: Min

last: Pan

first: Amardeep

last: Kaur

first: David

last: Larsen

last: Reiss


title: Halobacterium delta-ura3 growth with added uracil: time course

overall_design:
Halobacterium NRC-1 delta-ura3 strain was grown in shaken (220RPM) complete medium liquid culture at 37°C in duplicate flasks.  20µg/ml uracil was added to the media.  Samples were selected at 6 timepoints during the growth of this organism representing different phases of growth (e.g. early exponential, logrithmic, stationary etc.).

RNA extractions were performed using the Stratagene Absolutely RNA Miniprep Kit and RNA quality checked with the Agilent Bioanalyzer and with Oligo Microarrays were fabricated at the Institute for Systems Biology Microarray Facility. The arrays contain 4 spots per unique 70-mer oligonucleotides for each of 2400 non-redundant genes in Halobacterium NRC-1 Labeling, hybridization and washing have been previously described (Baliga et al. 2002) with 10 μg of RNA from the sample and reference. RNA from the final time point of a replicate experiment was used as the reference. Bias in dye incorporation was accounted for by reversing the labeling dyes (dye-flip). Raw data was processed and converted into log10 ratios with lambda (λ) values determined by a maximum likelihood method.Baliga, N. S., Pan, M., Goo, Y. A., Yi, E. C., Goodlett, D. R., Dimitrov, K., Shannon, P., Aebersold, R., Ng, W. V. & Hood, L. (2002) Proc Natl Acad Sci U S A 99:14913-84.
Keywords: growth curve, archaea, halobacterium

first: Linh

last: Hoang

first: Ewa

last: Kalisiak

first: Trent

last: Northern

first: Sunia

last: Trauger

first: Gary

last: Siuzdak

first: Nitin

last: Baliga


title: Halobacterium growth with added uracil: time course

last: Tenenbaum

overall_design:
Halobacterium NRC-1 was grown in shaken (220RPM) complete medium liquid culture at 37°C in duplicate flasks.  20µg/ml uracil was added to the media.  Samples were selected at 7 timepoints during the growth of this organism representing different phases of growth (e.g. early exponential, logrithmic, stationary etc.).

RNA extractions were performed using the Stratagene Absolutely RNA Miniprep Kit and RNA quality checked with the Agilent Bioanalyzer and with Oligo Microarrays were fabricated at the Institute for Systems Biology Microarray Facility. The arrays contain 4 spots per unique 70-mer oligonucleotides for each of 2400 non-redundant genes in Halobacterium NRC-1 Labeling, hybridization and washing have been previously described (Baliga et al. 2002) with 10 μg of RNA from the sample and reference. RNA from the final time point of a replicate experiment was used as the reference. Bias in dye incorporation was accounted for by reversing the labeling dyes (dye-flip). Raw data was processed and converted into log10 ratios with lambda (λ) values determined by a maximum likelihood method.Baliga, N. S., Pan, M., Goo, Y. A., Yi, E. C., Goodlett, D. R., Dimitrov, K., Shannon, P., Aebersold, R., Ng, W. V. & Hood, L. (2002) Proc Natl Acad Sci U S A 99:14913-84.
Keywords: growth curve, archaea, halobacterium


title: Gene expression response to silica treatment in wild-type C57 black 6 mice vs Rag1 knockout, NK-depleted mice

status: Public on Dec 19 2009

city: Missoula

first: Corbin

last: Schwanke

state: MT

department: Biomedical and Pharmaceutical Sciences

institute: University of Montana

summary: The lung is constantly exposed to potentially pathogenic particles and microorganisms. It has recently become evident that not only innate, but also adaptive immune responses to particulates such as crystalline silica (SiO2) entering the respiratory tract are complex and dynamic events. Although the cellular mechanisms and anatomical consequences involved in the development of silicosis have been extensively studied, they still remain poorly understood.  Based on their capacity for immune regulation, lymphocytes may play a role in determining the respiratory response to environmental challenge by SiO2. The objective of this study was to characterize the impact of SiO2 exposure on respiratory immune processes, with particular emphasis on evaluating the importance of lymphocytes in the murine silicosis model.  Therefore, we utilized lymphopenic mice including NK deficient, Rag1-/- or a combination (Rag1-/- NK depleted) and demonstrated that SiO2-induced fibrosis and inflammation occur independently of T, B, NK T, and NK cells.  Studies in Rag1-/- mice further suggest that lymphocytes may participate in controlling SiO2-induced inflammation through modulation of the Nalp3 inflammasome. This observation may have clinical relevance in the treatment of inflammatory and fibrotic lung diseases that are either refractory or respond sub-optimally to current therapeutics.

