title: Effects of environmental chemicals on development of neuronal cell lineages derived from mouse ES cells

status: Public on Oct 10 2009

city: tsukuba

first: Sone

last: Hideko

state: ibaraki

department: Center for Environmental Risk Research

institute: National Institute for Environmental Studies

summary: This study provides a comprehensive evaluation of changes in gene expression during treatment with environmental chemicals in embryonic bodies derived from mouse embryonic stem (ES) cells.  ES cells were maintained under the feeder cells in phenol red-free DMEM Medium (supplemented with 15% FBS, 100uM Non-essential amino acids (NEAA), 1000U/ml Leukemia inhibitory factor(LIF), 100uM 2-mercaptoethanol(2-ME), and 0.5% penicillin/streptomycin). Cells were gently washed in warm PBS and transferred to phenol red-free DMEM Medium (supplemented with 15% KnockOut Serum Replacement, 100uM NEAA, 100uM 2-ME, and 0.5% penicillin/streptomycin) in Microsphere array (MSA300F) and exposed with low and high levels of each chemical just after removing LIF from the culture media. Prior to collection, cells were washed in warm PBS, resuspended and briefly incubated in the QIAGEN RLT buffer, and finally collected in triplicate at 48 hours. Following RNA isolation, the best RNA yields for each replicate set was selected for target preparation and microarray processing.

overall_design: 25 total samples: 1 vehcle, 12 chemicals and two doses of each chemical [Vehicle Control (0.1% dimethyl sulfoxide), estradiol (1nM and 10nM), dehydrotestosterone (1nM and 10nM) bisphenol A (1pM and 100pM), triiodothyronine (1nM and 10nM), dexamethasone (1nM and 10nM), 2,3,7,8-tetrachlorodibenzo-p-dioxin (1nM and 10nM), 4(OH)-2’3,3’4’-5’-pentachlo biphenyls (1nM and 10nM), thalidomide (100nM and 0.01mM), bis(2-ethylhexyl)phthalate (0.001mM and 0.1mM), permethrin (100nM and 0.01mM), cyclopamine (100nM and 0.01mM), methoprene acid (0.001mM and 0.1mM)]; 1 Timepoint [48 hours].

first: Hideko

last: Sone

first: Seiichiro

last: Ohsako


title: FEAT overexpression in NIH3T3

status: Public on Oct 02 2009

city: Fukuoka

first: Atsushi

last: Takahashi

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

department: Medical Institute of Bioregulation

country: Japan

institute: Kyushu University

summary: To evaluate whether FEAT has cellular functions relevant in oncogenesis, FEAT was overexpressed in NIH3T3 cells, which only weakly express FEAT protein, and the alterations in genome-wide transcriptional profiles were analyzed by microarrays.

overall_design: The ORF of human FEAT cDNA was subcloned into the pENTR3C entry vector of the Gateway cloning system (Invitrogen).  LR recombination with the pEF-DEST51 vector (Invitrogen) yielded the pEF-DEST51-FEAT plasmid that encodes FEAT driven by the elongation factor 1alpha promoter.  NIH3T3 cells were transfected with pEF-DEST51-FEAT using HilyMax (Dojindo Laboratories).  After 7 days of selection with 10 µg/ml blasticidin S (Kaken Pharmaceutical), colonies were picked and screened for clones in which FEAT protein was overexpressed.  Three clones, FEAT-3, -15, and -20 were used in further studies.  The ccdB gene in the pEF-DEST51 vector was deleted to construct the pEF-DEST51-∆ccdB plasmid, which was stably transfected into NIH3T3 cells to obtain control cell lines, named ∆ccdB-1, -2, and -3.

first: Kosho

last: Murayama

first: Kenzaburo

last: Tani


title: plusGDNF and minusGDNF comparison using U74Av2 and 430A arrays

status: Public on Sep 29 2009

city: New YOrk

first: Benson

middle: Che-i

last: Lu

state: NY

department: Genetics and Development

country: USA

institute: Columbia University Medical Center

summary: Isolated mouse ureteric buds from E11.5 were grown in Matri-gel plus or minus GDNF.  Differential gene expression was analyzed between the "plus" and "minus" GDNF ureteric buds.

overall_design: 3 "plus GDNF" and 2 "minus GDNF" chips were analyzed with different pooled samples for each chip (U74Av2 and 430A). Sample comparisons and statistical analysis were performed using dChip 1.3, using the Comparison Analysis feature to identify genes differentially expressed between the two groups. The following filtering criteria were used: the “lower limit” for fold-change between the means of the +GDNF and -GDNF samples must exceed 1.2 with a 90% confidence limit, and the absolute difference between the two group means must exceed 100.

middle: C

first: Frank

middle: D

last: Costantini


title: Role of ICOS:ICOSL interaction in acute GVHD

status: Public on Sep 14 2009

city: Munich

first: Guenther

middle: HS

last: Richter

address: Parzivalstr. 16

department: Pediatrics & Children's Cancer Research Center

country: Germany

institute: Klinikum rechts der Isar, TU-Muenchen

summary: Inducible co-stimulator (ICOS) interaction with its ligand (ICOSL) is involved in several T cell effector functions. While blockade of ICOS:ICOSL interaction in chronic graft versus host disease (GVHD) seems benefi cial, results for acute GVHD remain controversial. To further elucidate its role in acute GVHD, C57BL / 6 mice were lethally irradiated and reconstituted with allogeneic spleen cells in the absence or presence of ICOSL-blocking mAb. Mice reconstituted with allogeneic spleen cells experienced severe GVHD and died untreated within 6 – 9 days after transplantation. Mice treated with an anti-ICOSL mAb starting from day 3 after transplantation gained weight again and survived for at least additional 12 days, although the treatment was already stopped at day 11 after transplantation. In contrast, the anti-ICOSL treatment starting from day 0 did not prevent GVHD. The diff erence between therapeutic (day 3) and prophylactic (day 0) anti-ICOSL treatment was independent of CD25 + CD4 + regulatory T cells since their depletion did not abrogate the therapeutic eff ect of ICOSL blockade. Microarray analysis revealed IFN- γ and chemokine up-regulation in spleen cells of prophylactically treated mice, emphasizing kinetic dependence of acute GVHD modulation via blockade of ICOS:ICOSL interaction.

overall_design: B6 recipients were irradiated with 10.0 Gray, administered from a 137 Cs source. Splenocytes from C3H mice were prepared as single cell suspensions in PBS, depleted of red blood cells and counted. 2 – 3 × 10^7 C3H splenocytes in a volume of 200 μl were transplanted into B6 recipients via tail vein injection (4 mice per group per experiment) 4 – 6 h after irradiation. Mice in the treatment group with anti-ICOSL mAb and their respective controls, received 500 μg mAb i. p starting at day 0 or day 3, followed by subsequent injections of 200 μg of mAb every other day. At day 4 after transplantation RNA of spleen cells was prepared and subjected to microarray analysis. Combined RNA from allogeneic transplanted mice was hybridized onto 2 independent arrays.

first: Andreas

last: Mollweide

first: Martin

last: Staege

first: Stefan

last: Burdach


title: Gene Expression Profiles of a Progression Model of Human Ovarian Cancer

status: Public on Sep 11 2009

city: Pune

first: Sharmila

last: Bapat

address: NCCS Complex, Ganeshkhind

country: India

institute: National Centre for Cell Science

summary: We have earlier reported the establishment of a comprehensive in vitro panel of 19 isogenic cell lines from a patient with Grade IV serous adenocarcinoma (Bapat et al. Cancer Research. 2005).  In this study, one of the cell lines termed as A4 at early passes (less than ~20) was assessed as being non-tumorigenic since it failed to exhibit anchorage independence growth in soft agar and form tumors in nude mice. After further culture (more than 20 passages in vitro), the cells expressed all features suggestive of transformation including capabilities of anchorage independence growth, clonogenecity and reproducibility of the human disease in mice models as assessed through tumor and ascites formation in nude mice, and serial transplantion of tumor-derived cells over 3-4 mouse generations. The tumors generated in nude mice were also identified to be histologically similar to the primary tumor of the patient.  A4 cells thus represent a single tumorigenic clone that underwent transformation in vitro, and hence may be considered to be an ovarian tumor progression model.

overall_design: Two-condition experiment,  Samples for hybridization included – (i) Non-tumorigenic A4 cells at passage 15 that were designated A4p15 – RNA labeled with Cy3; and (ii) Transformed A4 cells at passage 84 that were designated A4p84  – RNA labeled with Cy5.  Three samples of each were chosen for hybridization.

middle: A


title: Mouse alveolar rhabdomyosarcoma and wild-type skeletal muscle

status: Public on Aug 27 2009

city: San Antonio

first: Koichi

last: Nishijo

state: TX

address: 7703 Floyd Curl Dr.

department: Greehey Children's Cancer Research Institute I

institute: University of Texas Health Science Center at San Antonio

summary: The highly aggressive muscle cancer alveolar rhabdomyosarcoma (ARMS) is one of the most common soft tissue sarcoma of childhood, yet the outcome for unresectable and metastatic disease is dismal and unchanged for nearly 3 decades. To better understand the pathogenesis of this disease and to facilitate novel preclinical approaches, we previously developed a conditional mouse model of ARMS by faithfully recapitulating the genetic mutations observed in the human disease, i.e. activation of Pax3:Fkhr fusion gene with either p53 or Cdkn2a inactivation. In this report we show that this model recapitulates the immunohistochemical profile and the rapid progression of the human disease. We demonstrate that Pax3:Fkhr expression increases during late preneoplasia, but that tumor cells undergoing metastasis are under apparent selection for Pax3:Fkhr expression. At a whole genome level, a cross-species gene set enrichment analysis and metagene projection study showed that our mouse model is most similar to human ARMS when compared to other pediatric cancers. We have defined an expression profile conserved between mouse and human ARMS as well as a Pax3:Fkhr signature, including the target gene, SKP2. We further identified 7 “druggable” kinases over-expressed across species. The data affirms the accuracy of this genetically engineered mouse model.

overall_design: 6 mouse alveolar rhabdomyosarcoma tumors and 3 wild-type skeletal muscles were analyzed.

first: Charles

last: Keller


status: Public on Aug 15 2009

city: Philadelphia

first: Lewis

last: Chodosh

state: PA

address: 612 BRB II/III 421 Curie Blvd

institute: University of Pennsylvania

summary:
Analysis of Gene Expression in PTHrP-/- Mammary Buds Supports a Role for BMP Signaling and MMP2 in the Initiation of Ductal Morphogenesis.
Parathyroid hormone-related protein (PTHrP) acts on the mammary mesenchyme and is required for proper embryonic mammary development. In order to understand PTHrP’s effects on mesenchymal cells, we profiled gene expression in WT and PTHrP-/- mammary buds, and in WT and K14-PTHrP ventral skin, at E15.5. By cross-referencing the differences in gene expression between these groups, we identified 35 genes potentially regulated by PTHrP in the mammary mesenchyme, including 6 genes known to be involved in BMP signaling. One of these genes was MMP2. We demonstrated that PTHrP and BMP4 regulate MMP2 gene expression and MMP2 activity in mesenchymal cells. Using mammary bud cultures, we demonstrated that MMP2 acts downstream of PTHrP to stimulate ductal outgrowth. Future studies on the functional role of other genes on this list should expand our knowledge of how PTHrP signaling triggers the onset of ductal outgrowth from the embryonic mammary buds.

overall_design:
Five experimental groups (WT mammary buds, PTHrP-/- mammary buds, WT ventral skin, K14WT ventral skin, K14-PTHrP ventral skin). Three replicates in each group.

