title: Glucagon regulates Hepatic Kisspeptin1 to Impair Insulin Secretion in Diabetes Mellitus

status: Public on Apr 01 2014

city: Charlottesville

first: Stephen

last: Turner

address: 1670 Discovery Drive

institute: Signature Science, LLC

summary: Glucagon and insulin are counter-regulatory pancreatic hormones that precisely control blood glucose homeostasis1. Type 2 diabetes mellitus (T2DM) is characterized by inappropriately elevated blood glucagon2-5 levels as well as insufficient glucose stimulated insulin secretion (GSIS) by pancreatic ß-cells6. Early in the pathogenesis of T2DM, hyperglucagonemia is observable antecedent to ß-cell dysfunction7-9; and in mice, liver-specific activation of glucagon receptor-dependent signaling results in impaired GSIS10. However, the mechanistic relationship between hyperglucagonemia, hepatic glucagon action, and ß-cell dysfunction remains poorly understood. Here we show that glucagon action stimulates hepatic production of the neuropeptide kisspeptin1, which acts in an endocrine manner on ß-cells to suppress GSIS. In vivo glucagon administration acutely stimulates hepatic kisspeptin1 production, and kisspeptin1 is increased in livers from humans with T2DM and from mouse models of diabetes mellitus. Synthetic kisspeptin1 potently suppresses GSIS in vivo and in vitro from normal isolated islets, which express the kisspeptin1 receptor Kiss1R. Administration of a Kiss1R antagonist in diabetic Leprdb/db mice potently augments GSIS and reduces glycemia. Our observations indicate in the pathogenesis of T2DM an endocrine mechanism sequentially linking hyperglucagonemia via hepatic kisspeptin1 production to impaired insulin secretion. In addition, our findings suggest Kiss1R antagonism as a therapeutic avenue to improve ß-cell function in T2DM.

overall_design: Total RNA from L-Δprkar1a KO mice compared to control D-glucose mice

first: Woo-Jin

last: Song

first: Mehboob

last: Hussain


title: Osteoblast Gene Expression in Response to Bicc1 Knockdown

status: Public on Mar 25 2014

first: Charles

middle: R

last: Farber

state: VA

department: Center for Public Health Genomics

country: USA

institute: University of Virginia

summary: We recently identified Bicc1 as a regulator of osteoblast differentiation and bone mass.  Bicc1 encodes an RNA-binding protein.  Here, we have used siRNA to decrease Bicc1 expression in primary calvarial osteoblasts.  Illlumina microarrays were then used to profile global gene expression changes.

overall_design: The experiment consisted of 16 total samples in 4 treatment groups (N=4 replicates per treatment).  The treatment groups were osteoblasts treated with 1). control scrambled siRNA, 2) Bicc1_1 siRNA, 3) Bicc1_2 siRNA and 3) Bicc1_3 siRNA.  Cells were isolated, transfected and 48 hours later RNA was isolated and hybridized to arrays.


title: Timecourse analysis of Ezh2-dependent gene expression by SVZ NSCs during differentiation

status: Public on May 02 2014

city: San Francisco

first: William

last: Hwang

state: CA

address: Lim Lab - Box 0525, 35 Medical Center Way

department: Neurosurgery

institute: UCSF

summary: Previous work had established that Ezh2-deleted neural stem cells (NSCs) from the postnatal mouse subventricular zone (SVZ) had a deficit in both proliferation and neuronal differentiation both in vivo and in vitro.  Ezh2-deleted NSCs in an Ink4a/Arf-deleted background proliferated normally but still displayed a neurogenesis defect, suggesting that Ezh2 is necessary for the proper expression of genes responsible for neuronal differentiation.  Our results identify genes that are differentially regulated between control and Ezh2-deleted SVZ NSCs during differentiation.

overall_design: Total RNA obtained from SVZ NSCs 0, 1, 2, 4, and 7 days after switching from proliferation to differentiation media.

middle: W

first: Daniel

middle: A

last: Lim

first: Kevin

last: Kelley

first: Michael

middle: C

last: Oldham


title: Expression analysis of Mll3 knockdown p53-/- HSPC vs. control p53-/- HSPC

status: Public on Mar 19 2014

city: Chengdu

first: Chong

last: Chen

state: Sichuan

address: 17 Renmin S. Road-No. 3

department: State Key Laboratory of Biotherapy

country: China

institute: Sichuan University

summary: Recurring deletions of chromosome 7 and 7q [-7/del(7q)] occur in myelodysplastic syndromes and acute myeloid leukemia (AML) and are associated with poor prognosis. However, the identity of specific tumor suppressors on 7q remains elusive.  Using RNAi and CRISPR/Cas9 approaches, we show that a ~50% reduction in gene dosage of the mixed lineage leukemia 3 (MLL3) gene, located on 7q36.1, cooperates with other events occurring in -7/del(7q) AMLs to promote leukemogenesis. Mll3 suppression impairs the differentiation of HSPC. Interestingly, Mll3 suppressed leukemias, like human -7/del(7q) AMLs, are refractory to conventional chemotherapy but sensitive to the BET inhibitor JQ1. Thus, our mouse model functionally validates MLL3 as a haploinsufficient 7q tumor suppressor, and suggests a therapeutic option for this aggressive disease.

overall_design: Total RNA obtained from sorted lin-ckit+ hematopoietic stem and progenitor cells of recipient mice transplanted with shRen;p53-/- or shMll3;p53-/- cells at 6 weeks after transplant

first: Yu

last: Liu

first: Scott

last: Lowe


title: Peroxidasin is essential for eye development

city: Neuherberg

first: Martin

last: Irmler

state: Bayern

address: Ingolstaedter Landstrasse 1

department: Institute of Experimental Genetics

country: Germany

institute: Helmholtz Zentrum München GmbH

summary: Mutations in Peroxidasin (PXDN) cause severe inherited eye disorders in humans, such as congenital cataract, corneal opacity, and developmental glaucoma. The role of peroxidasin during eye development is poorly understood. Here we describe the first Pxdn mouse mutant which was induced by ENU (N-ethyl-N-nitrosourea) and led to a recessive phenotype. Sequence analysis of cDNA revealed a T3816A mutation resulting in a premature stop codon (Cys1272X) in the peroxidase domain. This mutation causes severe anterior segment dysgenesis and microphthalmia resembling the manifestations in patients with PXDN mutations. The proliferation and differentiation of the lens is disrupted in association with aberrant expression of transcription factor genes (Pax6 and Foxe3) in mutant eyes. Additionally, Pxdn is involved in the consolidation of the basement membrane and lens epithelium adhesion in the ocular lens. Lens material including γ-crystallin is extruded into the anterior and posterior chamber due to local loss of structural integrity of the lens capsule as a secondary damage to the anterior segment development leading to congenital ocular inflammation. Moreover, Pxdn mutants exhibited an early-onset glaucoma and progressive retinal dysgenesis. Transcriptome profiling revealed that peroxidasin affects the transcription of developmental and eye diseases-related genes at early eye development. These findings suggest that peroxidasin is necessary for cell proliferation and differentiation and for basement membrane consolidation during eye development. Our studies provide pathogenic mechanisms of PXDN mutation-induced congenital eye diseases.

overall_design: Total RNA obtained from homozygote embryos E12.5 and  wildtype embryos E12.5, each sample include 4 eyes of two embryos

first: Johannes

last: Beckers

first: Marion

last: Horsch


title: Simple Derivation of Transgene-Free iPS Cells by a Dual Recombinase Approach

status: Public on Mar 29 2014

address: Ingolstaedter Landstr. 1

institute: Helmholtz Zentrum Muenchen

summary:
Induced pluripotent stem cells (iPSCs) can be derived from somatic cells by the introduction of the transcription factors Oct4, Sox2, Klf4 and cMyc using various methods. Here, we describe a new approach for the derivation of murine iPSCs using a polycistronic non-viral inducible vector integrated into pseudo attP sites via the C31 integrase-mediated site-specific recombination and subsequent vector excision by Cre recombinase.
The pluripotency of the derived iPSCs was proved by in vitro and in vivo tests. The derived transgene-free iPSCs reactivated the endogenous pluripotency genes like e.g. Oct4, Sox2 and Nanog and the global gene expression profiles of iPSCs lines are highly similar to ESCs and distinct from parental murine fibroblasts. We demonstrated the differentiation potential of iPSCs by generation cells of the three germ layers as well as we successfully created germline chimeric mice from transgene-free iPSCs. In this study, we presented an efficient method for the generation of transgene-free iPSCs using dual-recombinase technology.

overall_design: expression data of iPSCs/ESCs/MEFs

first: Anna

last: Pertek

first: Ralf

last: Kühn


title: Expression analysis of OSK and Sall4+OSK reprogramming cells sorted for expression of miR-290 and/or miR-302.

status: Public on Mar 31 2014

first: Ron

last: Parchem

address: 35 Medical Center Way

summary: MEFs were infected with Oct4, Sox2, Klf4 (+/- Sall4), sorted for miR-290/302 reporter expression at day 9 (OSK) or 12 (Sall4+OSK), and then profiled. Resulting iPSCs were also profiled. Mouse ES cells were differentiated and sorted for miR-290/302 reporter expression during Fgf/Activin differentiation (day 4 or day 7).

overall_design: Performed in biological triplicate. Biological triplicate samples represent three independent lines. Total RNA collected with Trizol. All processing conducted at the UCLA Neuroscience Genomics Core. MouseRef-8 v2.0 Expression BeadChips.

first: Robert

last: Blelloch


title: Dynamic Pax3:Foxo1a expression of alveolar rhabdomyosarcoma

city: Portland

first: Ken

last: Kikuchi

state: OR

address: 3181 S.W. Sam Jackson Park Road

department: Pediatrics

institute: Oregon Health & Science University

summary: To define the specific function of Pax3:Foxo1a in G2/M stage, we compared whole mRNA expressions of mouse alveolar rhabdomyosarcoma tumor cells in G2/M stage (4N) with or without Pax3:Foko1a knockdown (si_YFP or si_control).

overall_design: The exerimental plan will include triplicate samples for sorted cells at G1/G0 (2N) and G2/M (4N) and dupicate samples for S (3N) phase cells for a total of 16 samples.

last: Keller


title: Genome Wide Expression of Mammary Epithelial Populations in Slug (SNAI2) WT vs Slug Null Mice

status: Public on Mar 08 2014

city: Boston

first: Charlotte

last: Kuperwasser

address: 75 Kneeland St

institute: Tufts University

summary: This experiment shows differential expression of genes in the luminal, basal and stromal subpopulations from SNAI2+/+ and SNAI2 LacZ/LacZ mammary epithelial cells.

overall_design: Luminal, basal and stromal populations were sorted from SNAI2+/+ and SNAI2 LacZ/LacZ mammary epithelial cells based on expression of CD49f and Epcam.

first: Sarah

last: Phillips


title: Comparative analysis of mouse oral cancer cell lines

status: Public on Apr 13 2014

city: St. Louis

first: ravindra

last: uppaluri

address: 660 South Euclid Avenue

institute: Washington University

summary: A comparative microarray analysis of  indolent or aggressive mouse oral cancer cell lines was performed to identify gene expression signatures and specific molecules involved in aggressive tumor growth.

overall_design: We compared 3 indolent cell lines (MOC1, MOC22, MOC23) to 1 aggressive line and it's derivatives (MOC2, MOC2-7 and MOC2-10).  We also included a cell line generated from a lymph node metastasis of the MOC2 tumor.  The lines were all analyzed in triplicated except for MOC1 which was done in quadruplicate. Finally, we included duplicate samples of primary, normal C57BL/6 oral keratinocytes grown in the same media as the MOC cell lines.

