title: Expression data of lung tissues from ICR mice treated with or without single-walled carbon nanotubes (SWCNTs)

status: Public on Jul 09 2011

city: Taipei

first: Huei-Wen

last: Chen

address: No.1, Sec.1, Re-Ai Rd

department: Medical College

country: Taiwan

institute: National Taiwan University

summary:
The SWCNTs can induce airway hyper-responsiveness (AHR) and chronic obstructive pulmonary disease (COPD)-like changes in mice model. The SWCNTs can induce clusters of proteinases, chemokines/cytokines, and macrophage receptors triggered signaling, which might play critical roles in the SWCNTs-induced pathological changes, including chronic inflammation and tissues remodeling.
We used microarrays to detail the global programme of gene expression underlying and identified distinct classes of up-regulated genes during this process.

overall_design: Lung tissues from adult ICR mice (6 weeks old) treated with or without single dose of 0.5 mg SWCNTs by intratrachael instillation were collected and homogenated under liquid nitrogen for RNA extraction and hybridization on Affymetrix microarrays. Since our data showed that the SWCNTs could induce significantly pulmonary granuloma and COPD-like lesion. Two time points of the samples have been collected for microarray analysis: day 1 after SWCNTs treatment as the acute phase responses; day 7 as the sub-chronic responses. We tried to compare the SWCNTs-regulated gene expression profiles with the PF68-treated (as the solvent control) to identify the possible mechanisms of SWCNTs-induced toxicity in lung.

first: Wan-Yu

last: Hsieh

first: Cheng-Chung

last: Chou

first: Chao-Chi

last: Ho

first: Sung-Liang

last: Yu

first: Hsuan-Yu

first: Han-Yi

first: Pan-Chyr

last: Yang


title: Maffucci tumours

status: Public on Jul 19 2011

city: Leiden

first: Twinkal

middle: Chandubhai

last: Pansuriya

state: Zuid-Holland

address: Albinusdreef 2

department: Pathology

country: Netherlands

institute: LUMC

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

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

overall_design: Refer to individual Series


title: ETV5 Mediated Downstream Gene Activation in Spermatogonial Stem Cells

status: Public on Jul 15 2011

city: Philadelphia

first: xin

last: wu

state: PA

address: 3850 baltimore Ave,

department: Animal Biology

country: USA

institute: School of Veterinary Medicine, University of Pennsylvania

summary:
Insight into mechanisms controlling gene expression in the spermatogonial stem cell (SSC) will improve our understanding of the processes regulating spermatogenesis and aid in treating problems associated with male infertility.
In this study we explored the global gene expression profiles of glial cell line-derived neurotrophic factor (GDNF) regulated transcription factors, Ets variant gene 5 (Etv5), B-cell CLL/lymphoma 6, member B (Bcl6b) and POU domain, class-3 transcription factor-1 (Pou3f1). We reasoned that these three factors may function as a core-set of transcription factors, regulating genes responsible for maintaining the SSC population. Using transient short-interfering RNA oligonucleotides (siRNA) to individually target Etv5, Bcl6b and Pou3f1 within mouse SSC cultures, we examined changes to the global gene expression profiles associated with these transcription factors. While there were only modest overlaps in the target genes regulated by the three factors, ETV5 was found to be a critical downstream regulator of GDNF signaling that mediated the expression of several known SSC self-renewal related genes including, Bcl6b  and LIM homeobox 1 (Lhx1). Notably, ETV5 was identified as a regulator of Brachyury and CXC chemokine Receptor, type 4 (Cxcr4), and we show that ETV5 binding to the Brachyury gene promoter region is associated with an active state of transcription. Moreover, in vivo transplantation of SSCs following silencing of Brachyury significantly reduced the number of donor cell-derived colonies formed within recipient mouse testes. These results suggest Brachury is of biological importance, and functions as part of GDNF/ETV5 signaling to promote self-renewal of mouse SSCs cultured in vitro.

overall_design: Microarray gene expression analysis was conducted with Affymetrix Mouse 430 2.0 GeneChips (Affymetrix Inc.).Following with gene knockdown, total RNA from spermatogonial stem cells  was converted to cDNA.  There are total 16 samples (Four groups and four samples per group) Negative control (N), Bcl6b Knockdown (B), Etv5 knockdown (E), and Pou3f1 knockdown (O), respectively.

first: Xin

last: Wu

first: Ralph

middle: L

last: Brinster


title: MYST4 (QKF/KAT6B/MORF) transcriptional targets in the adult dorsal cortex and E12.5 embryonic dorsal telencephalon

status: Public on Jul 08 2011

city: Parkville

first: Gordon

middle: K

last: Smyth

state: Vic

address: 1G Royal Pde

department: Bioinformatics

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

summary: MYST4 (QKF/KAT6B/MORF) is an important regulator of brain development and function through its regulation of gene expression. Genetic targets of MYST4 are currently unknown. We have therefore carried out microarrays comparing gene expression in wild type and Qkf mouse tissues, namely the dorsal cortex and E12.5 dorsal telencephalon, to elucidate genetic targets of MYST4.

overall_design: RNA was extracted for hybridization to arrays from 3 pairs of wild type and Qkf gt/gt mutant adult dorsal corticies and 3 pairs of wild type and Qkf gt/gt mutant E12.5 dorsal telencephalons

first: Bilal

middle: N

last: Sheikh

first: Tim

last: Thomas

first: Anne

last: Voss


title: WT vs c-Maf KO fetal liver macrophage

status: Public on Jul 06 2011

city: Tsukuba

first: Manabu

last: Kusakabe

state: IBARAKI

address: 1-1-1, Tennodai,

department: Department of Anatomy and Embryology

country: Japan

institute: University of Tsukuba

summary:
Homozygous disruption of c-Maf led to embryonic lethality and impaired erythroblastic island formation. c-Maf is expressed in the fetal liver macrophages. It suggests that macrophages are responsible for the lethality of c-Maf knock-out embryos. To search downstream genes of c-Maf, we surveyed genes associated with macrophage function by microarray analysis.
keywords: c-Maf, macrophage, erythroblastic islands,

overall_design: WT (c-Maf WT) and c-Maf KO (c-Maf KO) fetal liver macrophages were sorted by a FACSAria cell sorter. Total RNAs from those macrophages were prepared using RNeasy Kit. Genes down-regulated in c-Maf KO macrophages were searched by GeneSpring software.

first: Kazuhiko

last: Uchida

first: Satoru

last: Takahashi


title: Tissue-specific genetic regulation of splicing and expression (gene-level)

city: New York

first: Erin

middle: L.

last: Heinzen

state: NY

department: Institute for Genomic Medicine

institute: Columbia University

summary: Numerous genome-wide screens for polymorphisms that influence gene expression have provided key insights into the genetic control of transcription. Despite this work, the relevance of specific polymorphisms to in vivo expression and splicing remains unclear. We carried out the first genome-wide screen, to our knowledge, for SNPs that associate with alternative splicing and gene expression in human primary cells, evaluating 93 autopsy-collected cortical brain tissue samples with no defined neuropsychiatric condition and 80 peripheral blood mononucleated cell samples collected from living healthy donors. We identified 23 high confidence associations with total expression and 80 with alternative splicing as reflected by expression levels of specific exons. Fewer than 50% of the implicated SNPs however show effects in both tissue types, reflecting strong evidence for distinct genetic control of splicing and expression in the two tissue types. The data generated here also suggest the possibility that splicing effects may be responsible for up to 13 out of 84 reported genome-wide significant associations with human traits. These results emphasize the importance of establishing a database of polymorphisms affecting splicing and expression in primary tissue types and suggest that splicing effects may be of more phenotypic significance than overall gene expression changes.

overall_design: We evaluated 93 autopsy-collected cortical brain tissue samples with no defined neuropsychiatric condition and 80 peripheral blood mononucleated cell samples collected from living healthy donors. Affymetrix Human ST 1.0 exon arrays were used to assess exon and transcript expression levels for all samples used in the study. Replicate analyses were not performed.  Exon array sample preparation from total RNA was conducted based on standard Affymetrix protocols.  Data were normalized separately within PBMC and brain sets Affymetrix PLIER protocol with a sketch-quantile normalization procedure (Affymetrix Expression Console).  Normalized files include brain core transcripts (NABRAINSETCOMBplier-gene-core.summary), brain all transcripts (NABRAINSETCOMBplier-gene-full.summary), brain core exons (NABRAINSETCOMBplier-exon-core.summary), brain all exons (NABRAINSETCOMBplier-exon-all.summary), PBMC core transcripts (NAPBMCfullsetplier-gene-core.summary), PBMC all transcripts (NAPBMCfullsetplier-gene-full.summary), PBMC core exons (NAPBMCfullsetplier-exon-core.summary), PBMC all exons (NAPBMCfullsetplier-exon-all.summary).  all, full and core definitions are provided by Affymetrix.

first: David

middle: B

last: Goldstein


title: IKKa-mediated signaling circuitry regulates early B lymphopoiesis during hematopoiesis

status: Public on Jul 02 2011

city: Frederick

first: Mumtaz

last: Yaseen

state: Maryland

address: 1050 Boyles Street

institute: NCI

summary: Multiple transcription factors regulate B cell commitment, which coordinates with myeloid–erythroid lineage differentiation. One such factor, NF-kB, has long been speculated to regulate early B cell development; however, this issue remains controversial. IKKa is required for splenic B cell maturation, but not for bone marrow (BM) B cell development. Here, we unexpectedly found defective BM B cell development and an increased myeloid–erythroid lineages in kinase-dead IKKa (KA/KA) knock-in mice. Markedly increased cytosolic p100, an NF-kB2 inhibitory form, and reduced nuclear NF-kB p65, RelB, p50, and p52, as well as IKKa, was observed in KA/KA splenic and BM B cells. Several B- and myeloid–erythroid-cell regulators, including Pax5, were deregulated in KA/KA BM B cells. Using fetal liver and BM congenic transplants, and IKKa deletion from early hematopoietic cells in mice, this defect was identified as B cell intrinsic and as an early event during hematopoiesis. Re-expression of IKKa, Pax5, or combined NF-kB molecules promoted B cell development, but repressed myeloid–erythroid cell differentiation in KA/KA BM B cells. Together, these results demonstrate that IKKa regulates B-lineage commitment via combined canonical and noncanonical NF-kB transcriptional activity to target Pax5 expression during hematopoiesis.

overall_design: Microarray analysis was performed on RNA isolated from the BM of B220+ cells isolated from 4-week old WT and KA/KA mice using affymetrix mouse 430 2.0 array chip, containing 45,000 genes, at the Laboratory of Molecular Technology SAIC-Frederick. Data were normalized, and log2 transformations were generated using Partek software (St. Louis, MO, USA).