Differentially expressed genes are listed in the following supplementary files:
GSE17654_List1a-Higher_in_KO_Buds_than_WT_Buds.txt
GSE17654_List1b-Lower_in_KO_Buds_than_WT_Buds.txt
GSE17654_List2a-Higher_in_WT_Skin_than_WT_Buds.txt
GSE17654_List2b-Lower_in_WT_Skin_than_WT_Buds.txt

first: Julie

last: Hens

first: Pamela

last: Dann

first: Minoti

last: Hiremath

first: Tien-chi

last: Pan

first: John

last: Wysolmerski


title: GSK3 activates telomerase by regulating dynamic behaviour of multiple transcription factors converging on the hTERT gene

status: Public on Aug 03 2009

city: Glasgow

first: W.

middle: Nicol

last: Keith

state: Lanarkshire

address: Center for Oncology and Applied Pharmacology, University of Glasgow, CRUK Beatson Laboratories, Garscube Estate, Switchback Road

country: United Kingdom

institute: The University of Glasgow

summary: Telomerase controls cell immortality and is a promising cancer target. Understanding transcriptional regulation of the catalytic subunit hTERT is critical to realise effective telomerase therapeutics. GSK3 inhibition suppresses hTERT expression.

overall_design: A2780 ovarian adenocarcinoma cells were cultured continuously for 21 days in the presence of DMSO or 2.5mM GSK3 inhibitor 6-bromoindirubin-3’-oxime (BIO) with replenishment weekly on days 1 and 4. Cells were subcultured, counted, and RNA samples taken.

first: Alan

middle: E

last: Bilsland

first: Stacey

last: Hoare

first: Katrina

last: Stevenson

first: Jane

last: Plumb

first: Natividad

last: Gomez-Roman

first: Claire

last: Cairney

first: Sharon

last: Burns

first: Kyle

last: Lafferty-Whyte

first: Jon

last: Roffey

first: Tim

last: Hammonds

first: W

middle: N


title: Genetic loci that regulate healing and regeneration in LG/J and SM/J mice

status: Public on Jul 27 2009

first: Louise

last: Showe

address: 3601 Spruce St

institute: The Wistar Institute

summary: MRL mice display unusual healing properties. When MRL ear pinnae are hole punched, the holes close completely without scarring, with re-growth of cartilage, and reappearance of both hair follicles and sebaceous glands. Studies using (MRL/lpr x C57BL/6)F2 and backcross mice first showed that this phenomenon was genetically determined and that multiple loci contributed to this quantitative trait. The lpr mutation itself, however, was not one of them. In the present study, we examined the genetic basis of healing in the Large (LG/J) mouse strain, a parent of the MRL mouse and a strain that shows the same healing phenotype. LG/J mice were crossed with Small (SM/J) mice and the F2 population was scored for healing and their genotypes determined at >200 polymorphic markers. As we previously observed for MRL and (MRL x B6) F2 mice, the wound healing phenotype was sexually dimorphic with female mice healing more quickly and more completely than male mice. We found quantitative trait loci (QTL) on chromosomes (chr) 9, 10, 11, and 15. The heal QTL on chrs 11 and 15 were linked to differential healing primarily in male animals, whereas QTL on chrs 9 and 10 were not sexually dimorphic. A comparison of loci identified in previous crosses with those in the present report using LG/J x SM/J showed that loci on chrs 9, 11 and 15 co-localized with those seen in previous MRL crosses, whereas the locus on chr 10 was not seen before and was is contributed by SM/J.

overall_design: Illumina v6 arrays used for tissue from punched SM/J and LG/J ear holes. Triplicate samples were used for each strain and each timepoint.

first: Elizabeth

middle: P

last: Blankenhorn

first: Gregory

last: Bryan

first: Andrew

middle: V

last: Kossenkov

first: LiseDesquenne

last: Clark

first: Xiang-Ming

last: Zhang

first: Celia

last: Chang

first: Wenhwai

last: Horng

first: Susan

middle: L

last: Pletscher

first: James

middle: M

last: Cheverud

first: Ellen

last: Heber-Katz


title: Effects of FSH on testicular mRNA transcript levels in the hypogonadal mouse

status: Public on Aug 18 2009

city: Oxford

first: Dilair

last: Baban

address: Roosevelt Drive

department: Wellcome Trust Centre Human Genetics

institute: University of Oxford

summary:
In the normal mouse the pituitary gonadotrophins determine development, maturation and physiological regulation of the testis with follicle-stimulating  hormone (FSH) activating the Sertoli cell and luteinising hormone (LH) the Leydig cell. To look at the potential interaction of cell types within the testis following hormone stimulation we have investigated the effect of rFSH on testicular gene expression in the hypogonadal (hpg) male mouse. Due to a deletion in the gene encoding gonadotrophin-releasing hormone (GnRH), FSH and LH levels are at the lower limit of detection in the circulation and mice remain in a pre-pubertal state throughout life unless given exogenous hormone.
Here we have addressed important question of changes in the global gene expression profile of testicular tissue following hormone stimulation (rFSH) for 12, 24 and 72h following injections compared to control untreated hpg males of the same age.
Keywords: Hormone Response, Testicular gene expression Profile

overall_design: Adult 10 week old hpg males were injected sc with 8 I.U. of rFSH (Gonal F, Serono Pharmaceuticals) in 0.2ml of PBS (Sigma,UK) every 12 h for 12, 24 and 72 h. Mice were killed one hour after the last injection by cervical dislocation, testes dissected out, weighed and snap frozen in liquid nitrogen. Tissue was stored at -70oC until use. RNA was extracted using Qiagen RNeasy Lipid Tissue Mini kit (Qiagen, Valencia, CA) according to the manufacturer’s instructions and quantified on a NanoDrop ND-1000 (NanoDrop Wilmington, DE). RNA quality was checked using the Agilent bioanalyzer 2100 (Agilent, Santa Clara, CA). Testicular gene expression was examined in four individual mice at 12 and 72 h and 3 mice at 24h using high-density oligonucleotide mouse MOE430A arrays (Affymetrix, Santa Clara, CA), comparison was made with a group of 7 untreated hpg males of the same age.

first: Margaret

middle: H

last: Abel

first: Peter

last: O’Shaughnessy

first: Harry

last: Charlton


title: Transcriptome profiling reveals novel Disabled-2-associated downstream effectors in mouse embryonic stem cells (ESC)

status: Public on Aug 12 2009

city: Taoyuan

first: Chien-Ling

last: Huang

address: 259 Wen-Hwa 1st Road, Kwei-Shan

country: Taiwan

institute: Chang Gung University

summary:
Disabled-2 (DAB2) is up-regulated when ESC were cocultured with OP9 stromal cells for mesodermal colony formation. Expression of DAB2 short hairpin small interfering RNA (shDAB2) altered ESC cell-cell adhesion that subsequently affected colony formation and mesoderm differentiation competence.
To further unveil the molecular mechanisms associated with the phenotypic change of shDAB2-expressing ES cells, comprehensive profiling of DAB2-regulated molecules in shDAB2-ES cells (ES-V9 and 285-4) were performed by Affimatrix microarray.

overall_design: Total RNAs from vector control (ES-V9) and shDAB2-expressing (285-4) ESC were isolated by Trizol (Invitrogen) and were further purified using the RNeasy mini kit (Qiagen). For profiling of mRNA expression, the purified total RNAs were then subjected to microarray analysis (Affymetrix gene chip mouse 430A).

first: Ching-Ping

last: Tseng


title: HEK293 stably expressing Autoimmune regulator protein

city: Tartu

first: Tõnis

last: Org

address: Riia 23

department: Institute of Molecular and Cell Biology

country: Estonia

institute: University of Tartu

summary: Auto Immune REgulator (AIRE) protein expression in HEK293 cells

overall_design:
Three cell-lines where used in the study:

HEK293-NC; control cell-line expressing yellow fluorescent protein (YFP)

HEK-AIRE1, HEK-AIRE2; two different clone-derived Autoimmune regulator protein expressing cell-lines

HEK-AIRE-D312A; cell line expressing Autoimmune regulator protein with D312A mutation in the first PHD finger

With all cell-lines three independent experiments were performed.

first: Ana

last: Rebane

first: Kai

last: Kisand

first: Martti

last: Laan

first: Uku

last: Haljasorg

first: Reidar

last: Andreson

first: Pärt

last: Peterson


title: Gene expression programs of histologically distinct stages of prostate carcinogenesis in Nkx3.1; Pten mutant mice

status: Public on Nov 01 2009

city: Cincinnati

first: Bruce

middle: J

last: Aronow

state: OH

institute: Cincinnati Children's Hospital Medical Center

summary:
Key histological and growth progression characteristics of human prostate cancer are phenocopied in mouse models that have been subjected to androgen level depletion and engineered for hemizygosity of candidate prostate cancer tumor suppressor genes Nkx3.1 and Pten. To characterize their relative transcriptomes and identify a genomic basis for their relevance to human prostate cancers, we compared mouse prostate tumors expression profiles to those from a panel of human prostate cancer isolates and to normal and benign prostates. Human prostate cancers and mouse prostate tumor models both exhibit the activation of genes associated with growth, cell cycle control, and inhibition of differentiation (CDKN2A, CDKN2B, CDKN2C, CEBPB, CEBPG, CSF1, CTSS, DMBT1, EGFR, PLCG2, PXN, SPP1, TNFSF9), and conversely, diminished expression of genes associated with normal prostate differentiation and function. All tumors also exhibit dysregulated expression of genes associated with inflammation, the disruption of prostate-associated ER stress pathways, as well as with oxidative stress, energy metabolism, cell adhesion, and stress response. Immunoinflammatory and altered cell adhesion process-associated genes exhibited prominent expression in early stage tumors. In contrast, metastatic human prostate cancer samples eliminated the expression of most immunoinflammatory-associated transcripts. Cross-species comparisons of molecular programs that are shared or distinguishing of Nkx3.1; Pten mutant mouse models and human adenocarcinomas clearly delineate core tumorigenesis programs associated with cell cycle activation and loss of differentiation. Compared to locally spreading mouse and human tumors, metastatic prostate cancer exhibits greatly reduced expression of immunoinflammatory and adhesion genes, implying that immuno-inflammatory activation may enable first stages of tumorogenesis, but suppress metastasis. These results provide a novel framework to identify stage-specific biomarkers and candidate targets for combinatorial therapeutics. The complex role of inflammation suggests a need for additional caution in countering metastasis.