first: Ravindra

last: Uppaluri


title: Low-density lipoprotein receptor-5 contributes to whole body metabolism by regulating fatty acid metabolism in the osteoblast

status: Public on Mar 14 2014

first: Charles

last: Farber

summary: Wnt signaling is critical for normal skeletal development as well as whole-body metabolic function.  In this study, we described a previously unrecognized function for Wnt-Lrp5 signaling in the osteoblast that allows bone to acquire the resources necessary to fuel bone formation.  Mice lacking the Lrp5 co-receptor specifically in osteoblasts and osteocytes exhibit the expected reductions in postnatal bone mass and also develop peripheral adiposity with corresponding reductions in energy expenditure.  Conversely, mice expressing a high-bone mass mutant Lrp5 allele are leaner with reduced plasma triglyceride and free fatty acid levels.  In this context, Wnt-initiated signals downstream of Lrp5, but not Lrp6, regulate the expression of key enzymes required for fatty acid β-oxidation.  These results suggest that Wnt-Lrp5 signaling regulates basic cellular activities beyond those associated with fate-specification and differentiation in bone and that the skeleton influences global energy homeostasis via mechanisms independent of osteocalcin and glucose metabolism

overall_design: Total RNA isolated from cultures of Lrp5-deficient osteoblasts differentiated for 7 days in vitro compared to control osteoblasts

first: Ryan

last: Riddle


title: Transcriptional response of kidney tissue after 177Lu-octreotate administration in mice

status: Public on Mar 05 2014

city: Göteborg

first: Emil

last: Schüler

address: Gula stråket 2B

country: Sweden

institute: University of Gothenburg

summary: Transcriptomic profiling of normal mouse kidney cortex and medulla following 177Lu irradiation

overall_design: Total RNA was isolated from fresh-frozen tissue samples

first: Nils

last: Rudqvist

first: Toshima

middle: Z

last: Parris

first: Britta

last: Langen

first: Khalil

last: Helou

first: Eva

last: Forssell-Aronsson


title: NUP98-PHF23

status: Public on Mar 06 2014

city: Bethesda

first: Yuelin

middle: Jack

last: Zhu

state: MD

address: 9000 Rockville Pike

department: Genetics Branch, Center for Cancer Research

institute: NCI

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Gene expression study of leukemic and premalignant hematopoietic tissues from NUP98-PHF23 (NP23) mice.

summary: NUP98-PHF23 is oncogenic and results in a Hoxa/b + Meis1 overexpression in NP23 leukemias and in premalignant (clinically healthy) hematopoietic tissues.

overall_design: Gene expression profiles from AML, pre-T LBL and B-ALL were compared to wild type bone marrow, thymus and spleen tissues respectively. Similarly, gene expression profiles from premalignant (clinically healthy) NP23 bone marrow, thymus and spleen were compared to wild type bone marrow, thymus and spleen tissues respectively. 106A and 748T lymphoblastic cell lines were compared to wild type thymic tissue.

first: Sheryl

middle: M

last: Gough

first: Fan

last: Lee

middle: L

last: Walker

first: Marbin

last: Pineda

first: Sven

last: Bilke

first: Paul

middle: S

last: Meltzer

first: Peter

middle: D

last: Aplan


title: Genome-wide analysis of pancreas gene expression induced by maternal diet

status: Public on Mar 04 2014

city: Cleveland

first: James

last: Hester

state: Ohio

address: 9500 Euclid Avenue

department: Genomic Medicine

institute: Cleveland Clinic

summary:
The aim of this study is to characterize transcriptional changes induced by maternal diet in several adult tissues and to test whether differences in DNA methylation or microRNA expression could explain these changes.
--------------------------
Note: non-normalized values and associated raw data cannot be located by the submitter

overall_design: Total RNA from offspring of mothers fed high fat or low fat diets


title: Genome-wide analysis of white adipose tissue gene expression induced by maternal diet


title: Genome-wide analysis of muscle gene expression induced by maternal diet


title: Genome-wide analysis of liver gene expression induced by maternal diet


title: Genome-wide analysis of heart gene expression induced by maternal diet


title: Genome-wide analysis of expression in various tissues in response to maternal diet

summary:
Note: non-normalized values and associated raw data cannot be located by the submitter

This SuperSeries is composed of the SubSeries listed below.


title: Genome-wide analysis of brain gene expression induced by maternal diet


title: Gene expression profile of liver tissue in carbon tetrachloride (CCl4)-treated mouse treated with erlotinib

status: Public on Feb 28 2014

city: Dallas

first: Yujin

last: Hoshida

state: TX

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

summary:
Gene-expression profiles of liver tissue of cabon tetrachloride (CCl4)-treated mouse and the effect of erlotinib
Hepatocellular carcinoma (HCC) is the sixth most common solid tumor worldwide and the third leading cause of cancer-related death. Given the lack of successful treatment options, chemoprevention in high-risk patients has been proposed as an alternative strategy. Mounting evidence supports a role for epidermal growth factor (EGF) during chronic liver disease and hepatocellular transformation. We address the hypothesis that blocking the EGF-EGF receptor (EGFR) pathway may be an effective strategy for inhibiting fibrogenesis and hepatocarcinogenesis. A rat model of diethylnitrosamine (DEN)-induced cirrhosis was used to examine the effects of erlotinib on underlying chronic liver disease and HCC formation. The DEN-induced rat model closely resembles disease progression in humans both pathologically and molecularly. Erlotinib significantly prevented the development of HCC tumor nodules in a dose-dependent fashion. Further, erlotinib inhibited the activation of hepatic stellate cells and prevented fibrogenesis. Erlotinib also reduced hepatotoxicity and improved liver function. Finally, a gene expression signature predictive of poor survival in human cirrhosis patients was reversed in response to erlotinib. Our data demonstrate for the first time that EGFR inhibition prevents liver fibrogenesis. Further, our results suggest that erlotinib is a potentially effective HCC chemoprevention strategy through inhibition of cirrhosis progression which can be monitored at the molecular level.

overall_design: Animals received humane care according to the criteria outlined in the “Guide for the Care and Use of Laboratory Animals” of the National Academy of Sciences. All animals were maintained in accordance with the institutional guidelines of the Massachusetts General Hospital Subcommittee on Research Animal Care. Strain A/J male mice (Jackson Laboratory, Bar Harbor, ME) were treated three times a week for 18 weeks with either 0.1cc of a 40 percent solution of CCl4 (Sigma) in olive oil or with vehicle control by oral gavage.  Mice were sacrificed at 19 weeks after a one-week washout to eliminate acute effects of CCl4.  The liver was sectioned and fixed in phosphate-buffered 10% formaldehyde for histological analysis.  The remaining portions of the liver were collected in RNase-free tubes and snap-frozen in liquid nitrogen.  Frozen tissues were stored at -80°C until use.

first: Bryan

last: Fuchs

first: Tsutomu

last: Fujii

first: Suguru

last: Yamada

first: Gregory

middle: Y

last: Lauwers

first: Christopher

last: McGinn

first: Lan

last: Wei

first: Toshihiko

last: Kuroda

first: Michael

last: Lanuti

first: Supriya

last: Gupta

first: Andrew

last: Crenshaw

first: Robert

last: Onofrio

first: Bradley

last: Taylor

first: Wendy

last: Winckler

first: Todd

last: Golub

first: Kenneth

middle: K

last: Tanabe


title: WT and FcgKO peritoneal MF response to IL4

status: Public on Mar 01 2014

city: New Haven

first: Ruslan

last: Medzhitov

state: CT

address: PO Box 208011 300 Cedar Street TAC S660

department: Immunobiology

institute: Yale University

summary: Emerging data suggest that many immunoreceptors, all of which use a conserved ITAM-module for their signaling, can couple with members of additional classes of membrane receptors to deliver unique signal(s) to the cell. Using functional and gene expression analysis we describe the role for the tonic signaling through Fcg-chain, the major ITAM-module of the innate immune system, in modifying cytokine responses in MF.

overall_design: Peritoneal MF were left unstimulated or were stimulated in duplicates for 6 hrs with IL4. cDNA was analyzed using 8-sample Mouse Ref-8 v2.0 Illumina array.  Expressed genes were defined as those with p<0.05, and their relative expression values were calculated using average of two WT unstimulated samples as calibrator.

first: Medzhitov

last: Ruslan


title: Bone marrow macrophage (BMMF) response to IFNgR+FcgRI coincidence detection

summary: Different cell types that make an organism use a small number of identical signaling modules to integrate external cues and elicit diverse functions.  How the specificity of functional outcomes is achieved is unclear. It must lie within the context in which the external cue is perceived and integrated by the target cell. Within the innate immune system, we discovered communication between two classes of heterologous receptors designed to integrate external cues into context-specific response. Using IFNgR as an example, we describe the structural and functional collaboration between cytokine receptors and the ITAM signaling module, in this case the Fcg-chain at the plasma membrane of phagocytes. Receptor coupling allowed IFNg to modify FcgRI responses during IgG-mediated phagocytosis and to specify cell autonomous antimicrobial functions.

overall_design: BMMF were left unstimulated or were stimulated in duplicates for 6 hrs with IFNγ, IgG2a-opsonised SRBC or both. cDNA was analyzed using 8-sample Mouse Ref-8 v2.0 Illumina array.  Expressed genes were defined as those with p<0.05, and their relative expression values were calculated using unstimulated cells as calibrator. IgG2a against SRBC was produced by hybridoma TIB111 from ATCC


title: The effect of chronic Rapamycin on the transcriptome of old mouse liver

status: Public on Feb 07 2014

city: Saint Louis

first: Wilson

middle: Chun Yim

last: Fok

state: MO

address: 660 S Euclid Ave

department: Hematology

institute: Washington University in St. Louis

summary: Analysis of the effect of gene expression in the livers of old mice (25 months of age) fed rapamycin chronically (21 months) from 4 months of age.

overall_design:
Total RNA extracted from livers of 25 month old C57BL6/J male and female mice started on control or 14 ppm rapamycin (Rapa) from 4 months of age on 21 months of treatment.
Number of samples total: 69, with 19 samples in Control males, 13 samples in Rapa males, 16 samples in Control Females, and 21 samples in Rapa Females

first: Alex

last: Bokov

first: Yidong

last: Chen

first: Yiqiang

last: Zhang

first: Adam

last: Salmon

first: Martin

last: Javors

first: William

last: Wood

first: Yongqing

first: Kevin

last: Becker

first: Arlan

last: Richardson

first: Viviana

last: Perez


title: A role for the ITAM signaling module in specifying cytokine receptor functions


title: Heart tissue from Nelf-b CreER mice

city: San Antonio

first: Haihui

last: Pan

state: Texas

address: 8403 Floyd Curl Dr.

department: Molecular Medicine

institute: University of Texas Health Science Center at San Antonio

summary: Negative elongation factor (NELF) is known to enforce promoter-proximal pausing of RNA polymerase II (Pol II), a pervasive phenomenon observed across multicellular genomes.  However, the physiological impact of NELF on tissue homeostasis remains unclear.  Here we show for the first time that whole-body conditional deletion of the B subunit of NELF (NELF-B) in adult mice results in cardiomyopathy and impaired response to cardiac stress. Tissue-specific knockout of NELF-B confirms its cell-autonomous function in cardiomyocytes.  NELF directly supports transcription of those genes encoding rate-limiting enzymes in fatty acid oxidation and the tricarboxylic acid (TCA) cycle.  NELF also shares extensively transcriptional target genes with peroxisome proliferator-activated receptors alpha (PPARalpha), a master regulator of energy metabolism in myocardium.  Mechanistically, NELF helps stablize the transcription initation complex at the metabolism-related genes.  Our findings strongly indicate that NELF is part of the PPARalpha-mediated transcription regulatory network that maintains metabolic homeostasis in cardiomyocytes.

overall_design: 3 Nelf-b f/f and 3 Nelf-b f/f; CreER female mice were injected with Tamoxifen at 8 wk old. Heart tissue were harvested at 20 wks old and used for RNA preparation.

