title: Comparison of bone marrow-derived macrophages from BALB/c and C57BL/6 mice with and without interferon-gamma stimulation.

city: Greifswald

first: Maren

last: Depke

address: F.-L.-Jahn-Str. 15a

department: Department of Functional Genomics

institute: E.-M.-Arndt-University Greifswald, University Medicine Greifswald, Interfaculty Institute for Genetics and Functional Genomics

summary:
ABSTRACT
Macrophages are essential components of the innate immune system and crucial for pathogen elimination in early stages of infection. We previously observed that bone marrow-derived macrophages (BMM) from C57BL/6 mice exhibited increased killing activity against Burkholderia pseudomallei compared to BMM from BALB/c mice. This effect was particularly pronounced when cells were treated with IFN-γ. To unravel mechanisms that could explain these distinct bactericidal effects, a comparative combined proteome and transcriptome analysis of untreated and IFN-γ treated BALB/c and C57BL/6 BMM under standardized serum-free conditions was carried out. We found differences in gene expression/ protein abundance belonging to cellular oxidative and antioxidative stress systems. Genes/ proteins involved in the generation of oxidant molecules and the function of phagosomes (respiratory chain ATPase, lysosomal enzymes, cathepsin) were predominantly higher expressed/ more abundant in C57BL/6 BMM. Components involved in alleviation of oxidative stress (peroxiredoxin, mitochondrial superoxide dismutase) were more abundant in C57BL/6 BMM as well. Thus, C57BL/6 BMM seemed to be better equipped with cellular systems that may be advantageous in combating engulfed pathogens. Simultaneously, C57BL/6 BMM were well protected from oxidative burst. We assume that these variations co-determine differences in resistance between BALB/c and C57BL/6 mice observed in many infection models.

Biological significance:
In this study we performed combined transcriptome and proteome analyses on BMM derived from two inbred mouse strains that are frequently used for studies in the field of host-pathogen interaction research. Strain differences between BALB/c and C57BL/6 BMM were found to originate mainly from different protein abundance levels rather than from different gene expression. Differences in abundance of respiratory chain complexes and phagosomal proteins as well as differential regulation of components belonging to various antioxidant stress systems help to explain long-known differences between the mouse strains concerning their different susceptibility in several infection models.

overall_design: In this study 12 samples were analyzed. They are classified into four groups: BMM of Balb/c mice medium control, BMM of Balb/c mice interferon gamma treated,  BMM of C57Bl/6 mice medium control, and BMM of C57Bl/6 mice interferon gamma treated. Each of the four groups contains 3 biological replicates.

first: Katrin

last: Breitbach

first: Ivo

last: Steinmetz

first: Uwe

last: Völker


title: Expression data by ACLY knockdown

status: Public on Apr 13 2014

city: Tokyo

first: Toshiro

last: Migita

address: 2-1-6 Kami-kitazawa, Setagaya-ku

country: Japan

institute: Tokyo Metropolitan Institute of Medical Science

summary: De novo lipogenesis is activated in most cancers. Several lipogenic enzymes are implicated in oncogenesis and represent potential cancer therapeutic targets. RNA interference-mediated depletion of ATP citrate lyase (ACLY), the enzyme that catalyzes the first step of de novo lipogenesis, leads to growth suppression in a subset of human cancer cells. Here we demonstrate the molecular basis and potential biomarkers for ACLY-targeting therapy. First, suppression of cancer cell growth by ACLY depletion involves down-regulation of fatty acid elongase ELOVL6 at the transcriptional level. Lipid profiling revealed that ACLY depletion alters fatty acid composition in triglyceride; increased palmitate and decreased longer fatty acids, in accordance with ELOVL6 down-regulation. Second, ACLY depletion increases reactive oxygen species (ROS), whereas addition of antioxidant reduces ROS and attenuates the growth suppression. Third, ACLY depletion or ROS stimulation induce phosphorylation of AMP-activated protein kinase (AMPK), a sensor of energy and lipid metabolism. Analysis of various cancer cell lines revealed that the levels of AMPK phosphorylation (p-AMPK) correlate with the basal ROS levels, and that cancer cells with low basal p-AMPK (i.e., low basal ROS) levels are highly susceptible to ACLY depletion-mediated growth suppression. Finally, in clinical colon cancer tissues, p-AMPK levels are significantly decreased in aggressive tumors and correlate with the levels of 8-hydroxydeoxyguanosine, a hallmark of ROS stimulation. Together, these data suggest that ACLY inhibition suppresses cancer growth via palmitate-mediated lipotoxicity, and p-AMPK could be a predictive biomarker for its therapeutic outcome.

overall_design: Two cell lines are treated with ACLY siRNA. The samples include controls of each cell line.

first: Hiroyuki

last: Seimiya


title: Expression profile of PC-3-derived cell lines from transendothelial migration or in vivo metastasis

status: Public on Apr 10 2014

city: Iowa City

first: Qin

last: Huang

address: 5-509 Bowen Science Bldg

department: Molecular  Physiology and Biophysics

country: USA

institute: University of Iowa

summary:
Metastatic colonization involves cancer cell lodgment or adherence in the microvasculature and subsequent migration of those cells across the endothelium into a secondary organ site. To study this process further, we analyzed both in vitro and in vivo migration of human PC-3 prostate cancer cells . We isolated 6 subpopulation of cells: TEM4-18 were isolated from in vitro transendothelial migration of PC-3  cells; GS672.Ug, GS683.LALN and JD1203.Lu are single passaged in vivo cell lines from TEM4-18; GS689.Li and GS694.LAd are twice passaged in vivo cell lines from PC-3 cells. All the subpopulations crossed an endothelial barrier more efficiently and more aggressive in a murine metastatic colonization model than parental PC-3 cells. Microarray and FACS analysis of these cells showed that the expression of many genes previously associated with leukocyte trafficking and cancer cell extravasation were either unchanged or down-regulated. These cells exhibited characteristic molecular markers of an epithelial-to-mesenchymal transition, including frank loss of E-cadherin expression and upregulation of the E-cadherin repressor ZEB1.
We used microarray to detail the global programme of gene expression underlying cancer metastasis.

overall_design: We wanted to compare the expression profiles of cells that had undergone transendothelial migration in vitro or metastasis in vivo. TEM4-18 was generated from the parental PC-3 that was plated onto a confluent human microvascular endothelial cell line from the lung and allowed to migrate across this monolayer. GS672.Ug were isolated from urogenital after intravenous injection of PC-3 cells. GS683.LALN and JD1203.Lu were isolated from lung after intravenous injection of TEM-418 cells. JD549.Ki  were isolated from kidney after intravenous injection PC-3 cells. GS689.Li and GS694.LAd were isolated from liver and left adrenal after intravenous injection of JD549.Ki. All the cell lines are analyzed once except duplicate for TEM4-18 in this experiment for a total of 7 samples in this microarray. All other five sublines were then compared to TEM4-18 cells for changes in gene expression.

first: Justine

middle: M

last: Drake

first: Garth

last: Strohbehn

first: Tom

last: Bair

first: Michael

last: Henry


title: mTORC1 controls the systemically-induced adaptive regulation of stem cell quiescence into GAlert

city: Palo Alto

first: Joseph

middle: T

last: Rodgers

state: CA

address: 3801 Miranda Ave

institute: Stanford University

summary:
A unique property of many adult stem cells is their ability to exist in a non-cycling, quiescent state. Although quiescence serves an essential role in preserving stem cell function until the stem cell is needed in tissue homeostasis or repair, defects in quiescence can lead to an impairment in tissue function, the extent to which stem cells can regulate quiescence is unknown. Here, we show that the stem cell quiescent state is composed of two distinct functional phases: G0 and an “alert” phase we term GAlert, and that stem cells actively and reversibly transition between these phases in response to injury-induced, systemic signals. Using genetic models specific to muscle stem cells (or satellite cells (SCs)), we show that mTORC1 activity is necessary and sufficient for the transition of SCs from G0 into GAlert and that signaling through the HGF receptor, cMet is also necessary. We also identify G0-to-GAlert transitions in several populations of quiescent stem cells. Quiescent stem cells that transition into GAlert possess enhanced tissue regenerative function. We propose that the transition of quiescent stem cells into GAlert functions as an 'alerting' mechanism, a novel adaptive response that positions stem cells to respond rapidly under conditions of injury and stress without requiring cell cycle entry or a cell fate commitment.
We performed microarray analysis on muscle stem cells, harvested immediately after isolation, to investigate the transcriptional response these cells have to injury and the role of mTORC1 and cMet have in this response

overall_design: At least 2 weeks after tamoxifen treatment, to induce recombination and expression of the Rosa26rYFP lineage tracer in Pax7 expressing muscle stem cells using a Pax7-CreER driver, YFP+ cells were FACS purified from hindlimb muscles of animals that were noninjured (quiescent satellite cells (QSCs)) or from hindlimb muscle contralateral to muscles where we induced a BaCl2 injury (contralateral satellite cells (CSCs)). We compared the response of wild-type (WT) muscle stem cells to the response elicited by muscle stem cells with conditional ablation of TSC1, Rptor, or cMet genes. Immediately after FACS purification of cells, total RNA was extracted, processed, labeled, and hybridized to Affymetrix Mouse Gene 1.0 ST arrays. Each biological replicate is a pooled sample of muscle stem cells isolated from 3-4 mice.

first: Thomas

middle: A

last: Rando


title: Activating CD8 T cell clones via the T cell receptor complex in the absence and presence of cyclosporine A

status: Public on Apr 14 2014

city: New Haven

first: Raymond

middle: Morris

last: Johnson

state: CT

department: Med/Infectious Diseases

institute: Yale University

summary:
Comparison of a cyclosporine-resistant murine CD8 T cell clone to a cyclosporine-sensitive murine T cell clone during activation (CSA = Cyclosporine A)
Chronic allograft rejection is the leading cause of morbidity/mortality in solid organ and bone marrow transplant patients.  It occurs in the setting of potent calcineurin and mTOR inhibitor therapies, implying that T cells mediating chronic rejection can function with compromised calcineurin-NFAT or IL-2 receptor signaling pathways.  In murine models the T cells mediating allograft rejection in the setting of calcineurin inhibitor therapy are CD8 T cells making IFN-gamma without a requirement for perforin.  It is not known whether these pathologic T cells are a unique subset or how they function.  In parallel other animal model research has shown that alloepthelial cells residing in the donor organ are critical targets for rejection.  While investigating T cell-alloepithelial cell interactions, we discovered an unusual alloreactive CD8 T cell population that recognized MHC class II I-Abm12.  A CD8 T cell clone derived from that population was intrinsically-resistant to cyclosporine and rapamycin without prior exposure to either in vivo or in vitro.  Microarray analysis comparing the novel CD8 T cell clone to a conventional CD8 CTL clone specific for MHC class I Kbm1 suggested that the TCR signaling pathway responsible for cyclosporine-resistance utilized the Aryl Hydrocarbon Receptor (AHR).

overall_design: Two T cell clones x 2 experimental conditions x 4 replicates

first: Jeanette

last: McClintick


title: Expression data for T47D cells treated with 2mM hydroxyurea

status: Public on Apr 22 2014

city: Bethesda

first: Lea

last: Jessop

state: MD

address: 8717 Grovemont Circle 127

department: DCEG

institute: NCI

summary:
RAD51B, a paralog of RAD51, have been associated with breast cancer risk in genome-wide association studies. The underlying biological mechanism through which germline genetic variation in RAD51B confers susceptibility to breast cancer is not well understood. Here we investigate the molecular function of RAD51B in breast cancer cell lines.
We used microarrays to detail the global gene expression to identify classes of genes that are regulated  differnetly post DNA damages as a result of RAD51B depeletion.