Keywords: tumor stage

overall_design: 26 Affymetrix MOE430A microarrays

first: Walter

last: Jessen

first: Cory

last: Abate-Shen


title: Gene expression profiles during osteoclastogenesis

status: Public on Aug 08 2009

city: Tokyo

first: Masamichi

last: Takami

address: 1-5-8, Hatanodai, Shinagawa

department: School of Dentistry

institute: Showa University

summary:
Expressions of mRNA in osteoclast precursors treated with RANKL and M-CSF for 0, 24, and 72 h.
We used DNA microarray to analyze the changes in mRNA expressions during osteoclastogegesis.

overall_design: Osteoclast precursors were induced from mouse bone marrow cells by M-CSF for 3 days and treated with RANKL. WE extracted total RNA and analyzed by DNA microarray.

first: Ayako

last: Mochizuki

first: Baohong

last: Zhao

first: Ryutaro

last: Kamijo


title: Gene expression profiling of mouse epidermal keratinocytes

status: Public on Aug 07 2009

city: Madrid

first: Ramon

last: Garcia-Escudero

state: Madrid

address: Avda Complutense 40, Ed 70A

department: Biomedical Innovation

country: Spain

institute: CIEMAT

summary:
DNA microarray technology is a powerfull tool for genome-wide gene expression analysis of biological samples.  Here we review the methodology for expression profiling analysis of skin tissue or purified keratinocytes from mice. We explained the methodology and protocols for RNA preservation and purification, RNA quality and integrity tests, and DNA microarray technology types that can be used. Furthermore, using a dataset of mice samples, we explained how to perform chip raw data preprocessing and normalization, differential expression analysis, as well as gene-clustering and funcional analysis of gene deregulation.
Keywords: comparison skin tissue versus primary keratinocytes

overall_design: We performed a comparison between tissue and cultured, extracting the genes and gene family functions that characterize the differences between both type of samples. Similarly, we compared gene expression patterns that distinguish samples from newborn mice relative to adult animals.

first: Jesus

last: Paramio


title: Gene expression changes by 2,4-dinitrochlorobenzene in human bulge-derived keratinocytes

status: Public on Sep 30 2009

city: Nishinomiya

first: Yoshie

last: Yoshikawa

state: Hyogo

address: 1-1 Mukogawa-cho

department: Genetics

institute: Hyogo College of Medicine

summary:
In the epidermis, keratinocytes are involved in physical and first-line immune protection of the host. In this work, we analyzed molecular responses after the addition of contact sensitizers, 2,4-dinitrochlorobenzene (DNCB) using cultured human keratinocytes from the bulge region of a plucked hair follicle (bulge-derived keratinocytes; BDKs) in comparison with neonatal human epidermal keratinocytes NHEK and human monocytic leukemia THP-1. The changes in gene expression by the treatment of DNCB in BDKs were different from those in THP-1. Many genes orchestrating keratinocyte differentiation, which interact TGF-β and BMP signaling pathway, were significantly up-regulated in response to DNCB.

Keywords: Comparison analysis of gene expression changes by the treatment of DNCB

overall_design: three cell strains composed of four samples; two BDKs established from different donors, NHEK, and THP-1. One replicate per array.

first: Yusuke

last: Sasahara

first: Yukio

last: Kitano

first: Nozomi

last: Kanazawa

first: Hiroki

last: Shima

first: Tomoko

last: Hashimoto-Tamaoki


title: Whole genome analysis of Sertoli cell gene expression by retinoblastoma-1

status: Public on Sep 02 2009

city: Houston

first: Martin

last: Matzuk

address: One Baylor Plaza

department: Pathology

institute: Baylor College of Medicine

summary: Analysis of the regulation of gene expression profiles by retinoblastoma-1 in Sertoli cells. Conditional knockout of Rb1 in Sertoli cells led to progressive infertiliy in male mice that occured between 10 and 14 weeks of age. Results of gene expression studies performed on 6 week-old purified Sertoli cells helped elucidate the key role of RB1 in mature, differentiated Sertoli cells.

overall_design: Total RNA was obtained from 6 week-old Sox9-GFP labeled Sertoli cells that were fluorescently sorted (FACSAriaII cell sorter, BD)

first: Roopa

last: Nalam

first: Claudia

last: Andreu-Vieyra

first: Robert

last: Braun

first: Haruhiko

last: Akiyama


title: A gene expression signature classifying telomerase and ALT immortalization II

status: Public on Nov 02 2009

first: W.

last: Keith

summary:
A gene expression signature classifying telomerase and ALT immortalisation reveals an hTERT regulatory network and suggests a mesenchymal stem cell origin for ALT

Telomere length is maintained by 2 known mechanisms, activation of telomerase or alternative lengthening of telomeres (ALT).  The molecular mechanisms regulating the ALT phenotype are poorly understood and it is unknown how the decision of which pathway to activate is made at the cellular level.  We have shown previously that active repression of telomerase gene expression by chromatin remodelling of the promoters is one mechanism of regulation, however other genes and signalling networks are likely to be required to regulate telomerase and maintain the ALT phenotype.  Using gene expression profiling we have uncovered a signature of 1305 genes to distinguish telomerase positive and ALT cell lines.  By combining this with gene expression profiles of liposarcoma tissue samples we refined this signature to 297 genes significantly associated with telomere maintenance mechanism.  Network analysis of known direct interactions between genes within this signature revealed a regulatory signalling network consistent with a model of hTERT repression in ALT cell lines and liposarcomas.  This network expands on our existing knowledge of hTERT regulation and provides a platform to understand differential regulation of hTERT in different tumour types and normal tissues.  In addition we show evidence to suggest a novel mesenchymal stem cell origin for ALT immortalisation in cell lines and mesenchymal tissues.

Keywords: cell type comparison, gene expression

overall_design: Immortal cell lines, normal cell strains and hMSC samples were all performed in duplicate. Liposarcoma samples were run as single samples apart from S904R (Peritoneal_Liposarcoma_ALT_2) which was run in duplicate.

first: Kyle

last: Lafferty-Whyte

first: Claire

last: Cairney

first: Malcolm

middle: B

last: Will

first: Nedime

last: Serakinci

first: Maria-Grazia

last: Daidone

first: Nadia

last: Zaffaroni

first: Alan

last: Bilsland

first: W


title: Maternal Diabetes alters Transcriptional Programs in the Developing Embryo

status: Public on Jul 21 2009

city: Baton Rouge

last: Kappen

state: LA

address: 6400 Perkins Road

department: Developmental Biology

institute: Pennington Biomedical Research Center

summary:
Diabetic embryopathy can affect any developing organ system, although cardiovascular malformations, neural tube defects and caudal dysgenesis syndrome are the most prominent congenital malformations. We hypothesize that the metabolic imbalance occurring in diabetic pregnancy de-regulates tissue specific gene expression programs in the developing embryo. In order to identify genes whose expression is affected by maternal diabetes, we analyzed gene expression profiles of diabetes-exposed mouse embryos by using Affymetrix microarrays. We identified 129 genes with altered expression levels; 21 genes had increased and 108 genes had decreased expression levels in diabetes-exposed embryos relative to controls. A substantial fraction of these genes (35) are essential for normal embryonic development as shown by functional studies in mouse models. The largest fraction of diabetes-affected genes was in transcription factor and DNA-binding/chromatin remodeling functional categories (19%), which directly affect transcription. These findings suggest that transcriptional regulation in the developing embryos is perturbed by maternal diabetes and that transcriptional regulation plays a major role in the responses of embryos to intrauterine exposure to diabetic conditions. Interestingly, we found the expression of hypoxia-inducible factor 1 α (Hif1α) deregulated in the embryos exposed to the conditions of maternal diabetes. Since hypoxic stress is associated with the complications of diabetic pregnancy, we performed a post-hoc analysis of our microarray data with a specific focus on known HIF1 target genes. Of 39 genes detected in our microarrays, the expression changes of 22 genes (20 were increased and two genes were decreased in diabetes-exposed embryos) were statistically significant. These results indicate that HIF1-regulated pathways are affected in diabetes-exposed embryos. These results strongly suggest that de-regulation of hypoxia/HIF1 activated pathways could be the one of the key molecular events associated with the exposure to the teratogenic intrauterine environment of a diabetic mother.
Keywords: Comparative studies of embryonic response to maternal diabetes

overall_design: Total RNA was isolated from whole embryos at embryonic day 10.5 (E10.5). Five diabetes-exposed embryos (2 of 5 embryos had neural tube defects; NTD) were compared to  two control embryos. Diabetes was induced in female FVB mice (aged 7-9 weeks) by streptozotocin Embryos were isolated only from dams that were classified as diabetic with the blood glucose levels > 250 mg/dl from the mating day until the day of embryo harvest. Five ug  of total RNA was reverse-transcribed, and biotin-labeled cRNA probe generated using the Affymetrix labeling kit and protocol per manufacturers instructions. Probes were then hybridized to the Affymetrix 430A 2.0 genome chip with 14,338 genes. Following washing and staining, the chips were scanned using the Affymetrix GeneChip 3000 scanner in Genetic Microarray Core Facility at the University of Nebraska Medical Center. Images were analyzed using Affymetrix GCOS imaging software. Quality metric parameters including noise level, background, and the efficiency of reverse transcription were ascertained for all hybridizations. The expression levels and the “call” of “Present”, “Marginal”, “Absent” for each probe set were determined by the comparison of the signal intensity of matched and mismatched oligonucleotide probes for the gene sequence.

first: Gabriela

last: Pavlinkova

first: Michael

last: Salbaum


title: Langerhans cells from aryl hydrocarbon receptor deficient mice

status: Public on Sep 22 2009

city: Dusseldorf

first: Charlotte

last: Esser

address: Auf´m Hennekamp 50

department: Molecular Immunology

institute: IUF

summary:
The arylhydrocarbon receptor is a ligand inducible transcription factor. Known to control xenobiotic metabolizing enzymes, it also affects - depending on the cell type - numerous other genes, either directly or indirectly. With respect to the immune system, persistent activation leads to immunosuppression. We asked how the AhR is involved in Langerhans cells. These antigen presenting cells of the skin are responsible for allergies against chemicals (thus xenobiotic metabolism might be relevant) and a recently detected endogenous ligand, FICZ made by UVB radiation from tryptophane, is particularly abundant in the skin.

Keywords: comparison gene deficient mouse cells with wild-type

overall_design: ear skin epidermal sheets from AhR exon2 deficient mice and wildtype C57BL/6 mice were isolated and cultivated for 16 hours in standard medium. Tissues were then homogenized and Langerhans cells isolated via BSA gradient and cell sorting to greater 95% purity. RNA was preparedand amplified prior to chip-hybridization using the MessageAmp™ Kit of Ambion (Woodward St. Austin, USA). RNA was biotinylated (Enzo Bio Array™HighYield™ RNA transcript labeling kit (Affymetrix, High Wycombe, UK)) and purified. RNA was hybridized to MOE430A gene chips (Affymetrix).

first: Bettina

last: Jux


title: Illumina HapMap (1M)

city: San Diego

last: Illumina Inc.

state: CA

address: 9885 Towne Centre Drive

institute: Illumina Inc.

summary: HapMap samples

overall_design: 125 samples from Illumina_1M_Samples_1-63.zip and Illumina_1M_Samples_64-125.zip


title: A TGFB Responsive Gene Expression Signature is Associated With More Severe Skin and Lung Disease in Diffuse Scleroderma

status: Public on Sep 15 2009

city: Hanover

first: Jennifer

last: Sargent

state: NH

address: Dartmouth College; HB7400

institute: Dartmouth Medical School

summary: Primary dermal fibroblasts from patients with dSSc and healthy controls were treated with TGF beta for up to 24h and the genome-wide patterns of gene expression measured on DNA microarrays. 894 genes were identified as TGF beta-responsive in 4 independent cultures of dermal fibroblasts (2 healthy control and 2 dSSc patients).  The 894 genes in the TGF beta-responsive signature are associated with induction of growth factor signaling, collagen synthesis and extracellular matrix deposition.

overall_design:
Common reference design; we used Universal Human Reference RNA (Stratagene) as our reference for every array; For every hybridization sample RNA was always labeled with Cy3, and reference RNA was always labeled with Cy5

All processed data is displayed as log2 of the LOWESS-normalized Cy5/Cy3 ratio and was multiplied by negative 1 for analysis in the associated publication.