first: Zhanyong

last: Guo

first: Craig

last: April

first: Jian-Bing

last: Fan

first: Degeng

last: Wang

first: Rong

last: Li


title: Modification of T cell responses by stem cell mobilization requires direct signalling of the T cell by G-CSF and IL-10

status: Public on Feb 03 2014

city: Brisbane

first: Glen

last: Boyle

state: Queensland

address: 300 Herston Road Herston

department: Department of Cell and Molecular Biology, Cancer Program

country: Australia

institute: QIMR Berghofer Medical Research Insitute

summary: The majority of allogeneic stem cell transplants are currently undertaken using G-CSF mobilized peripheral blood stem cells. G-CSF has diverse biological effects on a broad range of cells and IL-10 is a key regulator of many of these effects. Using mixed radiation chimeras in which the haematopoietic or non-haematopoietic compartments were wild-type (WT), IL-10–/–, G-CSFR–/– or combinations thereof we demonstrated that the attenuation of alloreactive T cell responses after with G-CSF mobilization required direct signalling of the T cell by both G-CSF and IL-10. IL-10 was generated principally by radio-resistant tissue, and was not required to be produced by T cells. G-CSF mobilization significantly modulated the transcription profile of CD4+CD25+ regulatory T cells, promoted their expansion in the donor and recipient and their depletion significantly increased graft-versus-host disease (GVHD). In contrast, stem cell mobilization with the CXCR4 antagonist AMD3100 did not alter the donor T cell’s ability to induce acute GVHD. These studies provide an explanation for the effects of G-CSF on T cell function and demonstrate that IL-10 is required to license regulatory function but T cell production of IL-10 is not itself required for the attenuation GVHD. Although administration of CXCR4 antagonists is an efficient means of stem cell mobilization, this fails to evoke the immunomodulatory effects seen during G-CSF mobilization. These data provide a compelling rationale for considering the immunological benefits of G-CSF in selecting mobilization protocols for allogeneic stem cell transplantation.

overall_design: Single colour, Illumina MouseRef-8 v2.0 Beadarrays.

first: Kelli

middle: P

last: MacDonald

first: Laetitia

last: Le Texier

first: Ping

first: Helen

last: Morris

first: Rachel

last: Kuns

first: Katie

middle: E

last: Lineburg

first: Lucie

last: Leveque

first: Alistair

last: Don

first: Kate

last: Markey

first: Slavica

last: Vuckovic

first: Frederik

last: Otzen Bagger

first: Bruce

last: Blazar

first: Geoffrey

last: Hill


title: The effect of Rapamycin on the transcriptome of old mouse liver

first: Wilson

last: Fok

first: Alex

last: Bokov

first: Yidong

last: Chen

first: Yiqiang

last: Zhang

first: Adam

last: Salmon

first: Martin

last: Javors

first: William

last: Wood

first: Yongqing

first: Kevin

last: Becker

first: Arlan

last: Richardson

first: Viviana

last: Perez


title: WT and FcgKO peritoneal MF response to IFNg

first: Ruslan

last: Medzhitov

overall_design: Peritoneal MF were left unstimulated or were stimulated in duplicates for 6 hrs with IFNγ. cDNA was analyzed using 8-sample Mouse Ref-8 v2.0 Illumina array.  Expressed genes were defined as those with p<0.05, and their relative expression values were calculated using average of two WT unstimulated samples as calibrator.

first: Medzhitov

last: Ruslan


title: EMT-induced stemness and tumorigenicity are fueled by an oncogenic EGF/Ras pathway

status: Public on Feb 19 2014

city: Singapore

first: Tuan Zea

last: Tan

address: 14 Medical Drive, #11-01, Singapore

department: Cancer Science Institute Singapore

country: Singapore

institute: National University of Singapore

summary: Pre-EMT GIF14 cells treated with TGF-β1

overall_design: Total RNA obtained from isolated GIF-14 cells from untreated and TGF-β1-treated sample

first: Dominic

last: Voon

first: Jason

last: Koo

first: Tony

middle: T

first: Yoshiaki

last: Ito


title: The effect of short term Rapamycin on the transcriptome of old mouse liver

first: Wilson

summary: Analysis of the effect of gene expression in the livers of old mice (25 months of age) fed rapamycin short term (6 months) Rapamycin from 19 months of age.

overall_design:
Total RNA extracted from livers of 25 month old C57BL6/N male and female mice started on control or 14 ppm rapamycin (Rapa) from 19 months of age on 6 months of treatment.
Number of samples total: 42, with 10 samples in Control males, 12 samples in Rapa males, 9 samples in Control Females, and 11 samples in Rapa Females

first: Alex


title: Restless Legs Syndrome-associated variant in MEIS1 confers altered gene expression in embryonic ganglionic eminences

status: Public on Jan 29 2014

last: Irmler

summary: Genome-wide association studies (GWASs) identified the MEIS1 locus for Restless Legs Syndrome (RLS), but causal single nucleotide polymorphisms (SNPs) and the functional relevance have remained to be elucidated. The MEIS1 locus contains an exceptionally large number of highly conserved non-coding regions (HCNRs), which potentially function as cis-regulatory modules. We analyzed the HCNRs in the RLS-associated linkage disequilibrium (LD) block for allele-dependent enhancer activity in both zebrafish and mouse, comparing the protective and risk alleles of RLS-associated common variants. We found one enhancer, harboring the lead SNP rs12469063, which showed an allele-dependent reduction of reporter gene expression exclusively in the embryonic ganglionic eminences at developmental stage E12.5. Notably, the reporter activity overlapped with the endogenous telencephalic Meis1 expression domain, which co-localized with transcripts of all four validated RLS loci. Thus, the developing telencephalon represents the first neuroanatomic region implicated for RLS based on GWAS findings.

overall_design: Total RNA obtained from 2-3 male and female mice E12.5 (wildtype, heterzygote, homozygote) and 3-4 male heterozygote and wildtype mice (adult)

first: Johannes

last: Beckers

first: Marion

last: Horsch


title: Profiling of microRNA expression in hepatocellular carcinoma cells with overexpression of G protein alpha 12 active mutant

status: Public on Feb 04 2014

city: Seoul

first: Sang Geon

last: Kim

state: Seoul

address: San56-1, Sillim-dong, Kwanak-gu

department: College of Pharmacy

country: South Korea

institute: Seoul National University

summary: Heterotrimeric guanine nucleotide-binding proteins (G proteins) transmit extracellular signals from cell surface G protein-coupled receptors to intracellular effector molecules. Attention has been paid to the Gα12 family members because they mediate cell invasion, migration, and tumorigenesis. In our findings, Gα12 levels were higher in human HCCs than non-tumorous liver tissues. Array analyses using Huh7 cells stably transfected with Gα12QL (an active mutant form) enabled us to extract the microRNAs dysregulated by Gα12 active mutant. Of them, miR-122 was most greatly decreased. In addition, we found decreases of miR-200b/a, miR-192/215 levels. Dysregulation of the microRNAs changed the levels of key proteins associated with HCC cell migration/invasion.

overall_design: Huh7 hepatoma cells were transfected with pCMV or the plasmid encoding for activated mutant of Gα12 (Gα12QL). Stable transfectants were selected by incubating the cells in culture medium containing Geneticin for 3 weeks. We performed a miRNA microarray for the identification of global microRNA expression changes using WT-Huh7 and Huh7-Gα12QL cells. RNA for each set was harvested from quadruple plates.

first: Yoon-Mee

last: Yang

first: Woo-Hyung

last: Lee

first: Hye-Sun

last: Jung

first: Sang-Geon


title: Genome wide analysis of genes expressed in late G1/S phase of the cell cycle in PMCA4 knockout (P4KO) and P4KO rescued with PMCA4a primary vascular smooth muscle cells

status: Public on Jan 21 2014

city: Toronto

first: Mansoor

last: Husain

state: Ontario

address: Room TMDT-3-910, 101 College St.

department: Toronto Gen. Hosp. Res Institute

country: Canada

institute: University Health Network

summary: Husain lab cell proliferation in vitro experimental data showed that electroporating PMCA4a cDNA into P4KO cells rescued the  G1 arrest phenotype in P4KO primary vascular smooth muscle cells (VSMC). This microarray documents the different gene expression profiles of P4KO and P4KO+PMCA4a VSMC at the late G1/S stage in serum synchronized cell populations (n=4 populations for each genotype).

overall_design: Serum synchronized late G1/S stage cell populations  (P4KO and P4KO+PMCA4a) were employed to extract total RNA which was used for microarray analysis.

first: Talat

last: Afroze


title: Genome wide analysis of genes expressed in early G1 phase of the cell cycle in PMCA4 wild type and PMCA4 knockout primary vascular smooth muscle cells

summary:
Husain lab cell proliferation in vitro experimental data showed a G1 arrest in PMCA4 knockout primary vascular smooth muscle cells (VSMC). This microarray documents the
different gene expression profiles of PMCA4 wild type and knockout cells at the early G1 stage in serum synchronized cell populations (n=4 populations for each genotype).

overall_design: Serum synchronized cell populations were Hoechst labeled and flow sorted for early G1 sub-populations (PMCA4 WT n=4; PMCA4 KO n=4) and total RNA from sorted cells was used for microarray analysis.


title: Genome wide analysis of genes expressed in late G1/S phase of the cell cycle in PMCA4 wild type (P4WT), PMCA4 knockout(P4KO), P4KO rescued with PMCA4b and P4KO rescued with Vector primary vascular smooth muscle cells

summary:
Husain lab cell proliferation in vitro experimental data showed that electroporating PMCA4b cDNA into P4KO cells rescued the  G1 arrest phenotype in P4KO primary vascular smooth muscle cells (VSMC). This microarray documents the
different gene expression profiles of P4WT, P4KO, P4KO+PMCA4b and P4KO+Vector VSMC at the late G1/S stage in serum synchronized cell populations (n=4 or 5 populations for each genotype).

overall_design: Serum synchronized late G1/S stage cell populations  (P4WT, P4KO, P4KO+PMCA4b and P4KO+Vector) were employed to extract total RNA which was used for microarray analysis.


title: Interplay of host microbiota, genetic perturbations, and inflammation promotes local development of intestinal neoplasms in mice [BeadArray]

status: Public on Feb 12 2014

city: New York

first: Gerold

last: Bongers

state: NY

address: 1425 Madison Ave, 12-26A

department: Immunology Institute

institute: Icahn School of Medicine at Mount Sinai

summary:
The preferential localization of some neoplasms, such as serrated polyps, in specific areas of the intestine suggests that non-genetic factors may be important for their development. To test this hypothesis, we took advantage of transgenic mice that expressed HB-EGF throughout the intestine, but develop serrated polyps only in the cecum.
Here we show that a host-specific microbiome was associated with serrated polyps, and that alterations of the microbiota induced by antibiotic treatment or by embryo-transfer rederivation markedly inhibited the formation of serrated polyps in the cecum. Mechanistically, development of serrated polyps was associated with a local decrease in epithelial barrier-function, bacterial invasion, production of antimicrobials, and increased expression of several inflammatory factors such as IL-17, Cxcl2, Tnf-α, and IL-1. Increased number of neutrophils were found within the serrated polyps, and their depletion significantly reduced polyp growth.
Together these results indicate that non-genetic factors contribute to the development of serrated polyps and suggest that the development of these intestinal neoplasms in the cecum is driven by the interplay between genetic changes in the host, an inflammatory response, and a host-specific microbiota.

overall_design: Paired design; Surrounding and SP samples were obtained from the same mouse (n=3; mouse 1, 2, 3)

first: Michelle

last: Pacer

first: Thais

middle: H

last: Geraldino

first: Lili

last: Chen

first: Zhengxiang

last: He

first: Daigo

last: Hashimoto

first: Glaucia

last: Furtado

first: Jordi

last: Ochando

first: Kevin

last: Kelley

first: Jose

last: Clemente

first: Miriam

last: Merad

first: Harm

last: van Bakel

first: Sergio

last: Lira


title: Regulated Splicing of Plasma Membrane Ca2+ ATPase-4 (PMCA4) Controls Cell Cycle Progression in Vascular Smooth Muscle Cells