overall_design: T47D cells were first transfected with either non-targeting (control; siCON) or RAD51B-targeting (experimental; siRAD51B) siRNA, then followed by 24hr treatment of 2mM hydroxyurea (HU). Total RNA were extracted at the end of the treatment for microarray analysis. Three biological replicates were carried out for both control and experimental samples.

first: Phoebe

last: Lee

first: Chaoyu

last: Wang


title: Polycomb proteins link Proliferation with DNA Replication

status: Public on Apr 15 2014

city: Milan

first: Sri Ganesh

last: Jammula

address: Via Adamello 16

country: Italy

institute: IFOM-IEO

summary: Polycomb proteins control proliferation and cellular transformation regulating DNA replication independently of cell cycle checkpoints

overall_design: Total RNA was extracted from MEF cells (derived from Ola129 mice) transiently transfected with Ezh2 specific and control esiRNA oligos 48 hrs. post-transfection.

first: Andrea

last: Piunti

first: Sri

middle: G

first: Diego

last: Pasini


title: Alternative Splicing of MBD2 Supports Self-Renewal in Human Pluripotent Stem Cells [HG-U133_Plus_2]

status: Public on Apr 18 2014

city: Rochester

first: Hu

last: Li

state: MN

address: 200 First Street, Gonda Building G19-408

department: Molecular Pharmacology & Experimental Therapeutics

institute: Mayo Clinic

summary: Using global gene expression and proteomic analyses, we identified a molecular signature in human embryonic and induced pluripotent stem cells that suggested a central regulatory role for RNA splicing in self-renewal.  Through genetic and biochemical approaches, we established reciprocal functional links between the master regulatory factor OCT4 and SFRS2, a member of the serine/arginine-rich family of splicing factors. SFRS2 regulates expression of two isoforms of the methyl-CpG-binding protein MBD2 that play opposing roles in human ESC and during the reprogramming of fibroblasts.  Both the MBD2a isoform expressed in fibroblasts and the MBD2c isoform found in pluripotent cells bind OCT4 and NANOG promoters in human ESC, but only MBD2a interacts with NuRD chromatin remodeling factors.  Members of the miR-301 and miR-302 families provide additional regulation by targeting SFRS2 and the somatic specific MBD2a isoform. These data are consistent with a model in which OCT4, SFRS2, and MBD2 participate in a positive feedback loop to regulate proteome diversity in support of self-renewal in pluripotent cells.

overall_design: We isolated RNA from human iPS cells, different human fibroblasts and human embryonic stem cells for hybridization to the Affymetrix gene expression microarrays.

first: James

middle: J

last: Collins


title: Comparison of haploid and diploid clones of KBM7 cancer cell line

city: Cambridge

first: Yegor

last: Smurnyy

state: MA

address: 250 Massachusetts Ave

institute: Novartis Institutes for Biomedical Research

summary:
The series were performed to study the changes in gene expression upon diploidization of KBM7 cancer (CML) cell line. The line can exist either as a clone with 24 chromosomes (nearly haploid) or with
48 chromosomes (nearly diploid). Gene expression patterns are largely ploidy-independent, as suggested by this experiment

overall_design: Single cell derived clones of KBM7 cell line were grown. Included 7 haploid and 10 diploid clones, each with 2 independent total RNA extraction/microarray run. Also included peripheral blood mononuclear cells (PBMC) samples for comparison purposes.

first: Yan

last: Feng


title: Expression data from undifferentiated human ES cell line, khES3 grown using complete, leucine or lysine deprived media

status: Public on Apr 17 2014

city: Yokohama

first: nobuaki

last: shiraki

address: 4259-B-25 Nagatsuta-cho, Midori-ku

department: School of Life Science and Technology

institute: Tokyo Institute of Technology

summary:
In undifferentiated human ES cells, 48hr Leucine deprivation (delta Leu) or Lysine deprivation (delta Lys) led to apoptosis.
We used microarrays to detail the mollecular mechanism of cell-death caused by Leu, Lys deprivation in undifferentiated ES cells.

overall_design: Cells were harvested at undifferentiated stages for RNA extraction and hybridization on Affymetrix microarrays. We performed gene expression profiles of undifferentiated khES3 cells cultured in complete (comple),Leu or Lys deprivation for 5 hr.

first: Nobuaki

last: Shiraki

first: Tomonori

last: Tsuyama


title: PAX6 Regulates Melanogenesis in the Retinal Pigmented Epithelium through Feed-Forward Regulatory Interactions with MITF

status: Public on Apr 08 2014

city: Tel Aviv

first: Ruth

last: Ashery-Padan

state: Select a State or Province

address: Tel Aviv University

department: Department of Human Molecular Genetics and Biochemistry

country: Israel

institute: Tel-Aviv University

summary: During organogenesis, PAX6 is required for establishment of various progenitor subtypes within the central nervous system, eye and pancreas. PAX6 expression is maintained in a variety of cell types within each organ, although its role in each lineage and how it acquires cell-specific activity remain elusive. Herein, we aimed to determine the roles and the hierarchical organization of the PAX6-dependent gene regulatory network during the differentiation of the retinal pigmented epithelium (RPE). Somatic mutagenesis of Pax6 in the differentiating RPE revealed that PAX6 functions in a feed-forward regulatory loop with MITF during onset of melanogenesis. PAX6 both controls the expression of an RPE isoform of Mitf and synergizes with MITF to activate expression of genes involved in pigment biogenesis. This study exemplifies how one kernel gene pivotal in organ formation accomplishes a lineage-specific role during terminal differentiation of a single lineage.

overall_design: The data contains 3 control and 3 Pax6 negative samples representing biological repeats. Each sample was prepared from RPE dissected from E15.5 transgenic animals, either Pax6loxP/loxP or Pax6loxP/loxP;DctCre.

first: Shaul

last: Raviv

last: Padan


title: A novel EMT-selective small molecule induces ER stress

status: Public on Apr 09 2014

first: Yu-xiong

address: 9 Cambridge Center

institute: Whitehead Institute

summary:
Carcinoma cells can acquire key malignant traits by reprogramming their differentiation state via an epithelial-to-mesenchymal transition (EMT). Cancer cells that undergo EMT become invasive and resist a wide range of therapies including most chemotherapy drugs and radiation.  Such cells are also able to efficiently seed primary and metastatic tumors, making them functionally indistinguishable from tumor-initiating or cancer stem-like cells (TICs or CSCs). Therefore, there is significant interest in finding vulnerabilities of cancer cells that have undergone EMT.
A potent EMT-selective small molecule was discovered through a large-scale chemical screen. We used microarray analysis to understand the biological effects of this compound.

overall_design: HMLE_ctrl (human MECs, infected with a pBabe-shGFP retrovirus) and HMLE_Twist (human MECs, infected with a pBabe-Twist retrovirus) cells were treated with solvent control (DMSO), 5 µM or 10 µM of Cmp302 for 6 hours. Microarray analysis was performed to profile global gene expression.

first: Ethan

middle: S

last: Sokol

first: Piyush

middle: B

last: Gupta


title: Expression data from human monocyte derived macrophages infected with adenovirus expressing HIV-1 Vpr

city: Toronto

first: Muhammad

middle: Atif

last: Zahoor

state: Ontario

address: 101 College St.

country: Canada

institute: University Health Network

summary:
HIV-1 Vpr protein is a multifunctional protein which perturbs human transcriptome and interacts with a number of cellular proteins. In this study, we have attempted to explore the efffects of Vpr on human transcriptome and have identified several genes which are involved in innate immune respone and cell signaling pathways.
We used the microarray analysis to elucidate the differnetail expression pattern of differnet genes in human macrophages infected with HIV-1 Vpr. As result we found that HIV-1 Vpr protein leads to the induction of various interferon stimualted genes (ISGs) and chemokines in human macrophages.

overall_design: Human monocytes-derived macrophages (MDMs) were isolated from peripheral blood mononuclear cells (PBMCs) from two healthy donors and were infected with recombinant adenoviruses either expressing HIV-1 Vpr or ZsGreen1 as a control. At 48 hours post-infection, RNA was isolated and subjected to microarray analysis.

first: Guangai

last: Xue

first: Keisuke

last: Fukumoto

first: Aida

last: Yoko


title: Adenovirus promotes host cell anabolic glucose metabolism via MYC activation

city: Los Angeles

first: Nicholas

middle: Alexander

last: Graham

address: 570 Westwood Blvd, CNSI 4338

department: Molecular and Medical Pharmacology

institute: University of California, Los Angeles

summary:
Adenovirus infection leads to increased glycolytic metabolism in host cells. Expression of a single gene product encoded within the E4 early transcription region, E4ORF1, is sufficient to promote increased glycolytic flux in cultured epithelial cells.
E4ORF1 reprograms cellular glucose metabolism by augmenting MYC-dependent transcription of metabolic genes.

overall_design: To gain insight into the mechanism by which E4ORF1 promotes increased glycolytic flux, we conducted a global microarray analysis of changes in RNA expression in MCF10A cells induced to accutely express ORF1 versus an empty vector.

first: Minh

last: Thai

first: Thomas

last: Graeber

first: Heather

last: Christofk


title: Expression data during plantaris muscle regrowth following two weeks of hind limb suspension in young adult mice

status: Public on Apr 16 2014

city: Lexington

last: Chaillou

state: KY

address: University of Kentucky, Department of Physiology, 800 Rose Street

institute: Department of Physiology

summary: Global gene expression patterns were determined from microarray results on day 1, 3, 5, 7, 10 and 14 during plantaris muscle regrowth following two weeks of hind limb suspension in young adult mice (5 months).

overall_design: For each time point, one Affymetrix chip (Mouse Gene 1.0 ST) was used with 100 ng of total RNA derived from a pooled sample of the left plantaris muscle from six animals.

first: Janna

middle: R

last: Jackson

first: Jonathan

middle: H

last: England

first: Jonah

middle: D

last: Lee

first: Karyn

last: Esser

first: Esther

middle: E

last: Dupont-Versteegden

first: John

last: McCarthy


title: Gene expression analysis of Cbfb-deficient LSK and GMP

status: Public on Apr 05 2014

city: Saint Louis

first: Takeshi

last: Egawa

state: MO

address: 660 South Euclid

department: Pathology and Immunology

institute: Washington University School of Medicine

summary: Runx/Cbfb heterodimers play important roles in the development of hematopoietic cells in mouse embryos and adults. In order to identify genes that are regulated by Runx/Cbfb, we purified Lin– c-kit+ Sca1+ (LSK) cells and Lin– c-kit+ Sca1– CD16/32+ (GMP) cells from Vav1-iCre x Cbfb(F/F) and Vav1-iCre x Cbfb(F/+) mice and profiled gene expression using microarray.

overall_design: 200,000 LSK and GMP cells were purified separately from two 7 week old Vav1-iCre x Cbfb(F/F) mice and two Vav1-iCre x Cbfb(F/+) mice by cell sorting. The purity was higher than 98%. Total RNA was extracted using the NucleoSpin RNA XS kit (Macherey-Nagel), amplified using a PicoSL RNA amplification kit (Nugen) and biotinylated with Encore biotin module (Nugen). Labeled RNA was hybridized to Mouse Gene 1.0ST microarrays (Affymetrix) according to the manufacturer’s instruction.