middle: Y

last: Balkhi

first: J

last: Willette-Brown

first: F

last: Zhu

first: Zhisong

last: Chen

first: S

last: Liu

first: D

middle: C

last: Guttrdige

first: Michael

last: Karin

first: Yinling

last: Hu


title: Profile of gene expression signatures on DT40 cell for bursal-derived peptides

city: Nanjing

first: Pu

middle: Yan

address: No. 1, Weigang

country: China

institute: Nanjing Agriculture University

summary: To further elucidate the mechanism of bursal-derived bioactive peptides on avian B cell proliferation on the broad molecular level, we have employed whole genome microarray expression profiling as a discovery platform to examine gene expression patterns during BP5 and BSP-II treatment in DT40 cell culture system. Analysis of our expression microarray data in this manner defined 3163 genes up-regulated and 3539 genes down-regulated by BP5 treatment and 3117 genes up-regulated and 3531 genes down-regulated by BSP-II treatment at 95% confidence, with a commonly regulated gene set of 2253 upregulated genes and 2083 downregulated genes. Various pathways were significantly impacted by BP5 and BSP-II treatment, and gene Ontology annotations show changes in the expression of molecules involved in DT40 cell with BP5 and BSP-II treatment. Expression of 12 genes (FGF3, RAP1B, TCEB1, CSNK2A1, DNMT1, HIF1A, HDAC1, FZR1, GDF3, FGF8, IRF7, and SKP1) from this signature was quantified in the RNA samples by QRT-PCR, confirming low variability between the predicted response patterns.

overall_design: BP5 and BSP-II induced gene expressions in DT40 cell were measured at 4 hours after exposure to doses of 0.02ug/ml and 2ug/ml, respectively.  Two independent experiments were performed using different cells for each experiment.Three independently generated populations of cells were used for these experiments.

first: Xiu

last: Feng


title: Tissue-specific genetic regulation of splicing and expression


title: The RANK IVVY Motif-regulated Genes in Osteoclastogenesis

status: Public on Jul 05 2011

city: Birmingham

first: Dongquan

state: AL

address: 1717 11th Ave South

department: Medicine

institute: Univ of Alabama at Birmingham

summary:
By carrying out a systematic structure/function study of the RANK cytoplasmic domain, we previously identified a specific 4-a.a. RANK motif (IVVY535-538) which plays a critical role in osteoclastogenesis by mediating commitment of macrophages to the osteoclast lineage. We have recently validated the role of this IVVY motif in osteoclastogenesis in vivo by generating knockin (KI) mice bearing inactivating mutations in the RANK IVVY motif. This microarray experiment was performed to determine whether the IVVY motif is involved in regulating gene expression in osteoclastogenesis.
We used microarrays to detail the global programme of gene expression underlying cellularisation and identified distinct classes of up-regulated genes during this process.

overall_design: Bone marrow macrophages isolated from wild-type (WT) or knockin (KI) mice were plated in 60-mm tissue culture dishes and treated with M-CSF (44ng/ml) and RANKL (100ng/ml) for 24 hours. Each genotype has three triplicates. Total RNA was isolated for microarray analysis using mouse chips (type 430.2.0) at the Microarray Shared Facility at the University of Alabama at Birmingham.

first: Zhenqi

last: Shi

first: Xu


title: The UBC9 E2 SUMO conjugating enzyme binds the PR-Set7 histone methyltransferase to facilitate target gene repression

city: Los Angeles

first: Judd

last: Rice

state: California

address: 1450 Biggy Street

institute: University of Southern California

summary: To detect genes whose expression is signigicantly altered upon depletion of pr-SET7

overall_design: Total RNA obtained from 4 days post-transfection of control pSuperior empty plasmid and pSuperior pr-SET7 shRNA plasmid


title: Neurod6 expression defines new retinal amacrine cell subtypes and regulates their fate

status: Public on Jul 01 2011

city: Cambridge

first: Jeremy

last: Kay

state: MA

address: 52 Oxford Street

institute: Harvard University

summary:
The goal of this experiment was to define gene expression patterns of two mouse retinal neuron subsets that express the Thy1-mitoCFP-P (MP) transgene.
The two populations expressing the MP transgene are: 1) non-GABAergic, non-glycinergic amacrine cells; and 2) a subset of OFF-type bipolar cells.

overall_design:
We used the VC1.1 monoclonal antibody, which labels amacrine cells (ACs) but not bipolar cells, to separately purify the AC and bipolar populations that express the MP transgene.
Two biological replicates, originating from different litters, were collected for each sample. RNA was extracted from sorted cells and prepared for hybridization to Affymetrix microarrays.

first: Joshua

middle: R

last: Sanes


title: Microarray data of differentiating embryonic stem cells overexpressing the transcription factor Msgn1

first: Ravindra B

last: Chalamalasetty

state: MD

address: 1050 Boyles St, Bldg 539,Rm205

department: Cancer and Developmental Biology

institute: National Cancer Institute-Frederick

summary:
During mammalian gastrulation, pluripotent epiblast stem cells migrate through the primitive streak to form the multipotent progenitors of the mesoderm and endoderm germ layers. Msgn1 is a bHLH transcription factor and is a direct target gene of the Wnt/bcatenin signaling pathway. Msgn1 is expressed in the mesodermal compartment of the primitive streak and is necessary for the proper development of the mesoderm. Msgn1 mutants show defects in somitogenesis leading to a lack of trunk skeletal muscles, vertebra and ribs.
To study the molecular and cellular function of Msgn1 in Embryonic Stem Cells (ESC), we have generated doxycycline inducible gain-of-function ESC to overexpress Msgn1 in ESC. In order to identify Msgn1 targets, we performed transcriptional profiling of Msgn1 expressing ES cells and found that upon induction of Msgn1, multiple genes in the Notch pathway were differentially expressed compared to the uninduced cells. Moreover, Whole Mount Insitu Hybridization analysis in Msgn1 null mutants revealed that these Notch pathway genes required Msgn1 for their proper expression in vivo. Our studies demonstrate that Msgn1 is a critical effector of the Wnt pathway during mammalian somitogenesis, mediating crosstalk between the Wnt and Notch pathways.

overall_design: Inducible A2lox-Flag Msgn1 ES cells were differentiated to form Embryoid bodies (EBs) for 2 days. Flag-Msgn1 was induced on day 2 with doxycycline and samples were collected at three time points, 12h, 24h and 48h after addition of doxycycline. Uninduced cells were used as controls. Experiments were performed in triplicate

first: Ravindra

first: Terry

middle: P

last: Yamaguchi


title: Expression data from Mouse embryo

city: Oobu

first: Yuko

last: Katoh-Fukui

address: 35genngo ,moriokamachi

institute: National Inastitute for Longevity Sciences

summary:
Mice lacking the function of the PcG protein CBX2 (also known as M33) show defects in gonadal, adrenal, and splenic development. In particular, XY knockout mice develop ovaries but not testes, and the gonads are hypoplastic in both sexes.
To clarify the molecular basis of the defects, RNA prepared from both wild type and KO gonads were subjected to microarray analyses.

overall_design: Mouse embryonic gonads of Cbx2 knockout (KO) were sectioned and recovered at E11.5  for RNA extraction and hybridization on Affymetrix microarrays. Four different genotypes of embryos at E11.5 (XY WT, XX WT, XY Cbx2 KO, and XX Cbx2 KO) were frozen in OCT compound without fixation. They were sectioned to 30 μm slices and stained with hematoxylin. The developing gonadal cells localized by GATA4 immunostaining and morphology were prepared using a Laser Microdissection System. The specimens prepared from two or three individuals were combined into one group, and three groups were prepared for each genotype.

first: Ken-ichirou

last: Morohashi


title: Ionizing radiation in GI tract of Tweak KO mice

first: Suzanne

last: Szak

address: 14 Cambridge Ctr

department: Drug Discovery

institute: BiogenIdec, Inc.

summary: TWEAK/Fn14 signaling may regulate the expression of genes involved in epithelial repair and mucosal inflammation. Comparing the gene signatures in WT and TWEAK KO mice will inform the biology of TWEAK/Fn14 pathway in the GI tract.

overall_design: Mice were treated with 3 Gy of ionizing radiation. After 6h and 24h mice were sacrificed, and whole colon and jejunum were harvested, and RNA was isolated from these tissues. Each CEL file represents a different mouse.

first: Rei

last: Kawashima

first: Yuki

middle: I

last: Kawamura

first: Tomoyuki

last: Oshio

first: Aoi

last: Son

first: Motomi

last: Yamazaki

first: Teruki

last: Hagiwara

first: Toshihiko

last: Okada

first: Ping

last: Wu

first: Yutaka

middle: J

first: Fumio

last: Konishi

first: Oki

last: Miyake

first: Emiko

last: Takeshita

first: Yukio

last: Saito

first: Linda

last: Burkly

first: Taeko

last: Dohi


title: Identification of downstream transcriptional targets of Dlx5 during early mouse inner ear (otocyst/otic vesicle) development

city: Chicago

first: Samin

last: Sajan

state: IL

address: 920 E. 58th Street, CLSC 317

institute: University of Chicago

summary:
Several transcription factors are known to be expressed in discrete regions of the otic vesicle and Dlx5 is one of those that is expressed highly in the presumptive dorsal vestibular region. Mice lacking Dlx5 have vestibular defects. Specifically, they fail to form the endolymphatic duct (a defect visible as early as E10) as well as the anterior and posterior semi-circular canals. The lateral canal does form but is smaller, whereas the saccule, the utricle and the cochlea appear relatively normal. The goal of this study was to use microarrays to identify differentially expressed genes between wild-type and Dlx5-null otic vesicles microdissected from E10 and 10.5 and identify downstream targets of Dlx5 by searching the immediate 3kb promoter regions of the differentially expressed genes for homeodomain binding sites followed by chromatin immunoprecipitation in an otic vesicle-derived cell line over-expressing Dlx5.
Normal vestibular morphogenesis is compromised in mice lacking Dlx5, a member of the Distal-less family of homeobox transcription factors.  We identified its direct downstream targets in the developing mouse inner ear by gene expression profiling wild-type and Dlx5 null otic vesicles from embryonic stages E10 and E10.5.  Four hundred genes were differentially expressed in mutants when compared to wild-type in at least one of the two stages. To further constrain the list of likely direct targets of Dlx5, we examined the genomic DNA sequences in the 3kb promoter regions immediately proximal to the transcriptional start sites of these genes.   We searched for (i) one or more previously described binding site for Dlx5, (ii) one or more novel 12bp-long motifs with a canonical homeodomain response element (HDRE) shared by promoters of two or more genes, and (iii) 100% conservation of the 12bp-long HDRE-containing motifs in promoter regions of human orthologs.  Forty genes passed one or more of these filters, 12 of which are known to be expressed in the developing otic vesicle in domains that at least partially overlap with that of Dlx5 in one or both stages that we examined. Chromatin immunoprecipitation using a Dlx5 antibody confirmed direct binding of Dlx5 to promoter regions of seven of these genes (Atbf1, Bmper, Large, Lrrtm1, and Msx1, all of which were down-regulated in mutants, and Ebf1 and Lhx1, both of which were up-regulated in mutants) in an otic vesicle-derived cell line over-expressing Dlx5. Gene expression profiling of this cell line showed that Bmper and Lrrtm1 transcripts were up-regulated, further supporting their identification as direct targets of Dlx5 activity.

overall_design: Otic vesicles from wild-type and Dlx5-null embryos were microdissected from mouse developmental stages E10 and E10.5 and expression profiled in duplicate for each stage and genotype. Dlx5-transfected and empty vector-transfected 2B1 cell line samples were also profiled in duplicate (independent cell cultures).

middle: A

first: John

last: Rubenstein

first: Mark

last: Warchol

first: Michael

last: Lovett


title: Expression data from the node and primitive streak (NPS) regions from WT and Wnt3a null embryos

status: Public on Jun 30 2011

first: Terry. P

last: Yamaguchi

address: 1050 Boyles St, Bldg 539,Rm218

summary: The goal of this project was to elucidate the target genes and transcriptional networks activated by Wnt3a during gastrulation, a complex morphogenetic process in which the embryonic germ layers are formed and the vertebrate body plan is established.