overall_design: 2 replicates each of WT C57Bl6 saline treated, WT C57Bl6 silica treated, RagKO saline treated and RagKO silica treated.

first: Celine

last: Beamer

first: Andrij

last: Holian


title: Gene expression analysis of Ox40-cre/ROSA-YFP CD4+ T cell subsets

status: Public on Sep 22 2009

city: San Francisco

first: Mark

last: Klinger

state: CA

address: 513 Parnassus Avenue, Box0414

department: Microbiology and Immunology

institute: University of California, San Francisco

summary:
An Ox40-cre allele was used for lineage marking of CD4 T cells.  Naive T cells that had previously expressed OX40 demonstrated a partially activated phenotype that was distinct from that of the majority of naive T cells.  These results are consistent with a minor subpopulation of naive T cells being dependent on strong signaling responses to thymic self ligands.

Keywords: T cell population comparison.  Characterization of a novel subpopulation of naive T cells.

overall_design: Four types of T cells were sorted from mice (naive, CD44lo, CD44hi and Treg).

first: Nigel

last: Killeen


title: WT vs Hypomethylated Forebrain Gene Expression

status: Public on Dec 12 2009

city: Los Angeles

first: Masakazu

last: Namihira

address: 695 Charles E. Young Dr.

department: Human Genetics

institute: UCLA

summary: DNA methylation is a major epigenetic factor regulating genome reprogramming, cell differentiation, developmental gene expression.  To understand the role DNA methylation in CNS neurons, we generated conditional Dnmt1 mutant mice that possess ~90% hypomethylated cortical and hippocampal cells in the dorsal forebrain from E13.5 on.   The mutant mice were viable with a normal lifespan, but displayed severe neuronal cell death between E14.5 to 3-weeks postnatally.   Accompanied with the striking cortical and hippocampal degeneration, adult mutant mice exhibited neurobehavioral defects in learning and memory in adulthood.  Unexpectedly, a fraction of Dnmt1-/- cortical neurons survived through postnatal development, so that the residual cortex in mutant mice contained 20-30% of hypomethylated neurons throughout the life.  Hypomethylated excitatory neurons exhibited multiple defects in postnatal maturation including abnormal dendritic arborization and impaired neuronal excitability.  The mutant phenotypes are coupled with deregulation of those genes involved in neuronal layer-specification, cell death, and the function of ion channels.  Our results suggest that DNA methylation, through its role in modulating neuronal gene expression, plays multiple roles in regulating cell survival, neuronal migration and maturation in the CNS.

overall_design: We compared gene expression patterns in Wildtype and DNA methylation deficient (Emx1-cre; Dnmt1 mutant) mouse dorsal cortex. We performed 3 replicates using different each individual mouse strain. The Sample GSM350992 table is the average log ratio for the 3 replicatesArrays were performed in triplicate.

first: Leah

middle: K

last: Hutnick

first: Guoping

last: Fan


title: Halobacterium NRC-1 ura3 parent strain and VNG1451C deletion mutant in response to growth in rich medium

status: Public on Sep 08 2009

first: Amy

last: Schmid

institute: Institute for Systemsbiology

summary: Gene regulatory networks play an important role in coordinating biochemical fluxes through diverse metabolic pathways.  The modulation of enzyme levels enables efficient utilization of limited resources as organisms dynamically acclimate to nutritional fluctuations in their environment.  Here we have identified and characterized a novel nutrient-responsive transcription factor from the halophilic archaea, VNG1451C. In this experiment we used whole-genome microarray analysis in the VNG1451C deletion mutant vs. H. salinarum NRC-1 ura3 parent strain in rich medium during growth to show that the expression of many metabolic genes is perturbed in the VNG1451C deletion mutant.