first: Chun

last: Chou


title: Contribution of the STAT1alpha and STAT1beta isoforms to IFN-gamma mediated innate immunity

status: Public on Apr 04 2014

city: Vienna

first: Claus

last: Vogl

state: Vienna

address: Veterinaerplatz 1

department: Biomedical Sciences

country: Austria

institute: University of Veterinary Medicine, Vienna

summary: The transcription factor STAT1 is essential for interferon- (IFN) mediated protective immunity in humans and mice. Two splice isoforms of STAT1, STAT1α and STAT1β, differ with regard to a C-terminal transactivation domain, which is absent in STAT1β. Dimers of STAT1β are therefore considered transcriptionally inactive and potential competitive inhibitors of STAT1α. Contrasting this view, generation and analysis of mice deficient for either STAT1α or STAT1β demonstrated transcriptional activity of the STAT1β isoform and its enhancement of innate immunity. Gene expression profiling in primary cells revealed overlapping, but also non-redundant and gene-specific activities of STAT1α and STAT1β in response to IFNγ. Consistently, both isoforms mediated protective, IFNγ-dependent immunity against the bacterium Listeria monocytogenes, although with remarkably different efficiency. In contrast, STAT1α and STAT1β were largely redundant for transcriptional responses to IFNα/β and for IFNα/β-dependent antiviral activity. Collectively, our data shed new light on how STAT1 isoforms contribute to antimicrobial immunity.

overall_design: We treated macrophages of Stat1 delta alpha and Stat1 delta beta isoforms as well as Stat1 KO and Stat1 Wt mice with IFN gamma and Listeria to reveal differences in gene expression between isoforms and the two control genotypes.

first: Christian

last: Semper

first: Nicole

last: Leitner

first: Caroline

last: Lassnig

first: Matthias

last: Parrini

first: Michael

last: Rammerstorfer

first: Karin

last: Lorenz

first: Doris

last: Rigler

first: Simone

last: Müller

last: Kolbe

first: Thoms

last: Rülicke

first: Thomsa

last: Decker

first: Mathias

first: Birgit

last: Strobl


title: Time series expression data during phosphate limitation for E. coli K12 JP6015/pMU91

status: Public on Apr 03 2014

city: Stuttgart

first: Tom

last: Schuhmacher

address: Allmandring 31

department: Institute of Biochemical Engineering

country: Germany

institute: University of Stuttgart

summary:
A fermentation strategies with phosphate feeding was applied to elongate transition inti phosphate limitation for an tryptophan overproducing E. coli strain
High frequency sampling together with the applied fermentation strategy should provide high resolution insights into regulatory regimes involved in phosphate response

overall_design: The first sampling timepoint was set as a reference time point after 2,5 h fermentation time to cover phosphate excess conditions. Additional 9 sampling time points were selected based on process dynamics as soon as the phosphate concentrations became sensitive

first: Ralf

last: Takors


title: Reconstructing and reprogramming the tumor propagating potential of glioblastoma stem-like cells: ChIP-seq

first: Esther

last: Rheinbay

address: 7 Cambridge Center

institute: Broad Institute

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Developmental fate decisions are dictated by master transcription factors (TFs) that interact with cis-regulatory elements to direct transcriptional programs. Certain malignant tumors may also depend on a cellular hierarchy reminiscent of normal development but superimposed on underlying genetic aberrations. In glioblastoma (GBM), a subset of stem-like tumor- propagating cells (TPCs) appears to drive tumor progression and underlie therapeutic resistance, yet remain poorly understood. Here, we identify a core set of neurodevelopmental TFs (POU3F2, SOX2, SALL2, OLIG2) essential for GBM propagation. These TFs coordinately bind and activate TPC-specific regulatory elements, and are sufficient to fully reprogram differentiated GBM cells to ‘induced’ TPCs that recapitulate the epigenetic landscape and phenotype of native TPCs. We reconstruct a TF network model that highlights critical interactions and identifies novel therapeutic targets for eliminating TPCs. Our study establishes the epigenetic basis of a developmental hierarchy in a devastating malignancy, provides detailed insight into the underlying gene regulatory programs, and suggests attendant therapeutic strategies.

overall_design:
Histone modification profiling for H3K27ac and transcription factors in glioblastoma cell line reprogramming

The raw data files have been submitted to dbGAP.

first: M

middle: L

last: Suvà

first: E

first: S

last: Gillespie

first: B

last: Bernstein


title: Monozygotic twins discordant for recessive dystrophic epidermolysis bullosa phenotype highlight the role of TGF-β signalling in modifying disease severity

city: Genoa

first: Paolo

last: Uva

address: Via Gerolamo Gaslini, 5

institute: IRCCS Istituto Giannina Gaslini

summary: Recessive dystrophic epidermolysis bullosa (RDEB) is a genodermatosis characterized by fragile skin forming blisters that heal invariably with scars. It is due to mutations in the COL7A1 gene encoding type VII collagen, the major component of anchoring fibrils connecting the cutaneous basement membrane to the dermis. Identical COL7A1 mutations often result in inter- and intra-familial disease variability, suggesting that additional modifiers contribute to RDEB course. Here, we studied a monozygotic twin pair with RDEB presenting markedly different phenotypic manifestations, while expressing similar amounts of collagen VII. Genome-wide expression analysis in twins' fibroblasts showed differential expression of genes associated with TGF-β pathway inhibition. In particular, decorin, a skin matrix component with anti-fibrotic properties, was found to be more expressed in the less affected twin. Accordingly, fibroblasts from the more affected sibling manifested a profibrotic and contractile phenotype characterized by enhanced α-smooth muscle actin and plasminogen activator inhibitor 1 expression, collagen I release and collagen lattice contraction. These cells also produced increased amounts of proinflammatory cytokines interleukin 6 and monocyte chemoattractant protein-1. Both TGF-β canonical (Smads) and non-canonical (MAPKs) pathways were basally more activated in the fibroblasts of the more affected twin. The profibrotic behaviour of these fibroblasts was suppressed by decorin delivery to cells. Our data show that the amount of type VII collagen is not the only determinant of RDEB clinical severity, and indicate an involvement of TGF-β pathways in modulating disease variability. Moreover, our findings identify decorin as a possible anti-fibrotic/inflammatory agent for RDEB therapeutic intervention.

overall_design: Primary fibroblast cultures from biopsies from two twins affected by recessive dystrophic epidermolysis bullosa were analyzed. Each hybridization was performed in biological triplicate and in technical duplicate.

first: Teresa

last: Odorisio

first: Michela

last: Di Salvio

first: Angela

last: Orecchia

first: Giovanni

last: Di Zenzo

first: Eugenia

last: Piccinni

first: Francesca

last: Cianfarani

first: Antonella

last: Travaglione

first: Barbara

last: Bellei

first: Andrea

last: Conti

first: Giovanna

last: Zambruno

first: Daniele

last: Castiglia


title: Gene expression patterns of distinct human endothelial precursor cells

city: Taipei City

first: Tse-Shun

last: Huang

address: No.155, Sec.2, Linong Street

department: Institute of Microbiology and Immunology

country: Taiwan

institute: National Yang-Ming University

summary:
Early EPCs (eEPCs) appear at less than 1 week in culture dishes, whereas late EPCs (LEPCs) appear late at 2-4 weeks. Distinct angiogenic properties between these two EPC subpopulations have been disclosed by the angiogenesis assay: late EPCs, but not eEPCs, form vascular networks de novo and are able to incorporate into vascular networks. On the contrary, eEPCs, but not late ones, indirectly augment tubulogenesis even when physically separated by a Transwell membrane, implying the involvement of a cytokine-based paracrine mechanism.
Microarrays are great tools to “snapshot” the transcriptome profiles, and thus provide deeper insights into gene expressions and microRNA-gene interactions.

overall_design: Cord blood mononuclear cells (MNCs) were Histopaque-1077 isolated and plated in endothelial growth medium-2 on fibronectin-coated six-well plates at 37°C. After 3 days of culturing, attached eEPCs appeared, and medium and nonadherent cells were removed. Thereafter, the medium were replaced every 2 days, and a certain number of eEPCs continued to grow into the LEPCs colonies, which emerge 2–4 weeks after the start of MNC culture. Total RNA of early and late EPCs were extracted and evaluated with Affymetrix GeneChip Human U133 plus 2.0

first: Jaw-Wen

last: Chen

first: Jerry

last: Lo

first: Yu-Neng

last: Chueh

first: Yi-Chieh

last: Cheng

first: Hua-Yong

last: Wang

first: Po-Hsun

first: Chih-Ching

last: Lin

first: Hung-Jui

first: Shing-Jyh

last: Chang

first: Hsei-Wei


title: Genome-wide Scan for Methylation Profiles in Keloids

status: Public on Apr 02 2014

city: Detroit

first: Ana

middle: C

last: deCarvalho

state: MI

address: 2799 West Grand Blvd.

department: Department of Neurosurgery

institute: Henry Ford Hospital

type: Methylation profiling by genome tiling array

summary: Genome wide DNA methylation profiling of normal skin and keloid samples. The Illumina Infinium 450k Human DNA methylation Beadchip v1.1 was used to obtain DNA methylation profiles across approximately 485577 CpGs in keloid and normal samples. Samples included 6 normal skin, 6 Keloid.

overall_design: Bisulphite converted DNA from the 12 samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip v1.1

first: Jones

last: Lamont

first: George

last: Divine


title: mRNA expression profiles in far-infrared treated human endothelial precursor cells

summary: High glucose impairs the angiogenic activities of late endothelial precursor cells (EPC). We found that far infrared (FIR) treatment restored partially the activity of late EPC. However, the mechanisms are unclear. We performed gene expression microarray analysis to assess the expression profiles of high glucose-treated late EPC with or without FIR treatment.

overall_design: Late EPCs isolated from peripheral blood were cultured in high glucose condition for 48 hours, and then treated with or without FIR radiation for 30 minutes. Total RNA were extracted and evaluated with the Affymetrix GeneChip Human U133 plus 2.0 arrays.


title: Antibiotics induce redox-related physiological alterations as part of their lethality

first: Jason

last: Yang

address: 415 Main St, Rm 2017

department: Biological Engineering

institute: MIT / Broad Institute

summary:
Deeper understanding of antibiotic-induced physiological responses is critical to identifying means for enhancing our current antibiotic arsenal. Bactericidal antibiotics with diverse targets have been hypothesized to kill bacteria, in part, by inducing production of damaging reactive species. This notion has been supported by many groups, but recently challenged. Here we robustly test the hypothesis using biochemical, enzymatic and biophysical assays along with genetic and phenotypic experiments. We first used a novel intracellular hydrogen peroxide (H2O2) sensor, together with a chemically diverse panel of fluorescent dyes sensitive to an array of reactive species, to demonstrate that antibiotics broadly induce redox stress. Subsequent gene expression analyses reveal that complex antibiotic-induced oxidative stress responses are distinct from canonical responses generated by supra-physiological levels of H2O2. We next developed a method to dynamically quantify cellular respiration and found that bactericidal antibiotics elevate oxygen consumption, indicating significant alterations to bacterial redox physiology. We further show that catalase or DNA mismatch repair enzyme overexpression, as well as antioxidant pre-treatment limit antibiotic lethality, indicating that reactive oxygen species causatively contribute to antibiotic killing. Critically, the killing efficacy of antibiotics was diminished under strict anaerobic conditions, but could be enhanced by exposure to molecular oxygen or addition of alternative electron acceptors, suggesting that environmental factors play a role in killing cells physiologically primed for death. This work provides direct evidence that bactericidal antibiotics, downstream of their target-specific interactions, induce complex redox alterations that contribute to cellular damage and death, thus supporting an evolving, expanded model of antibiotic lethality.
Here, we used microarrays to analyze oxidative stress responses to bactericidal antibiotic treatment in wildtype and mutant E coli

sample_organism: Escherichia coli str. K-12 substr. MG1655

overall_design: WT or mutant E coli cells were grown to OD ~0.3. Untreated cells were harvested at time 0 as controls. Treated cells given the appropriate chemical perturbation and harvested 1 hour post-treatment. All experiments were performed in technical triplicate.