overall_design: To identify downstream targets of Wnt3a, transcriptional profiling was performed using Affymetrix GeneChips on both wildtype and Wnt3a null embryos at embryonic days (E) 7.75-8.  In order to maximize the likelihood of identifying direct target genes of Wnt3a, RNA was isolated from the node and primitive streak (NPS) region, an area where Wnt3a is highly expressed and at a time 12-18 hours before the morpholical phenotype of Wnt3a mutants becomes apparent.

first: William

last: Dunty Jr

first: Kristin

last: Biris

first: Terry


title: Gene expression profiling of in vivo derived induced and natural FOXP3+ regulatory T cells in the mouse

city: Milwaukee

first: Martin

last: Hessner

state: WI

address: 8701 Watertown Plank Road

department: Pediatrics

institute: Medical College of Wisconsin

summary:
The relative contribution of induced and natural Foxp3+ regulatory T cells (iTreg and nTreg cells, respectively) to the maintenance of tolerance is unknown.  We examined their respective roles by in vivo adoptive transfer immunotherapy of newborn Foxp3-deficient BALB/c mice.  Survival, weight gain, tissue infiltration, T cell activation, and the concentration of proinflammatory cytokines were used as outcome measurements.  Treatment with iTreg cells alone was not successful.  While effective in preventing death, treatment with nTreg cells alone was associated with chronic inflammation and autoimmunity.  Outcomes markedly improved when conventional T (Tconv) cells were transferred together with the nTreg cells, where 10% of the peripheral Treg cell pool was derived by in-situ conversion.  This enhancement depended upon the capacity of Tconv cells to express Foxp3.
The gene expression profile of in vivo derived iTreg cells was similar to the established nTreg cell genetic signature.  These results identify iTreg cells as an essential regulatory subset that supplements tolerance maintained by nTreg cells.

overall_design:
Purified cells sorted by flow cytometry from 4-8 treated mice(pooled EGFP+ Thy1.1+ iTreg cells with that of EGFP+ Thy1.1+ nTreg cells sorted from the spleens and lymph nodes of treated mice) were used to generate total RNA for each iTreg and nTreg array set, which was labeled and hybridized to Affymetrix 430 2.0 GeneChips in accordance to the manufacturer’s protocol. Three sets of arrays were performed, and the results were averaged. Both iTreg and nTreg array sets were compared to a) naïve CD4+EGFP– Tconv cells from Foxp3EGFP mice and b) in vitro derived iTreg cells 72 hours after Foxp3 induction, generated earlier. The subset of probe sets whose expression increased or decreased by twofold or more relative to Tconv cells as a common standard was identified and used for further analysis.

Naïve CD4+EGFP– Tconv cells from Foxp3EGFP mice and in vitro derived iTreg cells 72 hours after Foxp3 induction datasets obtained from GSE14415:
Naïve CD4+EGFP– Tconv cells from Foxp3EGFP mice: GSM360171 - GSM360173
In vitro derived iTreg cells 72 hours after Foxp3 induction: GSM360147 - GSM360151

first: Dipica

last: Haribhai

first: Shuang

last: Jia

first: Brandon

last: Edwards

first: Jennifer

last: Ziegelbauer

first: Mary

last: Williams

first: Shun-Hwa

last: Li

first: Pippa

middle: M

last: Simpson

first: Nita

middle: H

last: Salzman

first: Talal

last: Chatila

first: Calvin


title: expression data in lung of mice bearing inducible FGF18 transgene

city: Creteil

first: Roberto

last: Incitti

address: 51, av. du General de Lattre de Tassigny

country: France

institute: Universite Paris 12 (as of January 2010)

summary:
Better understanding alveolarization mechanisms could help improving prevention and treatment of diseases characterized by reduced alveolar number, especially bronchopulmonary dysplasia (BPD). Although signaling through fibroblast growth factor (FGF) receptors is essential for alveolarization, involved ligands are unidentified. FGF18 whose expression peaks during alveolar septation is likely to be involved. Herein, a mouse model of inducible, lung-targeted FGF18-transgene was used to advance the onset of FGF18 expression, and genome-wide expression changes were determined.
keywords: transgenic mice, alveolarization, angiogenesis, fibrosis, epithelial-mesenchymal transition.

overall_design: Four pairs of simple and double transgenic pups issued from 4 different litters were selected on the basis of FGF18 transgene induction. RNA from the mice lung were extracted and hybridized on Affymetrix microarrays.

first: Jacques

last: Bourbon

first: Marie-Laure

last: Franco-Montoya


title: Expression data from FOG1+/- (or FOG1+/+) and FOG1 ki/ki mouse megakaryocyte (Meg)

status: Public on Jun 28 2011

first: Yuhuan

last: Wang

address: 3615 Civic Center Blvd

institute: The Children's Hospital of Philadelphia

summary:
The transcription co-factor FOG1 interacts with the chromatin remodeling complex NuRD to mediate gene activation and gene repression during hematopoiesis. We have generated mice with a targeted mutation in the endogenous Fog1 locus that results in an N-ternimal mutation in FOG1 that disrupts the interaction with NuRD.
We used gene expression microarrays to explore the global transcriptional programs regulated by FOG1 and NuRD in megakaryocytic cells to aid in understanding its role during hematopoiesis.

overall_design: Bovine serum albumin (BSA) gradient centrifugation was used to isolate maturated megakaryocutes from mouse

first: Xiang

last: Yu

first: Gerd

last: Blobel

first: Mortimer

last: Poncz


title: Immunoprotective properties of sertoli cells: potential genes and pathways that confer immune privilege for sertoli cell transplantation and in the testis

status: Public on Jun 23 2011

city: Pullman

first: Timothy

middle: J.

last: Doyle

state: WA

address: 100 Dairy Road

department: School of Molecular Biosciences

institute: Washington State University

summary: Immune privileged Sertoli cells (SC) survive when transplanted across immunological barriers and prolong the survival of co-transplanted allogeneic and xenogeneic cells in rodent models. However, the mechanism for this survival and protection remains unresolved. We have recently identified a mouse Sertoli cell line (MSC-1) that lacks some of the immunoprotective abilities associated with primary SC. The objective of this study was to compare the survival and gene expression profiles of primary SC and MSC-1 cells to identify factors or immune-related pathways potentially important for SC immune privilege. Primary SC or MSC-1 cells were transplanted as allografts to the renal subcapsular area of naïve BALB/c mice and cell survival was analyzed by immunohistochemistry. Additionally, transcriptome differences were investigated by microarray and pathway analyses. While primary SC were detected within the grafts with 100% graft survival throughout the 20-day study, MSC-1 cells w  ere rejected between 11 and 14 days with 0% graft survival at 20 days post-transplantation. Microarray analysis identified 3198 genes that were differentially expressed with a ± 4-fold or higher level in primary SC. Cluster and pathway analyses indicate that the mechanism of SC immune privilege is likely complex with multiple immune modulators being involved such as immunosuppressive cytokines and complement inhibitors, lipid mediators for controlling inflammation, and junctional molecules that control leukocyte movement in and out of the immune privileged space. Further study of these immune modulators will increase our understanding of SC immune privilege and in the long-term lead to improvements in transplantation success.

overall_design:
We conducted microarray and pathway analyses to identify genes and immune-related pathways differentially regulated by aggregated primary Sertoli cells and MSC-1 cell line.
Aggregated 19 to 20-day mice primary Sertoli cells and MSC-1 cell line were used to determine the global transcriptome differences important for the survival and protection of transplanted cells.

first: Gurvinder

last: Kaur

first: Saroja

last: Putrevo

first: Emily

last: Dyson

first: Mathey

first: William

middle: T

last: McCunniff

first: Kwan

last: Kim

first: Jannette

last: Dufuour


title: Gene expression comparison among spleen dendritic cells, brain microglia, brain dendritic cells and bone marrow monocytes

status: Public on Jun 22 2011

first: Kang

last: Liu

department: Microbiology

summary: To understand the functional relationship between brain dendritic cells (brain DCs) and other myeloid cells, we compared the gene expression profile of m/chDCs to that of bone marrow monocytes, brain microglia and classical spleen CD8+ and CD8- DCs.  In order to obtain enough brain DCs for mRNA extraction, we expanded brain DCs with in vivo Flt3L treatment before purification.

overall_design: This study includes data from FACs Aria-purified brain DCs, bone marrow monocytes, brain microglia and classical spleen CD8+ and CD8- DCs. The genearray was performed to compare expression of cell surface endocytic receptor, cytokine receptors, TLRs, transcription factors, molecules for antigen processing and presentation. Each Series consists of 3 individuall samples

first: Matthew

last: Meridith


title: Gene expression analysis of mantle cell lymphoma (MCL) combined with laser microdissection

status: Public on Jun 25 2011

city: Kurume

first: Yoshizo

last: Kimura

institute: Kurume university

summary: Wnt3 signaling pathway plays a central role in lymphomagenesis, and that specific mitotic regulators facilitate transformation into more aggressive forms.

overall_design: For initiation, we compared the tumor cells of MCL in situ (n=4) with normal mantle zone B-lymphocytes (n=4), which were selected by laser microdissection.For transformation, we selected the overlapping genes differentially expressed between both cMCL (n=4) vs aMCL (n=5) and classical vs aggressive areas in iMCL (n=2).

first: Fumiko

last: Arakawa


title: Regulatory mechanisms of TSG-6 (TNF-alfa-induced protein-6: Tnfip6)-deficient and wild-type synovial fibroblasts

first: Tibor

last: Glant

address: 1735 West Harrison

department: Orthopedic Surgery

institute: Rush University Medical Center

summary:
BALB/c mice are susceptible to proteoglycan (PG) aggrecan-induced arthritis (PGIA), and the absence of TSG-6 further increases susceptibility and local inflammatory reactions, including neutrophil invasion into the joints. To gain insight into the mechanisms of TSG-6 action, synovial fibroblasts were isolated from wild-type and TSG-6-KO mice, cultured and exposed to various agents affecting either the TSG-6 expression and/or modify the intracellular function of TSG-6.
In the present microarray studies, we have identified differences in gene expression by fibroblasts isolated from wild-type or TSG-6-KO mice

Keywords: Genetic modification

overall_design: In this study we compared the gene expression profile of 42 fibroblast cultures from mouse synovial samples. Fifteen samples were wild-type and 27 samples were TSG-6 knockout. In these two genotype groups fibroblasts were treated with TNFa, LPS, TSG-6, HA, or HA+TSG-6, and were compared to untreated samples in the same genotype group. We also compared the same treatments between KO and WT.

first: Katalin

last: Mikecz

first: Anna

last: Laszlo


title: Exon array analysis in primary human fibroblasts

status: Public on Jun 17 2011

city: College Park

first: Kan

last: Cao

address: 2219 Bioscience Research building

department: CBMG

institute: University of Maryland

summary: Exon usage analysis in in vitro cultured fibroblast cells. To assay the genome-wide splicing changes during cellular senescence, we performed splicing analysis on young and old normal fibroblasts, and in fibroblasts +/- tert (telomerase protein subunit Tert immortalized).

overall_design: We analyzed primary fibroblasts from 5 healthy subjects at various passages and from 2 Hutchinson-Gilford Progeria Syndrome (HGPS) patients using the Affymetrix Human Exon 1.0 ST platform. Two or three technical replicates were performed.

