title: trkB.T1 WT versus trkB.T1 KO expression data following spinal cord injury (SCI)

status: Public on Aug 05 2013

city: Baltimore

first: Susan

last: Dorsey

address: 655 West Lombard Street

department: School of Nursing

institute: University of Maryland Baltimore

summary:
We profiled spinal cord tissue at the site of a moderate contusion injury at the level of the thoracic spinal cord
We examined several timepoints following injury, including sham and days 1,3 and 7 following injury and compared differential expression of genes within a genotype and across genotypes (trkB.T1KO/trkB.T1WT) at each timepoint.

overall_design: Tissue was profiled at baseline (sham) condition and then 1, 3 and 7 days after thoracic moderate contusion injury

first: Alan

middle: I

last: Faden


title: Menin-regulated genes in bone marrow B-cell progenitors

city: Hanover

first: Bin

middle: E

last: Li

state: New Hampshire

address: Remsen 725

department: Genetics

country: USA

institute: Dartmouth College

summary:
MLL1 translocations encode fusion proteins retaining the N-terminus of MLL1, which interacts with the tumor suppressor, menin. This interaction is essential for leukemogenesis, thus is a promising drug target. However, wild-type MLL1 plays a critical role in sustaining hematopoietic stem cells (HSCs), therefore disruption of an essential MLL1 cofactor would be expected to obliterate normal hematopoiesis. Here we show that rather than working together as a complex, menin and MLL1 regulate distinct pathways during normal hematopoiesis, particularly in HSCs and B-cells. We demonstrate the lack of genetic interaction between menin and MLL1 in steady-state or regenerative hematopoiesis and in B-cell differentiation despite the fact that MLL1 is critical for these processes. In B-cells, menin- or MLL1-regulated genes can be classified into three categories: 1) a relatively small group of co-regulated genes including previously described targets Hoxa9 and Meis1 but also Mecom and Eya1, and much larger groups of 2) exclusively menin-regulated and 3) exclusively MLL1-regulated genes. Our results highlight the large degree of independence of these two proteins and demonstrate that menin is not a requisite cofactor for MLL1 during normal hematopoiesis. Furthermore, our data support the development of menin-MLL1 disrupting drugs as safe and selective leukemia targeting agents.
We performed gene expression analysis to determine the genes deregulated in B-cell progenitors upon loss of menin.

overall_design: Fraction B pro-B cells (defined as B220+CD43+HSA+BP-1- BM cells) were sorted from four MenF/F and four Rag1-cre;MenF/F mice of three weeks old. Total RNA was amplified once, labeled, fragmented and hybridized to Affymerix GeneChip Mouse Genome 430 2.0 array.

first: Patricia

last: Ernst


title: Sphingosine-1-phosphate phosphatase 1 regulates keratinocyte differentiation and epidermal homeostasis

status: Public on Aug 09 2013

city: Bethesda

first: WeiPing

last: Chen

state: MD

address: Bldg 8, Room 1A11, NIDDK/NIH

department: GCL

institute: NIDDK/NIH

summary: Sphingosine 1-phosphate (S1P) is a bioactive lipid whose levels are tightly regulated by its synthesis and degradation. Intracellularly, S1P is dephosphoryled by the actions of two S1P-specific phosphatases, sphingosine 1-phosphate phosphatase 1 and 2.  To identify the physiologic functions of S1P phosphatase 1, we have studied mice with its gene, Sgpp1, deleted. Sgpp1-/- mice appeared normal at birth but during the first week of life, they exhibited stunted growth, suffered desquamation, and most died before weaning. Interestingly, the epidermal permeability barrier developed normally during embryogenesis.  Sgpp1 -/- pups and surviving adults exhibited epidermal hyperplasia and abnormal expression of keratinocyte differentiation markers. Keratinocytes isolated from Sgpp1 -/- skin had increased intracellular S1P levels, and expressed a gene expression profile that indicated enhanced differentiation. The results reveal S1P metabolism as a regulator of keratinocyte differentiation and epidermal homeostasis.

overall_design: Comparison of KO vs. WT with five replications per treatment sample

first: Maria

middle: L

last: Allende

first: Laura

middle: M

last: Sipe

first: Galina

last: Tuymetova

first: Weiping

first: Richard

last: Proia


title: Gene expression profile in the spleen of mice fed Lactobacillus brevis KB290

city: Nasushiobara

first: Yuichiro

last: Fukui

state: Tochigi

address: 17 Nishitomiyama

department: Nature & Wellness Research Department

country: Japan

institute: Research Institute, Kagome Co., Ltd.