first: Daniel

last: Dwyer

first: Peter

last: Belenky

first: James

last: Collins

first: Graham

last: Walker


title: Epigenomic profiling of stemness, differentiation and primary tissues in human glioblastoma

status: Public on Apr 11 2014

first: Esther

last: Rheinbay

type: Expression profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Mouse gastric adenocarcinoma

city: Goyang

first: Hark

middle: Kyun

last: Kim

address: 323 Ilsanro

department: Biomolecular Function Research Branch

country: South Korea

institute: National Cancer Center

summary: We have created mice by performing gastric epithelium-specific knockout of common tumor suppressor genes.

overall_design: Mice with transgene were monitored for spontaneous gastric cancer. Gene expression profiles were obtained from fresh frozen mouse primary gastric cancer samples.

first: Hark-Kyun


title: IFNb-1a in-vivo treatment induces the expression and signaling of IFNAR1 and inhibits Th17 responses in PBMCs derived from CIS patients

status: Public on May 15 2014

city: Chapel Hill

first: Silva

last: Markovic-Plese

state: NC

address: 105 Mason Farm Rd

institute: University of North Carolina at Chapel Hill

summary: IFNb has been used as a first line therapy for relapsing remitting multiple sclerosis (RRMS).  Since only a few studies have addressed the role of endogenous IFNb in the pathogenesis of the disease, our objective was to characterize its role in the transcriptional regulation of pathogenic Th17 cytokines in patients with RRMS.  In-vitro studies have demonstrated that IFNb inhibited IL-17A, IL-17F, IL-21, IL-22 and IFN-b secretion in CD4+ lymphocytes through the induction of suppressor of cytokine secretion (SOCS)1 and 3.  We found that patients with RRMS have increased serum and cerebrospinal fluid (CSF) Th17 (IL-17A and IL-17F) cytokine levels in comparison to the control subjects, suggesting that deficient endogenous IFNbeta secretion and/or signaling may contribute to the dysregulation of those pathogenic cytokines in CD4+ cells.  We identified that the endogenous IFNb from serum of RRMS patients induced a significantly lower IFN-inducible gene expression in comparison to healthy controls (HCs).  In addition, in-vitro studies have revealed a deficient endogenous and exogenous IFNb signaling in CD4+ cells derived from MS patients. Interestingly, upon inhibition of the endogenous IFNb signaling by silencing interferon regulatory factor (IRF)7 gene expression, the resting CD4+ T cells secreted significantly higher level of IL-17A, IL-17F, IL-21, IL-22 and IL-9, suggesting that endogenous IFNb suppresses the secretion of these pathogenic cytokines. In-vivo recombinant IFNb-1a treatment induced IFNAR1 and its downstream signaling molecules’ gene expression, suggesting that treatment may reconstitute a deficient endogenous IFNbeta regulation of the CD4+ T-cells’ pathogenic cytokine production in MS patients.

overall_design: Gene expression changes induced by IFNβ−1a were tested using Affymetrix Human Genome U133 (HG-U133) arrays (Affymetrix) that contain 45,000 probe sets representing 39,000 transcripts derived from approximately 33,000 human genes. 107 PBMCs per condition derived from 15 CIS patients were stimulated with plate-immobilized αCD3 (1 μg/ml) and αCD28 (5 μg/ml) mAb (BD Biosciences) in the absence or presence of IFNβ-1a (1000 U/ml) (EMD Serono Inc) for 24 h in serum-free medium (Gibco). Cells were harvested and the total RNA was isolated using a Rneasy kit (Quiagen). Arrays were hybridized for 16 hours at 45oC in the GeneChip® Hybridization Oven 640 (Affymetrix). The arrays were washed and stained with R-phycoerythrin streptavidin in the GeneChip® Fluidics Station 400 (Affymetrix). The arrays were scanned with a Hewlett Packard GeneArray Scanner. Affymetrix GeneChip® Microarray Suite 5.0 software was used for washing, scanning and basic analysis.

first: Yazhong

last: Tao

first: Xin

last: Zhang

first: Jianping

last: Jin

first: Yunan

last: Tang


title: p53 constrains progression to anaplastic thyroid carcinoma in a Braf-mutant mouse model of papillary thyroid cancer.

first: A

last: Bhutkar

address: 77 Massachusetts Avenue

institute: MIT

summary: Anaplastic thyroid carcinoma (ATC) has among the worst prognosis of any solid malignancy.  The low incidence of the disease has in part precluded systematic clinical trials and tissue collection, and there has been little progress in developing effective therapies.  BRAF and TP53 mutations co-occur in a high proportion of ATC, particularly those associated with a precursor papillary thyroid carcinoma (PTC).  In order to develop an adult-onset model of BRAF-mutant anaplastic thyroid carcinoma, we generated a novel thyroid-specific CreER transgenic mouse.  We utilize a Cre-regulated BrafV600E mouse and a conditional Trp53 allelic series to demonstrate that p53 constrains progression from papillary to anaplastic thyroid carcinoma.  Gene expression and immunohistochemical analyses of murine tumors identified the cardinal features of human ATC including loss of differentiation, local invasion, distant metastasis and rapid lethality.  We employed small animal ultrasound imaging to monitor autochthonous tumors, and show that treatment with the selective BRAF inhibitor PLX4720 improved survival, but did not lead to tumor regression or suppress signaling through the MAPK pathway.  Combination of PLX4720 and the MEK inhibitor PD0325901 more completely suppressed MAPK pathway activation in mouse and human ATC cell lines, and improved the structural response and survival of ATC-bearing animals.  This model expands the limited repertoire of autochthonous models of clinically aggressive thyroid cancer, and these data suggest that small molecule MAPK pathway inhibitors hold clinical promise in the treatment of advanced thyroid carcinoma.

overall_design: Total RNA from five murine papillary thyroid carcinoma (PTC) tumors and five murine anaplastic thyroid carcinoma (ATC) tumors was analyzed.

first: David

last: McFadden

first: Amanda

last: Vernon

first: Philip

middle: M

last: Santiago

first: Raul

last: Martinez-McFaline

first: Arjun

first: Denise

last: Crowley

first: Martin

last: McMahon

last: Sadow

first: Tyler

last: Jacks


title: Follicular B (FoB) cells purified from miR-17-92 tKO mice

status: Public on Apr 01 2014

city: La Jolla

first: Steven

last: Head

address: 10550 N Torrey Pines Rd

institute: The Scripps Research Institute

summary: We have generated a miR-17~92 fl/fl allele whose expression can be turned off conditionally by Cre recombinase in the miR-106a-363-/-;miR-106b-25-/- background. The mice were crossed to CD19-Cre mice to turn off the expression of miR-17~92 specifically in B cells.

overall_design:
Follicular B(FoB) cells were purified from CD19-Cre;miR-17~92 fl/fl;miR-106a-363;miR-106b~25 mice (tKO1, tKO2, tKO3) and CD19-cre (Control1, Control2, Control3) by MACS depletion of cells positive for CD9, CD43, and CD93 (also known as AA4.1).
The purity of follicular B cells was examined by flow cytometry and was greater than 95% for all samples. Total RNA was extracted using RNeasy kit (QIAGEN).

first: Changchun

last: Xiao

first: Hyun

middle: Y


title: Germline Aberrations of PAX5 Cause Susceptibility to pre-B cell Acute Lymphoblastic Leukemia

status: Public on Apr 06 2014

city: Memphis

first: Shann-Ching

last: Chen

state: TN

address: 262 Danny Thomas Place

department: Pathology

institute: St. Jude Children's Research Hospital

summary: A novel heterozygous germline variant, c.547G>A (p.Gly183Ser), in the paired box protein encoding gene, PAX5, was found to segregate with disease in two unrelated kindreds with autosomal dominant pre-B cell acute lymphoblastic leukemia (ALL). Leukemic cells from both families exhibited 9p deletion, with loss-of-heterozygosity and retention of the mutant PAX5 allele at 9p13. Two additional sporadic ALL cases with 9p loss demonstrated PAX5 Gly183 substitution in the leukemic cells. Functional and gene expression analysis of the PAX5 germline variants demonstrated reduced transcriptional activity. These data extend the role of PAX5 alterations in the pathogenesis of pre-B ALL, and implicate PAX5 in a novel syndrome of germline susceptibility to pre-B cell neoplasia.

overall_design: We analyzed 10 samples of J558 murine myeloma cells infected with MSCV-Puro-IRES-GFP (PIG) empty vector (EV; three independent replicates), MSCV-PIG Pax5 WT (WT; three independent replicates), and MSCV-PIG Pax5 G183S (Mut; four independent replicates). Cells were selected with puromycin after infection for 5-7 days, subsequently cells were sorted for GFP and IgM expression by FACS.

first: Sohela

last: Shah

first: Kasmintan

middle: A

last: Schrader

first: Esmé

last: Waanders

first: Andrew

last: Timms

first: Joseph

last: Vijai

first: Cornelius

last: Miething

first: Jeremy

last: Wechsler

first: Jun

last: Yang

first: James

last: Hayes

first: Robert

last: Klein

first: Jinghui

first: Gang

last: Wu

first: Mike

last: Rusch

first: Panduka

last: Nagahawatte

first: Jing

last: Ma

first: Guangchun

last: Song

first: Lei

last: Wei

first: Paul

last: Meyers

first: Deepa

last: Bhojwani

first: Suresh

last: Jhanwar

first: Peter

last: Maslak

last: Fleisher

first: Jason

last: Littman

first: Lily

last: Offit

first: Rohini

last: Rau-Murthy

first: Megan

last: Harlan-Fleischut

first: Xiaoni

last: Gao

first: Christopher

last: Manschreck

first: Thomas

last: Kitzing

first: Vundavalli

middle: V

last: Murty

first: Susana

last: Raimondi

first: Roland

middle: P

last: Kuiper

first: Annet

last: Simons

first: Joshua

last: Schiffman

first: Sharon

last: Plon

first: Kenan

last: Onel

last: Wheeler

first: Deborah

last: Ritter

last: Ziegler

first: Kathy

last: Tucker

first: Rosemary


title: Follicular B (FoB) cells purified from miR-17-92 tKO mice, stimulated with LPS/IL-4, 13.5hr

first: Steven

last: Head

summary: We have generated a miR-17~92 fl/fl allele whose expression can be turned off conditionally by Cre recombinase in the miR-106a-363-/-;miR-106b-25-/- background. The mice were crossed to CD19-Cre mice to turn off the expression of miR-17~92 specifically in B cells and stimulated LPS/IL-4 for 13.5hr.

overall_design:
Follicular B(FoB) cells were purified from CD19-Cre;miR-17~92 fl/fl;miR-106a-363;miR-106b~25 mice (TKO1, TKO2, TKO3) and WT (WT1, WTl2, WT3) by MACS depletion of cells positive for CD9, CD43, and CD93 (also known as AA4.1). The purified B cells were stimulated with LPS/IL-4 for 13.5hr in B cell media.
The purity of follicular B cells was examined by flow cytometry and was greater than 95% for all samples. Total RNA was extracted using RNeasy kit (QIAGEN).