first: Ausra

last: Milano

first: Swati

last: Bhattacharyya

first: John

last: Varga

first: Kari

last: Connolloy

first: Howard

middle: Y

last: Chang

last: Whitfield


title: murine T-cells from wildtype and Gfi1 knockout mice

city: Essen

first: Ludger

last: Klein-Hitpass

address: Virchowstr. 173

department: Universitaetsklinikum

institute: Institut fuer Zellbiologie

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

overall_design: Refer to individual Series

first: Pargmann

last: Denise

first: Yücel

last: Raif

first: Kosan

last: Christian

first: Saba

last: Ingrid

first: Klein-Hitpass

last: Ludger

first: Heyd

last: Florian

first: Dittmer

last: Uff

first: Möröy

last: Tarik


title: Gene expression analysis study in curcumin treated and control Y79 cells

status: Public on Jul 11 2009

city: Bangalore

first: Sugandan

last: Sivamani

address: 259, Apurva

department: Microarray Data Analysis

institute: Genotypic

summary: Gene expression analysis study in curcumin treated (20µM curcumin treated Y79 cells) and control Y79 cells (Suspension Y79 cells). Source were Y79 retinoblastoma cell line from human.

overall_design:
Organism used: Homo sapiens
* Slides: Gene Expression Whole Human Genome 4x44k
* Starting material: Cells in RNA later
* RNA Samples used: Control Y79 and Treated_Curcumin
* Labeling kit: Agilents Low input RNA linear amplification Kit one color
Labeling Method: T7 promoter based-linear amplification to generate labeled complementary RNA
* Total RNA and cRNA Purification Kit: Qiagen's RNeasy minikit
* Hybridization Kit: Agilent's In situ Hybridzation kit

Hybridization protocol The fragmented cRNA were mixed with 25ul of 2x GE Hybridization Buffer (Agilent). About 45ul of the resulting mixture was applied to the Microarray and hybridized at 65degC for 17 hours in an Agilent Microarray Hybridization Chamber (SureHyb: G2534A) with Hybridization Oven. After hybridization, slides were washed with Agilent Gene expression Wash Buffer I for 1 minute at room temperature followed by a 1 min wash with Agilent Gene expression Wash Buffer II for 37C. Slides were finally rinsed with Acetonitrile for cleaning up and drying. Scan protocol Laser detection of Cyanine 3 and Cyanine 5 fluorescence is performed using a confocal scanning instrument containing two tuned lasers, which excite Cyanine dyes at the appropriate wavelengths. Description Microarrays were scanned on an Agilent scanner (G2565AA) at 100% laser power, 30% PMT.Data extraction was carried out with Agilent Feature Extraction software (version 9.1), and normalization was done using linear per array algorithm according to the manufacturer's protocol. Data processing Feature extracted data was analyzed using GeneSpring GX v 7.3.1 software from Agilent. Normalization of the data was done in GeneSpring GX using the recommended one color Per Chip and Per Gene Data Transformation: Set measurements less than 0.01 to 0.01, Per Chip: Normalize to 50th percentile, Per Gene: Normalize to Specific Samples. Further quality control of normalized data was done using correlation based condition tree to eliminate bad experiments. Differentially regulated Genes were filtered with cutoff of > 1.5 for Up regulation and < 0.55 for Down Regulation were obtained. Differentially regulated genes were clustered using gene tree to identify significant gene expression patterns.

first: SeethaLakshmi

last: Thiagu

first: Subramaniam

last: Krishnakumar


title: Gene expression analysis study in cerulenin treated and control Y79 cells

summary: Gene expression analysis study in cerulenin treated - 7µg/ml cerulenin treated Y79 cells and control Y79 cells

overall_design:
Organism used: Homo sapiens
* Slides: Gene Expression Whole Human Genome 4x44k
* Starting material: Cells in RNA later
* RNA Samples used: Control Y79 and Treated_Cerulenin
* Labeling kit: Agilents Low input RNA linear amplification Kit one color
* Labeling Method: T7 promoter based-linear amplification to generate labeled complementary RNA
* Total RNA and cRNA Purification Kit: Qiagen's RNeasy minikit
* Hybridization Kit: Agilent's In situ Hybridzation kit

Hybridization protocol  The fragmented cRNA were mixed with 25ul of 2x GE Hybridization Buffer (Agilent). About 45ul of the resulting mixture was applied to the Microarray and hybridized at 65degC for 17 hours in an Agilent Microarray Hybridization Chamber (SureHyb: G2534A) with Hybridization Oven. After hybridization, slides were washed with Agilent Gene expression Wash Buffer I for 1 minute at room temperature followed by a 1 min wash with Agilent Gene expression Wash Buffer II for 37C. Slides were finally rinsed with Acetonitrile for cleaning up and drying.
Scan protocol  Laser detection of Cyanine 3 and Cyanine 5 fluorescence is performed using a confocal scanning instrument containing two tuned lasers, which excite Cyanine dyes at the appropriate wavelengths.
Description  Microarrays were scanned on an Agilent scanner (G2565AA) at 100% laser power, 30% PMT.Data extraction was carried out with Agilent Feature Extraction software (version 9.1), and normalization was done using linear per array algorithm according to the manufacturer's protocol.
Data processing  Feature extracted data was analyzed using GeneSpring GX v 7.3.1 software from Agilent. Normalization of the data was done in GeneSpring GX using the recommended one color Per Chip and Per Gene Data Transformation: Set measurements less than 0.01 to 0.01, Per Chip: Normalize to 50th percentile, Per Gene: Normalize to Specific Samples. Further quality control of normalized data was done using correlation based condition tree to eliminate bad experiments. Differentially regulated Genes were filtered with cutoff of > 1.5 for Up regulation and < 0.55 for Down Regulation were obtained. Differentially regulated genes were clustered using gene tree to identify significant gene expression patterns.

first: Vandana

last: Narayanan


title: Microarray data from murine C3H/10T1/2 and 3T3 L1 adipocytes

status: Public on Aug 30 2009

city: Research Triangle Park

first: James

last: Rong

state: NC

address: 5 Moore Drive

institute: GlaxoSmithKline

summary:
Growing evidence indicates that PPARγ agonists, such as rosiglitazone (RSG,), induce adipose mitochondrial biogenesis. Using microarrays, we systematically analyzed nucleus-encoded mitochondrial gene expression in two common murine adipocyte models, 3T3 L1 and C3H/10T1/2 adipocytes, and aimed to further establish the direct role of RSG, and capture the temporal changes in mitochondrial gene transcription during this process.

Keywords: Time course in two cell types

overall_design: Fully differentiated 3T3 L1 and C3H/10T1/2 adipocytes were treated with RSG, or DMSO vehicle for 1, 2, 4, 7, 24, and 48 hrs, and total RNA was extracted for microarray analysis.

first: Vivian

last: Zhang

middle: X


title: Human Adrenocortical Tumors: normal cortex vs inactive adenoma vs cortisol secreting adenoma vs adrenocortical cancer

status: Public on Jul 01 2009

city: Budapest

first: Zsófia

last: Tömböl

address: Szentkirályi u. 46.

department: 2nd Department of Medicine

country: Hungary

institute: Semmelweis University

summary: Transcriptional profiling of human adrenocortical tumors. Gene expression profile of normal adrenal cortex, hormonally inactive adenoma, cortisol-secreting Cushing-adenoma and primary adrenocortical cancer tissues were compared. The goal of this study was to identify significant differences in the gene expression of these groups. Further aim was to reveal biologically relevant pathogenetic pathways altered at transcriptional and posttranscriptional level, as well.

overall_design: mRNA expression profiles of normal adrenal cortex, inactive adenoma, cortisol secreting adenoma and primary adrenocortical cancer tissues were compared. Biological replicates: 4 samples per each experimental group were investigated. Whole genome expression analysis was performed in a two-colour microarray design by comparing individual samples to a uniform reference pool of all samples examined on Agilent Whole Human Genome 4x44 K microarray platform.

first: Peter

last: Szabó

first: Viktor

last: Molnár

first: Zoltán

last: Wiener

first: Gergely

last: Tölgyesi

first: Attila

last: Patócs

first: András

last: Falus

first: Károly

last: Rácz

last: Igaz


title: Blood pooling experiments on ophthalmalogic phenotypes with Illumina arrays

city: Brisbane

first: Stuart

last: Macgregor

state: Queensland

address: 300 Herston Road

department: Genetic Epidemiology

country: Australia

institute: Queensland Institute of Medical Research

summary:
In this study 3 pooling experiments were performed. In each of the 3 cohorts, a 'case' and a 'control' blood pool was compared - the goal being to identify single nucleotide polymorphisms with significantly different estimated pooling allele frequencies between cases and controls. For cohort 1, 100 individuals with blue eye color were placed in one pool (the 'control' pool) and 100 individuals with brown eye color were placed in another pool ( the 'case' pool). In cohort 2, 131 individuals with age-related macular degeneration were placed in one pool, with 216 control individuals in another pool. In cohort 3, 100 individuals with pseudoexfoliation syndrome were placed in a case pool - in this case the cohort 2 control sample was used as 'controls'. The blue/brown pools were hybridized to Illumina HumanHap550 arrays. The cohort 2 and 3 pools were hybridized to Illumina 1M arrays. After processing, the raw data are summarized to give pooling allele frequency estimates for each pool.
The abstract from the paper describing these data is as follows: Genome-wide association studies (GWAS) have now successfully identified important genetic variants associated with many human traits and diseases. The high cost of genotyping arrays in large datasets remains the major barrier to wider utilization of GWAS. We have developed a novel method in which whole blood from cases and controls respectively is pooled prior to DNA extraction for genotyping. We demonstrate proof of principle by clearly identifying the associated variants for eye color, age-related macular degeneration and pseudoexfoliation syndrome in cohorts not previously studied. Blood pooling has the potential to reduce GWAS cost by several orders of magnitude and dramatically shorten gene discovery time. This method has profound implications for translation of modern genetic approaches to a multitude of diseases and traits yet to be analysed by GWAS, and will enable developing nations to participate in GWAS.

overall_design: Pools were typed with Illumina arrays. Estimates of pooling allele frequency were obtained.

first: Jamie

last: Craig

first: Alex

middle: W

last: Hewitt

last: MacGregor


title: Homeobox gene IRX1 is a tumor suppressor gene in gastric carcinoma

status: Public on Jul 30 2009

city: Shanghai

first: Yingyan

last: Yu

address: Shanghai Ruijin 2nd Road No.197

department: Department of Surgery

country: China

institute: Shanghai Ruijin Hospital

summary: To explore the functon of IRX1 in gastric cancer, we employed whole genome microarray expression profiling as a discovery platform to identify gene expression changes in three samples. We constructed the eukaryotic expression vector pEGFP-IRX1. The pEGFP-IRX1 expression vector was transfected into SGC-7901 gastric cancer cells by Lipofectamine 2000. The IRX1 protein was mainly observed in nuclei. Naive SGC7901 and empty vector pEGFP-N1 transfected cells were used as controls.

overall_design: Gene expression profiles were compared between parental gastric cancer cell line SGC7901 and cells transfected with pEGFP-IRX1 and pEGFP-N1.

first: Xiaobo

last: Guo

first: W

middle: R

last: Liu

first: Lei

first: Z

middle: G

last: Zhu


title: Expression data from estradiol-treated fetal urogenital sinus mesenchyme cells

status: Public on Jun 27 2009

city: Columbia

first: Julia

last: Taylor

state: MO

address: 114 Lefevre Hall

department: Biological Sciences

institute: University of Missouri

summary: Developmental estrogen exposure causes permanent alterations to mouse prostate development.  Fetal prostatic mesenchyme cells regulate epithelial cell proliferation and differentiation, and alterations to mesenchymal regulation of prostate epithelial cell proliferation and differentiation may lead to permanent changes in gland structure and function.  Our goal was to understand how mesenchymal cells convert estrogen signaling to stimuli that affect epithelial cells. We used microarrays to identify estrogen-induced transcriptomal changes in primary cultures of fetal mouse prostate mesenchymal cells.