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

overall_design: Refer to individual Series


title: Switching of the Relative Dominance Between Feedback Mechanisms in Lipopolysaccharide-Induced NF-kB Signaling

status: Public on Jan 14 2014

first: Timothy

middle: G

last: Myers

address: 50 South Drive, Room 5509

department: Research Technologies Branch

institute: National Institute of Allergy and Infectious Diseases

summary: The bacterial product lipopolysaccharide (LPS) stimulates nuclear factor kB (NF-kB) signaling, which results in the production of proinflammatory cytokines, such as tumor necrosis factor-alpha (TNF-alpha), as part of the immune response. NF-kB target genes also include those encoding proteins that inhibit NF-kB signaling through negative feedback loops. By simultaneously studying the dynamics of the nuclear translocation of the NF-kB subunit RelA and the activity of a Tnf-driven reporter in a mouse macrophage cell line, Sung et al. found that the gene encoding RelA was also a target of NF-kB. Synthesis of RelA occurred only at higher concentrations of LPS and constituted a positive feedback loop that dominated over existing negative feedback mechanisms. Genes expressed in response to a high concentration of LPS were enriched for those involved in innate immune responses. Together, these data suggest that the RelA-dependent positive feedback loop enables macrophages to mount an effective immune only above a critical concentration of LPS.

overall_design: Bone-marrow-derived macrophage (BMDM) cells were stimulated with zero, low, and high concentration of LPS separately for 4hrs. Two replicates for each condition.

first: Myong

last: Sung

first: Ning

last: Li

first: Qizong

last: Lao

first: Rachel

last: Gottschalk

first: Gordon

last: Hager

first: Iain

last: Fraser


title: Strain-specific Innate Immune Signaling Pathways Determine Malaria Parasitemia Dynamics and Host Mortality

status: Public on Jan 13 2014

summary: Malaria infection triggers vigorous host immune responses; however, the parasite ligands, host receptors and the signaling pathways responsible for these reactions remain unknown or controversial. Malaria parasites primarily reside within red blood cells (RBCs), thereby hiding themselves from direct contact and recognition by host immune cells. Host responses to malaria infection are very different from those elicited by bacterial and viral infections and the host receptors recognizing parasite ligands have been elusive. Here we investigated mouse genome-wide transcriptional responses to infections with two strains of Plasmodium yoelii (N67 and N67C) and discovered differences in innate response pathways corresponding to strain-specific disease phenotypes. Using in vitro RNAi gene knockdown and knockout mice, we demonstrated that a strong IFN-I response triggered by RNA Polymerase III and melanoma differentiation-associated protein 5 (MDA5), not Toll-like receptors (TLRs), binding of parasite DNA/RNA contributed to a decline of parasitemia in N67-infected mice. We showed that conventional dendritic cells were the major sources of early IFN-I, and that surface expression of phosphatidylserine (PS) on infected RBC (iRBC) might promote their phagocytic uptake, leading to the release of parasite ligands and the IFN-I response in N67 infection. In contrast, an elevated inflammatory response mediated by CD14/TLR and p38 signaling played a role in disease severity and early host death in N67C-infected mice. In addition to identifying cytosolic DNA/RNA sensors and signaling pathways previously unrecognized in malaria infection, our study demonstrates the importance of parasite genetic backgrounds in malaria pathology and provides important information for studying human malaria pathogenesis.

overall_design: Spleen RNA from mice, 4 days post infection with Plasmodium yoelii (strain N67 or N67C), or mock infection (N). Replicates from 6 individual mice per condition.

first: Jian

last: Wu

first: Linjie

last: Tian

first: Xiao

last: Yu

first: Sittiporn

last: Pataradilokrat

first: Weishi

first: Yanwei

last: Qi

first: Amir

last: Zeituni

first: Sethu

last: Nair

first: Steve

last: Crampton

first: Marlene

last: Orandle

first: Silvia

last: Bolland

first: Chen

middle: F

first: Carole

last: Long

first: John

last: Coligan

first: Rongfu

last: Wang

first: Xin-zhuan

last: Su


title: Microarray analysis of Nurr1 and Foxa2 synergisitic effect for DA neuron induction

status: Public on Jan 16 2014

first: Sang-Hun

last: Lee

address: 222 Wangsimni-ro, Seongdong-gu

department: biochemistry and molecular biology

institute: College of medicine, Hanyang University

summary: Analysis of dopaminergic neuronal gene expression changes by Nurr1 and/or Foxa2 overexpression. Result provides that Foxa2 potentiates Nurr1-induced DA neuronal phenotype gene expression.

overall_design: To identify the syergism of Nurr1 and Foxa2 for developing DA neural precursors, neural precusor cells (NPCs) isolated from embryonic brain were treated control, Nurr1, Foxa2 and Nurr1-Foxa2 retrovirus. After treatment of retroviruses, NPCs were cultrued in N2 media withdrawn mitogen (bFGF, EGF) for differetiation of DA neuron. Total RNA was obtained from NPCs in differentiation day 2.

first: Sang-Hoon

last: Yi

first: Xibiao

last: He


title: EGFR inhibition prevents liver cirrhosis and hepatocellular carcinoma

first: Yujin

last: Hoshida

sample_organism:
Mus musculus
Rattus norvegicus

platform_organism:
Mus musculus
Rattus norvegicus


title: IMPACT OF CARDIOMYOCYTE-SPECIFIC BMAL1 DELETION ON MYOCARDIAL GENE EXPRESSION, METABOLISM, AND CONTRACTILE FUNCTION

status: Public on Jan 01 2014

city: Birmingham

first: Molly

last: Bray

state: AL

address: 1720 2nd Avenue N, RPHB 230H

department: Genetics

institute: University of Alabama at Birmingham

summary: Circadian clocks are cell autonomous, transcriptionally-based, molecular mechanisms that confer the selective advantage of anticipation, enabling cells/organs to respond to environmental factors in a temporally appropriate manner. Critical to circadian clock function are two transcription factors, CLOCK and BMAL1. Previous studies in our laboratory have highlighted roles for CLOCK in cardiac physiology/pathophysiology. Here, we describe transcriptional, metabolic, and functional consequences of cardiomyocyte-specific Bmal1 knockout (CBK). Microarray analysis revealed 2037 differentially expressed genes in CBK hearts, many of which were previously identified in cardiomyocyte-specific Clock mutant (CCM) hearts. Subsequent analysis showed that Beta-hydroxybutyrate dehydrogenase 1 mRNA, protein, and enzymatic activity are markedly depressed in both CBK and CCM hearts, as is myocardial Beta-hydroxybutyrate oxidation, revealing a novel role for the circadian clock in ketone body utilization. A number of genes encoding for collagen isoforms were identified as oscillating in a time-of-day-dependent manner in wild-type, but not CBK, hearts, including col3a1, col4a1, and col4a2. Chronic induction of collagen isoform genes in CBK hearts was associated with severe age-dependent depression of cardiac function. Development of cardiomyopathy in CBK mice was associated with early mortality; all CBK mice die by one year of age. These studies highlight novel critical functions for BMAL1 in the heart, including regulation of ketone body metabolism and the extracellular matrix.

overall_design: RNA from whole hearts collected every 3 hours for 24 hours from wildtype and CBK mice was isolated and analyzed using MouseRef-8_V2 BeadChips (Illumina, Inc.).  The 24-hour data were examined for rhythmicity using cosinor analysis and differences in rhythmicity between genotype groups were further examined for differences in the model fitting parameters.

first: Martin

last: Young

first: Rachel

middle: A

last: Brewer

first: Betty

last: Pat

first: William

last: Ratcliffe

first: Rodrigo

last: Garcia

first: Maximiliano

last: Grenett

first: Tana

last: Birky

first: Bradley

middle: W

last: Peden

first: Billy-Joe

last: Ammons


title: Circulating miRNAs spectra in plasma of multiple myeloma patients compared with healthy individuals

city: Nanjing

first: Lijuan

last: Chen

address: 300 Guangzhou Road

institute: the First Affiliated Hospital of Nanjing Medical University, Jiangsu Province Hospital

summary:
MicroRNAs (miRNAs) are a class of small non-coding single-stranded RNAs whose dysregulation of expression plays an important role in cancer development. Circulating miRNAs are novel biomarkers in several cancers. Thus, we explored whether the miRNAs in plasma could be useful clinical biomarkers for multiple myeloma (MM) patients.
The expression levels of four miRNAs in plasma were upregulated while eight miRNAs were downregulated in MM patients compared with healthy controls according to microarray.

overall_design: MiRNA microarray was conducted to determine deregulated miRNAs in plasma of 9 MM patients and 7 healthy controls.

first: Xiaoyan

last: Qu


title: Transcriptional Response to transgenic BRAF(V600K) in the intestinal epithelium

status: Public on Dec 31 2013

city: Berlin

first: Markus

last: Morkel

address: Charitéplatz 1

department: Dept. of Pathology

institute: Charité - Universitätsmedizin Berlin

summary:
We have analysed transcriptional effects of BRAF(V600K) in the intestinal epithelium of transgenic mice that harbour an inducible BRAF(V600K) transgene.
Mice used in this experiment were compound transgenic for a stem-cell specific Lgr5-EGFP Reporter and either an inducible TdTomato-2A-BRAF(V600K) transgene or an inducibe TdTomato-luciferase transgene.

overall_design: Transgenes were induced by doxycycline (4mg/ml) treatment provided in a 1% sucrose solution in the drinking water of transgenic mice for 24h. Intestinal crypts were isolated by filtering (70um) following a PBS/EDTA incubation step. Single cell suspensions were made by digestion of crypts in 500ug/ml trypsine and 0.8u/ml DNAseI for approx. 20min at RT. Cell populations for profiling were isolated by FACS, using an Aria SOPR (BD), equipped with a 70um nozzle.

first: Pamela

last: Riemer


title: Time-course gene expression profiles of gefitinib-sensitive or -resistant lung adenocarcinoma cells stimulated with EGF, in the presence or absence of gefitinib, EGF receptor tyrosine kinase-specific inhibitor

city: Minato-ku

first: Noriko

last: Gotoh

state: Tokyo

department: Institute of Medical Science

country: Japan

institute: The University of Tokyo

summary: Gefitinib, an epidermal growth factor receptor (EGFR) tyrosine kinase inhibitor (TKI), induces substantial clinical responses for non-small cell lung cancer (NSCLC) cells harboring EGFR activating mutations, but most of them invariably develop resistance. By generating a gefitinib resistance (PC9GR) from a human NSCLC-derived drug sensitive cell line (PC9), we studied differences of transcription dynamics between them by the aid of a computational decoupling of hidden regulatory signals from time course gene expression profiles. Given a collection of transcription factors (TFs) and their regulatory targets, the method captured temporally-synchronized shifts in evolving expression of target genes sharing each TF regulatory  unit, and drew underlying regulatory signals. The analysis identified sterol regulatory element binding protein 1 (SREBP-1) as a key regulatory agent that facilitates the maintenance  of drug tolerance, involving transcription controls of a G1-specific cyclin dependent kinase inhibitor whose expression was specifically elevated in PC9, but in turn, reduced in PC9GR

overall_design: Gefitinib-resistance cell line (PC9GR) was established derived from lung adenocarcinoma cell line PC9. PC9 cells and PC9GR cells were treated with the four different conditions, control (No treatment), EGF-treatment, gefitinib-treatment, and both gefitinib and EGF-treatment. In each condition, the gene expression was measured at 26 time points during 24 hrs.