first: Cao

last: Kan

first: Francis

last: Collins


title: Expression data from newborn mouse brain expressing a constitutively active PDGFRb

status: Public on Jun 15 2011

city: Oklahoma City

first: Lorin

last: Olson

state: Oklahoma

address: 825 NE 13th St

institute: Oklahoma Medical Research Foundation

summary:
To identify targets of PDGFRb signaling and potentially new markers for pericyte activation, we used microarray analysis to compare gene expression in control and mutant pericytes expressing a constitutively active PDGFRb.
We chose 1 day after birth as a time point for analysis because the number of pericytes and morphology of the vasculature is similar between mutants and controls at this time.

overall_design: We dissociated P1 mouse brains and isolated microvessel fragments with their associated pericytes by affinity to anti-PECAM-coated magnetic beads. RNA was then isolated from four control (wild type) and four mutant (PDGFRb D849V knockin) brains, and then used to prepare labeled samples for array hybridization.

middle: E

first: Philippe

last: Soriano


title: Comparison of polysomal profiles of murine adult normal, tumor, and recruited olig2 cells

first: Elena

last: Fomchenko

department: Cancer Biology and Genetics

institute: Memorial Sloan Kettering Cancer Center

summary:
Comparison of polysomal profiles of murine adult olig2 cortical progenitors, murine tumor olig2 cells derived from hPDGF-B-driven glioblastomas, and murine olig2 proliferative recruited glioma cells contributing to the tumor mass but not derived from the cell of origin

An unbiased way to define a cell population lies in identification of its gene expression signature and subsequent comparison to gene expression signatures of known normal or cancer cells to define its position on the axis of tumorigenesis. To quantify similarities and differences in the expression profiles of recruited cells and tumor cells using microarray analysis, we used the bacTRAP technology that allows immunoprecipitation of polysomes from specific cell types in vivo (Heiman et al 2008, Doyle et al 2008). We compared polysomal expression profiles of hPDGFb-driven Ntv-a Ink4a/Arf+/- olig2 mouse glioma cells representing a histologically defined glioma population, recruited olig2 cells derived from Ink4a/Arf+/- olig2 RP-eGFP mice transplanted with non-fluorescent glioma cells, and normal adult cortical olig2 mouse progenitors, using Affymetrix 430 mouse 2.0 chips and Genespring GX10 software (Doyle et al 2008, Heiman et al 2008). Translational profiles of recruited olig2 cells and glioma olig2 cells were similar to each other and clearly distinct from the normal olig2 progenitors, majority of the differences accounted for by the “statistically significantly changed” set of mRNAs (ANOVA, p<0.05), and sample clustering reduced upon removal of the ANOVA-tested mRNA set. Unsupervised hierarchical mRNA clustering likewise indicated that recruited olig2 cells clustered more closely to glioma olig2 cells. The caveat is that olig2 expression in the adult normal brain of bacTRAP olig2 RP-eGFP mice labels both progenitors and mature oligodendrocytes, while recruited and tumor olig2 cells are almost entirely progenitors; therefore, some of the differences seen in the comparative analysis of normal, tumor and recruited olig2 cells may in part result from the shift in relative abundance of different progenitor and mature olig2 cell populations.

Normal olig2 progenitors were collected from three replicates of pooled cortices of three olig2 RP-eGFP bacTRAP reporter mice. Mouse gliomas induced by injection of a non-fluorescent RCAS-hPDGFb (Shih et al 2004) or by transplantation of muring glioma cells derived from Ntv-a gliomas induced by the non-fluorescent RCAS-hPDGFb were collected from Ntv-a olig2 RP-eGFP bacTRAP reporter mice and immunoprecipitated; each tumor was processed as a separate sample. Briefly, mouse tissues were collected into ice-cold cyclohexamide-containing buffer, homogenized, cells were lysed in NP-40 and DHPC-containing buffer, centrifuged at 20,000g for 15 min, supernatant incubated with anti-eGFP-conjugated protein G beads 30 min at 4C, washed and RNA collected using Trizol reagent as per manufacturer’s instructions (Doyle et al., 2008; Heiman et al., 2008). RNA was purified, concentrated using Qiagen RNeasy kit, its quality confirmed by Agilent Bioanalyzer, 15ng per sample amplified using Affymetrix Two-Cycle Amplification kit and hybridized to Affymetrix 430 mouse 2.0 chips as described in Doyle et al., 2008; Heiman et al., 2008. Data was analyzed using Genespring GX10 software, as described in the text and in Doyle et al., 2008; Heiman et al., 2008. Briefly, samples were normalized using GCRMA, filtered to remove probe sets with low intensity, and analyzed using ANOVA (p<0.05) with SNK post-hoc and Benjamini and Hochberg FDR multiple testing correction. Probe quality, Pearson’s correlation, hierarchical clustering, heatmaps, gene profile plots were generated using Genespring GX10 software. Pathway analysis was performed using Ingenuity as per manufacturer’s instructions.

overall_design: Gliomas are thought to form by clonal expansion from a single cell-of-origin, and progression-associated mutations to occur in its progeny cells. Glioma progression is associated with elevated growth factor signaling and loss of function of tumor suppressors Ink4a, Arf and Pten. Yet, gliomas are cellularly heterogeneous; they recruit and trap normal cells during infiltration. We performed lineage tracing in a retrovirally mediated, molecularly and histologically accurate mouse model of hPDGFb-driven gliomagenesis. We were able to distinguish cells in the tumor that were derived from the cell-of-origin from those that were not. Phenotypic, tumorogenic and expression analyses were performed on both populations of these cells. Here we show that during progression of hPDGFb-induced murine gliomas, tumor suppressor loss can expand the recruited cell population not derived from the cell-of-origin within glioma microenvironment to dominate regions of the tumor, with essentially no contribution from the progeny of glioma cell-of-origin. Moreover, the recruited cells can give rise to gliomas upon transplantation and passaging, acquire polysomal expression profiles and genetic aberrations typically present in glioma cells rather than normal progenitors, aid progeny cells in glioma initiation upon transplantation, and become independent of PDGFR signaling. These results indicate that non-cell-of-origin derived cells within glioma environment in the mouse can be corrupted to become bona fide tumor, and deviate from the generally established view of gliomagenesis.

first: Ana

last: Milosevic

first: Daviana

last: Martinez

first: Victoria

last: Isakova

first: Karim

last: Helmy

first: Amanda

last: Katz


title: Effect of fasting on human skeletal muscle mRNA levels

status: Public on Jun 08 2011

city: Iowa City

first: Christopher

last: Adams

state: IA

address: 540G EMRB, 200 Hawkins Drive

institute: University of Iowa

summary: The goal of these studies was to determine the effects of fasting on skeletal muscle mRNA levels in healthy human subjects.

overall_design: Seven healthy adult human subjects fasted for 40 hours and then a muscle biopsy (fasting sample) was obtained from the vastus lateralis muscle.  Immediately after the first muscle biospy, subjects then ate a mixed meal.  Six hours after the first muscle biopsy, a second muscle biopsy (fed sample) was obtained from the contralateral vastus lateralis muscle.  In each subject, mRNA levels under fasting conditions were normalized to mRNA levels under fed conditions, which were set at 1.


title: Role of NFBD1 in global gene expression

status: Public on Jun 16 2011

city: New Haven

first: Vince

last: Schulz

state: CT

address: 333 Cedar St. LMP 4085

department: Department of Pediatrics

institute: Yale University

summary: NFBD1 (nuclear factor with BRCT domains 1), also known as MDC1 (mediator of DNA damage signaling 1), is a protein involved in the ATM signaling pathway in response to DNA damage.  In addition to a role in signaling, NFBD1 possesses transactivation activity, suggesting that it may influence transcription. Furthermore, NFBD1 affects p53-mediated transcription in the presence of the DNA damaging agent adriamycin.  Our goal was to determine if NFBD1 affects global gene expression with or without ionizing radiation-induced DNA damage.  Moreover, we sought to separate p53-dependent from p53-independent events.  Illumina microarray analysis was carried out on RNA extracted from cells treated with and without NFBD1 shRNA and/or p53 shRNA in the presence and absence of DNA damage.  Surprisingly, we found that the expression of NFBD1-regulated genes was changed in both the presence and absence of DNA damage.  Furthermore, most NFBD1-regulated genes were regulated independently of p53.  The identification of NFBD1-regulated genes was confirmed with a second NFBD1-directed shRNA sequence.

overall_design:
The role of NFBD1 in global gene expression both in the presence and absence of ionizing radiation was determined. p53-dependent and p53-dependent events regulated by NFBD1 depletion were studied.

U2OS cells were treated with control, NFBD1 shRNA, and/or p53 shRNA-expressing retrovirus. Cells were then treated with ionizing radiation and total RNA was isolated for Illumina microarray analysis.

first: Kathleen

last: Wilson

first: Vincent

first: David

last: Tuck

middle: F

last: Stern


title: Expression profiling of Irgm1-/- (Lrg-47) HSCs

city: Houston

first: Megan

last: Baldridge

state: TX

address: One Baylor Plaza

department: Molecular and Human Genetics

institute: Baylor College of Medicine

summary:
To assess gene expression changes in Irgm1 (Lrg-47) deficient HSCs

Keywords: genetic modification, knockout

overall_design: A total of 6 samples were analyzed: 3 experimental replicates of Irgm1 HSCs were compared with 3 control replicates of WT HSCs

last: Weksberg

first: Katherine

last: King

first: Stuart

last: Chambers

first: Nathan

last: Boles

first: Margaret

last: Goodell


title: Tet2 loss leads to increased hematopoietic stem cell self-renewal and myeloid transformation

city: LYON

first: Jiri

last: ZAVADIL

state: Other

address: 150 COURS ALBERT THOMAS

institute: IARC WHO

summary:
Recurrent somatic mutations in TET2 and in other genes that regulate the epigenetic state have been identified in patients with myeloid malignancies and in other cancers.  However, the in vivo effects of Tet2 loss have not been delineated.   We report here that Tet2 loss leads to increased stem-cell self-renewal and to progressive stem cell expansion. Consistent with human mutational data, Tet2 loss leads to myeloproliferation in vivo, notable for splenomegaly and monocytic proliferation. In addition, haploinsufficiency for Tet2 confers increased self-renewal and myeloproliferation, suggesting that the monoallelic TET2 mutations found in most TET2-mutant leukemia patients contribute to myeloid transformation.  This work demonstrates that absent or reduced Tet2 function leads to enhanced stem cell function in vivo and to myeloid transformation.
These studies show that a ubiquitin ligase-substrate pair can orchestrate the molecular program of HSC differentitiation

overall_design: Gene expression profiles from WT and Tet2-/- sorted LSK and myeloid progenitors (CMP and GMP) were compared using genome wide mRNA expression profiling by Affymetrix genechip arrays (Mouse 430 2.0) and key targets were validated by chromatin immunoprecipitation experiments.

first: Kelly

last: Moran-Crusio

first: Linsey

last: Reavie

first: Alan

last: Shih

first: Omar

last: Abdel-Wahab

first: Dephine

last: Ndiaye-Lobry

first: Camille

last: Lobry

first: Maria

last: Figueroa

first: Aparna

last: Vasanthakumar

first: Jay

last: Patel

first: Xinyang

last: Zhao

first: Fabiana

last: Perna

first: Suveg

last: Pandey

first: Jozef

last: Madzo

first: Chunxiao

last: Song

first: Qing

last: Dai

first: Chuan

last: He

first: Sherif

last: Ibrahim

first: Miloslav

last: Beran

last: Zavadil

first: Stephen

last: Nimer

first: Ari

last: Melnick

first: Lucy

last: Godley

first: Iannis

last: Aifantis

first: Ross

middle: L

last: Levine


title: A latent pro-survival function for the mir-290-295 cluster in mouse embryonic stem cells.