first: Changchun

last: Xiao

first: Hyun

last: Jin


title: Gene expression analysis of CD4+ CD8+ thymocytes [Affymetrix]

city: Freiburg

first: Pierre

middle: Daniel

last: Cauchy

state: Baden-Württemberg

address: Breisacher Str. 115

department: Zentrum für Translationale Zellforschung

institute: University Medical Center Freiburg

summary:
We performed ChIP-Seq for hallmark TFs (Ets1, Runx1), histone modification marks (H3K4me1, H3K4me2, H3K4me3, H3K27me3, H3K36me3), total RNA Pol II, short RNA-Seq as well as nucleosome mapping mainly in murine Rag2 -/- thymocytes. We also performed ChIP-Seq for E47 as well as nucleosome mapping, gene expression microarray analysis in CD4+ CD8+ DP thymocytes. Overall, we find a key role for the transcription factor Ets1, contributing towards alpha beta T cell lineage commitment via differential transactivation of stage-specific genes orchestrated by dynamic, co-association -mediated chromatin remodeling, as well as transcription dependent generation of a specialized chromatin structure at the TCR beta locus.
Genome-wide analysis via ChIP-Seq for Ets1, Runx1, total RNA Pol II binding,  H3K4me1, H3K4me2, H3K4me3, H3K27me3, H3K36me3, short RNA-Seq, Mnase-Seq in murine Rag2 -/- thymocytes, ChIP-Seq for E47, Mnase-Seq and gene expression microarray analysis in DP thymocytes

overall_design:
Genome-wide analysis via ChIP-Seq for Ets1, Runx1, total RNA Pol II binding,  H3K4me1, H3K4me2, H3K4me3, H3K27me3, H3K36me3, short RNA-Seq, Mnase-Seq in murine Rag2 -/- thymocytes, ChIP-Seq for E47, Mnase-Seq and gene expression microarray analysis in DP thymocytes

This Series represents gene expression microarray data.

first: Joaquin

last: Zacarias-Cabeza

first: Laurent

last: Vanhille

first: Frederic

last: Koch

first: Romain

last: Fenouil

first: Angelica

last: Santana

first: Aleksandra

last: Pekowska

first: Ahmad

last: Maqbool

first: Hélène

last: Holota

first: Aurélien

last: Griffon

first: Jean

last: Imbert

last: Ferrier

first: Salvatore

last: Spicuglia

first: Jean-Christophe

last: Andrau


title: Follicular B (FoB) cells purified from miR-17~92 TG and miR-17~92 tKO mice

last: Head


title: Inhibition of BET bromodomain proteins as a therapeutic approach in prostate cancer

status: Public on Mar 31 2014

city: London

first: Matteo

last: Righi

state: London

address: The MediaWorks, 191 Wood Ln

country: United Kingdom

institute: Autolus Therapeutics

summary: We analyzed transcriptional changes in 4 prostate cancer cell lines following treatment with the BET inhibitor I-BET762 using  Affymetrix Human Genome U133 Plus 2.0 Arrays.

overall_design: Four prostate cancer cell lines (NCI-H660, VCaP, LNCaP, PC-3) were treated with DMSO (control) or I-BET762 at 0.5uM or 10uM concentrations for 24 hours. Two biological replicates are included for each treatment group.

first: Anastasia

last: Wyce

first: Yan

last: Degenhardt

first: Yuchen

last: Bai

first: BaoChau

last: Le

first: Susan

last: Korenchuk

first: Ming-Chih

last: Crouthamel

first: Charles

middle: F

last: McHugh

first: Robert

last: Vessella

first: Caretha

last: Creasy

first: Peter

middle: J

last: Tummino

first: Olena

last: Barbash


title: Expression Data from murine control and IL6ralpha-deficient macrophages stimulated with Interleukin-6

status: Public on Mar 30 2014

city: Heidelberg

first: Jan

last: Mauer

state: BW

address: Im Neuenheimer Feld, 583

institute: BioMed X Innovation Center

summary:
IL-6 induces IL4ralpha expression in macrophages. This mechanism is necessary to promote macrophage polarization towards an M2-phenotype and is crucial to limit the inflammatory response both upon obesity and LPS-endotoxemia.
In this dataset, we include the expression data obtained from primary murine bone marrow-derived macrophages from control and IL6ralpha-deficient macrophages (n=4vs4) stimulated with interleukin-6 (IL-6)

overall_design: 8 samples were analyzed to compare control and IL6ralpha-deficient macrophages for their gene expression profiles upon stimulation with IL-6

first: J

last: Brüning


title: Suppression of inflammation in psoriasis blood after IL-17 treatment with ixekizumab

city: New York

first: Mayte

last: Suarez-Farinas

state: NY

address: 1425 Madison Ave, L2-70C, Box 1077,

institute: Mount SinaiSchool of Medicine

summary: The effect of anti-IL-17 treatment on systemic inflammation is not fully understand. Using cDNA microarray, genomic analysis methods such as GSEA and ingenuity, we characterized the transcriptional changes in the blood of psoriasis patients afer systemic neutralization of IL-17 compared to baseline (before treatment).  We also compared the whole blood-derived transcriptome between psoraisis patients at baseline and healthy volunteers to examine systemic inflammation in psoriasis patients.

overall_design: total RNA was extratced from whole blood from psoriasis patients at baseline and after two weeks of treatment; total RNA was extracted from the whole blood of healthy individuals

last: Suárez-Fariñas

first: Claire

middle: Q

last: Wang

first: James

middle: G

last: Krueger

middle: W

last: Hoffman


title: Gene expression profiles induced by overexpression of PDEF in MCF10A mammary epithelial cell line

status: Public on Mar 29 2014

city: Boston

first: Joan

middle: S.

last: Brugge

address: 240 Longwood Avenue

department: Department of Cell Biology

institute: Harvard Medical School

summary: Recent studies suggest that PDEF is required for secretory cell differentiation in several epithelial tissues. To investigate PDEF in the mammary gland, we examined the effect of this transcription factor on gene expression using microarray based profiling of MCF-10A cells. These cells are non-transformed mammary epithelial cells that express protein and gene expression programs of basal epithelial cells and undetectable levels of endogenous PDEF. Bioinformatics analysis of the genes induced or repressed by PDEF overexpression in MCF10A cells revealed a striking effect on expression of luminal and myoepithelial cell markers.

overall_design: Six samples were harvested 26 hours after retroviral infection with either vector control or PDEF.  Each condition was performed in triplicate.

first: Gilles

last: Buchwalter

first: Michele

last: Hickey

first: Anne

last: Cromer

first: Laura

last: Selfors

first: Ruwanthi

middle: N

last: Gunawardane

first: Jason

last: Frishman

first: Rinath

last: Jeselsohn

first: Craig

last: Jordan

first: Rachel

last: Schiff

middle: S

first: Myles

last: Brown


title: Gene expression profiles induced by shRNA-mediated knockdown of PDEF in MCF7 mammary epithelial cell line

summary: Microarray gene expression analysis was performed in MCF7 cells transduced with a non-specific shRNA or PDEF-targeting shRNA, and both subjected to hormone depletion for 48 hours. Analyses of differentially expressed genes combined with gene ontology revealed a downregulation of cell cycle related-genes and an upregulation of apoptosis-related genes in PDEF knockdown cells. These target genes constitute potential effectors of the pro-survival role of PDEF.

overall_design: Four samples were harvested after lentiviral infection with either non-specific shRNA control or PDEF-targetting shRNA.  All samples were subjected to hormone depletion for 48 hours.  Each condition was performed in duplicate


title: Gene expression profiling of naïve bone marrow-resident granulocyte monocyte precursors (GMPs) and TSLP-elicited splenic GMP-like cells

status: Public on Mar 28 2014

city: Philadelphia

first: Mark

middle: C.

last: Siracusa

state: PA

address: 421 Curie Blvd

department: Microbiology

institute: UPenn

summary:
Extramedullary hematopoiesis (EMH) refers to the differentiation of hematopoietic stem cells (HSCs) into effector cells that occurs in compartments outside of the bone marrow. Previous studies linked pattern recognition receptor (PRR)-expressing HSCs, EMH and immune responses to microbial stimuli. However, the factors that regulate EMH and whether EMH operates in broader immune contexts remain unknown. Here, we demonstrate a previously unrecognized role for thymic stromal lymphopoietin (TSLP) in promoting the population expansion of progenitor cells in the periphery and identify that TSLP-elicited progenitors differentiate into effector cells including macrophages, dendritic cells and granulocytes that contribute to TH2 cytokine responses. The frequency of circulating progenitor cells was also increased in allergic patients with a gain-of-function polymorphism in TSLP, suggesting the TSLP-EMH pathway may operate in human disease. These data identify that TSLP-induced EMH contributes to the development of allergic inflammation and indicate that EMH is a conserved mechanism of innate immunity.
In this study, we performed gene expression profiling to examine how the transcriptional signatures compared between TSLP-elcited GMP-like cells and naïve bone marrow-resident GMPs.

overall_design: Splenic TSLP-elicited GMP-like cells (CD3-, CD4-, CD5-, CD8-, CD19-, CD11b-, CD11c-, NK1.1-, FcεRI-, CD34+ c-kit+) were sort-purified from the spleen of C57BL/6 mice on day 5 post-TSLP-cDNA treatment. BM-resident GMPs (CD3-, CD4-, CD5-, CD8-, CD19-, CD11b-, CD11c-, NK1.1-, FcεRI-,  Sca1- c-kit+ CD34+ CD16/32+) were sort-purified from mice that received a control-cDNA injection.

first: David

last: Artis


title: Distinct activation of positive and negative regulatory immune genes during an evolving T cell response to diphencyprone (DPCP) in human skin

last: Suarez-Farinas

summary: We sought to characterize delayed-type hypersensitivity (DTH) responses elicited by topical hapten DPCP in normal human skin

overall_design: Comparison of transcriptomes among DPCP- and placebo-treated skin at different time points

first: Nicholas

last: Gulati

last: Suárez-Fariñas


title: The distribution of genomic variations in human iPSCs is related to replication timing reorganization during reprogramming [Affymetrix]

city: Rochester

first: Hu

last: Li

address: 200 First Street, Gonda Building G19-408

institute: Mayo Clinic

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

summary:
Cell fate change involves significant genome reorganization, including change in replication timing, but how these changes are related to genetic variation has not been examined. To study how change in replication timing that occurs during reprogramming impacts the copy number variation (CNV) landscape, we generated genome-wide replication timing profiles of induced pluripotent stem cells (iPSCs) and their parental fibroblasts. A significant portion of the genome changes replication timing as a result of reprogramming, indicative of overall genome reorganization. We found that early and late replicating domains in iPSCs are differentially affected by copy number gains and losses, and that in particular CNV gains accumulate in regions of the genome that change to earlier replication during the reprogramming process. This differential relationship was present irrespective of reprogramming method. Overall, our findings reveal a functional association between reorganization of replication timing and the CNV landscape that emerges during reprogramming.