title: Global transcriptomic profiling of hypoxic ischemia in an in vivo neonatal mouse model: cortex

city: Hobart

first: Minghui Jessica

state: Tasmania

address: Menzies Research Institute, University of Tasmania, Private Bag 24

department: Neuroscience group

institute: Menzies Research Institute

summary: Hypoxia-ischemia (HI) brain damage is one of the most common causes of neonatal brain injuries, amidst other conditions such as intrauterine infection and perinatal cerebral hemorrhage (Bracci et al., 2006). HI, occurring during the perinatal period, severely affects brain integrity resulting in detrimental long-term neurological morbidity in terms of motor, intellectual, educational and neuropsychological performance deficits (e.g. cerebral palsy, mental retardation, learning disability and epilepsy), and even neonatal mortality  (Cowan et al., 2003; Ferriero, 2004; van Handel et al., 2007; Shalak and Perlman, 2004). Current therapeutic interventions fail to provide substantial reversal of HI brain injuries and improvement in overall cognitive function. Recent clinical studies demonstrated that post-HI hypothermia provide moderate neuroprotection but fail to show any significant reduction in neonatal morbidity and mortality (Shankaran et al., 2005). We would like to investigate the transcriptional effects of HI on neonatal brain, and if hypoxic pre-conditioning is beneficial to the reduction of brain damage.

overall_design: Microarray analysis was performed on the cortex of neonatal brains using Illumina mouse Ref8 V2 genechips. The right common carotid artery was exposed through a ventral midline neck incision and permanently occluded by electrocoagulation, The wound was sutured and mouse pups were returned to their mother for 1.5–2 h. Sham control and pre-conditioned mice (n = 4) underwent the identical procedure, without carotid artery occlusion.  Pups were then placed in an 8% O2/92% N2 humidified chamber at 37°C for 1 h with tissue extraction taking place 3h, 8h and 24h thereafter (n=4 respectively). Sham controls were included in this study too (n=4 respectively).

first: Nam

last: Cheung

first: Minghui

first: Peter

last: Crack

first: Jayapal

last: Manikandan


title: Mouse Endothelial Progenitor Cell (EPC) Lines - Illumnia Array

status: Public on Dec 30 2013

city: Tampa

first: Jeff

last: Russell

state: FL

address: 12902 Magnolia Drive

department: Head and Neck/Endocrine

institute: Moffitt Cancer Center

summary: Mouse EPCs were harvested from lung tissue and cultured in hypoxic chambers (2% FiO2) for 48 hrs and then transferred to regular incubators. Cell lines were then stained for the uptake of the acetylated form of low density lipoprotein. These cells were then sorted by flow cytometry and labeled as EPC_acLDL cells. Finally, high passage EPC_acLDL cells (p16-20) were collected and labeled as EPC_late cells. The three cell lines were then grown up, harvested, and RNA isolated and submitted in duplicate for Illumina array analysis of gene expression.

overall_design: 3 samples, in duplicate: EPC, EPC_acLDL, and EPC_Late

first: Jeffery


title: Global transcriptomic profiling of hypoxic ischemia in an in vivo neonatal mouse model: Striatum

overall_design: Microarray analysis was performed on the striatum of neonatal brains using Illumina mouse Ref8 V2 genechips. The right common carotid artery was exposed through a ventral midline neck incision and permanently occluded by electrocoagulation, The wound was sutured and mouse pups were returned to their mother for 1.5–2 h. Sham control and pre-conditioned mice (n = 4) underwent the identical procedure, without carotid artery occlusion.  Pups were then placed in an 8% O2/92% N2 humidified chamber at 37°C for 1 h with tissue extraction taking place 3h, 8h and 24h thereafter (n=4 respectively). Sham controls were included in this study too (n=4 respectively).

first: Nam-Sang

first: Minghui-Jessica


title: miR-135b exerts metastatic activity in the ErbB2 driven mammary carcinogenesis

status: Public on Dec 01 2013

city: Torino

first: Raffaele

last: Calogero

state: To

address: Via Nizza 52

department: Molecular Biotechnology Center

country: Italy

institute: University of Torino

summary: In view of the roles played by miRNAs in cancer progression, we performed a microarray analysis aimed at identifying  miR-135b target genes in breast cancer cells. Detection of transcripts affected by silencing of mir-135b was done using a time course at 24, 48 and 72 h both transfecting cell with mir-135b  specific miRIDIAN microRNA Hairpin Inhibitor or miRIDIAN microRNA Hairpin Inhibitor negative control. Each experimental condition was repeated three times and analysed on on MOUSEREF-8 V2 Illumina bead chips. Genome studio was used to generate raw intensity signal without normalization. Data log2 transformation and loess normalization was performed with oneChannelGUI. Data were filtered using an IQR filter (i.e. only genes characterized by an IQR > 0.25, were retained for further analysis). Detection of differentially expressed transcripts was also performed with oneChannelGUI, using masigpro package with default parameters. Data were visualized by hierarchical clustering, as log2 ratio between anti-miR135b and the negative control using TMEV software. The subset of transcripts characterized by an increase in expression as consequence of a reduction of expression of miR135b were selected. MicroRNA target data for mir135b were retrieved from miranda database (microRNAsmiranda.mouse_predictions_S_C_aug2010.txt, http://www.microrna.org/microrna/home.do). Miranda data and transcripts increasing their expression upon silencing of miR135b were intersected to find the genes in common.

first: Elena

last: Quaglino

first: Maddalena

last: Arigoni

first: Elisabetta

last: Ercole

first: Federica

last: Riccardo

first: Daniela

last: Cantarella

first: Francesca

last: Orso

first: Guido

last: Forni

last: Cavallo


title: Transcriptional program for induced delta cell on day10

status: Public on Nov 20 2013

city: Cambridge

first: Weida

last: Li

state: MA

address: 7 Divninity Avenue

institute: Harvard University

summary: Direct lineage conversion of adult cells is a promising approach for regenerative medicine.  A major challenge of lineage conversion is to generate specific subtypes of cells, closely related cells with distinct properties.  The pancreatic islets contain three major hormone-secreting endocrine subtypes:  insulin+ β-cells, glucagon+ α-cells, and somatostatin+ δ-cells.  We previously reported that a combination of three transcription factors, Ngn3, Mafa, and Pdx1, directly reprogram pancreatic acinar cells to β-cells.  We now show that acinar cells can be converted to δ-like and α-like cells by Ngn3 and Ngn3+Mafa respectively.  Thus, three major islet endocrine subtypes can be derived by acinar reprogramming.  Ngn3 promotes establishment of a generic endocrine state in acinar cells at the onset of reprogramming in addition to promoting δ-specification.  Mafa and Pdx1 suppress δ-specification in α- and β-cell formation.  These studies identify a set of defined factors whose combinatorial actions reprogram acinar cells to distinct islet endocrine subtypes in vivo.

overall_design: induced beta cells samples at day 10 collected for the microarray

first: Qiao

last: Zhou


title: Gene expression in alpha SMA Cre-labeled cells in periosteum during early fracture callus formation

status: Public on Nov 27 2013

city: Grafton

first: Brya

last: Matthews

state: Auckland

address: 85 Park Rd

department: Molecular Medicine and Pathology

country: New Zealand

institute: University of Auckland

summary: Fracture healing is a process that involves many cell populations. In this study we characterized gene expression in a subset of cells involved in fracture healing. αSMACreERT2 mice crossed with Ai9 reporter mice that express tdTomato fluorescent protein after Cre-mediated activation were used as an experimental model. αSMA-expressing cells were labeled by tamoxifen administration, then periosteal cells from the tibia were isolated two days later (controls), or tibial fractures were performed and periosteum/soft callus tissue was collected after 2 and 6 days. The tdTomato positive cell population was isolated by flow cytometry, and subjected to microarray analysis. Histology and cell surface marker analysis indicates that αSMACreERT2 labels a mainly mesenchymal population in the periosteum that expands after fracture, and contributes to both osteogenic and chondrogenic elements of the fracture callus. We were therefore able to examine gene expression in a defined population during the early stages of fracture healing.

overall_design: Total RNA was obtained from the tomato positive cells within the periosteal compartment of fractures from αSMACreERT2/Ai9 mice. Control animals were given 2 doses of tamoxifen, and periosteum was collected and labeled cells sorted (8-9 sex-matched mice per group). Fractures were performed after the second dose of tamoxifen, and tomato positive cells from periosteum/callus tissue were isolated 2 and 6 days after fracture (4-8 animals per sample pooled). 3 replicates for each sample are included.

first: Ivo

last: Kalajzic


title: Robust Differentiation of Islet Progenitors into Functional Insulin-secreting Cells by Suppression of Key Transcription Regulators

status: Public on Nov 01 2013

city: Perth

first: Munish

last: Mehta

state: WA

address: L6, Rear 50 Murray Street

department: Diabetes Research Unit

institute: Harry Perkin Institute of Medical Reasearch

summary: Gene profiling revealed that differentiation was accompanied by suppression of a range of transcription regulator genes typical of islet progenitor cells.  In order to understand molecular mechanisms of differentiation, transcriptome-wide gene expression analysis was performed on purified islet progenitors  at days 0, 1 and 4 of differentiation together with adult islets as a control.

first: F

middle: X

last: Jiang

first: Q

last: Nguyen

first: M

first: G

last: Morahan


title: Combined treatment of rapamycin and dietary restriction has a larger effect on the transcriptome and metabolome of liver

status: Public on Nov 08 2013

city: Saint Louis

first: Wilson

last: Fok

address: 660 S Euclid Ave

department: Hematology

institute: Washington University in St. Louis

summary: Rapamycin (Rapa) and dietary restriction (DR) have consistently been shown to increase lifespan. To investigate whether Rapa and DR affect similar pathways in mice, we compared the effects of feeding mice ad libitum (AL), Rapa, DR, or a combination of Rapa and DR (Rapa + DR) on the transcriptome and metabolome of the liver. The principal component analysis shows that Rapa and DR are distinct groups. Over 2500 genes are significantly changed with either Rapa or DR when compared with mice fed AL; more than 80% are unique to DR or Rapa. A similar observation was made when genes were grouped into pathways; two-thirds of the pathways were uniquely changed by DR or Rapa. The metabolome shows an even greater difference between Rapa and DR; no metabolites in Rapa-treated mice were changed significantly from AL mice, whereas 173 metabolites were changed in the DR mice. Interestingly, the number of genes significantly changed by Rapa + DR when compared with AL is twice as large as the number of genes significantly altered by either DR or Rapa alone. In summary, the global effects of DR or Rapa on the liver are quite different and a combination of Rapa and DR results in alterations in a large number of genes and metabolites that are not significantly changed by either manipulation alone, suggesting that a combination of DR and Rapa would be more effective in extending longevity than either treatment alone.

overall_design:
Total RNA extracted from livers of 8 month old C57BL6/J mice started on ad libitum (AL), 40% dietary restriction (DR), 14 ppm rapamycin (Rapa), and 14 ppm rapamycin + 40% dietary restriction (Rapa+DR) from 2 months of age on 6 months of treatment.
Number of samples total: 46, with 11 samples in AL, 11 samples in DR, 12 samples in Rapa, and 12 samples in Rapa+DR

middle: C

first: Alex

last: Bokov

first: Jon

last: Gelfond

first: Yiqiang

last: Zhang

first: Mark

last: Doderer

first: Yidong

last: Chen

first: Martin

last: Javors

first: Bill

last: Wood

first: Yongqing

first: Kevin

last: Becker

first: Arlan

last: Richardson

first: Viviana

middle: I

last: Perez


title: Genome-wide analysis of E17.5 pituitary gland gene expression of control and Insm1 mutant mice

status: Public on Oct 20 2013

first: Jochen

last: Welcker

address: Robert-Rössle-Str. 10

institute: MDC Berlin

summary: The Insm1 gene encodes a zinc finger factor expressed in many endocrine organs. We show here that Insm1 is required for differentiation of all endocrine cell types in the pituitary. Thus, in Insm1 mutant mice, hormones characteristic of the different pituitary cell types (thyroid, follicle and melanocyte stimulating hormone, adrenocorticotrope hormone, growth hormone and prolactin) are absent or produced at markedly reduced levels. The differentiation deficit is accompanied by an up-regulated expression of components of the Notch signaling pathway. Further, skeletal muscle-specific genes are ectopically expressed, indicating that Insm1 blocks a muscle-specific expression program. Since Insm1 is also essential for differentiation of endocrine cells in the pancreas, intestine and adrenal gland, it is emerging as a transcription factor that acts in a pan-endocrine manner. The Insm1 factor contains a SNAG domain at its N-terminus, and we show here that the SNAG domain recruits histone modifying factors (Kdm1a, Hdac1/2 and Rcor1-3) and other proteins implicated in transcriptional regulation (Hmg20a/b and Gse1). Deletion of the SNAG domain in mice disrupted differentiation of pituitary endocrine cells, and resulted in an upregulated expression of components of the Notch signaling pathway and ectopic expression of skeletal muscle-specific genes. Our work demonstrates that Insm1 acts in the transcriptional network that controls differentiation of endocrine cells in the anterior pituitary gland, and requires the SNAG domain to exert this function in vivo.