status: Public on Jun 18 2011

first: Charles

middle: Arthur

last: Whittaker

institute: Koch Institute

summary: MicroRNAs (miRNAs) post-transcriptionally regulate the expression of thousands of distinct mRNAs. While some regulatory interactions help to maintain basal cellular functions, others are likely relevant in more specific settings, such as response to stress. Here we describe such a role for the mir-290-295 cluster, the dominant miRNA cluster in mouse embryonic stem cells (mESCs). Examination of a target list generated from bioinformatic prediction, as well as expression data following miRNA loss, revealed strong enrichment for apoptotic regulators, two of which we validated directly: Caspase 2, the most highly conserved mammalian caspase, and Ei24, a p53 transcriptional target. Consistent with these predictions, mESCs lacking miRNAs were more likely to initiate apoptosis following genotoxic exposure to gamma irradiation or doxorubicin. Knockdown of either candidate partially rescued this pro-apoptotic phenotype, as did transfection of members of the mir-290-295 cluster. These findings were recapitulated in a specific mir-290-295 deletion line, confirming that they reflect miRNA functions at physiological levels. In contrast to the basal regulatory roles previously identified, the pro-survival phenotype shown here may be most relevant to stressful gestations, where pro-oxidant metabolic states induce DNA damage. Similarly, this cluster may mediate chemotherapeutic resistance in a neoplastic context, making it a useful clinical target.

overall_design: Three replicates of mouse embryonic stem cells with Dicer (CTRL) compared to three replicates of mouse embryonic stem cells lacking Dicer (CRE)

first: Grace

middle: X

last: Zheng

first: Arvind

last: Ravi

first: J

last: Calabrese

first: Lea

last: Medeiros

first: Oktay

last: Kirak

first: Lucas

last: Dennis

first: Rudolf

last: Jaenisch

first: Christopher

last: Burge

first: Phillip

last: Sharp


title: Global gene expression profiling of spontaneous hepatocellular carcinoma in B6C3F1 mice: Similarities in the molecular landscape to human liver cancer.

status: Public on Jun 07 2011

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

summary: Hepatocellular carcinoma (HCC) is an important cause of morbidity and mortality worldwide. Although the risk factors of human HCC are well known, the molecular characterization of this disease is complex, and treatment options in general remain poor. The use of rodent models to study human cancer has been extensively pursued both through genetically engineered rodents and rodent models used in carcinogenicity and toxicology studies. In particular, the B6C3F1 mouse used in the National Toxicology Program (NTP) 2-year bioassay has been used to evaluate the carcinogenic effects of environmental and occupational chemicals, and other compounds. The high incidence of spontaneous HCC in the B6C3F1 mouse has challenged its use as a model for chemically induced HCC in terms of relevance to the human disease. Using global gene expression profiling, we identify the dysregulation of several mediators similarly altered in human HCC, including re-expression of fetal oncogenes, upregulation of protooncogenes, downregulation of tumor suppressor genes, and abnormal expression of cell cycle mediators, growth factors, apoptosis regulators, and angiogenesis and extracellular matrix remodeling factors. Although important differences in etiology and pathogenesis remain between human and mouse HCC, there are important similarities in global gene expression and the types of signaling networks dysregulated in mouse and human HCC.  These data provide further relevance for the use of this model in hazard identification of compounds with potential human carcinogenicity risk, and may help in better understanding mechanisms of tumorigenesis due to chemical exposure in the NTP 2-year carcinogenicity bioassay.

overall_design: Six spontaneous hepatocellular carcinomas and six normal livers (as controls) from 2-year-old B6C3F1 mice.

first: Mark

last: Hoenerhoff

first: Arun

last: Pandiri

first: Stephanie

last: Lahousse

first: Hue-Hae

last: Hong

first: Tai-Vu

last: Ton

first: Tiwanda

last: Masinde

first: Scott

last: Auerbach

first: Kevin

last: Gerrish

first: Pierre

last: Bushel

first: Keith

last: Shockley

first: Robert

last: Sills


title: Mouse conjunctival forniceal gene expression during postnatal development and its regulation by Kruppel-like factor 4

city: Pittsburgh

first: Shivalingappa

middle: Kottur

last: Swamynathan

state: PA

address: 203 Lothrop Street Room 1025

department: Ophthalmology

institute: University of Pittsburgh

summary:
Purpose: To identify the changes in postnatal mouse conjunctival forniceal gene expression and their regulation by Klf4 around eye opening stage when the goblet cells first appear.
Methods: Laser-capture-microdissection was used to collect conjunctival forniceal epithelial cells from postnatal-day (PN) 9, PN14 and PN20 wild-type (WT), and PN14 Klf4-conditional null (Klf4CN) mice, where goblet cells are absent, developing, present, and missing, respectively. Microarrays were used to compare gene expression among these four groups. Expression of selected genes was validated by Q-RT-PCR, and spatiotemporal expression assessed by in situ hybridization.  Results: We identified 668, 251, 1160 and 139 genes that were upregulated and 492, 377, 1419 and 57 genes that were downregulated between PN9 and PN14, PN14 and PN20, PN9 and PN20, and PN14 WT and Klf4CN conjunctiva, respectively. Transcription factors Spdef, FoxA1 and FoxA3 that regulate goblet cell development in other mucosal epithelia, and epithelial specific Ets (ESE) transcription factor family members were upregulated during conjunctival development. Mesenchymal-epithelial transition (MET) was favored and diverse pathways related to glycoprotein biosynthesis, mucosal immunity, signaling, endocytic and neural regulation were affected during conjunctival development. Conjunctival Klf4-target genes differed significantly from the previously identified corneal Klf4-target genes, implying tissue-dependant regulatory targets for Klf4.
Conclusions: We have identified the changes in gene expression accompanying mouse conjunctival development and the role of Klf4 in this process. These studies provide new probes to study conjunctival epithelial development and function, and reveal that the gene regulatory network required for goblet cell development is conserved across different mucosal epithelia.

overall_design: Three independent samples in each of four developmental groups

first: Divya

last: Gupta

first: Stephen

last: Harvey

first: Naftali

last: Kaminski


title: Splitting Function enables Dual Feedback Regulation to Control JAK2/STAT5 Signaling for a Wide Ligand Range

city: Lübeck

first: Hauke

last: Busch

state: Schleswig-Holstein

address: Ratzeburger Allee 160

department: Lübeck Institute of Experimental Dermatology

country: Germany

institute: University of Lübeck

summary:
Cellular signal transduction is governed by multiple feedback mechanisms to elicit robust cellular decisions.  We combined mathematical modeling and extensive time-resolved data sets in primary erythroid progenitor cells and dissected the roles of the two transcriptional feedback regulators of the SOCS family, CIS and SOCS3 in JAK2/STAT5 signaling. Our model revealed that both feedbacks are most effective at different ligand concentration ranges.
To identify the relevant transcriptional feedback regulators that are involved in attenuation of Epo-induced JAK2-STAT5 signaling in addition to CIS, we performed a time-resolved genome-wide expression profiling of murine erythroid progenitor cells at the colony forming unit erythroid (CFU-E) stage up to 24 and 7 hours after EPO stimulation and in control, repectively. The analysis   identified SOCS3 as the only further de novo regulated gene upon Epo-induced JAK2-STAT5 signaling. From subsequent mathematical modeling, we calculated the STAT5 response in previously unobserved Epo concentrations, which provided a quantitative link between cell survival and the integrated response of STAT5 in the nucleus. In conclusion, our combined modeling approach revealed novel insights into the orchestrated action of feedback control to regulate STAT5-mediated survival decisions over a broad range of ligand concentrations.

overall_design: Freshly sorted CFU-E cells were starved for 1 h in Panserin 401 supplemented with BSA and 50 µM β-Mercaptoethanol. Subsequently, cells were stimulated with 0.5 U/ml Epo or left untreated and RNA was extracted at different time points (0,1,2,3,4,5,6,7,8,14,19,24 hrs after Epo stimulation and at 0,1,2,3,4,5,6,7 hrs without Epo treatment) using the RNeasy Mini Plus Kit (Qiagen, Hilden, Germany).

first: Julie

last: Bachmann

first: Norbert

last: Gretz

first: Ursula

last: Klingmüller


title: Variegated gene expression caused by cell-specific long-range DNA interactions

city: Utrecht

first: Elzo

last: de Wit

address: Uppsalalaan 8

institute: Hubrecht Institute

type:
Expression profiling by array
Other

summary: Mammalian genomes contain numerous DNA elements with potential transcription regulatory function but unknown target genes. We used transgenic, gain-of-function mice with an ectopic copy of the beta-globin locus control region (LCR) to better understand how regulatory elements dynamically search the genome for target genes. We find that the LCR samples a restricted nuclear sub-volume in which it forms preferential contacts with genes controlled by shared transcription factors. One contacted gene, betah1, located on another chromosome, is upregulated, providing genetic demonstration that mammalian enhancers can function between chromosomes. Upregulation is not pan-cellular but confined to selected ‘jackpot’ cells significantly enriched for inter-chromosomal LCR-betah1 interactions. This implies that long-range DNA contacts are relatively stable and cell-specific and, when functional, cause variegated expression. We refer to this as spatial effect variegation (SEV). The data provide a dynamic and mechanistic framework for enhancer action, important for assigning function to the one- and three-dimensional structure of DNA.

overall_design:
A knock-in mouse strain was compared to a wild-type FVB strain. The knock-in mouse strain carries a human beta-globin LCR in the Rad23a locus. We performed 4C for the Rad23a locus in the knock-in and the wild-type strain. Biological replicates were analyzed in a reversed dye orientation.
At the RNA level these mice were characterized with Affymetrix expression arrays. We analyzed three biological replicates for the WT and the knock-in.

first: Daan

last: Noordermeer

first: Petra

last: Klous

first: Wouter

last: de Laat


title: Beta cell overexpression of HSD11B1 in high fat fed mice

city: Edinburgh

first: Donald

last: Dunbar

address: 47 Little France Crescent

department: Centre for Cardiovascular Science

country: United Kingdom

institute: University of Edinburgh

summary: To model the potential diabetogenic effects of higher level of HSD11B1 in b-cells of the pancreas in vivo, we created a transgenic model overexpressing HSD11B1 under the mouse insulin I promoter (MIP-HSD1) in diabetes-prone C57Bl/KsJ mice. KsJ wild type and MIP-HSD1 heterozygous mice have been high fat fed for 12 weeks. Pancreata have been perfused with collagenase and islets isolated by hand picking. Isolated islets (around 500) coming from at least 3 mice (around 200/mice) have been directly lysed in Trizol. Total RNA have been extracted by Trizol plus RNA Purification Kit (invitrogen).

overall_design: Four biological replicates per group: Wild type KsJ mice on High Fat diet (KsJ1, KsJ2, KsJ3, KsJ4) and MIP-HSD1 transgenic mice on High Fat diet (MIP1, MIP2, MIP3, MIP4) were used to prepare RNA for microarray analysis.