overall_design: Urogenital sinus mesenchymal cells were obtained from CD-1 male mouse fetuses at gestation day 17 and cultured in the presence of 0.1 μM estradiol .

first: Catherine

last: Richter

first: Atsuko

last: Suzuki

first: Hajime

last: Watanabe

first: Taisen

last: Iguchi

first: Toshihiro

last: Shioda

first: Kathryn

last: Coser

first: Frederick

middle: S

last: vom Saal


title: Reversible and irreversible anchorage independent growth in skin cells

status: Public on Jun 01 2009

city: Richland

first: Katrina

last: Waters

state: WA

address: 902 Battelle Blvd; MSIN J4-18

department: Biological Sciences Division

institute: Pacific Northwest National Laboratory

summary:
We have investigated the regulation of anchorage-independent growth (AIG) by basic fibroblast growth factor (bFGF) and 12-O-tetradecanoyl phorbol-13-acetate (TPA) in JB6 mouse epidermal cells in the context of wound repair versus carcinogenesis responses.  bFGF induces an unusually efficient but reversible AIG response, relative to TPA-induced AIG which is irreversible.  Distinct global gene expression profiles are associated with anchorage-independent colonies arising from bFGF-stimulated JB6 cells, relative to colonies arising from fully tumorigenic JB6 cells (RT101), including genes exhibiting reciprocal regulation patterns.  Thus, while TPA exposure results in commitment to an irreversible and tumorigenic AIG phenotype, the AIG response to bFGF is reversible with essentially complete restoration of normal cell cycle check point control following removal of bFGF from growth medium.  These results are consistent with the physiological role of bFGF in promoting wound healing, and suggest that natural mechanisms exist to reverse transformative cellular phenotypes associated with carcinogenesis.

Keywords: cell phenotype comparison

overall_design: To determine whether there were shared transcriptional effects between reversible and irreversible AIG, we performed global microarray analyses on colonies isolated from soft agar for both bFGF-treated JB6 cells and fully tumorigenic JB6 cells from the RT101 cell line.  Gene expression changes associated with colony formation were determined by comparison to respective monolayer control cells.

first: Thomas

last: Weber


title: Gene expression in a Highly Tumorigenic Cells (HTC) purified from Urothelial Cancer

status: Public on May 28 2009

city: Baltimore

first: Luigi

last: Marchionni

state: MD

address: 1550 Orleans St., CRB2, Room 1M52

department: Oncology

institute: Johns Hopkins University

summary: We used DNA microarrays to compare RNA transcript expression from distinct cell populations sorted by FACS with an antibody against the 67Kd laminin receptor (67LR), and showing distinct tumorigenicity in vivo.

overall_design: Sorted cells were derived by digesting xenografted sw 780 tumors into single cell suspensions. Differential gene expression was assessed by direct comparisons of labeled moieties, using a dye-swap design and biological replication. Hybridizations were performed on Agilent (Santa Clara, CA) Whole Human Genome DNA microarrays (hgug4112a). Three different samples were analyzed: 1) Urothelial cancer cells expressing 67LR (67LR+, BRIGHT); 2) Urothelial cancer cells not expressing 67LR (67LR-, DIM); 3) Control sorted urothelial cancer cells (BULK, containing both BRIGHT and DIM cells). In this series we provide normalized single channel intensities, aligned with the corresponding raw expression data.


title: Transcriptome analysis of freshly sorted and expanded regulatory and conventional T cells

status: Public on May 20 2009

city: Regensburg

first: Christian

last: Schmidl

address: Franz-Josef-Strauss-Allee 11

institute: Rengensburg Center for Interventional Immunology

summary: Transcriptome analysis of freshly sorted regulatory T cells (CD4+CD25+) and conventional T cells (CD4+CD25-) and of expansion cultures of regulatory T cells (CD4+CD25+CD45RA+) and conventional T cells (CD4+CD25-).

overall_design: Three biological replicates were performed of freshly sorted Treg and Tconv cells each. Four replicates of Treg expansion cultures sorted into CD45RA+/- subpopulations prior to RNA extraction were performed.

first: Maja

last: Klug

first: Michael

last: Rehli

first: Tina

last: Böld


title: Relapse-related molecular signature in lung adenocarcinomas identifies patients with dismal prognosis

status: Public on Jun 23 2009

city: Nagoya

first: Takashi

last: Takahashi

state: Aichi

address: 1-1 Kanokoden, Chikusa-ku

institute: Aichi Cancer Center

summary:
We identified a relapse-related molecular signature represented by 82 probes (RRS-82) through genome-wide expression profiling analysis of a training set of 60 patients. The robustness of RRS-82 in the selection of patients with a high probability of relapse was then validated with a completely blinded test set of 27 adenocarcinoma patients, showing a clear association of high risk RRS-82 with very poor patient prognosis regardless of disease stage. The discriminatory power of RRS-82 was further validated using an additional independent cohort of 30 Stage I patients who underwent surgery at a distinct period of time.

Keywords: Disease state analysis

overall_design: Expression profiles in 117 patients with lung adenocarcinomas.

first: Shuta

last: Tomida

first: Toshiyuki

last: Takeuchi

first: Yukako

last: Shimada

first: Chinatsu

last: Arima

first: Keitaro

last: Matsuo

first: Tetsuya

last: Mitsudomi

first: Yasushi

last: Yatabe


title: Primary Langerhans cells in mice treated with TCDD

status: Public on May 01 2009

first: Charlotte

last: Esser

summary:
The transcriptome of murine LC after 24 hours in vivo exposure to a moderate dose of 10 microgram 2,3,7,8-tetrachlorodibenzo-p-dioxin was studied.
It was found that mice, although they express the arylhydrocarbon receptor abundantly in LC, are inert to its activation. Target genes are not inducible, in contrast to many other cell types.
Keywords: toxic effect, single dose

overall_design: i.p. injection, isolation of cells after 24 hours, 95% sorting purity of LC.

first: Bettina

last: Jux

first: Markus

last: Frericks


title: Gene microarray analysis of mouse-brain endothelial cells exposure to Pertussis Toxin and B-oligomer

status: Public on Apr 29 2009

city: Burlington

first: Jeffrey

last: Bond

state: VT

address: 95 Carrigan Dri e

department: Microbiology and Molecular Genetics

institute: University of Vermont

summary:
Pertussis Toxin (PTX) regulated inflammatory and angiogenesis-related transcripts in endothelial cells from mouse brain(MBEC). Of ~14,000 mouse genes tracked, 34 showed altered expression in response to PTX, and most of these changes were dependent on the ADP-ribosyltransferase activity of the S1 subunit of the active holotoxin. More than one third of these genes have roles in inflammation and angiogenesis.
Keywords: response to treatment

overall_design: MBEC(passage1) cultured on collagen-coated glass chamber slides were treated with PTX and B-oligomer at 3ng/ml, or PBS as control. Six hours later, total RNA were isolated from the cells. Gene microarray were performed to identify early candidate genes that are affected by PTX. The experiment was repeated twice independently.

first: Changming

last: Lu

first: Steven

last: Pelech

first: Hong

last: Zhang

first: Karen

last: Spach

first: Elizabeth

last: Blankenhorn

first: Cory

last: Teuscher


title: Gene expression profiling of retinoblastoma Y79 cell line post EpCAM silencing using siRNA

first: Sugandan

last: Sivamani

summary: Retinoblastoma Y79 cell line was treated with specific siRNA to silence EpCAM gene expression in vitro and RNA was isolated for microarray experiment to study the changes in the whole gene expression profiling in the Y79 cell line. The study identified 465 up-regulated genes (>1.0 fold) and 205 down-regulated genes (<0.5 fold) in response to knockdown of Ep-CAM.

overall_design:
Organism used: Homo sapiens
Slides: Whole genome Human 4x44k array
Starting material: Cells in RNA Later
RNA Samples used: Control, siRNA1
Labeling kit: Agilent Low Input RNA Linear amplification kit
Labeling Method: T7 promoter based-linear amplification to generate labelled complementary RNA
Total RNA and cRNA Purification Kit: Qiagen’s RNeasy minikit
Hybridization Kit: Agilent In situ Hybridization Kit

Hybridization protocol
The fragmented cRNA were mixed with 25ul of 2x GE Hybridization Buffer (Agilent). About 45ul of the resulting mixture was applied to the Microarray and hybridized at 65degC for 17 hours in an Agilent Microarray Hybridization Chamber (SureHyb: G2534A) with Hybridization Oven. After hybridization, slides were washed with Agilent Gene expression Wash Buffer I for 1 minute at room temperature followed by a 1 min wash with Agilent Gene expression Wash Buffer II for 37C. Slides were finally rinsed with Acetonitrile for cleaning up and drying.
Scan protocol
Laser detection of Cyanine 3 and Cyanine 5 fluorescence is performed using a confocal scanning instrument containing two tuned lasers, which excite Cyanine dyes at the appropriate wavelengths.
Description  Microarrays were scanned on an Agilent scanner (G2565AA) at 100% laser power, 30% PMT.Data extraction was carried out with Agilent Feature Extraction software (version 9.1), and normalization was done using linear per array algorithm according to the manufacturer’s protocol.
Data processing
Feature extracted data was analyzed using GeneSpring GX v 7.3.1 software from Agilent. Normalization of the data was done in GeneSpring GX using the recommended one color Per Chip and Per Gene Data Transformation: Set measurements less than 0.01 to 0.01, Per Chip: Normalize to 50th percentile, Per Gene: Normalize to Specific Samples. Further quality control of normalized data was done using correlation based condition tree to eliminate bad experiments. Differentially regulated Genes were filtered with cutoff of > 1.5 for Up regulation and < 0.55 for Down Regulation were obtained. Differentially regulated genes were clustered using gene tree to identify significant gene expression patterns.

first: Moutushy

last: Mitra

first: Mallikarjuna

last: Kandalam

first: Ramashenkar

last: verma

first: Uma

last: Maheswari

first: Subramanian

last: Krishnakumar


title: Gene expression profiles of spontaneous metastasis in a K-ras/p53 mutant mouse model

status: Public on Apr 15 2009

city: Houston

first: Chad

last: Creighton

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

summary: The biologic basis for NSCLC metastasis is not well understood. Here we addressed this deficiency by transcriptionally profiling tumors from a genetic mouse model of human lung adenocarcinoma that develops metastatic disease owing to the expression of K-rasG12D and p53R172H. We identified 2,209 genes that were differentially expressed in distant metastases relative to matched lung tumors. Mining of publicly available data bases revealed this expression signature in a subset of NSCLC patients who had a poorer prognosis than those without the signature.

overall_design: Primary lung adenocarcinomas and metastases from p53R172H∆g/+ K-rasLA1/+ mice or syngeneic tumors were isolated, carefully dissected to remove the adjacent tissue, snap-frozen in liquid nitrogen and stored at -80° until use. Part of each dissected tumor was histologically evaluated by a board-certified pathologist.  Synthesis of cRNA and hybridization to Mouse Expression Array 430A 2.0 chips were performed.  Two-sided t-paired tests using log-transformed expression values determined significant differences between primary tumors and metastasis.