overall_design:
Analysis of genes regulated by Insm1 in embryonic day 17.5 pituitary gland.
Total RNA from pituitary glands of E17.5 control embryos was compared to E17.5 Insm1 mutant embryos.

first: Carmen

last: Birchmeier


title: Effect of propranolol on differential gene expression in peripheral blood monocytes from mice subject to repeated social defeat

status: Public on Nov 04 2013

city: Los Angeles

first: Steve

last: Cole

state: CA

address: 11-934 Factor Bldg, UCLA

department: Medicine

institute: UCLA School of Medicine

summary:
This study tested the effects of repeated social defeat (RSD) on gene expression in peripheral blood monocytes and examined the extent to which these effects were abrogated by the beta-adrenergic antagonist propranolol.
Study Type: Risk prediction

overall_design: Gene expression profiling was carried out on peripheral blood monocyte mRNA samples collected from 36 mice randomized to either 6 cycles of repeated social defeat (RSD, n=18) or to parallel home cage control (HCC, n=18) conditions.  Within each condition (RSD vs HCC), 9 animals were treated with the beta-adrenergic antagonist propranolol and 9 were treated with an equivalent volume of vehicle.  After 6 cycles of RSD or parallel HCC, blood samples were pooled into groups of n=3 samples in each condition, and Illumina Mouse Ref-8 BeadArray assays were performed on RNA from approximately 1 million CD11b+ peripheral blood mononuclear cells (i.e., monocytes) which were immunomagnetically isolated by MACS.  The primary research questions are 1) whether expression of pro-inflammatory genes is altered by RSD, and 2) whether treatment with propranolol abrogates these effects.


title: Transcriptional profile of WT, PRR and IFN-/- dendritic cells stimulated with poly IC in vivo

status: Public on Oct 01 2013

first: Paula

last: Longhi

address: 1230 York Av

institute: The Rockefeller University

summary: Analysis of the specific transcriptional changes on DCs provided by direct pattern recogition receptor (PRR) or IFNAR signaling that are required for DC maturation after poly IC stimulation. Results provide important information about the intricate differentiation process of DC maturation and the importance of type I IFNs for DC immunogenicity.

overall_design: WT/IFNA-/- or WT/PRR-/- mixed-chimera mice were injected with 50 ug Poly-IC i.p. in vivo 4 and 14 hr later, wild type and KO CD11chi CD3- DX5- B220- DCs were FACS sorted based on CD45.2 expression. Total RNA was isolated and expression profile was compared between unstimulated and activated WT and KO DCs.


title: The effects of Hmgb1 depletion on gene expression in murine cells

city: Milano

first: Riccardo

middle: Lorenzo

last: Rossi

state: MI

address: Via Trivulzio 10

department: Integrative Biology

institute: Fondazione INGM

summary: High Mobility Group Box 1 (HMGB1) is a highly abundant and evolutionarily conserved non-histone chromatin component with the ability to bind and bend DNA. The protein is involved in fundamental nuclear processes including nucleosome sliding, transcription, replication, V(D)J recombination and DNA transposition. To assess the functional impact of HMGB1 on transcription we performed gene expression profile analyses of mouse embryonic fibroblasts, wild-type or knockout for the Hmgb1 gene

overall_design: 2 genetic backgrounds: wild-type (Wt), Hmgb1-/- (KO), 3 biological replicates (rep1, rep2, rep3; S phase synchronized cells in duplicate only), no technical replicates. Each pair of wt and Hmgb1-/- MEFs was isolated from embryos born from a single Hmgb1+/- mother crossed with a Hmgb1 +/- male. Total RNAs from three pairs of MEFs, derived from three different mothers and cultured up to passage 3, were extracted using mirVana miRNA Isolation Kit (Ambion)  and analyzed on the Illumina BeadsArray platform.

first: Barbara

last: Celona

first: Alessandra

last: Agresti

first: Marco

last: Bianchi

first: Grazisa

last: Rossetti

middle: L

first: Massimiliano

last: Pagani


title: Ablation of coactivator Med1 switches the cell fate of dental epithelia to that generating hair [CL stage]

status: Public on Sep 23 2013

city: San Francisco

first: Yuko

last: Oda

address: 111N-MB 360 1700 Owens St, Suite 360

department: Endocrine Research

institute: VA Medical Center UCSF

summary: Cell fate is defined by specific transcriptional program. Here, we provide evidence that the transcriptional coactivator, Mediator 1 (MED1), is critical in determining the cell fate of ectodermal epithelia. MED1 ablation disrupted enamel formation and generated hair adjacent to the incisors. Deletion of MED1 altered the differentiation of dental epithelia to one expressing epidermal and hair genes similar to the skin. The cellular switch from dental to epidermal/hair lineage was characterized by abnormalities in MED1 deficient dental epithelial stem cells residing in cervical loop. MED1 deficiency caused a failure of dental epithelial stem cells to commit to the dental stratum intermedium regulated by Notch signaling. Instead, MED1 deficient cells retained stem cell potentials expressing Sox2. These cells were eventually adopted an epidermal fate probably through calcium provided through capillary networks, which is originally utilized for enamel formation. Our results demonstrate that MED1 regulates Sox2/Notch1 regulated cell lineage determination in dental epithelia. Our study also shows a potential to regenerate hairs by using genetically engineered dental tissues or cells outside of the skin.

overall_design: n=3 WT and KO (each sample contain dissected dental tissues from 3 mice combined)

first: Lizh

last: Hu

first: Thai

last: Nguyen

first: Frankie

last: Fong

first: Daniel

middle: D

last: Bikle


title: Ablation of coactivator Med1 switches the cell fate of dental epithelia to that generating hair [mixed stage]


title: Ablation of coactivator Med1 switches the cell fate of dental epithelia to that generating hair [maturation stage]

overall_design: n=4 WT and KO (each group contains dissected dental tissues from 3 mice combined)

first: Lizhi


title: Niche-based screening identifies small-molecule inhibitors of leukemia stem cells

status: Public on Sep 20 2013

first: Kimberly

last: Hartwell

address: 7 Cambridge Center

department: Cancer Program

institute: Broad Institute

summary: Efforts to develop more effective therapies for acute leukemia may benefit from high-throughput screening systems that reflect the complex physiology of the disease, including leukemia stem cells (LSCs) and supportive interactions with the bone-marrow microenvironment. The therapeutic targeting of LSCs is challenging because LSCs are highly similar to normal hematopoietic stem and progenitor cells (HSPCs) and are protected by stromal cells in vivo. We screened 14,718 compounds in a leukemia-stroma co-culture system for inhibition of cobblestone formation, a cellular behavior associated with stem-cell function. Among those that inhibited malignant cells but spared HSPCs was the cholesterol-lowering drug lovastatin. Lovastatin showed anti-LSC activity in vitro and in an in vivo bone marrow transplantation model. Mechanistic studies demonstrated that the effect was on-target, via inhibition of HMG-CoA reductase. These results suggest that statins should be re-evaluated as anti-leukemia agents, and illustrate the power of merging physiologically-relevant models with high-throughput screening.

overall_design:
Freshly isolated LSCe cells were treated with either 5µM BRD7116 or DMSO vehicle control for 6 hours in suspension in IMDM (12440053, Invitrogen), 10% FBS. Total RNA was extracted from the cells, labeled, and hybridized to MouseRef-8 v2.0 Expression BeadChips.
Hartwell, K.A. et al., In Press (full citation forthcoming)

first: Peter

last: Miller

first: Siddhartha

last: Mukherjee

first: Alissa

middle: R

last: Kahn

first: Alison

last: Stewart

first: David

middle: J

last: Logan

first: Joseph

middle: M

last: Negri

first: Mildred

last: Duvet

first: Marcus

last: Järås

first: Rishi

last: Puram

first: Vlado

last: Dancik

first: Fatima

last: AlShahrour

first: Thomas

last: Kindler

first: Zuzana

last: Tothova

first: Shrikanta

last: Chattopadhyay

last: Hasaka

first: Rajiv

last: Narayan

first: Mingji

last: Dai

first: Christina

last: Huang

first: Sebastian

last: Shterental

first: Lisa

last: Chu

first: J

last: Haydu

first: Jae

last: Shieh

last: Steensma

first: Benito

last: Munoz

first: Joshua

last: Bittker

first: Alykhan

last: Shamji

first: Paul

last: Clemons

first: Nicola

last: Tolliday

first: Anne

last: Carpenter

first: D

last: Gilliland

first: Andrew

last: Stern

first: Malcolm

last: Moore

last: Scadden

first: Stuart

last: Schreiber

first: Benjamin


title: The effect of miR-294 and miR-181 on the transcriptome during OSK reprogramming of MEFs

status: Public on Sep 15 2013

first: Robert

last: Blelloch

address: RMB1018, 35 Medical Center Way

department: Urology

institute: UCSF

summary: Study designed to determine the immediate effects of supplementing OSK reprogramming with miR-294 or miR-181. MEFs were infected on day 0, and transfected with miR-294, miR-181 or control mimic on day 1. On day 3 RNA was extracted. OSK infected MEFs samples were compared to non-infected MEFs and to fully reprogrammed iPSCs.

overall_design: Performed in biological triplicate, with each sample containing different OSK viral stocks, different preparations of MEFs and independent transfections. Biological triplicate iPSCs represent three independent and clonally expanded iPSC lines. Total RNA collected with Trizol. All processing conducted at the UCLA Neuroscience Genomics Core. MouseRef-8 v2.0 Expression BeadChips.

last: Judson


title: Th2 cytokine IL-4 is critical in initiating pulmonary vascular inflammation under hypoxic conditions and induces pulmonary vascular endothelial cell activation.

status: Public on Sep 19 2013

city: baltimore

first: chris

last: cheadle

state: MD

address: 5200 Eastern Ave

department: SOM

institute: JHU

summary:
IL-4-mediated pro-inflammatory vascular responses have been implicated in the pathogenesis of chronic cardiopulmonary diseases.
Our results show that hypoxia-induced collagen synthesis and early recruitment of inflammatory cells are significantly less in the lungs of IL-4 knockout (KO) mice than in those of wild-type mice.  In addition, we found that IL-4 significantly increased pro-inflammatory genes in primary pulmonary microvascular endothelial cells.

overall_design: This study was designed to identify the gene expression profile of IL-4-dependent pulmonary vascular inflammation induced by hypoxia.

first: Chris

last: Cheadle

first: Kazuyo

last: Kegan


title: Molecular Profiling of glucokinase-expressing cells from mouse hypothalamus

status: Public on Sep 13 2013

first: Sarah

last: Stanley

address: 1230 York Avenue

department: Dept of Molecular Genetics

institute: Rockefeller University

summary: Analysis of genes from glucokinase-expressing cells following immunoprecipitation of hypothalamic EGFP-tagged L10 ribosomal protein from Glucokinase-cre/Elongation factor 1 alpha 1 - lox stop lox - EGFPL10 mice

overall_design: mRNA obtained by immunoprecipitation in adult Gck-cre/EF1A1-LSL-EGFPL10 mice

first: Jeffrey

last: Friedman


title: mRNA expression in CD4+ CD25+ GITR+ regulatory T cells from WT and Bach2 KO mice

status: Public on Nov 14 2013

city: Madison

first: Eui Ho

last: Kim

state: Wisconsin

address: 2015 Linden Dr.