overall_design: Halobacterium salinarum NRC-1 (ATCC700922) ura3 parent and VNG1451C strains were grown in complex medium (CM; 250g/L NaCl, 20g/L MgSO4.7H2O, 3g/L sodium citrate, 2g/L KCl, 10g/L peptone) at 37ºC under full-spectrum white light. Biological replicate samples were removed throughout the growth curve at early log, mid log, late log, and stationary phase to measure genome-wide transcription.

first: Schmid

last: Amy

first: Koide

last: Tie

first: Pan

last: Min

first: Baliga

last: Nitin S.


title: Acetylation of p65 at lysine 314 is important for late NF-k(kappa)B-dependent gene expression

status: Public on Jan 10 2010

city: Zurich

first: Karin

last: Rothgiesser

address: Winterthurerstrasse 190

country: Switzerland

institute: Institute of Veterinary Biochemistry and Molecular Biology

summary: We provided earlier evidence that acetylation of p65 at lysines 310, 314 and 315 is important for the expression of a defined subset of genes; acetylation at these residues regulates both positively and negatively gene expression, in a gene-specific manner. These earlier studies provided a first glance of the functional relevance of p65 acetylation, since gene expression was measured only after 45 minutes of TNFα stimulation. In order to know if the requirement for site-specific acetylation is maintained for the same genes after longer exposure to TNFα, and to identify possible new genes regulated through p65 acetylation, we decided to extent our analysis to 3 hours of stimulation. For this, we used p65(-/-) MEFs complemented with non-acetylatable mutants, where the target lysines for acetylation were mutated to arginines.

overall_design: p65(-/-) cells complemented either with wild type p65, an empty plasmid as control (pTV), the acetylation-deficient double mutant K314/315R or the triple mutant KTR (K310/314/315R), were stimulated by TNFα for 3 hours and total RNA was isolated in three independent replicates from these cells. RNA was amplified, labeled and hybridized to the Agilent Whole Mouse Genome Array. After statistical analysis of the expression profiles, differentially expressed genes were identified.

first: Monika

last: Fey

first: Michael

middle: O

last: Hottiger


title: Dynamic responses of primary human bronchial epithelial cells to influenza virus, viral RNA and interferon-beta

status: Public on Mar 30 2010

city: Cambridge

first: Nir

last: Hacohen

state: MA

address: 7 Cambridge Center

institute: Broad Institute

summary: We  defined the major transcriptional responses in primary human bronchial epithelial cells (HBECs) after either infection with influenza or treatment with relevant ligands. We used four different strategies, each highlighting distinct aspects of the response. (1) cells were infected with the wild-type PR8 influenza virus that can mount a complete replicative cycle. (2) cells were transfected with viral RNA (‘vRNA’) isolated from influenza particles. This does not result in the production of viral proteins or particles and identifies the effect of RNA-sensing pathways (e.g., RIG-I.). (3) Cells were treated with interferon beta (IFNb), to distinguish the portion of the response which is mediated through Type I IFNs. (4) Cells were infected with a PR8 virus lacking the NS1 gene (‘DNS1’). The NS1 protein normally inhibits vRNA- or IFNb-induced pathways, and its deletion can reveal an expanded response to infection.

overall_design: HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNß (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ?NS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated

first: Sagi

last: Shapira

first: Bennett

last: Shum


title: Integrative Transcriptome Analysis Reveals Common Molecular Subtypes of Human Hepatocellular Carcinoma (HT-HG_U133A)

city: Dallas

first: Yujin

last: Hoshida

state: TX

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

summary: Hepatocellular carcinoma (HCC) is a highly heterogeneous disease, and prior attempts to develop genomic-based classification for HCC have yielded highly divergent results, indicating difficulty in identifying unified molecular anatomy. We performed a meta-analysis of gene expression profiles in data sets from eight independent patient cohorts across the world. In addition, aiming to establish the real world applicability of a classification system, we profiled 118 formalin-fixed, paraffin-embedded tissues from an additional patient cohort. A total of 603 patients were analyzed, representing the major etiologies of HCC (hepatitis B and C) collected from Western and Eastern countries. We observed three robust HCC subclasses (termed S1, S2, and S3), each correlated with clinical parameters such as tumor size, extent of cellular differentiation, and serum alpha-fetoprotein levels. An analysis of the components of the signatures indicated that S1 reflected aberrant activation of the WNT signaling pathway, S2 was characterized by proliferation as well as MYC and AKT activation, and S3 was associated with hepatocyte differentiation. Functional studies indicated that the WNT pathway activation signature characteristic of S1 tumors was not simply the result of beta-catenin mutation but rather was the result of transforming growth factor-beta activation, thus representing a new mechanism of WNT pathway activation in HCC. These experiments establish the first consensus classification framework for HCC based on gene expression profiles and highlight the power of integrating multiple data sets to define a robust molecular taxonomy of the disease.