first: Jon

last: Kurie

first: Dror

last: Berel

first: Don

last: Gibbons

first: Wei

last: Lin


title: Molecular signatures of N-nitroso compounds in Caco-2 cells: implications for colon carcinogenesis

status: Public on Apr 01 2009

city: Maastricht

first: Dennie

last: Hebels

address: Universiteitssingel 50

department: Health Risk Analysis and Toxicology

country: Netherlands

institute: Maastricht University

summary:
N-nitroso compounds (NOC) are genotoxic compounds and animal carcinogens, and may play a role in human cancer development. Since the gastro-intestinal tract is an important route of exposure, we hypothesize that NOC exposure targets genetic processes relevant in colon carcinogenesis. To investigate this, we analysed the transcriptomic effects of genotoxic concentrations of two nitrosamides, N-methyl-N'-nitro-N-nitrosoguanidine (MNNG, 1µM) and N-methyl-N-nitrosurea (MNU, 1mM), and four nitrosamines, N-nitrosodiethylamine (NDEA, 50mM), N-nitrosodimethylamine (NDMA, 100mM), N-nitrosopiperidine (NPIP, 40mM), and N-nitrosopyrrolidine (NPYR, 100mM), in the human colon carcinoma cell line Caco-2. Gene Ontology gene group, consensus motif gene group and biological pathway analysis revealed that nitrosamides had little effect on gene expression after 24 hours of exposure, whereas nitrosamines had a strong impact on the transcriptomic profile. Analyses showed modifications of cell cycle regulation and apoptosis pathways for nitrosamines which was supported by flow cytometric analysis. We found additional modifications in gene groups and pathways of oxidative stress and inflammation, which suggest an increase in oxidative stress and pro-inflammatory immune response upon nitrosamine exposure, although less distinct for NDMA. Furthermore, NDEA, NPIP and NPYR most strongly affected several developmental motif gene groups and pathways, which may influence developmental processes. Many of these pathways and gene groups are implicated in the carcinogenic process and their modulation by nitrosamine exposure may therefore influence the development of colon cancer. In summary, our study has identified pathway modifications in human colon cells which may be associated with cancer risk of nitrosamine exposure in the human colon.

Keywords: Comparison of genome-wide gene expression between different conditions

overall_design: The study investigated differential gene expression in Caco-2 cell line mRNA following 24 hours of exposure to six different N-nitroso compounds. Four biological replicates per sample compound. One compound per array, hybridized against vehicle control. Dye-swap between biological replicates 1 and 2, and 3 and 4.

first: Danyel

middle: D

last: Jennen

first: Jos

middle: C

last: Kleinjans

first: Theo

last: de Kok


title: Gene expression profiling of retinoblastoma Y79 cell line treated with scopoletin from Morinda citrifolia in vitro

summary: Retinoblastoma Y79 cell line was treated with scopoletin in vitro and RNA was isolated for microarray experiment to study the changes in the whole gene expression profiling in the Y79 cell line. The study identified 1675 up-regulated genes (>1.0 fold) and 1879 down-regulated genes (<-1 fold) in response to scopoletin treatment

overall_design:
Slides:Whole genome Human 4x44k array
* Starting material: Cells in RNA Later
* RNA Samples used: Y79_c_Noni Extract,Control
* Labeling kit: Agilent's Quick-Amp labeling Kit
* Labeling Method: T7 promoter based-linear amplification to generate labeled complementary RNA
* Total RNA and cRNA Purification Kit: Qiagen's RNeasy minikit Cat
* Hybridization Kit: Agilent's In situ Hybridzation kit
Hybridization protocol
The fragmented cRNA were mixed with 25ul of 2x GE Hybridization Buffer (Agilent). About 45ul of the resulting mixture was applied to the Microarray and hybridized at 65degC for 17 hours in an Agilent Microarray Hybridization Chamber (SureHyb: G2534A) with Hybridization Oven. After hybridization, slides were washed with Agilent Gene expression Wash Buffer I for 1 minute at room temperature followed by a 1 min wash with Agilent Gene expression Wash Buffer II for 37C. Slides were finally rinsed with Acetonitrile for cleaning up and drying.
Scan protocol
Laser detection of Cyanine 3 and Cyanine 5 fluorescence is performed using a confocal scanning instrument containing two tuned lasers, which excite Cyanine dyes at the appropriate wavelengths.
Description Microarrays were scanned on an Agilent scanner (G2565AA) at 100% laser power, 30% PMT.Data extraction was carried out with Agilent Feature Extraction software (version 9.1), and normalization was done using linear per array algorithm according to the manufacturer's protocol.
Data processing
Feature extracted data was analyzed using GeneSpring GX v 7.3.1 software from Agilent. Normalization of the data was done in GeneSpring GX using the recommended one color Per Chip and Per Gene Data Transformation: Set measurements less than 0.01 to 0.01, Per Chip: Normalize to 50th percentile, Per Gene: Normalize to Specific Samples. Further quality control of normalized data was done using correlation based condition tree to eliminate bad experiments. Differentially regulated Genes were filtered with cutoff of > 1.5 for Up regulation and < 0.55 for Down Regulation were obtained. Differentially regulated genes were clustered using gene tree to identify significant gene expression patterns.

first: Surendiran

last: Gangadharan

first: Seetha

last: Lakshmi

first: Mathivanan

last: Narayanaswamy


title: Human ES cells' gene expression difference compared with that of the adult cells including CCD-1079sk and IMR90

first: Jing

last: Liao

address: 320 Yue Yang Road

institute: Institute of Biochemistry and Cell Biology  Shanghai Institutes for Biological Sciences  Chinese Academy of Science

summary: Human ES cells had different gene expression level compared with that of the adult cells including CCD-1079sk and IMR90. This difference gave the human ES cells unique characteristics which could then be compared with other species' ES cells or iPS cells like mouse ES cells and Rat iPS cells by the homologue genes comparison to show which species' ES cells or iPS cells were more competitive with the other.

overall_design:
There were three replicates sample of the Human ES cells named 1, 2, 3.
And the adult cells were the mixture of CCD-1079sk and IMR90 named mix2. Human ES cells samples were labled with Cy3 and the mix2 were labled with Cy5. The data was process to show the human ES cells' gene expression difference compared with that of mix2.

first: Lei

last: Xiao

first: Chun

last: Cui

first: Huasheng

first: Xiaokun

last: Teng

first: Yi

last: Zhang


title: Presomitic mesoderm and somite-level tissue of 9.5 dpc Dll3 mutants

status: Public on Mar 11 2009

city: Tempe

first: Kenro

last: Kusumi

state: AZ

department: School of Life Sciences

institute: Arizona State University

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

overall_design: Refer to individual Series


title: Feedback control by the human microRNA, let-7, regulates expression of the RNA sielncing enzyme, Dicer

status: Public on Jun 30 2009

city: Berkely

first: Sanchita

last: Bhattacharya

address: 1 Cyclotron Rd

institute: MIT

summary:
let-7 regulates Dicer and HMGA2 expression and decrease the steady state levels of these genes
Keywords: miRNA inhibition and overexpression

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Three replicates of each sample

first: Gyorgy

last: Hutvagner

first: Herve

last: Seitz

first: Benjamin

last: Haley

first: Bradford

last: Stadler

last: Lewis

first: Phillip

last: Zamore


title: C57BL/6 C3H/HeJ apoE-/- mice - gene expression in aorta

status: Public on Feb 20 2009

city: Charlottesville

first: Weibin

last: Shi

state: VA

address: 480 Ray C Hunt Drive

department: Radiology

institute: University of Virginia

summary:
Inbred mouse strains C57BL/6J (B6) and C3H/HeJ (C3H) exhibit a marked difference in their susceptibility to atherosclerosis and the arterial wall has proven to be a source of the difference in atherosclerosis susceptibility.  Genome-wide gene expression analysis was conducted in aortic walls of the two strains.  Total RNA was extracted from aortas of 6-week-old female B6 and C3H apoE-deficient (apoE-/-) mice fed a chow or Western diet.  1514 genes in chow fed mice and 590 genes in Western fed mice were found to be differentially expressed between the two strains.  RNA was extracted from aorta using a Trizol protocol.  Total RNA was pooled in an equal amount from 4 mice for each group. Standard Affymetrix procedures were performed using 8ug of total RNA.
Microarrays were used to detect gene expression in aortic walls of two apoE-deficient mouse strains when fed a chow or western diet.

Keywords: atherosclerosis, arterial walls, C57BL/6, C3H/HeJ, Inbred strains, Hyperlipidemia, and Western diet

overall_design: 4 groups of mice were studied: C57BL/6 apoE-/- mice on chow diet (03-62_BC), C57BL/6 apoE-/- mice on Western diet (03-62_BW), C3H/HeJ apoE-/- mice on chow diet (03-62_CC), and C3H/HeJ apoE-/- mice on Western diet (03-62_CW). Mice were weaned at 3 weeks of age onto a chow diet. At 4 weeks of age, mice were switched onto a western diet or continued the chow diet for 2 additional weeks.


title: HRI Protects Erythroid Precursors in iron deficiency and beta-Thalassemia by Maintaining GATA-1 and Fog-1 Expression

summary:
Heme-regulated eIF2α kinase (HRI) is essential for the survival of erythroid precursors in iron and heme deficiency and it also plays a protective role in red blood cell diseases of erythroid protoporphyria and β-thalassemia. In this study, we demonstrated for the first time the impairment of GATA-1 and Fog-1 expressions in iron deficiency and the impairment of GATA-1 expression in β-thalassemia. Furthermore, HRI is necessary to maintain the GATA-1/Fog-1 induced functions in erythroid differentiation, cell cycle and cell survival by sustaining both expressions of GATA-1 and Fog-1 in iron deficiency and in β-thalassemia.
Keywords: Genetic modification

overall_design: Three replicates of gene chip profiling were performed for each condition, Wt+Fe, Wt-Fe, Ko+Fe and Ko-Fe.

first: Sijin

last: Liu

first: Anping

last: Han

first: Rajasekhar

last: Suragani

first: Wanting

last: Zhao

first: Rebecca

last: Fry

first: Mitchell

last: Weiss

first: Jane-Jane

last: Chen


status: Public on Jun 19 2009

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

summary:
Increased antigen cross-presentation but impaired cross-priming after activation of PPARγ is mediated by up-regulation of B7H1
Dendritic cells (DCs) are able to take up exogenous antigens and present antigen-derived peptides on MHC class I molecules, a process termed cross-presentation. The mannose receptor (MR), an endocytic receptor expressed on a variety of antigen-presenting cells (APCs), has been demonstrated to target soluble antigens exclusively towards cross-presentation. In this study, we investigated the role of the murine nuclear receptor peroxisome proliferator-activated receptor γ (PPARγ), a ligand-activated transcription factor with immunomodulatory properties, in MR-mediated endocytosis and cross-presentation of the model antigen ovalbumin (OVA). We could demonstrate both in vitro and in vivo that activation of PPARγ resulted in increased MR expression, which in consequence led to enhanced MR-mediated endocytosis and elevated cross-presentation of soluble OVA. Concomitantly, activation of PPARγ in DCs induced up-regulation of the co-inhibitory molecule B7H1, which, despite enhanced cross-presentation, caused an impaired activation of naive OVA-specific CD8+ T cells and the induction of T cell tolerance. These data provide a mechanistic basis for the immunomodulatory action of PPARγ which might open new possibilities in development of therapeutical approaches aimed at the control of excessive immune responses, e.g. in T cell-mediated autoimmunity.

overall_design: Comparison of murine mannose receptor negative versus mannose receptor positive bone marrow-derived DCs

first: Luisa

last: Klotz

first: Sabine

last: Classen

first: Andrea

last: Gaarz

first: Sven

last: Burgdorf

first: Christian

last: Kurts


title: Expression data of LPS-stimulated macrophages from wild-type, MyD88-/- and TRIF-/- mice.

status: Public on Feb 19 2009

city: Kyoto

first: Osamu

last: Takeuchi

state: Kyoto

address: Yoshida-konoe-cho, Sakyo-ku,

department: Grad School of Medicine

institute: Kyoto University

summary:
Lipopolysaccharide (LPS), a Toll-like receptor (TLR) 4 ligand, activates intracellular signaling via adaptors, MyD88 and TRIF, leading to the expression of various genes including proinflammatory cytokines.
We used microarrays to examine influence of MyD88 or TRIF deficiency in LPS-inducible gene expression.