department: Pathobiological Sciences

institute: University of Wisconsin-Madison

summary: Bach2 regulates homeostasis of foxp3+ regulatory T cells and protects against fatal lung disease in mice.

overall_design: Cells from WT and Bach2 KO spleen were isolated. CD4+ CD25+ GITR+ (Treg) cells were sorted by FACS sorting. Total RNAs were extracted from sorted Treg cells using by Rneasy Kit (Qiagen).

first: Eui

first: M

last: Suresh


title: Differential gene expression in peripheral blood leukocytes from mice subject to repeated social defeat

first: Steve

last: Cole

summary:
This study tested the effects of repeated social defeat (RSD) on gene expression in peripheral blood mononuclear cells (PBMC), and examined the extent to which these effects were abrogated by depletion of CD11b+ cells (monocytes).
Study Type: Risk prediction

overall_design: Gene expression profiling was carried out on peripheral blood mononuclear cell (PBMC) mRNA samples collected from 18 mice randomized to either 6 cycles of repeated social defeat (RSD, n=9) or to home cage control (HCC, n=9) conditions.  PBMC samples were pooled into 3 groups of n=3 samples in each condition, and Illumina Mouse Ref-8 BeadArray assays were performed on approximately 1 million total PBMC and 1 million PBMC from which CD11b+ cells were immunomagnetically depleted by MACS.  The primary research questions are 1) whether expression of pro-inflammatory genes is altered by RSD, and 2) whether depletion of CD11b+ cells (monocytes) abrogates these effects.


title: Expression analyses of inducible c-Fos expressing kerationcytes

status: Public on Sep 05 2013

first: Marc

last: Zapatka

address: Im Neuenheimer Feld 580

department: B060 Molecular Genetics

institute: German Cancer Research Center

summary:
Expression analyses comparing c-Fos expressing keratinocytes vs non-expressing controls.
Skin squamous cell carcinomas (SCCs) are the second most prevalent skin cancers. Chronic skin inflammation has been associated with the development of SCCs, but the contribution of skin inflammation to SCC development remains largely unknown. In this study we demonstrate that inducible expression of c-fos in the epidermis of adult mice is sufficient to promote inflammation-mediated epidermal hyperplasia leading to the development of pre-neoplastic lesions. Interestingly, c-Fos transcriptionally controls mmp10 and s100a7a15 expression in keratinocytes subsequently leading to CD4 T cell recruitment to the skin, thereby promoting epidermal hyperplasia. Combining inducible c-fos expression in the epidermis with a single dose of the carcinogen 7,12-Dimethylbenz(a)anthracene (DMBA) leads to the development of highly invasive SCCs, which are prevented by using the anti-inflammatory drug Sulindac. Moreover, human SCCs display a correlation between c-FOS expression and elevated levels of MMP10 and S100A15 proteins as well as CD4 T cell infiltration. Our studies demonstrate a bidirectional crosstalk between pre-malignant keratinocytes and infiltrating CD4 T cells in SCC development. Therefore, targeting inflammation along with the newly identified targets, such as MMP10 and S100A15, represent promising therapeutic strategies to treat SCCs.

overall_design: 5 different time points measured in triplicate comparing Dox-treated vs untreated c-FostetON keratinocytes

first: Eva

last: Briso

first: Erwin

last: Wagner

first: Zbigniew

last: Rogon


title: Regulation of constitutive and alternative splicing by PRMT5 reveals a role for Mdm4 pre-mRNA in sensing defects in the spliceosomal machinery (BeadChip)

city: Singapore

first: Julius

last: Müller

address: 61 Biopolis Drive

department: IMCB

institute: A*Star Singapore

summary: Protein Arginine MethylTransferase 5 (PRMT5) is known to mediate epigenetic control on chromatin and to functionally regulate components of the splicing machinery. In this study we show that selective deletion of PRMT5 in different organs leads to cell cycle arrest and apoptosis. At the molecular level, PRMT5 depletion results in reduced methylation of Sm proteins, aberrant constitutive splicing and in the Alternative Splicing (AS) of specific mRNAs. We identify Mdm4 as one of these mRNAs, which due to its weak 5’-Donor site, acts as a sensor of splicing defects and transduces the signal to activate the p53 response, providing a mechanistic explanation of the phenotype observed in PRMT5 conditional knockout mice. Our data demonstrate a key role of PRMT5, together with p53, as guardians of the transcriptome. This will have fundamental implications in our understanding of PRMT5 activity, both in physiological conditions, as well as pathological conditions, including cancer and neurological diseases.

overall_design: Total RNA was extracted from control Prmt5F/F, and Prmt5 depleted Prmt5F/FNes (Nestin-Cre) Neural Stem/Progenitors Cells (NPCs). The final cRNA samples were hybridized to Illumina MouseRef-8 V2 arrays in quadruplicates.

first: Marco

last: Bezzi

first: Shu

last: Teo

first: Wei

last: Mok

first: Sanjeeb

middle: K

last: Sahu

first: Leah

last: Vardy

first: Zahid

last: Bonday

first: Ernesto

last: Guccione


title: Modeling Pathogenesis of Primary Liver Cancer in Lineage Specific Cell Types

city: Copenhagen

first: Jesper

middle: B

last: Andersen

address: Ole Maaloes Vej 5

department: Biotech Research and Innovation Centre

country: Denmark

institute: Copenhagen University

summary: Classification of human liver cancer into biologically distinct subgroups suggests origin from different hepatic lineage cells. To clarify contribution of lineage stage in liver oncogenesis, we transduced H-Ras and SV40LT into hepatic progenitor cells (HPC), hepatoblasts (HB) and terminally differentiated adult hepatocytes (AH). Regardless of origin, all transformed cell types acquired common cancer stem cell characteristics in vitro and in vivo. However, expression analysis distinguished tumors of different cellular origin underscoring the contribution of lineage/stage-dependent genetic changes in malignant transformation. Notably, AH-derived tumors showed specific enrichment of c-Myc target genes. These data establish that any hepatic lineage cell can be a target for transformation and acquire common cancer stem cell traits via activation of diverse cell type specific pathways.

overall_design: Profiling of individual tumors derived by Ras/SV40 transformation of hepatic progenitor cell (oval cells), hepatoblasts (fetal) and adult hepatocytes

first: Agnes

last: Holczbauer

first: Snorri

middle: S

last: Thorgeirsson


title: Canonical Nlrp3 inflammasome activation links systemic age-related inflammation with functional decline

city: Baton Rouge

first: Ryan

last: Grant

state: LA

address: 6400 Perkins Rd

institute: Pennington Biomedical Research Center

summary:
This experiment was performed to analyze the contribution of NLRP3 inflammasome activation to age-related changes in hippocampal RNA.  The hypothesis was that decreased inflammasome activation would reduce hippocampal inflammation.
Results indicate that inflammasome knockout animals are protected from age-related changes in hippocampal gene expression

overall_design: Gene expression profiles of young (1 month) and old (21-23 month) wild type, CIAS -/- and ASC -/- mouse hippocampal tissue were compared.  Total mRNA was extracted using Trizol.

first: Yun-Hee

last: Youm

first: Vishwa

last: Dixit

first: Diana

last: Albarado

first: Anthony

last: Ravussin

first: Paul

last: Pistell

first: Susan

last: Newman

first: Amanda

last: Laque

first: Heike

last: Munzberg

first: Donald

last: Ingram

first: J

last: Salbaum


title: Transcriptome based identification of mouse cumulus cell markers that predict the developmental competence of their enclosed antral oocytes

status: Public on Sep 01 2013

city: Berlin

first: Alessandro

last: Prigione

state: Berlin

address: Robert-Roessle-Str. 10

institute: Max Delbrueck Center for Molecular Medicine

summary: The cumulus cells (CCs) that envelope antral and ovulated oocytes have been regarded as putative source of non-invasive markers of the oocyte developmental competence and a number of studies have observed a correlation between CCs gene expression, embryo quality and final pregnancy outcome. With the aim of identifying marker transcripts, we isolated CCs from antral mouse oocytes of known developmental incompetence (NSN-CCs) or competence (SN-CCs) and compared their transcriptomes.

overall_design: Total RNA was isolated from cumulus cells derived from oocytes with a SN or NSN chromatin organization.


title: The organizational effects of testosterone on brain DNA methylome

status: Public on Aug 29 2013

first: Tuck

middle: Cheong

last: Ngun

address: 695 Charles E Young Dr S Gonda 5524

department: Human Genetics

institute: UCLA

summary: Analysis of gene expression in the bed nucleus of the stria terminalis/preoptic area and striatum in response to perinatal testosterone exposure. The hypothesis tested was that differences in DNA methylation would be reflected in differences in gene expression.

first: Negar

last: Ghahramani

first: Pao-Yang

last: Chen

first: Yuan

last: Tian

first: Sangitha

last: Krishnan

first: Stephanie

last: Muir

first: Liudmilla

last: Rubbi

first: Arthur

middle: P

last: Arnold

first: Geert

last: de Vries

first: Nancy

last: Forger

first: Matteo

last: Pellegrini

first: Eric

last: Vilain


title: Ablation of coactivator Med1 switches the cell fate of dental epithelia to that generating hair

first: Yuko

last: Oda

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

overall_design: Refer to individual Series

first: Lizh

last: Hu

first: Thai

last: Nguyen

first: Frankie

last: Fong

first: Daniel

last: Bikle


title: Gene expression profile in melanomas from Pdk1-inactivated BrafV600E::Pten-/- mice

status: Public on Sep 17 2013

city: Durham

first: Jian-Liang

last: Li

state: NC

address: 111 TW Alexander Dr

institute: NIEHS

summary: Gene expression profiling was performed to access the changes in gene expression in melanomas from Pdk1-inactivated Brafv600E::Pten-/- mice.  The expression profiles of the BrafV600E::Pten-/-::Pdk1-/- were compared to the BrafV600E::Pten-/-::Pdk+/+ genotypes.  The analysis has identified several important signaling pathways in Pdk1-dependent melanomagenesis.

overall_design: Melanoma tumors from the BrafV600E::Pten-/-::Pdk1+/+ and BrafV600E::Pten-/-::Pdk1-/- genotypes were harvested and mRNA from each group was pooled to enable four biologically replicates analysis.

first: Marzia

last: Scortegagna

first: Jian

first: Ze’ev

last: Ronai


title: Profiling of hepatic progenitor cells isolated from Egfr fl/fl and Met fl/fl murine control livers

first: Jesper

last: Andersen

summary:
Transcriptomic profiling;
Determination of the transcriptomic similarity between Egfr fl/fl and Met fl/fl progenitor cells isolated from excised livers (n=3, each)

overall_design: Profiling of hepatic progenitor cells

first: Mitsuteru

last: kitade

first: Valentina

last: Factor

first: Snorri

last: Thorgeirsson


title: Transcriptome analysis of Brg1 deficient small intestinal epithelium in the context of normal and aberrant Wnt signalling

status: Public on Aug 07 2013

city: Cardiff

first: Aliaksei

last: Holik

address: Museum Avenue

department: School of Biosciences

country: United Kingdom

institute: Cardiff University

summary: Brg1 has been reported to act as a trans-activator for the Wnt pathway by interacting with beta-catenin. Given this interaction and the crucial role Wnt signalling plays in the intestinal homeostasis, we aimed to investigate the effect of Brg1 loss on gene expression in normal and Wnt activated small intestinal epithelium.