overall_design: Four hepatocellular carcinoma (HCC) cell line samples treated or untreated by TGF-beta

first: Sebastian

last: Nijman

first: Masahiro

last: Kobayashi

first: Jennifer

last: Chan

first: Jean-Philippe

last: Brunet

first: Derek

last: Chiang

first: Augusto

last: Villanueva

first: Philippa

last: Newell

last: Camargo

first: Supriya

last: Gupta

first: Jamie

last: Moore

first: Matthew

last: Wrobel

first: Jim

last: Lerner

last: Reich

first: Kenji

last: Ikeda

first: Masashi

last: Hashimoto

first: Goro

last: Watanabe

first: Stacey

last: Gabriel

first: Scott

last: Friedman

first: Hiromitsu

last: Kumada

first: Josep

last: Llovet

first: Todd

last: Golub


title: Halobacterium NRC-1 VNG1451C deletion mutant growth in defined medium with and without glucose

first: Amy

last: Schmid

summary: Gene regulatory networks play an important role in coordinating biochemical fluxes through diverse metabolic pathways.  The modulation of enzyme levels enables efficient utilization of limited resources as organisms dynamically acclimate to nutritional fluctuations in their environment.  Here we have identified and characterized a novel nutrient-responsive transcription factor from the halophilic archaea, VNG1451C. In this experiment we used whole-genome microarray analysis in the VNG1451C deletion mutant vs. H. salinarum NRC-1 ura3 parent strain in defined medium during growth with and without glucose to show that the expression of many metabolic genes is perturbed in the VNG1451C deletion mutant in response to this sugar.

overall_design: Halobacterium salinarum NRC-1 (ATCC700922) ura3 parent and VNG1451C strains were grown in complete defined medium (CDM; 20 amino acids at concentrations defined by Shand and Perez, 1999. NaCl 250g/L, MgSO4 20 g/L, KCl 1 g/L, NaH2PO4 0.167mM, Biotin 0.02mM, Thiamin 0.015mM, Folic acid 0.0113 mM, MnSO4 0.01mM, FeSO4, 0.01mM, glucose added at 10% w/v where indicated in sample files) at 37ºC under full-spectrum white light. Biological replicate samples were removed throughout the growth curve at early log, mid log, and stationary phase to measure genome-wide transcription.

first: Tie

last: Koide

first: Min

last: Pan

first: Nitin

last: Baliga


title: Microarray Profile of Gene Expression during Osteoclast Differentiation in Modeled Microgravity

first: Michael

last: Falduto

institute: GenUs BioSystems, Inc.

summary:
Microgravity leads to a 10-15% loss of bone mass in astronauts during space flight. Osteoclast is the multinucleated bone resorbing cell. In this study, we used NASA developed ground based Rotary Wall Vessel Bioreactor (RWV), Rotary Cell Culture System (RCCS) to simulate microgravity (μXg) conditions and demonstrated a significant increase (2-fold) in osteoclastogenesis compared to ground based control (Xg) mouse bone marrow cultures. We further determined the gene expression profiling of RAW 264.7 osteoclast progenitor cells in microgravity by agilent microarray analysis. Gene expression pattern was functional group clustered by transcriptome analysis using gene ontology tree machine (GOTM) for cell proliferation/survival, differentiation and function. We confirm the microgravity modulated gene expression critical for osteoclast differentiation by real-time RT-PCR and Western blot analysis in murine bone marrow cultures.
We identify transcription factors such as c-Jun, c-Fos, PU-1 critical for osteoclast differentiation is up-regulated in microgravity conditions. In addition, microgravity resulted in 2.3 and 2.0-fold increase in the level of cathepsin K and MMP-9 matrix metalloproteinase expression in preosteoclast cells involved in the bone resorption process respectively. We also demonstrate a significant increase in the expression levels of M-CSF receptor, c-Fms and PLCγ2 and S100A8 molecules that play an important role in Ca2+ signaling essential for osteoclast function. Further, microgravity stimulated preosteoclast cells showed elevated cytosolic Ca2+ levels compared to ground based control cells. Thus, microgravity regulated gene expression profiling in preosteoclast cells provide new insights in to molecular mechanisms and therapeutic targets of osteoclast differentiation/activation responsible for bone loss and fracture risk in astronauts during space flight mission.