summary:
Lactic acid bacteria confer a variety of health benefits. Here we investigate the mechanisms by which Lactobacillus brevis KB290 enhances cell-mediated cytotoxic activity. We fed a diet containing KB290 (3 × 10^9 colony-forming units/g) , or potato starch, to 9-week-old female BALB/c mice for 1, 4, 7, or 14 days and examined the cytotoxic activity of splenocytes was measured. RNA was extracted from the spleen and analyzed for gene expression by DNA microarray.
KB290 enhanced the cell-mediated cytotoxic activity of splenocytes. The Gene Ontology (GO) terms related to immune process were significantly enriched in up-regulated gene set for 7 days and the GO terms related to cellular process were enriched in down-regulated gene set on days 4 and 7. Among the GO terms related to immune process, positive regulation of T cell-mediated cytotoxicity was existed. Almost all of the genes included in the term encoded MHC class I molecules, which are involved in the presentation of antigen to CD8+ cytotoxic T cells. On the other hand, the over-represented Kyoto Encyclopedia of Genes and Genomes pathways among the up-regulated genes were those for natural killer cell-mediated cytotoxicity and antigen processing and presentation on day 1. Although the up-regulated genes involved in antigen processing and presentation for stimulation of CD8+ cytotoxic T cells were not observed on day 14, some genes involved in T cell and natural killer cell activation remained up-regulated until day 14. The sequential gene expression profiling reflected the changes in cytotoxic activity during KB290 feeding. These results suggest that the enhanced cytotoxic activity could have been caused both by activation of natural killer cells and by CD8+ cytotoxic T cells stimulated via MHC class I presentation.

overall_design: Specific-pathogen-free female BALB/c mice, aged 8 weeks, were purchased from Charles River Laboratories Japan, Inc. They (n = 48) were divided into two groups, control and KB290 (4 cages per group) with equal mean body weights. They were allowed to free access to a commercial normal diet CE-2 (CLEA Japan, Inc.) and sterile water during one-week acclimation period. Then, they received lyophilized KB290 for the treatment group diet (3x109 cfu/g) or 5.8% (w/w) potato starch (Nippon Starch Chemical) for the control group diet for 1, 4, 7, and 14 days. Daily intake of KB290 containing diet per treated mouse was 3.99g, or about 1 × 1010 cfu. On day 1, 4, 7, and 14, six mice in each group were euthanized and their spleens were sampled for Cell-mediated cytotoxicity and DNA microarray assay.

first: Erika

last: Sasaki

first: Nobuo

last: Fuke

first: Yuji

last: Nakai

first: Tomoko

last: Ishijima

first: Keiko

last: Abe

first: Nobuhiro

last: Yajima


title: Pax6 is required for normal cell cycle exit and the differentiation kinetics of retinal  progenitor cells.

status: Public on Aug 01 2013

city: Tel Aviv

first: Ruth

last: Ashery-Padan

state: Select a State or Province

address: Tel Aviv University

department: Department of Human Molecular Genetics and Biochemistry

country: Israel

institute: Tel-Aviv University

summary: The coupling between cell-cycle exit and onset of differentiation is a common feature throughout the developing nervous system, but the mechanisms that link these processes are mostly unknown. Although the transcription factor Pax6 was implicated in both proliferation and differentiation of multiple regions within the CNS, its contribution to the transition between these successive states remains elusive. To gain insight into the role of Pax6 during the transition from proliferating progenitors to differentiating precursors, we investigated cell-cycle and transcriptomic changes occurring in Pax6- retinal progenitor cells (RPCs). Our analyses revealed a unique cell-cycle phenotype of the Pax6-deficient RPCs, which included a reduced number of cells in the S phase, an increased number of cells exiting the cell cycle, and delayed differentiation kinetics of Pax6- precursors. These alterations were accompanied by co-expression of factors that promote (Ccnd1, Ccnd2, Ccnd3) and inhibit (P27kip1 and P27kip2) the cell cycle. Further characterization of the changes in transcription profile of the Pax6-deficient RPCs revealed abrogated expression of multiple factors which are known to be involved in regulating proliferation of RPCs, including the transcription factors Vsx2, Nr2e1, Plagl1 and Hedgehog signaling. These findings provide novel insight into the molecular mechanism mediating the pleiotropic activity of Pax6 in RPCs. The results further suggest that rather than conveying a linear effect on RPCs, such as promoting their proliferation and inhibiting their differentiation, Pax6 regulates multiple transcriptional networks which function simultaneously, thereby conferring the capacity to proliferate, assume multiple cell fates and execute the differentiation program into retinal lineages.

overall_design: The data contains 3 control and 3 Pax6 negative samples representing biological repeats. Each sample was prepared from ~1.8 million cells taken from the distal retina of either E12 alpha-Cre or Pax6 floxed alpha-Cre animals. Distally located retinal progenitors expressing Cre and eGFP were separated using FACS.