overall_design: We used VillinCreERT2 Cre recombinase and loxP targeted allels of Brg1 and Apc to generate 4 cohorts of conditional knock-out mice: Cre-negative controls (n=4), Brg1 deficient (n=4), Apc deficient (n=3) and double Brg1-Apc deficient (n=4). All mice were induced by 4x80mg/kg daily injections of Tamoxifen. Epithelium enriched (gut scrapes) samples of small intestine (jejunum) were collected at day 4 post induction. Loss of Brg1 expression in the small intestinal epithelium at this time point was confirmed by immunohistochemistry.


title: Rapamycin extends life span, but has limited effects on aging in mice

status: Public on Jul 29 2013

city: Neuherberg

first: Martin

last: Irmler

state: Bayern

address: Ingolstaedter Landstrasse 1

department: Institute of Experimental Genetics

institute: Helmholtz Zentrum München GmbH

summary: Rapamycin extends life span in mice, but it remains unclear if this compound also delays mammalian aging. Here, we present results from a comprehensive large-scale assessment of a wide rage of structural and functional aging phenotypes in mice. Rapamycin extended life span but showed few effects on a large number of systemic aging phenotypes, suggesting that rapamycin's effects on aging are largely limited to the regulation of age-related mortality and carcinogenesis.

overall_design: Total RNA obtained from 2-4 male mice of each analysed group (25 weeks old controls, 25 month old controls, 25 month old rapamycin treated)

first: Johannes

last: Beckers

first: Marion

last: Horsch


title: Whole genome profiling of liver sinusoidal endothelial cells (LSEC) before and after hepatectomy

status: Public on Aug 26 2013

city: Heidelberg

first: Junhao

address: Im Neuenheimer Feld 280

department: Division of Vascular Oncology and Metastasis

summary: compare acute gene expression changes in LSEC after hepatecomy

overall_design: WT C57BL/6N mice were either sham operated or underwent 2/3 hepatectomy. One day after operation, LSEC were isolated. RNA were immediatedly extracted for gene array.

first: Hellmut

last: Augustin


title: Liver gene expression profile _ wild type_ CYP7A1 transgenic

status: Public on Aug 15 2013

city: Rootstown

first: John

last: Chiang

state: OH

address: 4209 State Route 44

department: Biochemistry and Molecular Pathology

institute: Northeast Ohio Medical University

summary: Bile acids are not only physiological detergents facilitating nutrient absorption, but also signaling molecules regulating metabolic homeostasis. We reported recently that transgenic expression of CYP7A1 in mice stimulated bile acid synthesis and prevented Western diet-induced obesity, insulin resistance and hepatic steatosis. The aim of this experiment is to determine the impact of induction of hepatic bile acid synthesis on liver metabolism by determining hepatic gene expression profile in CYP7A1 transgenic mice. CYP7A1 transgenic mice and wild type control mice were fed either standard chow diet or high fat high cholesterol Western diet for 4 month. Hepatic gene expressions were measured by microarray analysis. Our results indicate that hepatic bile acid synthesis is closely linked to cholesterogenesis and lipogenesis, and maintaining bile acid homeostasis is improtant in hepatic metabolic homeostasis.

overall_design:
Male aged matched (~ 12-14 weeks) CYP7A1 transgenic mice and their wild type control littermates were fed a standard chow diet or a high fat (42%) high cholesterol (0.2%) diet (Harlan Teklad #88137) for 4 month Four groups (4 mice/group) are included in the experiments:
Group 1: WT _ Chow
Group 2: CYP7A1-tg + chow
Group 3: WT + Western diet
Group 4: CYP7A1-tg _ Western diet

Total liver mRNA was isolated with a RNeasy kit (Qiagen) and used for microarray analysis.

first: Banu

last: Gopalan

first: Shannon

last: Boehme

first: Jie

last: Cheng


title: Ectopic cerebellar cell migration causes maldevelopment of Purkinje cells and abnormal motor behaviour in Cxcr4 null mice

status: Public on Jul 12 2013

city: Tao-Yuan

first: Guo-Jen

last: Huang

address: 259 Wen-Hwa 1st Road

country: Taiwan

institute: Chang Gung University

summary: Transcriptome analysis revealed the most significantly affected pathways in the Cxcr4 deficient developing cerebellum are involved in extra cellular matrix receptor interactions and focal adhesion

overall_design: We isolated the cerebellum  WT (n=8) and CXCR4 KO(n=7) P1 mice, and run illumina mice gene expression array to compare the gene expression pattern between this two groups.


title: Identification of genes involved in SHH subgroup medulloblastoma using murine whole-body Sleeping Beauty insertional mutagenesis

status: Public on Jul 09 2013

city: Newcastle upon Tyne

first: Michael

middle: Stewart

last: Jackson

address: Central Parkway

department: Institute of Genetic Medicine

institute: Newcastle University

summary: Ptch+/- mice, which are predisposed to SHH subgroup medulloblastoma, were mutagenised using the Sleeping Beauty transposon to identify genes which increase the frequency of medulloblastoma formation. Gene expression in tumours was assessed both to investigate their relationship to human subgroup tumours, and to identify genes where expression was altered by mutagenesis.

overall_design: Total RNA isolated from tumours induced by SB mutagenesis were compared to normal cerebellum, tumours induced witout SB mutagenesis, and tumours from a distinct model of disease (GTML).

first: Steven

last: Clifford

first: Daniel

last: Williamson

first: Louis

last: Chesler

first: Hani

last: AlAfghani


title: Feminized behavior and gene expression in the striatum in a novel mouse model of Klinefelter Syndrome

first: Tuck

last: Ngun

summary: Analysis of gene expression in the striatum in a mouse model of Klinefelter Syndrome (the Sex Chromosome Trisomy model). The hypothesis tested was that feminization of partner preference was also reflected on a molecular level

overall_design: 4 different genotypes were analyzed (XX female, XY male, XXY male, XX male). There were 8-12 biological replicates per genotype for a total of 38 samples.

first: Negar

last: Ghahramani

first: Michelle

last: Creek

first: Shayna

last: Williams-Burris

first: Hayk

last: Barseghyan

first: Yuichiro

last: Itoh

first: Francisco

last: Sánchez

first: Rebecca

last: McClusky

first: Janet

last: Sinsheimer

first: Arthur

last: Arnold

first: Eric

last: Vilain


title: HepG2 treated with two Polycyclic Aromatic Hydrocarbons (benzo[a]anthracene & benzo[k]fluoranthene)

status: Public on Jul 22 2013

city: Seoul

first: Mi-Kyung

last: Song

address: 39-1 Hwawol-gok-dong, Wolsong-gil5, Seongbuk-gu-seoul

institute: Korea Institute of Science & Technology

summary: To gain deeper insight into the mechanism of toxicity, it is important to identify and characterize miRNAs profiles involved in responses to specific classes of toxicants in conjunction with their impact on gene expression levels. However, few reports have described the effects of toxicants on miRNA expression profiles. Taking into account the prominent role of miRNAs in cancer development, progression, cell cycle control, and proliferation-related processes, it is likely that miRNAs are involved in the toxic response induced by carcinogens. Polycyclic aromatic hydrocarbons (PAHs) are a well-characterized class of human carcinogens. In the present study, we documented the different expression profiles of miRNAs in environmental carcinogen-exposed HepG2 cells by miRNA microarray analysis.

overall_design: To evaluate the change in miRNA expression levels, human hepatocellular carcinoma (HepG2) cells were exposed to two PAHs (benzo[a]anthracene, benzo[k]fluoranthene) for 48 h. miRNA expression analysis was conducted using a 8x16k human miRNA microarray (Agilent Technologies, USA).

first: Jae-Chun

last: Ryu


title: Global transcriptomic profiling of hypoxic ischemia in an in vivo neonatal mouse model

status: Public on Dec 31 2013

city: Hobart

first: Minghui Jessica

last: Chen

address: Menzies Research Institute, University of Tasmania, Private Bag 24

department: Neuroscience group

institute: Menzies Research Institute


title: Feminized behavior and gene expression in the BNST/POA in a novel mouse model of Klinefelter Syndrome

city: Los Angeles

summary: Analysis of gene expression in the bed nucleus of the stria terminalis/preoptic area in a mouse model of Klinefelter Syndrome (the Sex Chromosome Trisomy model). The hypothesis tested was that feminization of partner preference was also reflected on a molecular level


title: Gene expression in mouse retinas with cone cyclic nucleotide gated channel deficiencies

status: Public on Jul 03 2013

city: Oklahoma City

first: Bart

last: Frank

state: OK

institute: OMRF

summary: The cone photoreceptor cyclic nucleotide-gated (CNG) channel is essential for central and color vision and visual acuity.  Mutations in the channel subunits CNGA3 and CNGB3 are associated with achromatopsia and cone dystrophy.  We investigated the gene expression profiles in mouse retina with CNG channel deficiency on a cone-dominant background, i.e., CNGA3-/-/Nrl-/- and CNGB3-/-/Nrl-/- mice, relative to Nrl-/- mice.

overall_design: Total RNA was isolated from 2 retinas per animal (CNGA3-/-/Nrl-/-, CNGB3-/-/Nrl-/-, and Nrl-/- mice). The background strain for these mutations was C57bl/6.

first: Xi-Qin

last: Ding


title: Smchd1 regulates autosomal genes subject to monoallelic expression

city: Parkville

first: Matthew

last: Wakefield

state: VIC

address: 1G Royal Parade

department: Bioinformatics

institute: Walter and Eliza Hall Institute

summary: Analysis of the genes that escape silencing in the MommeD1 allele of Smchd1

overall_design: Total RNA from E9.5 embryos compared in a two factor design - gender and Smchd1 genotype

first: Arne

last: Mould

first: Zhenyi

last: Pang

first: Miha

last: Pakusch

first: Ian

last: Tonks

first: Mitchell

last: Stark

first: Dianne

last: Carrie

first: Annica

last: Seidel

first: Jonathan

last: Ellis

first: Lutz

last: Krause

first: Marnie

middle: E

last: Blewitt

first: Graham

middle: F

last: Kay


title: Analysis of temporal gene expression responses during TNBS-induced colitis development

status: Public on Jul 08 2013

city: Leiden

first: Rob

last: Mariman

address: Vestwal 5

country: Netherlands

institute: TNO

summary: To obtain insight into the complex traits underlying the local pathophysiological response to the repeated colitis inductions with TNBS, whole genome gene expression was performed on RNA isolated from the distal colon tissue of 5 mice/timepoint

overall_design: Total RNA obtained from isolated from the distal colon of TNBS colitis mice (isolated on day  9, 14, 16, 21, 23, and 28) was compared to those healthy control mice

first: Bas

last: Kremer


title: Comparative analysis of transcriptional gene regulation indicates similar physiological response in mouse tissues at low absorbed doses from i.v. administered 211At

status: Public on Jul 02 2013

city: Gothenburg

first: Britta

last: Langen

address: Gula stråket 2B

department: Department of Radiation Physics

institute: Sahlgrenska Academy at University of Gothenburg

summary: Transcriptomic profiling of normal mouse lung, liver, kidney, and spleen tissue following 211At irradiation.

overall_design: Total RNA was isolated from fresh-frozen tissue samples.

first: Nils

last: Rudqvist

first: Toshima

middle: Z

last: Parris

first: Emil

last: Schüler

first: Khalil

last: Helou

first: Eva

last: Forssell-Aronsson


title: Microarray of wild type, Shp2 knock-out, Pten knock-out and double knock-out erythroblasts

city: Shanghai

first: Helen

middle: He

last: Zhu

address: 3rd Floor, Building 5, 1630 Dongfang Road

department: Stem Cell Center, Renji Hospital

institute: School of Medicine, Shanghai Jiaotong University

summary: the gene expression profiling results provide important information for the genes regulated by crosstalk between Shp2 and Pten mediated signal pathways

overall_design: Total RNA was extracted from CD71mid Ter119high erythroblasts isolated from the bone marrow of wide type, Shp2 knock-out, Pten knock-out and double knock-out mice

middle: H

first: Gen-Sheng

last: Feng