Keywords: Expression profiling by array

overall_design:
[Gene expression] We isolated RNA from normal human fibroblast derived iPS cells, normal human fibroblasts, and human embryonic stem cells for hybridization to the Affymetrix gene expression microarrays.
[CNV] We isolated genomic DNA from iPSCs derived with retroviral and episomal vectors and their parental fibroblast cells for hybridization to the Affymetrix Genome-Wide Human SNP 6.0 Array.

first: Junjie

last: Lu


title: Expression data from Escherichia coli after treatment with nalidixic acid (NA)

status: Public on Mar 27 2014

city: jerusalem

first: Hanna

last: Engelberg-Kulka

state: Israel

address: Ein Karem

department: Microbiology and Molecular Genetics

institute: The Hebrew University Hadassa Medical School

summary: Having found that LexA degradation was significantly higher under apoptotic like death (ALD) than under SOS conditions, we hypothesized that additional genes tightly regulated by LexA would be transcribed under ALD conditions.

overall_design: We used microarray analysis to test the transcription pattern of up-regulated genes in ALD. We added no NA (n.t.), 100 µg/ml NA, or 10 µg/ml NA to cultures of the WT MC4100relA+, or its ΔmazEF or ΔmazEFlexA3 derivatives.

first: Ariel

last: Erental

first: Yoav

last: Smith


title: Gene expression profiling in psoriatic lesional and non-lesional skin [brodalumab treatment]

city: Seattle

first: Jeannette

last: Bigler

state: WA

address: 3200 NE 92nd Street

institute: BJ Group, LLC

summary: To explore the psoriasis phenotype and pathways involved in psoriasis, we characterized gene expression in lesional and non-lesional skin from psoriasis patients. Furthermore, we explored the effects of various doses of brodalumab on lesional skin over time.

overall_design: From each of the 25 psoriasis patients, we obtained two pre-dose biopsies, one from a lesion and the other from non-lesional skin in the same general body geography, and two post-dose biopsies. Total RNA was extracted from 6mm punch biopsies that were split in half. A total of 99 samples were run on Affymetrix HU133 Plus 2.0 microarrays. There was no paired non-lesional sample for 'T_lesional_pre-dose' (skn55789).

first: Marty

last: Timour

first: Keith

last: Kerkof

first: Christopher

middle: B

last: Russell


title: PDEF knockdown and overexpression in mammary epithelial cells

first: Joan

last: Brugge

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

overall_design: Refer to individual Series

first: Gilles

last: Buchwalter

first: Michele

last: Hickey

first: Anne

last: Cromer

first: Laura

last: Selfors

first: Ruwanthi

last: Gunawardane

first: Jason

last: Frishman

last: Jeselsohn

last: Jordan


title: Analysis of the DNA methylome and transcriptome in granulopoiesis reveal timed changes and dynamic enhancer methylation

city: Stockholm

first: Karl

last: Ekwall

address: Alfred Nobels Alle 7

country: Sweden

institute: Karolinska Inst

summary: The study investigated the changes in DNA-methylation and gene expression during granulopoiesis. To this end CMP, GMP, PMC and PMN cell populations were isolated by FACS from bone marrow from healthy donors and analysed by CAGE as well as expression and DNA microarrays.

overall_design: Bisulphite converted DNA from biological triplicate samples of CMP, GMP, PMC and PMN cell poplulations were hybridised to the Illumina Infinium 450k Human Methylation Beadchip.

first: Michelle

last: Rönnerblad

first: Tor

last: Olofsson

first: Robin

last: Andersson

first: Iyadh

last: Douagi

first: Mohsen

last: Karimi

first: Sören

last: Lehmann

first: Ilka

last: Hoof

first: Albin

last: Sandelin

first: Masayohi

last: Itoh

first: Sayaka

last: Nago-Sato

first: Hideya

last: Kawaji

first: Timo

last: Lassmann

first: Piero

last: Carninici

first: Yoshihide

last: Hayashizaki

first: Alistair

middle: R

last: Forrest

first: Erik

last: Arner

first: Andreas

last: Lennartsson


title: Microarray Gene Expression for Undifferentiated Mesenchymal Stem Cells, Adipogenically Differentiated and Dedifferentiation cells

city: Berlin

first: Mujib

last: Ullah

address: Charitéplatz 1 10117 Berlin, Virchoweg11

department: Berlin-Brandenburg Center for Regenerative Therapies, Dept. of Rheumatology

institute: Charité-University Medicine Berlin

summary:
Bone marrow mesenchymal stem cells (MSC) were adipogenically differentiated followed by dedifferentiation. We are interested to know the new fat markers, adipogenic signaling pathways and dedifferentiation signaling pathways.Furthermore we are also intrested to know that how differentiated cells convert into dedifferentiated progenitor cells. To address these questions, MSC were adipogenically differentiated, followed by dedifferentiation. Finally these dedifferentiated cells were used for adipogenesis, osteogenesis and chondrogenesis. Histology, FACS, qPCR and GeneChip analyses of undifferentiated, adipogenically differentiated and dedifferentiated cells were performed. Regarding the conversion of adipogenically differentiated cells into dedifferentiated cells, gene profiling and bioinformatics demonstrated that upregulation (DHCR24, G0S2, MAP2K6, SESN3) and downregulation (DST, KAT2, MLL5, RB1, SMAD3, ZAK) of distinct genes play a curcial role in  cell cycle to drive the adipogenically differentiated cells towards an arrested state to narrow down the lineage potency. However, the upregulation (CCND1, CHEK, HGF, HMGA2, SMAD3) and downregulation (CCPG1, RASSF4, RGS2) of these cell cycle genes motivates dedifferentiation of adipogenically differentiated cells to reverse the arrested state. We also found new fat markers along with signaling pathways for adipogenically differentiated and dedifferentiated cells, and also observed the influencing role of proliferation associated genes in cell cycle arrest and progression.
We have differentiated bone marrow derived mesenchymal stem cells(MSC) into adipogenically differentiated cells followed by dedifferentiation. We are intrested to know new fat markers, signaling pathways for adipogenically differentiated and dedifferentiated cells, along to observe the genes associated with cell cycle arrest and progression. Results are also provide molecular insight into the process of adipogenesis and dedifferentiation.

overall_design: To study the adipogenic differentiation and dedifferentiation process along with "how adipogenically differentiated cells convert into dedifferentiated cells" on the molecular level, gene expression profiling with genome-wide Affymetrix HG-U133 Plus 2.0 olgonucleotide microarrays (Affymetrix, Santa Clara, CA, USA) was applied. In total, 12 GeneChips were performed for n=3 donors and 4 times (3x4=12): 3x P4 MSC (undifferentiated state), 3x adipogenically differentiated cells at day 15 (differentiated state), 3x dedifferentiated cells at day 7 (dedifferentiated state) and 3x dedifferentiated cells at day 35 (dedifferentiated state)

first: Stefan

last: Stich

first: Michael

last: Notter

first: Jan

last: Eucker

last: Sittinger

first: Jochen

last: Ringe


title: Cancer-Associated Fibroblasts Support Lung Cancer Stemness through Paracrine IGF-II/IGF1R/Nanog Signaling

status: Public on Mar 25 2014

city: Taipei

first: Wan-Jiun

last: Chen

address: No.1 Jen Ai Road section 1

institute: National Taiwan University

summary:
The CLS1/CAF co-culture maintained the cancer stemness. This cancer stemness was lost when the CAF feeder cells were removed during passaging.
To investigate the specific signaling pathways and markers of lung CSCs, we analyzed the gene expression profile of the CLS1 sphere after  CLS1/CAF co-culture and compared this profile with that obtained for CLS1 cells cultured without feeder cells through different passages (CLS1 p3, p6, and p14) and CLF1

overall_design: CLS1 sphere generated by co-culture with CAF and remove CAF to mimic cancer cell differentiation.  Four time points of the CLS1 after co-culture with CAF have been collected for microarray analysis:CLS1-2 p.3, p.6, p.8, p.14. We tried to compare theCLS1 sphere-regulated gene expression profiles with the CLS1-2 p.3, p.6, p.8, p.14  and CLF1 to identify the possible cross talk  mechanisms of CLF1 and CLS1 and the signaling pathways that maintain stem cell properties.

first: Chao-Chi

last: Ho

first: Chih-An

last: Lin

first: Wen-Cheng

last: Chu

first: Wan-Fen

last: Lee

first: Yu-Hui

last: Yang

first: Hsuan-Yu

first: Ker-Chau

last: li

first: Yee-Ming

first: Jen-Yi

first: Ping

last: Wu

first: Han-Yi

middle: E

last: Chou

first: Thai-Yen

last: Ling

first: Sung-Liang

last: Yu

first: Shin-Sheng

last: Yuan

first: Yu-Ju

middle: L

first: Yih-Leong

last: Chang

first: Huei-Wen

first: Pan-Chyr


title: The effect of genotype and in utero environment on inter-individual variation in neonate DNA methylomes (methylomes)

city: Singapore

first: Dennis

last: Wang

address: 30 Medical Drive

country: Singapore

institute: Singapore Institute for Clinical Sciences

summary:
We surveyed the genotypes and DNA methylomes of 237 neonates and found 1423 punctate regions of the methylome that were highly variable across individuals, termed variably methylated regions (VMRs), against a backdrop of homogeneity. Although methQTLs were readily detected in neonatal methylomes, genotype alone did not explain the majority of the VMRs.
We found that the best explanation for 75% of VMRs was the interaction of genotype with different in utero environments, including maternal smoking, maternal depression, maternal BMI, infant birth weight, gestational age and birth order.

overall_design: We surveyed the genotypes and DNA methylomes of 237 neonates and included 32 technical replicates

first: Joanna

middle: D

last: Holbrook


title: Combined microRNA/mRNA transcriptome analysis reveals angiogenic microRNAs-genes pathway of human late endothelial precursor cells.

city: Taipei City

first: Tse-Shun

last: Huang

address: No.155, Sec.2, Linong Street

institute: National Yang-Ming University

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


title: The distribution of genomic variations in human iPSCs is related to replication timing reorganization during reprogramming

first: Hu

last: Li

state: MN

department: Molecular Pharmacology & Experimental Therapeutics

type: Genome variation profiling by genome tiling array

first: Junjie

last: Lu


title: Steroid Receptor Coactivator 1 is an Integrator of Glucose and NAD(+)/NADH Homeostasis

city: Houston

first: David

last: Lonard

state: TX

address: 1 Baylor Plaza

department: Mol & Cell Biology-Mol.Regulation

institute: Baylor College of Medicine

summary: SRC-1 affects the expression of complex I of the mitochondrial electron transport chain, a set of enzymes responsible for the conversion of NADH to NAD(+). NAD(+) and NADH were subsequently identified as metabolites that underlie SRC-1's response to glucose deprivation. Knockdown of SRC-1 in glycolytic cancer cells abrogated their ability to grow in the absence of glucose consistent with SRC-1's role in promoting cellular adaptation to reduced glucose availability

overall_design: RNA profiling was used to examine the effects of SRC-1 perturbation on gene expression in the absence or presence of glucose.

first: Massoud

last: Motamed

first: Kimal

middle: I

last: Rajapakshe

first: Sean

middle: M

last: Hartig

first: Cristian

last: Coarfa

first: Robb

last: Moses

first: Bert

last: O'Malley


title: Expression data from lungs of Vldlr-/- mice and wild type (WT) B6129SF2/J mice that had received intranasal house dust mite (HDM) challenges to induce experimental asthma or saline, as a control.

city: Bethesda

first: Yanqin

last: Yang

state: Maryland

address: 10 Center Dr.

institute: NIH

summary:
The very low density lipoprotein receptor (VLDLR) is a multi-ligand receptor that mediates pleiotropic biological processes, such as brain development.
In this dataset, we include the expression data obtained from lungs from mice that had been challenged with house dust mite to induce experimental asthma or saline, as a control. These data are used to obtain genes that are differentially expressed in response to VLDLR signaling.

overall_design: We compared wild type and VLDLR knock out mice that had been sensitized and challenged with house dust mite or saline, as a control. There were total 16 samples with four biological relicates in each group.

first: Stewart

last: Levine


title: Expression data from primary Glioblastoma in adults

city: Leipzig

first: Edith

last: Willscher

address: Haertelstraße 16-18

institute: IZBI

summary:
Gene expression profiling revealed over-representation of a distinct (proneural-like) expression signature in long-term survivors that was linked to IDH1/2 mutation. However, among the IDH1/2-wildtype patients, tumors from long-term survivors did not show distinct gene expression profiles and included proneural, classical and mesenchymal glioblastoma subtypes.
We performed genome- and/or transcriptome-wide molecular profiling of primary tumor samples from 70 glioblastoma patients of the German Glioma Network, including 23 longterm survivors with >36 months overall survival (OS), 16 short-term survivors with <12 months OS, and 31 patients with intermediate OS

overall_design: For this study, we screened prospectively recruited patients with a histopathological reference diagnosis of glioblastoma, known KPS at diagnosis, information on extent of resection by early postoperative neuroimaging, available frozen tissue specimens from the initial operation, and documented clinical outcome.