title: Comparative analysis of genomic features of human HIV-1 infection and primate models of SIV infection

status: Public on Jun 03 2011

city: Charlestown

first: Matthew

last: Woods

address: 149 13th Street

department: Computational Biology Core

institute: The Ragon Institute of MGH, MIT, and Harvard

summary:
High levels of HIV-1 replication during the chronic phase of infection are usually associated with rapid disease progression (RP). However, a minority of HIV-infected individuals remain asymptomatic and show persistently high CD4+ T cell counts despite high viremia for many years (viremic non progressors, VNP). The latter profile is reminiscent of the non-pathogenic model of SIV infection in natural hosts such as the sooty mangabey. We used various genomic approaches to examine 66 RP and 6 VNP defined according to strict criteria. RP were characterized by depletion of protective HLA alleles, enrichment of HLA alleles associated with disease progression, and a characteristic transcriptome profile of CD4+ and CD8+ T cells similar to that observed in pathogenic SIV infection of rhesus macaque. In contrast, VNPs presented lower expression of interferon stimulated genes than RP, and shared with SIV-infected sooty mangabeys a common profile of regulation of a set of genes that includes CASP1, CD38, LAG3, TNFSF13B, SOCS1 and EEF1D. The estimated 8% of RP and 0.1% of VNP in human cohorts represent two subsets of HIV-infected individuals whose analysis may inform our understanding of HIV pathogenesis.
Selection criteria rapid progressors (RP): HIV seroconversion window <1 year WITH documented negative and positive serology or biological proof of primary infection. AND One of A) or B)   A) >2 CD4+ T cell counts below 350 cells/µl within 3 years of seroconversion AND no subsequent rise of CD4+ T cells above 350 cells/µl in the absence of ART.   B) ART initiated within 3 years of seroconversion AND CD4+ T cell count within 1 month of ART-start <350 cells/µl.  Selection criteria viremic non progressors (VNP): > 3 years of follow-up AND median HIV viremia from >3 measurements >100'000 viral RNA copies/ml AND HIV viremia consistently above 10’000 copies/ml AND CD4+ T cell count above 350 cells/µl AND no ART during follow-up.  Selection criteria elite/viremic controllers (EC): see Casado et al. 2010. Host and viral genetic correlates of clinical definitions of HIV-1 disease progression. PLoS ONE 5:e11079.

overall_design:
Total RNA from 41 samples obtained from CD4 T cells from HIV infected individuals to identify associations between gene expression and different distinct patterns of disease progression
Total RNA from 38 samples obtained from CD8 T cells from HIV infected individuals to identify associations between gene expression and different distinct

first: Margalida

last: Rotger

first: Judith

last: Dalmau

first: Andri

last: Rauch

first: Paul

last: McLaren

first: Steve

last: Bosinger

first: Raquel

last: Martinez

first: Netanya

middle: G

last: Sandler

first: Annelys

last: Roque

first: Julia

last: Liebner

first: Manuel

last: Battegay

first: Enos

last: Bernasconi

first: Patrick

last: Descombes

first: Itziar

last: Erkizia

first: Jacques

last: Fellay

first: Bernard

last: Hirschel

first: Jose

last: Miró

first: Eduard

last: Palou

first: Matthias

last: Hoffmann

first: Marta

last: Massanella

first: Julià

last: Blanco

first: Huldrych

last: Günthard

last: de Bakker

first: Daniel

last: Douek

first: Guido

last: Silvestri

first: Javier

last: Martinez-Picado

first: Amalio

last: Telenti


title: Gene expression profiling of uterine stromal cells isolated from Hand2 floxed and Hand2 ablated mice on day 4 of pregnancy

city: Urbana

first: Quanxi

last: Li

address: 2001 S lincoln Avenue

department: Comparative Bioscience

institute: Universit of Illinois at Urbana-Champaign

summary:
Our previous study revealed that the basic helix-loop-helix transcription factor Hand2 is a downstream target of progesterone signaling in mouse uterine stroma at the time of implantation. Further, conditional deletion of Hand2 in mouse uterus leads to implantation failure due to impaired uterine epithelial receptivity.
To identify the downstream targets of Hand2 in the uterus, we performed gene expression profling of uterine stromal cells isolated from Hand2-null mice and the corresponding controls on day4 of pregnancy (the time of implantation). The microarray results revealed elevated expression of mRNAs corresponding to several members of the fibroblast growth factor family in uterine stroma of Hand2-ablated mice. These factors act as paracrine mediators of mitogenic effects of estrogen on the epithleium. Thus, Hand2 is a critical regulator of the uteirne stromal-epithelial communication that directs proper steroid regulation conducive for establshment of pregnancy.

overall_design: We performed conditional ablation of Hand2 in the mouse uterus using the PRcre mouse model. As Hand2 expression is restricted to stromal comaprtment,  we isolated uterine stromal cells from day4 pregnant mice (n=5 for each genotype), purified total RNA from these cells, pooled these samples and then hybridized to high density affymetrix microarrays. Control vs. KO.

first: Indrani

middle: C

last: Bagchi

first: Milan

middle: K


title: Differential pancreatic islet global gene expression in young heterozygous Men1 mice and wildtype littermates

status: Public on Jun 02 2011

city: Uppsala

first: Margareta

last: Lejonklou

address: Entrance 70, UAS

department: Medical Sciences

country: Sweden

institute: Uppsala University Hospital

summary: Multiple Endocrine Neoplasia Tumor Syndrome type 1 (MEN 1) is an autosomal dominant tumor syndrome affecting individuals with a heterozygous germline mutaion of the MEN1 gene. MEN 1 carriers commonly develop parathyroid, anterior pituitary, duodenal and pancreatic endocrine tumors. The phenotype of existing mouse models for the MEN 1 syndrome, with a germline heterozygous (hz) Men1 gene inactivation, show close resemblance to the human MEN 1 syndrome. Menin, the protein encoded for by the MEN1/Men1 gene, lacks homology with known proteins, and evidence of its involvement in different cellular processes is steadily growing. Several interaction partners have been identified, involving different interaction sites on the menin protein. Accumulating evidence suggests a role for menin in transcriptional regulation, cell cycle control, apoptosis, chromatin modification and DNA damage response and repair. Loss of heterozygosity (LOH) of the MEN1 gene precedes tumor formation in the MEN 1 heterozygous pancreas. We set out to determine if there is a change in gene expression early on in the hz islet, as compared with islets in wildtype (wt) littermates, long before the LOH events occur. We performed a global mRNA expression microarray on islets from young, five-week-old, hz Men1 mice and their wt littermates, and we have subsequently corroborated a subset of the findings on the qPCR and protein level.

overall_design: Islets were isolated and RNA prepared from five five-week-old female mice heterozygous for the Men1 gene and five female wildtype littermates, and then a global gene expression microarray was performed.

first: Andreea

last: Barbu

first: Peter

last: Stålberg

first: Britt

last: Skogseid


title: Transcriptome transfer provides a model for understanding the phenotype of cardiomyocytes

city: Philadelphia

first: Tae

middle: Kyung

last: Kim

address: 3620 Hamilton Walk

department: Pharmacology

institute: University of Pennsylvania

summary: We show that the transfer of the adult ventricular myocyte (AVM) transcriptome into either a fibroblast or an astrocyte converts the host cell into a cardiomyocyte. Transcriptome-effected cardiomyocytes (tCardiomyocytes) display morphologies, immunocytochemical properties, and expression profiles of postnatal cardiomyocytes. Cell morphology analysis shows that tCardiomyoctes are elongated and have a similar length-to-width ratio as AVMs. These global phenotypic changes occur in a time-dependent manner and confer electroexcitability to the tCardiomyocytes. tCardiomyocyte generation does not require continuous overexpression of specific transcription factors; for example, the expression level of transcription factor Mef2c is higher in tCardiomyocytes than in fibroblasts, but similar in tCardiomyocytes and AVMs. These data highlight the dominant role of the gene expression profile in developing and maintaining cellular phenotype. The transcriptomeinduced phenotype remodeling–generated tCardiomyocyte has significant implications for understanding and modulating cardiac disease development.

overall_design: Transcriptome transfer can change one cell type to another cell type. We transfect cardiomyocyte transciptome into fibroblast and astrocyte. Transcriptomes from single cells are isolated and amplified and then hybridize on Affymetrix array.

first: James

last: Eberwine


title: The impact of a phytoestrogen-rich diet on cardiac gene expression in the context of HCM

city: Boulder

first: Leslie

last: Leinwand

state: CO

address: 3415 Colorado Ave

department: MCD Biology and BioFrontiers Institute

institute: University of Colorado at Boulder

summary:
A soy diet worsens the progression of an inherited form of hypertrophic cardiomyopathy (HCM) in male mice when compared to casein-fed mice. Females are largely resistant to this diet effect and better preserve cardiac function. We hypothesized that the abundant phytoestrogens found in soy are mainly responsible for this diet-dependent phenotype. Indeed, feeding male mice a phytoestrogen-supplemented casein-based diet can recapitulate the negative outcome seen when male mice are fed a standard soy-based diet.
To gain mechanistic insights into disease pathogenesis, we used Affymetrix microarrays to profile gene expression in left ventricular tissue from 2 month old HCM male and female mice as well as wild-type littermate controls. These mice were fed a phytoestrogen (genistein + daidzein)-supplemented casein-based diet. We identified a number of molecular pathways that could explain both the male and female phenotypes.

overall_design: Hearts from male and female wild-type or HCM C57BL/6 mice fed a phytoestrogen-supplemented (genistein and daidzein mix) casein-based diet were excised at 2 months of age. Total RNA was extracted from left ventricles. Biotin-labeled amplified RNA was hybridized to Affymetrix Mouse Genome 430 2.0 microarrays.

first: Elizabeth

middle: D

last: Luczak

first: Christopher

last: Haines

first: Pamela

last: Harvey

first: Kristen

last: Barthel

first: John

middle: P

last: Konhilas

last: Watson

first: Brian

last: Stauffer


title: Expression profile of OPC senescence

status: Public on Jun 01 2011

city: Sapporo

first: Toru

last: Kondo

address: Kita-15, Nishi-7, Kita-ku,

department: Institute for Genetic Medicine

institute: Hokkaido University

summary: To identify factors involved in OPC senescence, we compared gene expressions between OPC-CG4, OPC-FCS and OPC-Rev.

overall_design: We established OPC senescence model system, in which OPC become senescent in the presence of high concentration of FCS. This phenotypes were kept even when the medium was switched to their optimal serum-free medium.


title: Altered Gene Expression in Placentae from a Mouse Model of Diabetic Pregnancy

city: Baton Rouge

first: Claudia

last: Kappen

state: LA

address: 6400 Perkins Road

department: Developmental Biology

institute: Pennington Biomedical Research Center

summary:
AIMS/HYPOTHESIS: Pregnancies complicated by diabetes have a higher risk of adverse outcomes for mothers and children, including predisposition to disease later in life, such as metabolic syndrome and hypertension.  We hypothesized that adverse outcomes from diabetic pregnancies may be linked to compromised placental function.  Our goal in this study was to identify cellular and molecular abnormalities in diabetic placenta.

METHODS: Using a mouse model of diabetic pregnancy, placental gene expression was assayed at midgestation and cellular composition was analyzed at various stages. Genome-wide expression profiling was validated by quantitative PCR, and tissue localization studies were performed to identify cellular correlates of altered gene expression in diabetic placenta.