Keywords: Time course after LPS (100 ng/ml) stimulation

overall_design: Peritoneal macrophages from wild-type, MyD88-/- and TRIF-/- mice were stimulated with LPS for 0, 1 and 4 hours, followed by RNA extraction. Then hybridization on affymetrix microarrays was performed.

first: Kazufumi

last: Matsushita


title: Comparisons between liver tissues and freshly isolated hepatocytes from IkkβF/F and IkkβDhep (Ikkβ-deleted) mice

city: La Jolla

first: Dr. Hyam

middle: L.

last: Leffert

address: 9500 Gilman Drive

department: Pharmacology

institute: UCSD School of Medicine

summary: CD74, a Type II membrane glycoprotein and MHC class II chaperone (Ii), is normally expressed by cells associated with the immune system. CD74 also forms heterodimers with CD44 to generate receptors to macrophage migration inhibitory factor (MIF), a proinflammatory cytokine. Following targeted Cre-mediated deletion of Ikkβ in IkkβDeltaHep mice (a strain highly susceptible to chemically-induced hepatotoxicity and hepatocarcinogenesis), CD74 is abundantly expressed by hepatocytes throughout liver acini (as detected by specific Western blots and immunohistochemical stains); it is not observed in either control IkkβF/F hepatocytes or embryonic fibroblasts from Ikkβ-/- mice. Constitutive CD74 expression in IkkβDeltaHep hepatocytes is also accompanied by significantly augmented expression of CD44 and genes associated with antigen processing and host defense. These observations suggest that IkkβDeltaHep hepatocytes might directly respond to MIF signaling, accounting partly for the enhanced susceptibility of IkkβDeltaHep mice to hepatotoxins and hepatocarcinogens, and also might exhibit unusual immunological properties including antigen presentation.

overall_design: Total RNA samples were obtained from four 6-8 week-old male mice.  The four RNA samples were processed as described in the PROTOCOLS section below.

first: Katherine

last: Koch

first: Hyam


title: Comparison of human ES cells, mouse ES cells, rat iPS cells and their somatic cells.

status: Public on Mar 30 2009

first: Jing

last: Liao

department: Institute of Biochemistry and Cell Biology

sample_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

first: Lei

last: Xiao

first: Chun

last: Cui

first: Huasheng

first: Xiaokun

last: Teng

first: Yi

last: Zhang


title: IMR90 4hr bystander experiment  0.5Gy alpha particle strip dish format

status: Public on Dec 29 2008

city: New York

first: Shanaz

middle: Adi

last: Ghandhi

state: NY

address: 630, W 168th street

department: Center for Radiological Research

institute: Columbia University Medical Center

summary:
Radiation affects tissue and cellular integrity at the level of DNA, protein and  metabolites of the cell and extracellular space. The effects of radiation are not limited to targeted cells and tissue and radiation induced bystander   effects are significant to exposed individuals  in accidental or therapeutic situations. These non-targeted effects of radiation have been studied extensively at the low dose range where they appear to have adverse effects on cells and surrounding environments. The requirement of cellular contact and shared fluid media has been established as critical to the bystander effect yet there is not much known about the actual signaling mechanism and its ability to transmit the damaging effect over space and time. Experimental cell types and context within the tissue are also quite important to the nature and extent of this bystander effect and must be considered when drawing parallels at the organismal level. Our approach was to use a genomic level analysis of global mRNA expression in primary lung fibroblast cells to understand the cellular triggers and mechanism of the bystander effect. Gene ontology and pathway analyses suggested that the p53 induced transcriptional response appears muted in bystanders while cytokine and cell signaling mechanisms such as those controlled by NFkB and p38 MAPK are highly active in both populations. We validated a large number of genes that are significantly changed at 4hrs after irradiation in both irradiated and bystander populations. We investigated time course gene expression profiles of cyclooxygenase2 (PTGS2), interleukin 8 (IL8) and BCL2 related protein 2 (BCL2A1), as genes that are involved in cellular signaling via the  NFkB pathway, which revealed that there is a dramatic response at 0.5hr after irradiation followed by another wave at 4hr in both populations. The induction of interleukins such as cytokine IL8 and chemokine IL6 at the transcriptional level is both early and amplified and if followed by translation and secretion of these proteins could explain the concerted response seen in bystander cells. Our results are the first to show that there is a significant and distinct global response of cellular signaling genes  in bystander cells with some genes showing a response as early as 0.5hr after irradiation which implies a fast moving intercellular signal that leads to a concerted response in the irradiated and bystander  populations.

Keywords: gene expression fold change

overall_design: There are 12 total samples, 4 corresponding biological replicates of IMR90 cells that were not irradiated (control=C), irradiated (alpha=A) and bystander (B)

middle: A

first: Sally

last: Amundson


title: Time course progression of BMP4-treated hESC gene expressions under 4 % and 20 % oxygen conditions.

status: Public on May 10 2009

first: Toshihiko

last: Ezashi

address: 240a CS Bond Life Sciences Center

department: Animal Sciences

institute: University of Missouri-Columbia

summary:
H1 hESC were exposed to BMP4 (10 ng/ml) in absence of FGF2 for 0, 3, 12, 24, 72, and 120 h under both physiological (4 % O2) and atmospheric (20 % O2) conditions to identify candidate genes and gene networks associated with specification from totipotent precursor cells to trophoblast. RNA from cells under both conditions was isolated at each time point.
Approximately 32,000 probe sets (out of 40,391) provided a signal above background at one of the time points. Of these, 14,478 showed a ≥2-fold (plus or minus) change (p<0.05) under 4 % O2, and 18,580 under 20 % O2. The data indicate the potential usefulness of hESC grown in presence of BMP4 and absence of FGF2 for studying both the emergence of trophoblast from hESC precursors and for its subsequent differentiation over time, space and varied O2 concentrations.
Keywords: Genes and gene networks associated with specification from totipotent precursor cells to trophoblast

overall_design: Twelve sets of H1 hESC RNA were prepared from BMP4 treated cells for 0, 3, 12, 24, 72, and 120 h under both physiological (4 % O2) and atmospheric (20 % O2) and cultured on Matrigel coated six-well plate.

first: Laura

last: Schulz

first: Michael

last: Roberts


title: Regulatory and conventional T-cells

status: Public on May 11 2009

first: Christian

last: Schmidl

type: Genome binding/occupancy profiling by genome tiling array

type: Methylation profiling by genome tiling array


title: GAP-43 HZ and KO mouse barrel cortex show modifications in genes associated with synaptogenesis and barrel map formation

status: Public on Jun 01 2009

city: Syracuse

first: Frank

last: Middleton

address: 505 Irving Avenue

department: Neuroscience and Physiology

institute: SUNY Upstate Medical Univ

summary: Mice lacking the growth associated protein, GAP-43, (KO) show multiple deficits in forebrain axon guidance and cortical cell differentiation (Donovan and McCasland, 2005). As a result, GAP-43 KO mice fail to form barrels in mouse somatosensory cortex (S1) (Maier et al., 1999). GAP-43 heterozygous (HZ) mice show abnormalities in axonal pathfinding and show larger than normal barrels in layer IV S1 due to widely branched thalamocortical afferents (TCAs). Regardless of abnormalities during early development, HZ barrels become indistinguishable from WT by postnatal day 26. One explanation for these findings is that compensatory mechanisms may be activated in GAP-43 HZ cortex. We have used mRNA microarray expression analysis to gain a more comprehensive view of genes involved in GAP-43 signaling during barrel map formation. Using laser  microdissection , cortical cells of the barrel cortex were excised, RNA extracted and used in GeneChip analysis. Expression profiling and functional gene group analysis of RNA from WT, HZ, and KO cortex at postnatal day 5 was performed. We identified thousands of transcripts differentially expressed across the genotypes. Verification of selected changes in gene expression was accomplished using in situ hybridization. Our results suggest an adaptive modification in transcript expression of genes involved in cell-cell communication and synaptogenesis. These modifications appear important in forward and reverse signaling as well as maintaining synchrony between the cells. Compensatory up- and down regulation of synapse-associated genes may explain the reverse in HZ phenotype from P7 to P26. Moreover, these findings provide new insight into the role GAP-43 plays in several pathways associated with synaptogenesis and trans-synaptic signaling.

overall_design: 3 replicate RNA samples were prepared from laser microdissected barrel cortex samples of WT, HZ and KO mice at a single timepoint (postnatal day 5)

first: Emily

last: Kelly

first: James

last: McCasland

first: Ania

middle: K

last: Majewska


title: Lasp1 gene disruption is linked to enhanced cell migration and tumor formation

status: Public on Feb 12 2009

city: Augusta

first: Han

state: GA

department: IMMAG

institute: Medical College of Georgia

summary:
Chronic loss of Lasp1 alters the expression of other genes associated with cell motility/attachment, and/or other cellular functions.  Results provide new information showing that loss of Lasp1 leads to up- and down-regulation of genes involved in cell motility/attachment/growth.

Keywords: Genotype comparison

overall_design: Total RNA isolated from  Lasp1-/- MEFs compared to Lasp1+/+ MEFs.

first: Catherine

last: Chew

first: Xunsheng

last: Chen


title: Use of spermatozoal total RNA profiles to study gene-environment interactions in human germ cells

status: Public on Jan 28 2009

first: Joost

last: Linschooten

department: Health Risk Analysis & Toxicology

summary: Paternal exposure to genotoxic compounds is thought to contribute to diseases in their offspring. Therefore, mRNA profiles from sperm in ejaculates of cigarette smokers (N=4) were compared with non-smokers (N=4). Smoking behaviour was verified by assessing cotinine levels in seminal plasma. Gene-expression analysis was subsequently performed using microarray technology (Agilent human 4x44k) to investigate the use of gene-expression profiling as biomarker of gene-environment interactions in human testis

overall_design: The study investigated differential gene expression in spermatozoal RNA from 4 smokers as compared to 4 non-smokers. Two conditions: smoking or non-smoking. One individual per array, hybridized against a common reference sample.

middle: O

first: Frederik

last: van Schooten

first: Adolf

last: Baumgartner

first: Eduardo

last: Cemeli

last: van Delft

first: Diana

last: Anderson

first: Roger

last: Godschalk


title: Transcriptional profile of mouse lung during the fibrotic phase of the response to bleomycin

status: Public on Jul 07 2009

city: London

first: Chris

last: Scotton

address: 5 University Street

department: Medicine

institute: University College London

summary: Wildtype mice were given saline or bleomycin by oropharyngeal instillation. After 14 days, during the fibrotic phase of the response, lungs were dissected and total RNA was extracted and used for gene expression profiling. The aim was to identify those genes regulated during the development of fibrosis in this animal model of bleomycin-induced lung fibrosis.