first: Guido

last: Reifenberger

first: Ruthild

last: Weber

first: Vera

last: Riehmer

first: Kerstin

last: Kaulich

first: Henry

last: Wirth

first: Jens

last: Gietzelt

first: Bettina

last: Hentschel

first: Manfred

last: Westphal

first: Matthias

last: Simon

first: Gabriele

last: Schackert

first: Johannes

last: Schramm

first: Jakob

last: Matschke

first: Michael

middle: C

last: Sabel

first: Dorothee

last: Gramatzki

first: Jörg

last: Felsberg

first: Christian

last: Hartmann

first: Joachim

middle: P

last: Steinbach

first: Uwe

last: Schlegel

first: Wolfgang

last: Wick

first: Bernhard

last: Radlwimmer

first: Torsten

last: Pietsch

last: Tonn

first: Andreas

last: von Deimling

first: Hans

last: Binder

last: Weller

first: Markus

last: Loeffler


title: The effect of genotype and in utero environment on inter-individual variation in neonate DNA methylomes

first: Dennis

last: Wang


title: Calcineurin signaling regulates neural induction through antagonizing the BMP pathway

city: Stanford

first: Ahryon

last: Cho

state: CA

address: 300 Pasteur Dr

institute: Stanford University School of Medicine

summary: Calcineurin activity is required for neural differentiation of embryonic stem cells (ESC). We assessed gene expression changes at several time points of in vitro ESC to neural differentiation when calcineurin activity is inhibitied by its antagonist FK506 and Cyclosporin(CsA).

overall_design: d4, d6, d8, and d12 EBs of FK506/CsA treatment group (d3-8) and its non-treated control group were harvested from three independent experiments of in vitro differentiation of 46C mouse ESCs. Total RNA of each sample was extracted, reverse transcribed, labeled and hybridized to Affymetric Mouse Gene ST 1.0 Arrays.

first: Isabella

middle: A

last: Graef


title: Identification of candidate genes regulated by E4bp4 in murine bone marrow

status: Public on Mar 21 2014

city: London

first: Hugh

middle: JM

last: Brady

address: South Kensington

department: Life Sciences

institute: Imperial College

summary:
E4bp4 is essential for the development of natural killer (NK) cells. We sought to identify downstream targets of E4bp4 by comparing mRNA expression in wild type vs. E4bp4 knockout
Lineage-depleted bone marrow, which is enriched for haematopoietic progenitor cells. We then went on to validate these targets using real time PCR, genetic complementation assays and ChIP

overall_design: Total RNA was extracted from linege-depleted bone marrow from six wild type and six E4bp4 knockout mice. Labelled cDNA was hybridised to a GeneChip Mouse Gene 1.0 ST Array. The data generated was imported into GeneSpring GXv11 (Agilent) and normalised using the Robust Multi-Array (RMA16) algorithm. Genes were filtered on expression value between 20th and 100th percentile to remove those with very low or no expression across all the samples. A moderated t-test was applied to the data and p values were adjusted for multiple testing using a Benjamini-Hochberg False Discovery Rate correction.

first: Victoria

last: Male


title: Gene expression in primary human B cells sorted according to IL-10 secretion or not after 2 days of activation.

status: Public on Mar 24 2014

first: Pawel

last: Durek

address: Charitéplatz 1

institute: Deutsches Rheuma-Forschungszentrum

summary: To determine characterize human B cells that express IL-10 on a molecular level, we compared the global gene expression of primary CD19pos B cells secreting IL-10 or not, upon activation with anti-CD40, IL-4 and CpG for 2 days.

overall_design: Human B cells from healthy donors were sorted according to CD19 expression by magnetic cell separation. The cells were stimulated at 2.5E06 cells/ml by activating anti-CD40 mAb (1 µg/ml, clone 82111, RnD Systems), recombinant human IL-4 (10 ng/ml, Immunotools) and CpG2006 (3 µg/ml) for 2 days following restimulation for 3 h with phorbol myristate acetate (PMA, 10 ng/ml) and ionomycin (1 µg/ml). Staining of viable IL-10 secreting human CD19pos B cells was performed by the IL-10 capture assay according the manufacturers instructions (Miltenyi Biotec, n=2). Finally, the cells were sorted into IL-10posCD69pos and IL-10negCD69pos cells by flow cytometric cell sorting on a BD Aria II sorter (Becton Dickinson). Dead cells were excluded using propidium iodide. Total RNA was extracted using the RNeasy Mini kit (Qiagen). The integrity and amount of isolated RNA was assessed for each sample using an Agilent 2100 Bioanalyzer (Agilent, Waldbronn, Germany) and a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE). Double-stranded complementary RNA was synthesized from 1 µg total RNA using Message AmpII Biotin (Ambion, USA). Fifteen micrograms of fragmented cRNA of each sample were hybridized to four HG-U133A plus 2.0 GeneChips (Affymetrix). Hybridization was performed in a Hybridization Oven 640, and chips were washed and stained in the Fluidics Station 400 (both Affymetrix). Finally, the arrays were scanned with a GeneChip Scanner 3000 using the GCOS software, version 1.4, both Affymetrix. All relevant GCOS data of quality checked microarrays were analyzed with High Performance Chip Data Analysis (HPCDA, unpublished), using the BioRetis database (www.bioretis-analysis.de), as described and validated previously.

first: Guido

last: Heine

first: Gennadiy

last: Drozdenko

last: Grün

first: Hyun-Dong

last: Chang

last: Radbruch

first: Margitta

last: Worm


title: Influence of isolation procedure and storage condition on the ex vivo gene expression pattern in peripheral human effector/memory T helper lymphocytes

summary: Gene expression profiling of cells isolated ex vivo is a unique tool to assess gene expression in vivo. Exemplified for CD4+CD45RO+ effector/memory T helper (T E/M) lymphocytes of human peripheral blood, we have analyzed different isolation procedures and storage conditions for the introduction of bias.

overall_design: Cells from clinical samples can be sorted to high purity by a flow cytometric sorter and assessed for their gene expression pattern but storage/shipping conditions and often necessary pre-enrichment due to low initial population frequencies bears the danger of introducing artificial changes.   To test for changes introduced by different procedures, cells were enriched either by magnetic cell sorting (MACS) with Whole-Blood CD4 beads, density gradient centrifugation, alone or in combination with CD3 MACS, or by lysis of erythrocytes followed by MACS depletion of CD15+ cells prior to fluorescence-activated cell sorting (FACS) as CD3+CD4+CD45RO+ cells. A total of 7 different protocols were compared among each other and to T cells stimulated for 3 hours after isolation with Phorbol-12-myristate-13-acetate and Ionomycin (PMA/Iono). Preparation-induced de novo transcription was blocked in one of the protocols by addition of 2 µg/ml Actinomycin D (ActD).  To test for changes introduced by delays in sample preparation blood samples were drawn and either processed directly or kept at 4 °C or room temperature (RT) for 2 or 6 hours before T E/M cells were isolated. Gene expression was compared among the various cell preparations and to T E/M cells isolated from 1 day old buffy coat fractions stored at RT.  Sorted cells were lysed in TRIzol (Invitrogen) and frozen at -80°C until used for RNA extraction. Total RNA was extracted using the miRNeasy kit (Qiagen). The integrity and amount of isolated RNA was assessed for each sample using an Agilent 2100 Bioanalyzer (Agilent, Waldbronn, Germany) and a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE). Double-stranded complementary RNA was synthesized from 1 µg total RNA using Message AmpII Biotin (Ambion, USA). Fifteen micrograms of fragmented cRNA of each sample were hybridized to 26 HG-U133A plus 2.0 GeneChips (Affymetrix). Hybridization was performed in a Hybridization Oven 640, and chips were washed and stained in the Fluidics Station 400 (both Affymetrix). Finally, the arrays were scanned with a GeneChip Scanner 3000 using the GCOS software, version 1.4, both Affymetrix. All relevant GCOS data of quality checked microarrays were analyzed with High Performance Chip Data Analysis (HPCDA, unpublished), using the BioRetis database (www.bioretis-analysis.de), as described and validated previously.

first: Kerstin

last: Westendorf

first: Anna

last: Ohkrimenko

first: Joachim

first: Heidi

last: Schliemann

first: Jun

last: Dong


title: Expression data from HT29 intestinal epithelial cell line

status: Public on Mar 22 2014

city: Davis

first: Michael

last: George

address: 451 Health Sciences Drive

department: Medical Microbiology and Immunology

institute: University of California, Davis

summary:
The study recapitulates, through in vitro micropatterned co-cultures, interactions between HIV-infected T-lymphocytes and intestinal epithelial cells in order to investigate the mechanisms underlying the disruption of normal epithelial cell and barrier function during HIV infection. The co-culture method simplifies observation/monitoring of the two cell types and is particularly suited for laser microdissection-based retrieval of the epithelial cells for downstream gene expressions studies.
Microarrays were used to characterize changes in gene expression in HT29 epithelial cells co-cultured with Jurkat T-lymphocytes in the presence and absence of HIV infection

overall_design: Micropatterned co-cultures were generated of healthy or HIV-infected T-lymphocytes (Jurkat) and human intestinal epithelial (HT-29) cells whereby both cell types were positioned on the same surface in a price spatial configuration (micropattern).  HT29 celsl were then isolated by laser capture microdissection and used for RNA extraction and hybridization on Affymetrix U133 Plus2 microarrays.


title: Expression data from E16.5 mouse embryonic brain wild-type and knock-out conditions

status: Public on Mar 23 2014

city: Brighton

first: Fernando

last: Gomez-Herreros

address: Science Park Road, Falmer

department: GDSC

institute: University of Sussex

summary: In this dataset, we include the expression data obtained from dissected mouse 16.5 embryonic brains using 3 wild type and 3 Tdp2Δ1-3 individuals. These data are used to obtain 165 genes that are differentially expressed as a consequence of Tdp2 absence.

overall_design: The data (obtained from three independent pairs of wild type and TDP2D1-3 brains) was normalised using RMA (Robust Multi-Array Average) and genes changing 1.5 fold (corrected p-value cut-off:0.05) between Tdp2+/+ and Tdp2∆1-3

first: Rocio

last: Romero-Granados


title: Correlated DNA methylation clusters in whole blood

city: Shanghai

first: Yun

last: Liu

address: 130 Dong An Road

country: China

institute: Fudan University

summary:
Genome-wide DNA methylation level was studied to identify the clustering of correlated DNA methylation at CpGs in whole blood.
We used Illumina HumanMethylation450 BeadChip array to identify the clustering of correlated DNA methylation in whole blood from normal individuals from Baltimore Longitudinal Study of Aging (BLSA).

overall_design: Bisulphite converted DNA from normal individuals were hybridized to the Illumina Illumina HumanMethylation450 BeadChip arrays

first: Andrew

last: Feinberg


title: Expression data of patient-derived triple negative breast cancer xenograft tumors

city: Palo Alto

first: Haiyu

last: Zhang

address: 300 Pasteur Dr.

institute: Stanford University

summary:
Triple negative breast cancer (TNBC) is an aggressive subtype that lack targeted clinical therapies. In addition, TNBC is heterogeneous and was recently further sub-classified into seven TNBC subtypes that displayed unique gene expression patterns.
To develop therapeutic treatment regimens, we established seven patient-derived xenograft models from TNBC tumors. These xenograft models not only retained the histology and clinical markers of the corresponding patient tumors, but also bearing the same mutations and deletions identified in the patient tumors. Moreover, as part of evaluation of these models, we performed microarrays on the xenograft tumors to assess their TNBC subtypes.