RESULTS: We detected significantly altered gene expression in diabetic placenta for genes expressed in the maternal as well as those in the embryonic compartments.  We also found altered cellular composition of the decidual compartment. Furthermore, the junctional and labyrinth layers were reduced in diabetic placenta, accompanied by aberrant differentiation of spongiotrophoblast cells.

CONCLUSIONS/INTERPRETATION: Diabetes during pregnancy alters transcriptional profiles in the murine placenta, affecting cells of both embryonic and maternal origin, and involving several genes not previously implicated in diabetic pregnancies.  The molecular changes and abnormal differentiation of multiple cell types precede impaired growth of junctional zone and labyrinth, and placenta overall.  Whether these changes represent direct responses to hyperglycaemia or physiological adaptations, they are likely to play a role in pregnancy complications and outcomes, and have implications for developmental origins of adult disease.

overall_design: The STZ diabetic mouse model was used to investigate gene expression changes in diabetic placentae at E10.5. Placentae were dissected from 5 different FVB dams at embryonic day 10.5 under diabetic conditions and from 5 control dams. Gene expression profiles from five individual placentae from independent pregnancies per group were compared.


title: Expression profiles of mouse glioma-initiating cells.

summary: To identify factors involved in glioma-initiating cells (GICs), we compared gene expressions between GIC-like cells and non-GICs.

overall_design: p53-deficient Neural stem cells (NSCs), oligodendrocyte precursor cells (OPCs), and astrocytes (ASTs) were transfected with pCMS-EGFP-HRasL61 and pBabe-neo by electroporation and cultured in 0.5 mg/ml neomycin. The GFP-positive stable NSCs (NSCL61s), OPCs (OPCL61s) and ASTs (ASTL61s) were purified by flow cytometry. Total RNA was prepared using a RNeasy Mini Kit (QIAGEN) and used for the expression analysis.


title: Expression profiles from mouse prostate progenitor/stem cells treated with ethanol or 100nM 1,25 dihydroxyvitamin D3

city: Winston-Salem

first: Scott

last: Cramer

address: Medical Center Blvd

department: Cancer Biology

institute: Wake Forest University School of Medicine

summary:
A major goal in prostate stem cell biology is to identify genes, pathways, or networks that control self-renewal and multilineage differentiation.  We hypothesize that 1,25 dihydroxyvitamin D3 can induce differentiation of prostatic progenitor/stem cells, thus serving as an in vitro model with which to study the molecular mechanisms of stem cell differentiation by 1,25 dihydroxyvitamin D3.  1,25 dihydroxyvitamin D3 elicits its effects primarily through transcriptional regulation of genes, so microarray studies were used to gain insight into the cellular response to 1,25 dihydroxyvitamin D3.
We used microarrays to detail the global gene expression changes that occur upon 1,25 dihydroxyvitamin D3 treatment of prostatic progenitor/stem cells.

overall_design: Adult mouse prostate progenitor/stem cells were plated at 1 x 10^5 cells per 10 cm culture dish and grown to 70% confluency before treatment with vehicle (0.1% ethanol) or 100 nM 1,25(OH)2D3 in cell culture media (n = 3 or 4).  Cells were treated with control or experimental media for 6 hrs or 48 hrs before RNA isolation.  The RNA from 6 hrs and 48 hrs was used to probe Affymetrix 430A oligonucleotide arrays (GPL339).

first: Sophia

last: Maund

first: Wendy

middle: W

last: Barclay

first: Jason

last: Hipp


title: Timecourse expression data from sciatic nerve distal stump of C57BL/6 and C57BL/6 OlaHsd-Wlds mice.

city: Quebec

first: Ezequiel

last: Calvo

state: Quebec

address: 2705 Boul. Laurier

department: Molecular Endocrinilogy

country: Canada

institute: CRCHUL

summary: Wallerian degeneration (WD) involves the fragmentation of axonal segments disconnected from their cell bodies, segmentation of the myelin sheath, and removal of debris by Schwann cells and immune cells. The removal and downregulation of myelin-associated inhibitors of axonal regeneration and synthesis of growth factors by these two cell types are critical responses to successful nerve repair. Here, we analyzed the transcriptome of the sciatic nerve of mice carrying the Wallerian degeneration slow (WldS) mutant gene, a gene that confers axonal protection in the distal stump after injury, therefore causing significant delays in WD, neuroinflammation, and axonal regeneration.

overall_design: 56 C57BL6 mice and 56 C57BL/6 OlaHsd-Wlds mice were anesthetized with isoflurane and underwent a microcrush lesion of their left sciatic nerve at the mid-thigh level (exept naive mice, t0). At 0, 3, 7 and 14 days post-injury, mice were anesthetized and killed by cervical dislocation.   Sciatic nerves were collected and conective tissue removed. A 4-mm long sciatic nerve segment was taken from the nerve distal stump, starting at 1 mm distal from the lesion up to 5 mm distal. Distal nerve stumps were pooled by group and RNA extracted. Samples were hybridized to GeneChip® Mouse Genome 430 2.0 Array (Affymetrix). Biological replicate was done.

first: Benoit

last: Barrette

first: Nicolas

last: Vallières

first: Steve

last: Lacroix


title: mRNA expression data from iPSCs, ntESCs and iPSC-nt-ESCs

status: Public on May 31 2011

city: Shanghai

first: Guohui

last: Ding

address: 320 Yueyang Road

institute: Shanghai Institutes for Biological Sciences

summary:
We generated three kinds of genetically identical mouse reprogrammed cells: induced pluripotent stem cells (iPSCs), nuclear transfer embryonic stem cells (ntESCs) and iPSC-nt-ESCs that are established after successively reprogramming of iPSCs by nuclear transfer (NT). NtESCs show better developmental potential than iPSCs, whereas iPSC-nt-ESCs display worse developmental potential than iPSCs.
We used microarrays to distinguish the gene expression differences among three pluriptoent stem cells and identified that imprinted genes had a similar expression pattern in iPSCs and iPSC-nt-ESCs.

overall_design: We sought to obtain genetic identical pluripotent stem cell lines in order to minimize genetic variations among different reprogrammed cells. To that end, we established a genetically homogenous secondary reprogramming system, in which mouse embryonic fibroblasts (MEFs) carrying doxycycline (dox)-inducible lentiviruses expressing Oct4, Sox2, Klf4 and c-Myc were isolated and used as donors for different reprogramming experiments. We generated iPSCs after plating MEFs in the presence of dox in ES culture conditions, and then derived ntESCs after transplantation of the nucleus from the same MEFs into enucleated oocyte. Furthermore, we successively reprogrammed iPSCs by means of NT and established a set of nt-iPSC lines.  Pluripotent stem cells generated from different reprogramming strategies were for RNA extraction and hybridization on Affymetrix microarrays.

first: Jiarui

last: Wu

first: Jinsong

last: Li


title: Expression data from BCL6-YFP-positive Tfh cells, BCL6-YFP-negative Tfh cells, non-Tfh cells, and naïve helper T cells.

city: Yokohama

first: Takaharu

last: Okada

state: Kanagawa

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

department: Research Center for Allergy and Immunology

institute: RIKEN

summary: We found that a number of Tfh cells downmodulated BCL6 protein after their development, and we sought to compare the gene expression between BCL6-hi Tfh cells and BCL6-low Tfh cells.

overall_design: CD4+ T cells were sorted from immunized and non-immunized mice for RNA extraction and hybridization on Affymetrix microarrays. Bcl6yfp/+ OT-II cells were transferred to congenic recipient mice, and immunized with NP-OVA in CFA subcutaneously. Seven or ten days after immunization, cells were collected from draining lymph nodes, and sorted on FACSAria by the expression of CXCR5, PD-1 and BCL6-YFP. Naive CD4+ T cells were CD4+ CD44lo CD62Lhi cells from unimmunized mice.

first: Saya

last: Moriyama

first: Masahiro

last: Kitano


title: Microarrays of macrophages infected with smooth or rough Brucella suis

status: Public on Jun 24 2011

city: Ann Arbor

first: Yongqun

last: He

state: MI

address: 018 ARF, 1150 W. Medical Center Dr.

institute: University of Michigan

summary: The macrophage-Brucella interaction is critical for the establishment of a chronic Brucella infection.  Smooth virulent B. suis strain 1330 (S1330) prevents macrophage cell death. However, rough attenuated B. suis strain VTRS1 induces strong macrophage cell death. To further investigate the mechanism of VTRS1-induced macrophage cell death, microarrays were used to analyze temporal transcriptional responses of murine macrophage-like J774. A1 cells infected with S1330 or VTRS1.

overall_design: Murine J774.A1 macrophages were plated in T75 at 8 x 10^6 cells per flask one day prior to infection, and then infected with B. suis S1330 or VTRS1 at a MOI of 200:1. Total RNAs were isolated by TRIzol and further purified using Qiagen RNeasy Mini Kit (Qiagen, Valencia, CA) at 0, 1, 2, 4, 8, 24, and 48 h post infection. The RNA samples were stored at -80 ºC until an Agilent 2100 BioAnalyzer (Agilent Technologies, Palo Alto, CA) was used to assess the concentrations and quality of RNA samples. Total RNA (20 µg) per sample was used for hybridization with Affymetrix mouse GeneChip 430 2.0 array. Preparation of cDNA, hybridization, quality controls and scanning of the GeneChip 430 2.0 arrays were performed according to the manufacturer's protocol (Affymetrix, Santa Clara, CA) .


title: Expression data from E10.5 mouse otocyst

status: Public on May 23 2011

city: Bunkyo-ku Tokyo

first: Chisato

last: Fujimoto

address: 7-3-1 Hongo

institute: The University of Tokyo

summary:
We established a novel EGFP reporter mouse line (named Tg(ETAR-EGFP)14Imeg), which enables the placode-derived inner ear sensory cell lineage to be visualized and monitored. At E10.5, EGFP expression was detected in the ventral and dorsomedial region of the otocyst.
Using this reporter line and FACS-array technology, we performed gene expression profiling focused on the regional specificity of the otocyst.

overall_design: We sorted E10.5 otocyst epithelial cells of heterozygous mice into EGFP-positive and EGFP-negative cells for RNA extraction and hybridization on Affymetrix microarrays. We profiled the expression of the genes in FACS-enriched cell population and conducted transcriptome analysis.

first: Hiroyuki

last: Aburatani


title: Expression Data from Toxoplasma gondii Infected Murine Macrophages and Dendritic Cells

status: Public on May 29 2011

city: Cambridge

first: Kenneth

last: Hu

state: MA

address: 31 Ames Street

department: Biology

institute: Massachusetts Institute of Technology

summary:
We wanted to determine how type II versus type III Toxoplasma infection affect host gene expression
We infected mouse macrophage (RAW264.7 and J774) and dendritic (DC2.4) cell lines with type II (Me49) and type III (CEP)

overall_design: cells were grown in T75 until 80% confluency, then infected with parasites for 18 hours at MOI of 7. Then the RNA was harvested from the cells by Trizol.

first: Kirk

last: Jensen

first: Jeroen

last: Saeij


title: Expression Data from Toxoplasma gondii Infected Murine Bone Marrow-Derived Macrophages

summary:
We wanted to determine how  type I ROP16 affect host gene expression
We infected BMDM's from BALB/c with type I (RH) and type I (RH) ΔROP16

overall_design: BMDM's were plated, then infected with parasites for 18 hours. Then the RNA was harvested from the cells by Trizol.


title: Effect of anti-miR-33 treatment on gene expression in mouse macrophages from atherosclerotic plaques.

status: Public on May 20 2011

city: San Diego

first: Christine

last: Esau

state: CA

address: 3545 John Hopkins Court

institute: Regulus Therapeutics

summary:
Inhibition of miR-33 results in increased cholesterol efflux and HDL-cholesterol levels in mice. In this study we examined the effect of miR-33 inhibition in a mouse model of atherosclerosis and observed significant reduction in atherosclerotic plaque size. At the end of the study, gene expression in macrophages from the atherosclerotic plaques was assessed.
The results demonstrated a reduction in inflammatory gene expression and increased levels of mRNAs containing miR-33 binding sites.

overall_design: LDLR-/- mice on a Western diet with established atherosclerosis were switched to normal chow and treated with anti-miR-33, control anti-miR, or saline (n=4/group) for 4 weeks. Gene expression profiling was performed on macrophages in aortic plaques isolated at the end of the treatment period by laser capture microdissection.

first: Aaron

last: Chang


title: Identification and functional analysis of epigenetically silenced microRNAs in colorectal cancer cells

city: Cleveland

first: Angela

last: Ting

state: Ohio

address: 9500 Euclid Ave/NE50

department: Genomic Medicine

institute: Cleveland Clinic

summary:
Abnormal miRNA expression has been linked to the development and progression of human cancers, and such dysregulation can result from aberrant DNA methylation.  We combined the analysis of miRNA expression data deposited with empirical DNA methylation data in HCT116 and DKO colon cancer cells (SRA accession# SRP001414) to identify novel DNA methylation regulated miRNAs.