overall_design: Microgravity associated with space flight is a challenge for normal bone homeostasis. Astronauts experience 10-15% bone loss during a space flight mission. We aimed to determine the effect of simulated microgravity on osteoclast preosteoclasts cells. RAW264.7 cells (1.5 x 106 /ml) were loaded in RCCS with DMEM containing 10% FBS for 24 h. The cells were stimulated with RANKL (80ng/ml) for 24 h to obtain preosteoclasts in parallel with ground based control cells. Total RNA was isolated using RNAzol reagent (Biotecx Labs, Houston, TX) from control (Xg) and microgravity (μXg) subjected cells and hybridized with Agilent whole mouse genome 4x44K array system. Slides were washed and scanned on an Agilent G2565 microarray scanner. Data obtained were analyzed with Agilent feature extraction and GeneSpring GX v7.3.1 software packages (Genus biosystem, Inc. Northbrook, IL, USA).

first: Sambandam

last: Yuvaraj

first: Jeremy

last: Blanchard

first: Giffin

last: Dautridge

first: Srinivasan

last: Shanmugarajan

first: Ted

last: Bateman

first: Sakamuri

middle: V

last: Reddy


title: Double-Stranded RNA-Activated Protein Kinase Regulates early innate immune responses during RSV Infection

status: Public on Sep 23 2009

first: NIEHS

last: Microarray Core

summary: Respiratory Syncytial virus (RSV) is the most common cause of childhood viral bronchiolitis and lung injury. Inflammatory responses significantly contribute to lung pathologies during RSV infections and bronchiolitis but the exact mechanisms have not been completely defined. The double-stranded RNA-activated protein kinase (PKR) functions to inhibit viral replication and participates in several signaling pathways associated with innate inflammatory immune responses. Using a functionally defective PKR (PKR-/-) mouse model, we investigated the role of this kinase in early events of RSV-induced inflammation. Our data showed that bronchoalveolar lavage (BAL) fluid of infected PKR-/- mice had significantly lower levels of several innate inflammatory cytokines and chemokines. Histological examinations revealed that there was less lung injury in infected PKR-/- mice as compared to the wild type. A genome-wide analysis showed that several early anti viral and immune regulatory genes were affected by PKR activation. These data suggest that PKR is a signaling molecule for immune responses during RSV infections.

overall_design: 6-10 week old male WT (B6.129PF1/J) (The Jackson Labs, Bar Harbor, ME) and PKR-/-  mice were used in all experiments. Mice were housed and maintained in specific pathogen-free conditions and used in accordance with the regulations of the National Institutes of Health. The human long strain of RSV-A2 (originally from Dr. B.S. Graham, NIH) was propagated in HEp-2 cells (American Type Culture Collection). Viral stocks were prepared by harvesting HEp-2 cells in fresh medium and three quick freeze thaw cycles followed by high speed centrifugation (10,000 X g) to remove cellular debris.

first: Radiah

last: CornMinor

first: Gino

last: Limmon

first: Laura

last: Miller-DeGraff

first: Darlene

last: Dixon

first: Danica

last: Andrews

first: Randal

last: Kaufman

first: Farhad

last: Imani


title: Halobacterium salinarum NRC-1 growth curve

status: Public on Jun 25 2009

first: Tie

last: Koide

address: 1441 N 34th street

institute: Institute for Systems Biology

summary: Halobacterium salinarum NRC-1 was grown in CM media, at 37oC in a waterbath with agitation of 125 rpm under constant light. Analysis of transcriptional changes during growth, in addition to mapping of transcriptome structure under the same conditions, provided interesting insights about regulatory logic within prokaryotic coding regions.

overall_design:
Samples were collected at different cell densities, from OD ~0.2 to OD ~5.0.
2 biological replicates were conducted. For each sample, a dye-swap experiment was performed.

first: David

last: Reiss

first: Marc

middle: T

last: Facciotti

first: Min

last: Pan