overall_design: After obtaining IRB-approved informed written patient consent, breast cancer tissues were obtained fresh from Stanford Hospital and transplanted into the number 2 mammary fat pads of female NOD SCID mice (NOD.CB17-Prkdcscid/J, Jackson Laboratory West, Sacramento, CA, USA). Mice were maintained in pathogen-free animal housing. The established xenografts were subsequently passaged from mouse to mouse. Xenograft tumor tissues were frozen on dry ice for RNA isolation and microarray analysis.

first: Marc

last: Coram

first: Adam

last: Cohen

first: Andrea

middle: H

last: Bild

first: Stefanie

last: Jeffrey


title: Pre-BCR Signaling induce IgK Locus Accessibility by functional redistribution of Enhancer-mediated chromatin Interactions

city: Rotterdam

first: Ralph

last: Stadhouders

address: Dr. Molewaterplein 50

department: Pulmonary Medicine

country: Netherlands

institute: Erasmus Medical Center

summary: During B cell development the precursor B cell receptor (pre-BCR) checkpoint is thought to increase immunoglobulin k light chain (Igk) locus accessibility to the V(D)J recombinase. Accordingly, pre-B cells lacking the pre-BCR signaling molecules Btk or Slp65 showed reduced germline Vk transcription. To investigate whether pre-BCR signaling modulates Vk accessibility through enhancer-mediated Igk locus topology, we performed chromosome conformation capture and sequencing analyses. These revealed that already in pro-B cells the k enhancers robustly interact with the ~3.2 Mb Vk region and its flanking sequences. Analyses in wild-type, Btk and Slp65 single and double-deficient pre-B cells demonstrated that pre-BCR signaling reduces interactions of both enhancers with Igk locus flanking sequences and increases interactions of the 3’k enhancer with Vk genes. Remarkably, pre-BCR signaling does not significantly affect interactions between the intronic enhancer and Vk genes, which are already robust in pro-B cells. Both enhancers interact most frequently with highly used Vk genes, which are often marked by transcription factor E2a. We conclude that the k enhancers interact with the Vk region already in pro-B cells and that pre-BCR signaling induces accessibility through a functional redistribution of long-range chromatin interactions within the Vk region, whereby the two enhancers play distinct roles.

overall_design: We performed genome-wide expression profiling of FACS-purified B220+CD19+ pre-B cell fractions from wild-type (WT), Btk and Slp65 single and double deficient VH81x transgenic Rag1-/- mice (n=4 of each genotype). In these experiments non-VH81x transgenic Rag1-/- pro-B cells served as controls (n=3).

first: Saravanan

last: Yuvaraj

first: Marjolein

middle: J

last: de Bruijn

first: Rudi

middle: W

last: Hendriks


title: Mediating effects of miR-155 on the FceRI signaling responses of mast cells

status: Public on Mar 20 2014

city: Manchester

first: Silvia

last: Bulfone-Paus

address: Grafton Street

department: Faculty of Human and Medical Sciences

institute: University of Manchester

summary: MicroRNA 155 (miR-155) has been shown to regulate the gene expression of important players of physiological and pathological processes, like hematopoietic lineage differentiation, immunity and inflammation, viral infections, cancer and cardiovascular diseases, among others. Degranulation is an event in which mast cells, upon activation of the FceRI, release their granule content rich in vasoactive amines, proteases and TNFa. Additionally activation of the receptor promotes de novo synthesis of cytokines, chemokines and growth factors.  Analysis of bone marrow derived mast cells (BMMC) deficient in miR-155 showed a significant increase in FceRI mediated degranulation and in the release of cytokines like TNFa, IL-6 and IL-13.  In addition miR 155-/-  mice presented higher anaphylaxis reactions compared to WT mice.   Gene expression analysis of BMMC was performed in order to identify intermediaries of FceRI mediated degranulation under the control of miR-155. The results indicate that miR-155 regulates negatively the expression of the regulatory subunits of the kinase PI3Kgamma, Pik3r5 (p101) and Pik3r6 (p84, p87PIKAP), involved in Ca+ influx and degranulation.

overall_design: Total RNA from 3 independent cultures of WT and miR-155-/- BMMC treated with anti-DNP IgE and 20 ng/ml DNP-HSA for 1hr were used to performed gene expression analysis using the Affymetrix Genechip® Mouse Gene 1.0 ST

first: Diego

last: Goyeneche-Patino

first: Katharina

last: Biethahn


title: Expression data from isolated terminal end buds in mammary glands with or without Ovol2 deletion

status: Public on Mar 19 2014

city: Yokohama

first: Kazuhide

last: Watanabe

state: Kanagawa

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

department: Center for Integrative Medical Sciences

institute: Riken

summary: Epithelial cells possess remarkable plasticity, having the ability to become mesenchymal cells through alterations in adhesion and motility (epithelial-to-mesenchymal transition or EMT). Recent studies suggest that EMT endows differentiated epithelial cells with stem cell traits, posing the interesting question of how epithelial plasticity is properly restricted to ensure epithelial differentiation during tissue morphogenesis. Here we identify zinc-finger transcription factor Ovol2 as a key suppressor of EMT of mammary epithelial cells. Epithelia-specific deletion of Ovol2 completely arrests mammary ductal morphogenesis, and depletes epithelial stem/progenitor cell reservoirs. Further, Ovol2-deficient epithelial cells undergo EMT in vivo to become non-epithelial cell types, and that Ovol2 directly represses key EMT inducers such as Zeb1 and regulates stem/progenitor cell responsiveness to TGF-beta. We also provide evidence for a suppressive role of Ovol2 in breast cancer progression. Our findings underscore the critical importance of exquisitely regulating epithelial plasticity to balance stemness with epithelial differentiation in development and cancer.

overall_design: TEBs from control and conditional Ovol2-knockout mammary glands were physically isolated for RNA extraction and hybridization on Affymetrix microarrays. In order to identify primary changes, we analyzed TEBs from 24-25-day-old mice, when morphological differences between control and Ovol2 SSKO were still minimal.

first: Xing

last: Dai


title: Gene expression in human endometrial cancer tissues and serous papillary endometrial cancer cell line, SPAC-1L, treated by STAT1-siRNA and/or IFN-gamma

city: Kyoto

first: Budiman

last: Kharma

state: Kyoto

address: 54 Kawahara-cho, Shogoin, Sakyo-ku

department: Gynecology and Obstetrics

institute: Kyoto University Graduate School of Medicine

summary:
Endometrial cancer is one of the most common gynecologic malignancies, and patients with high grade disease, especially  serous papillary subtype (SPEC) are often related to the poor outcomes. Recent genome-wide analyses have revealed that SPEC exhibits gene expression profiles that are distinct from the endometrioid histologic subtype; therefore, it is important to identify the SPEC driver genes or pathways responsible for the inherently aggressive phenotypes and to develop SPEC-specific therapies to target these driver genes or pathways.
Through array-based analysis and immunohistochemical staining of human endometrial cancer tissue, STAT1 is identified high expressed, and can distinguish SPEC from other subtypes of endometrial cancer. In vitro and in vivo experiments show STAT1 role as a pro-survival factor in SPEC. STAT1 was identified as a master gene modulating “transcriptional pro-survival pathways” to enhance multiple malignant characteristics  These finding may suggest that targeting of STAT1, the SPEC driver gene, may provide the means to improve poor outcomes for patients with SPEC.

overall_design: We used microarrays to clarify the changes of gene expression along with STAT1-siRNA treatment and to confirm whether there are any changes on genes expression related to STAT1 pathway. We also used the microarray data to clarify genes signatures which can distinguish subtype of human endometrial cancers.

first: Tsukasa

last: Baba

first: Noriomi

last: Matsumura

first: Hyun

last: Kang

first: Junzao

last: Hamanishi

first: Ryusuke

last: Murakami

first: Ken

last: Yamaguchi

first: Yuko

last: Hosoe

first: Yumiko

last: Yoshioka

first: Masaki

last: Mandai

first: Ikuo

last: Konishi


title: Expression data from MCF7 and MCF7-LTED cells treated with YC-1

status: Public on Mar 17 2014

city: Barcelona

first: Miguel Angel

last: Pujana

address: Gran Via 199

country: Spain

institute: Institut Catala d'Oncologia IDIBELL

summary: To identify novel therapeutic opportunities for patients with acquired resistance to endocrine treatments in breast cancer, we applied a high-throughput drug screen. The IC50 values were determined for MCF7 and MCF7-LTED cells.

overall_design: MCF7 and LTED cells were treated with YC-1 for RNA extraction and hybridization on Affymetrix microarrays.

first: Helena

last: Aguilar

first: Miguel


title: Single cell gene expression of early E8.5 pioneer neural crest cells and paraxial mesoderm

status: Public on Mar 18 2014

city: Cincinnati

first: Rebekah

last: Karns

state: OH

address: 3333 Burnet Ave

department: Gastroenterology, Hepatology, & Nutrition

institute: Cincinnati Children's Hospital Medical Center

summary:
Laser capture microdissection (LCM) was used to isolate cells from the principal critical micro-regions, whose development, differentiation and signaling interactions are responsible for the construction of the mammalian face. At E8.5, as migrating neural crest cells begin to exit the neural fold/epidermal ectoderm boundary, we examined the facial mesenchyme, composed of neural crest and paraxial mesoderm cells, as well as cells from adjacent neuroepithelium.
For these 11 samples, we used a single cell isolation and cDNA generation protocol followed by a standard Affymetrix labeling protocol to better define the gene expression states of the early E8.5 pioneer neural crest and paraxial mesoderm cells.  Using a combination of statistical and expression level filtering criteria, we have identified expression patterns present within these embryonic cell populations.  The genes identified through this study are highly enriched for known critical genes as well as many genes not previously known to be cell type specific at this stage.

overall_design:
Mouse emrbyos were harvested at developmental stage E8.5 and single cells were captured from the neuroepithilium, neural crest, and paraxial mesoderm.  RNA was extracted, labelled, and quantified using the Mouse ST-l microarray.

for further details about this study contact steve.potter@cchmc.org (isolation and labeling) or bruce.aronow@cchmc.org (informatics)

first: Steve

last: Potter

first: Bruce

last: Aronow


title: Expression data from SKOV3 cells treated with SAHA or vehicle control

city: Boston

first: Panagiotis

last: Konstantinopoulos

state: MA

address: 450 Brookline Ave

institute: Dana Farber Cancer Institute

summary: We performed a microarray experiment to assess SAHA-induced changes in expression of genes of the homologous recombination DNA repair pathway

overall_design: SKOV-3 ovarian cancer cells were treated with 1µM SAHA or vehicle-control (0.01% DMSO) for 6 or 24 hours, harvested and processed for RNA isolation.  Data for both time-points for SAHA and vehicle-control treated cells were obtained in duplicate.  Total RNA was isolated using the Qiagen RNeasy Kit (Qiagen, Valencia, CA) according to manufacturer's instructions. cDNA synthesis and hybridization on oligonucleotide microarrays (U133 Plus 2.0 Array GeneChip, Affymetrix, Inc., Santa Clara, CA) were carried out using standard protocols.


title: Expression data from mouse whole bladders of cyclophosphamide-induced cystitis

first: Takeshi

last: Okinami

address: 54 Shogoin-Kawahara-Cho, Sakyo-ku

department: Department of Urology

summary:
To analyze the gene expression of non-bacterial bladdder inflammation, mouse cyclophosphamide(CYP)-induced model of cystitis was adapted.
Forty-eight hour after CYP or vehicle treatment, total RNA was extracted from CYP-treated group (CYP150) and control group (CYP0). We used microarrays to detail the gene expression underlying bladder inflammation.

overall_design: Five-week-old female Balbc/A mice were injected intraperitoneally with 150mg/kg body weight of CYP diluted in 15ml/kg body weight of saline. Mice injected with saline alone served as controls. Treated mice were killed 48 hours after administaration and the whole bladders harvested. Total RNA was extracted and microarray analysis was performed.