ABSTRACT:
Abnormal microRNA (miRNA) expression has been linked to the development and progression of several human cancers, and such dysregulation can result from aberrant DNA methylation.  While a small number of miRNAs is known to be regulated by DNA methylation, we postulated that such epigenetic regulation is more prevalent.  By combining MBD-isolated Genome Sequencing (MiGS) to evaluate genome-wide DNA methylation patterns and microarray analysis to determine miRNA expression levels, we systematically searched for candidate miRNAs regulated by DNA methylation in colorectal cancer cell lines.  We found 64 miRNAs to be robustly methylated in HCT116 cells and/or DNMT-1 and 3B doubleknock cells (DKO); eighteen of them were located in imprinting regions or already reported to be regulated by DNA methylation.  In the remaining
46 miRNAs, expression levels of 18 were consistent with their DNA methylation status.  Finally, 10 miRNAs were up-regulated by 5-aza-2'-deoxycytidine treatment and identified to be novel miRNAs regulated by DNA methylation.  Moreover, we demonstrated the functional relevance of these epigenetically silenced miRNAs by ectopically expressing select candidates, which resulted in inhibition of growth and migration of cancer cells. Our study also provides a reliable strategy to identify DNA methylation-regulated miRNAs by combining DNA methylation profiles and expression data.

overall_design: [miRNA expression]: Total RNA was extracted from 3 biological replicate sets of HCT116 and DMNT-1 and 3B double knock out HCT116 (DKO) colorectal cancer cells.


title: Expression data from human embryonic stem cells (hESCs) and Activin-induced/derived cells

status: Public on May 21 2011

city: Stanford

first: Si Wan

last: Kim

address: 300 Pasteur Drive M313

department: Genetics

institute: Stanford University

summary:
Nodal/Activin signaling directs mesendoderm specification in early vertebrate embryogenesis. We have characterized transcriptional profiling of human embryonic stem cells and Activin-treated cells at different timepoints.
In this dataset, we include the timecourse gene expression data obtained from hESC differentiation post Activin treatment, examining at day 0, 1, 3 and 5.

overall_design: Four biological replicates were used for day 0, three for day 1, three for day 3, and four for day 5. Cells were harvested and used for total RNA preparation using Trizol (Invitrogen). Gene expression was analyzed using GeneChip Human Exon 1.0 ST Array (Affymetrix).

first: Si

first: Zhengqing

last: Ouyang

first: Wing

last: Wong

first: Julie

last: Baker


title: Expression data from Rad21 knock-down in ES cells

status: Public on May 19 2011

city: Dresden

first: Maciej

last: Paszkowski-Rogacz

address: Tatzberg 47/49

department: UCC / Medical Faculty and University Hospital Carl Gustav Carus

institute: Technische Universität Dresden

summary:
The Cohesin complex has recently been described to regulate gene expression. We wanted to determine the gene expression profile specific in mouse ES cells after depletion of the Cohesin subunit Rad21.
We used microarrays to detail the global programme of gene expression underlying depletion of Rad21 and identified distinct early development related genes up-regulated and many pluripotency related genes downregulated.

overall_design: Rad21 was depleted in R1/E ES cells for 48h using esiRNAs against Rad21. An esiRNA against non-targeting Luciferase was used as a negative control

first: Anja

last: Nitzsche


title: Cell of origin in AML: Susceptibility to MN1-induced transformation is regulated by the MEIS1/abdB-like HOX protein complex

city: Gothenburg

first: Lars

last: Palmqvist

address: Sahlgrenska University Hospital

department: Institute of Biomedicine

institute: University of Gothenburg

summary: The molecular mechanism defining susceptibility of normal cells to oncogenic transformation may be a valuable therapeutic target. We characterized the cell of origin and its critical pathways in MN1 leukemias. Common myeloid (CMP), but not granulocyte-macrophage progenitors (CMP) could be transformed by constitutively overexpressed MN1. Complementation studies of CMP-signature genes in GMPs demonstrated that leukemogenicity of MN1 required the MEIS1/abdB-like HOX protein complex. Colocalization studies by ChIP-seq identified common chromatin targets of MN1 and MEIS1 that were associated with open chromatin and transcriptional activation. Transcriptional repression of MEIS1 target sites in established MN1 leukemias had antileukemic activity. As MN1 relies on but can not activate expression of MEIS1/abdB-like HOX proteins, transcriptional activity of these genes determines which cell is the cell of origin in MN1 leukemia.

overall_design: We have showed at the single cell level that CMPs, but not GMPs, are susceptible to MN1-induced transformation. To identify transcriptional differences between CMPs and GMPs that may explain this difference in susceptibilities to MN1 transformation we produced gene expression profiles (two biological replicates in each experimental arm) of bone marrow cells from MN1 leukemic mice and mature myeloid bone marrow cells (Gr1+/CD11b+) from healthy mice and compared those to already published gene expression profiles of CMPs and GMPs (Krivtsov, A.V., et al. (2006). Transformation from committed progenitor to leukaemia stem cell initiated by MLL-AF9. Nature 442, 818-822).

first: Michael

last: Heuser

first: Haiyang

last: Yun

first: Bob

last: Argiropoulos

first: Eric

last: Yung

first: Florian

last: Kuchenbauer

first: Gyeongsin

last: Park

first: Iyas

last: Hamwi

first: Courteney

last: Lai

first: Malina

last: Leung

first: Grace

last: Lin

first: Masayuki

last: Iwasaki

first: Nina

last: Thiessen

first: Gordon

last: Robertson

first: Martin

last: Hirst

first: David

last: Kent

first: Connie

last: Eaves

last: Cleary

first: Marco

last: Marra

first: Arnold

last: Ganser

first: Keith

middle: R

last: Humphries


title: Expression data of small intestine crypts and villi from mice with nutritional and genetic risk factors for intestinal tumors

city: Bronx

first: DONGHAI

last: WANG

state: NY

institute: Montefiore Medical Center

summary: Nutritional and genetic risk factors for intestinal tumors are additive on mouse tumor phenotypes, demonstrating that diet and genetic factors impact risk by distinct combinatorial mechanisms. We analyzed expression profiles of small intestine crypts and villi from mice with nutritional and genetic risk factors. The results advanced our understanding of the mechanistic roles played by major risk factors in the pathogenesis of intestinal tumors.

overall_design: Small intestine crypts and villi from mice with nutritional (Ain76A, NWD1, and NWD2) and genetic risk factors (WT, Apc1638N/+ and p21-/-) were collected for RNA extraction and analysis using the Affymetrix 3' IVT expression microarray. Three or four replicates per tissue/risk factor.

first: Donghai

last: Wang

first: Karina

last: Peregrina

first: Elena

last: Dhima

first: Elaine

middle: Y

first: John

middle: M

last: Mariadason

first: Leonard

middle: H

last: Augenlicht


title: Gene expression profile of mouse hematopoietic cells

city: Tokyo

first: Hitoshi

last: Ichikawa

address: 5-1-1 Tsukiji, Chuo-ku

institute: National Cancer Center Research Institute

summary: Each fraction of mouse hematopoietic cells  was purified by cell sorting from bone marrow of 8-week-old C57BL/6 mice, and its gene expression was analyzed.

overall_design: Two biological replicates of each fraction were analyzed using a Mouse Genome 430 2.0 array (Affymetrix).

first: Hiroyuki

last: Miyoshi


title: Gene expression profile of mouse hematopoietic stem cells

summary: Mouse CD34(-)KSL hematopoietic stem cells and CD34(+)KSL multipotent progenitors were purified by cell sorting from bone marrow of 8-week-old C57BL/6 mice, and their gene expression was analyzed.

overall_design: Two biological replicates of CD34(-)KSL hematopoietic stem cells and CD34(+)KSL multipotent progenitors were analyzed using a Mouse Genome 430 2.0 array (Affymetrix).


title: Transcriptional profiling of ex vivo isolated inflammed mouse lymphatic endothelial cells

city: Zurich

first: benjamin

last: vigl

address: W.-Pauli-Str. 10, HCI, G490

department: Institute of Pharmaceutical Sciences

country: Switzerland

institute: ETH Zurich

summary: Chemokines and adhesion molecules upregulated in lymphatic endothelial cells (LECs) during tissue inflammation are believed to enhance dendritic cell (DC) migration to draining lymph nodes (dLNs), but the in vivo control of this process is not well understood. By performing transcriptional profiling of LECs isolated from murine skin, we found that inflammation induced by a contact hypersensitivity (CHS) response upregulated the adhesion molecules ICAM-1 and VCAM-1 and inflammatory chemokines in LECs. Furthermore, lymphatic lineage markers like Prox-1, VEGFR3 and LYVE-1 were significantly downregulated during CHS. By contrast, skin inflammation induced by Complete Freund’s adjuvant (CFA) induced a different pattern of chemokine and lymphatic marker gene expression and almost no ICAM-1 up-regulation in LECs. In FITC painting experiments, DC migration to dLNs was more strongly increased in CFA- as compared to CHS-induced inflammation. Interestingly, DC migration did not correlate with the induction of CCL21 and ICAM-1 in LECs. However, the requirement for CCR7 signaling became further pronounced during inflammation, whereas CCR7-independent signals only had a minor role in enhancing DC migration. Collectively, these findings indicate that inflammation-induced DC migration is stimulus-dependent and only moderately enhanced by LEC-induced genes other than CCL21.

overall_design: Mouse ear skin single-cell suspensions were prepared by a fast protocol that minimizes the RNA degradation. Fluorescence-activated cell sorting (FACS) was used to sort lymphatic endothelial cells (LEC) from CHS inflammed and control skin. 4 pairs (each with one control and one CHS inflammed sample, sorted and extracted on the same day) of LECs were chosen based on the quality of extracted and amplified material. This gave 8 samples to analyze (4 biological replicates in each condition). Each sample was sorted from 3 mice.

first: Benjamin

last: Vigl

first: Cornelia

last: Halin