overall_design: Wildtype male C57Bl/6J mice (8-10 weeks old) were used in the study, with three mice per group. Bleomycin (1mg/kg body weight in 50μl of saline) or saline was administered by oropharyngeal installation as described previously by Lakatos et al, Exp Cell Res, 2006, under light halothane-induced anaesthesia. After 14 days, lungs were removed, blotted dry and the trachea and major airways were excised before the separated lobes were snap frozen in liquid nitrogen. Lungs were then pulverized under liquid nitrogen, and the resulting lung powder was used for total RNA extraction using Trizol. Following DNase-treatment, clean-up, cDNA synthesis and cRNA synthesis, samples were hybridized to Affymetrix MOE430A genechips using standard protocols. The data were analyzed using RMA with quantiles normalization.

first: Rachel

last: Chambers

first: Robin

last: Johns

first: YC

last: Lee


title: MEF wt versus Med23-/- KO after 20% Serum Stimulation

status: Public on Apr 14 2009

city: Berkeley

first: Michael

middle: Andrew

last: Balamotis

address: 1 Cycotron Rd. Bld. 84

department: Life Sciences

institute: Lawrence Berkeley National Lab

summary: Affymetrix MOE430A arrays. Mouse embryonic fibroblasts (MEFs) from E11 passaged through crisis. Starved in 0.5% FBS for 16 h then stimulated by 20% serum final concentration for 30 minutes. The purpose was to identify genes affected by the loss of MED23 protein (subunit of the mediator complex). Samples were assayed in duplicate (Set 1 and Set 2) for starved state and serum state cells.

overall_design: Cells starved in low-serum (0.5%) for 16 h then add final conc. 20% FBS for 30 minutes. Harvest total RNA from duplicate samples. One sample set is kept starved and serves as the baseline. The other set is stimulated. This is done for both wild-type cell and the Med23-/- KO cells. We looked for gene expression fold changes greater than 2 (plus or minus) to find genes affected for serum stimulation by the loss of MED23, looking in detail at immediate early genes like Egr1.

first: Jennitte

middle: L

last: Stevens

first: Arnold

last: Berk


title: Analysis of wild-type and C mutant human HPIV1 and interferon beta treatment in human respiratory epithelial A549 cells

status: Public on Dec 22 2008

city: Bethesda

first: Jim

last: Boonyaratanakornkit

address: 50 South Dr, Bldg 50, Rm 6513

department: LID

institute: NIH - NIAID

summary:
HPIV1 is an important respiratory pathogen in children and the most common cause of viral croup. We performed a microarray-based analysis of gene expression kinetics to examine how wild-type (wt) HPIV1 infection altered gene expression in human respiratory epithelial cells and what role IFN-beta played in this response. We similarly evaluated HPIV1-P(C-), a highly attenuated and apoptosis-inducing virus that does not express any of the four C proteins, and HPIV1-C(F170S), a less attenuated mutant that contains a single point mutation in C and, like wt HPIV1, does not efficiently induce apoptosis, to examine the role of the C proteins in controlling host gene expression. We also used this data to investigate whether the phenotypic differences between the two C mutants could be explained at the transcriptional level. Mutation or deletion of the C proteins of HPIV1 permitted the activation of over 2000 cellular genes that otherwise would be repressed by HPIV1 infection. Thus, the C proteins profoundly suppress the response of human respiratory cells to HPIV1 infection. Cellular pathways targeted by the HPIV1 C proteins were identified and their transcriptional control was analyzed using bioinformatics. Transcription factor binding sites for IRF and NF-kappaB were over-represented in some of the C protein targeted pathways, but other pathways were dominated by less known factors such as forkhead transcription factor FOXD1. Surprisingly, the host response to the C knockout and C(F170S) mutants was very similar, and thus the phenotypic differences between these two viruses could not be explained at the host cell transcriptional level.

Keywords: Time course; response to viral infection; response to IFN-beta

overall_design: A549 cells were infected with wt HPIV1, C(F170S), or P(C-) in triplicate, and RNA was isolated at 6, 12, 24, and 48 hours.  A549 cells were also treated with IFN-beta in triplicate, and RNA was isolated at 6 and 24 hours.  Mock infection/treatment was performed in triplicate at each corresponding time point.  Overall, 42 samples and microarrays were analyzed.


title: Met1 or DB7 tumor gene expression

status: Public on Nov 30 2008

first: Kent

last: Hunter

address: 37/4048 37 Convent Drive

department: Center for Cancer Research

institute: National Cancer Institute

summary:
Metastasis predictive gene signatures can result from either somatic mutation, inherited polyrmorphism or both.  This experiment is designed to look at the gene expression differences due to differences in somatic mutations in the initiating oncogene, PyMT.  Met1 is from a fully metastatic FVB mammary tumor cell line, DB7 contains a mutation that permits tumor formation, but suppresses metastatic ability.

Keywords: Basal transcription profiles

overall_design: Mammary tumors from adult F1 animals from (AKR/J x PyMT) and (DBA/2J x PyMT) outcrosses was collected and arrayed on Affymetrics chip to identify basal differences in gene expression between the different genotypes


title: TCDD induced gene expression changes in dendritic cells

status: Public on Nov 25 2008

city: Duesseldorf

first: Markus

last: Frericks

address: Auf'm Hennekamp 50

department: Immunology

institute: Institute for Environmental Research

summary: Effect of the over activation of the aryl hydrocarbon receptor on gene expression of spleen derived dendritic cells.

overall_design: 8-12 week old, female C57BL6 mice were injected 10 µg/kg TCDD i.p. or solvent control. After 24 h mice were sacrificed and splenic dendritic cells purified by MACS sorting.

first: Susanne

last: Stutte

first: Charlotte

last: Esser


title: Effects of calorie restriction and exercise on mammary gland gene expression in C57BL/6 mice

status: Public on Dec 24 2008

first: Jackie

last: Lavigne

address: 6120 Executive Blvd. Rm. 6114

department: DCEG

institute: NCI/NIH

summary:
We performed a factorial experiment examining the effects of calorie restriction (CR) and exercise (EX) in mice.  CR mice received 70% of calories but 100% of all other nutrients compared to AL mice.  Food consumption, weight gain, and physical activity levels were recorded for 6 weeks.
Diet and exercise treatments, both alone and in combination, had significant effects on body composition and levels of physical activity.  Affymetrix oligo microarrays were used to determine global gene expression patterns in mammary gland total RNA. CR and EX had some overlapping but primarily unique effects on mammary gene expression, with CR affecting a much larger number of genes.  The gene changes presented suggest that CR and EX influence mammary gland development and potentially carcinogenesis through distinct pathways.

Keywords: 2 X 2 factorial mouse experiment; ad lib; calorie restriction; exercise; exercise + calorie restriction. Endpoints: body composition; bone density; gene expression in mammary gland

overall_design: Female C57BL/6 mice (9 weeks old) were randomized into 4 experimental groups: 1) food consumed ad libitum (AL); 2) AL with access to running wheels (AL+EX); 3) 30% CR; and 4) 30% CR with access to running wheels (CR+EX). RNA samples from animal mammary glands were analysed by Affymetrix oligo-microarray platform, in particular 10 samples from AL group (control), 9 samples from AL+EX group,  9 samples from CR group and 9 samples from CR+EX group were analysed.

first: Michela

last: Padovani

first: Gadisetti

middle: V

last: Chandramouli

first: Susan

middle: N

last: Perkins

first: J

last: Barrett

first: Stephen

last: Hursting

first: L.

middle: M

last: Bennett

first: David

last: Berrigan


title: Effects of spaceflight on murine skeletal muscle gene expression

status: Public on Dec 28 2008

city: Charleston

first: Jeremy

last: Barth

state: SC

address: 173 Ashley Ave, BSB 627

institute: MUSC

summary: Spaceflight results in a number of adaptations to skeletal muscle, including atrophy and shifts towards faster muscle fiber types. To identify changes in gene expression that may underlie these adaptations, microarray expression analysis was performed on gastrocnemius from mice flown on the STS-108 shuttle flight (11 days, 19 hours) versus mice maintained on earth for the same period. Additionally, to identify changes that were due to unloading and reloading, microarray analyses were conducted on calf muscle from ground-based mice subjected to hindlimb suspension (12 days) and mice subjected to hindlimb suspension plus a brief period of reloading (3.5 hours) to simulate the time between landing and sacrifice of the spaceflight mice.

overall_design: There are five experimental groups in this study: 1) mouse gastrocnemius, spaceflight for 11 days 19hr, n=4; 2) mouse gastrocnemius, animal enclosure module for 11 days, 19h, n=4; 3) mouse calf muscle, hindlimb suspension for 12 days, n=5; 4) mouse calf muscle, hindlimb suspension for 12 days plus reloading for 3.5 hr, n=5; 5) mouse calf muscle, no experimental treatment, n=5.

last: Allen

first: Ted

last: Bateman


title: MOE430A Analysis of Dll3 mutant vs. wild-type 9.5 dpc somite-level tissue

status: Public on Mar 11 2009

first: Kenro

last: Kusumi

department: School of Life Sciences

institute: Arizona State University

summary:
Delta-like 3 (Dll3) is a divergent ligand and modulator of the Notch signaling pathway only identified so far in mammals. Null mutations of Dll3 disrupt cycling expression of Notch targets Hes1, Hes5, and Lfng, but not of Hes7.  Compared with Dll1 or Notch1, the effects of Dll3 mutations are less severe for gene expression in the presomitic mesoderm, yet severe segmentation phenotypes and vertebral defects result in both human and mouse.  Reasoning that Dll3 specifically disrupts key regulators of somite cycling, we carried out functional analysis to identify targets accounting for the segmental phenotype. Using microdissected embryonic tissue from somitic and presomitic mesodermal tissue, we identified new genes enriched in these tissues, including Limch1, Rphn2, and A130022J15Rik.  Surprisingly, we only identified a small number of genes disrupted by the Dll3 mutation. These include Uncx, a somite gene required for rib and vertebral patterning, and Nrarp, a
 regulator of Notch/Wnt signaling in zebrafish and a cycling gene in mouse. To determine the effects of Dll3 mutation on Nrarp, we characterized the cycling expression of this gene from early (8.5 dpc) to late (10.5 dpc) somitogenesis. Nrarp displays a distinct pattern of cycling phases when compared to Lfng and Axin2 (a Wnt pathway gene) at 9.5 dpc but appears to be in phase with Lfng by 10.5 dpc.  Nrarp cycling appears to require Dll3 but not Lfng modulation.  In Dll3 null embryos, Nrarp displayed static patterns.  However, in Lfng null embryos, Nrarp appeared static at 8.5 dpc but resumed cycling expression by 9.5 and dynamic expression at 10.5 dpc stages.  By contrast, in Wnt3a null embryos, Nrarp expression was completely absent in the presomitic mesoderm. Towards identifying the role of Dll3 in regulating somitogenesis, Nrarp emerges as a potentially important regulator that requires Dll3 but not Lfng for normal function.

overall_design: To enrich for genes in the somite level tissues that are specifically disrupted by Dll3 mutation, we compared microdissected tissues from wild-type and Dll3 mutant embryos. We generated biological replicate pools from Dll3+/+ (wild-type) or Dll3neo/neo embryos for a total of six pools. Microarray analysis using Affymetrix MOE430A arrays was carried out on the biological pool triplicates for both wild-type and mutant genotypes.

first: William

last: Sewell

first: Sewell

middle: B

last: Sparrow

first: Allanceson

middle: J

last: Smith

first: Dorian

last: Gonzalez

first: Eric

middle: F

last: Rappaport

first: Sally

last: Dunwoodie