first: Chen

last: Farhy

first: Micael

last: Elgart

first: Varda

last: Oron-Karni

first: Yotam

last: Menuchin

last: Asher-Padan


title: Induction of the mouse germ cell fate by transcription factors in vitro [exp1]

status: Public on Aug 04 2013

city: Kyoto

first: Fumio

last: NAKAKI

address: Yoshidakonoe-cho, Sakyo-ku

department: Graduate School of Medicine

institute: Kyoto University

summary: The germ cell lineage ensures the continuity of life through the generation of male and female gametes, which unite to form a totipotent zygote. We have established a culture system that recapitulates the mouse germ-cell specification pathway: Using cytokines, embryonic stem cells (ESCs)/induced pluripotent stem cells (iPSCs) are induced into epiblast-like cells (EpiLCs) and then into primordial germ cell-like cells (PGCLCs) with capacity both for spermatogenesis and oogenesis, creating an opportunity for understanding and regulating mammalian germ cell development in both sexes in vitro. Here we show that, without cytokines, simultaneous over-expression of three transcription factors (TFs), Blimp1 (also known as Prdm1), Prdm14 and Tfap2c (also known as AP2γ), directs EpiLCs, but not ESCs, swiftly and highly efficiently into a PGC state with endogenous transcription circuitry. The induction of the PGC state on EpiLCs minimally requires Prdm14 but not Blimp1 or Tfap2c. The TF-induced PGC state reconstitutes key transcriptome and epigenetic reprogramming in PGCs, but bypasses a mesodermal program that accompanies PGC specification in vivo and in vitro by cytokines including BMP4. Importantly, the TF-induced PGC-like cells robustly contribute to spermatogenesis and fertile offspring. Our findings provide not only a novel insight into the transcriptional logic that creates a germ cell state, but also a foundation for the TF-based reconstitution and regulation of mammalian gametogenesis.

overall_design: Aim of this analysis is characterization of transcription factor-induced primordial germ cells (TF-PGCLCs) compared with cytokine-induced primordial germ cells (Ck-PGCLCs) (Hayashi et al., 2011, Cell), epiblast-like cells (EpiLCs) (Hayashi et al., 2011, Cell), and embryonic stem cells (ESCs) and identification of genes differentially expressed among them. TF-PGCLCs induced by multiple combinations of TFs (Blimp1 (B), Prdm14 (P14), and Tfap2c (A) (BP14A), BP14, P14A, P14) on day 2 and 4 (for BP14A cells) of the induction were also compared. Parental clone without exogenous TFs cultured with doxycycline, are also included as a negative control. Ck-PGCLCs day 2 and day 4 samples, which are previously unreported, EpiLCs and ESCs used in this study were also included. Overexpression of exogenous three TFs in ESCs yields stella-ECFP (SC) positive cells, which were sorted and included in the analysis. cDNA samples, prepared from approximately 20,000 cells, were amplified with a quantitative global PCR method (Kurimoto et al., 2006, Nucleic Acids Research). Two biological duplicates for each cell type were analyzed. Samples from GSE30056 were also included and reanalysed (GSM1070855-GSM1070864).

last: Nakaki

first: Katsuhiko

last: Hayashi

first: Hiroshi

last: Ohta

first: Kazuki

last: Kurimoto

first: Yukihiro

last: Yabuta

first: Mitinori

last: Saitou


title: Induction of the mouse germ cell fate by transcription factors in vitro [exp2]

overall_design: Aim of this analysis is identification of genes whose expression was altered by each of key transcription factor for transcription factor-induced primordial germ cells (TF-PGCLCs) induction (Blimp1 (B), Prdm14 (P14), and Tfap2c (A)). Both of epiblast-like cells (EpiLCs) (Hayashi et al., 2011, Cell) and aggregates of EpiLCs cultured with doxycycline on day 1 were harvested for 5 cell lines, including BP14A (Clone #3-3), B (#2-4), P14 (#7-109), A (#8-2), and the parental clone (BVSCR26rtTA embryonic stem cells).  Total RNA was isolated and analyzed. Two biological duplicates for each cell type were included.


title: Location of indigenous human HSCs reveals functional properties of HSCs that are dictated by anatomic and cellular architecture of bone marrow II

city: Hamilton

first: Mickie

last: Bhatia

state: Ontario

address: 1200 Main Street West

department: Stem Cell and Cancer Research Institute (SCC-RI)

country: Canada

institute: McMaster University

summary: Demonstration of hematopoietic stem cells (HSCs) was first shown in the mouse and was dependent on recipient bone marrow (BM) to support in vivo multilineage hematopoietic reconstitution, thereby illustrating non-cell-autonomous requirements for HSC functions. Murine studies have defined microanatomic compartments in the BM comprised of osteoblasts, mesenchymal cells, subsets of vasculature, and innervating neural cells functioning as an HSC-supportive niche. Despite the potential clinical applications, analyses of putative HSCs in the BM of humans has not been examined. Here, using human bone biopsies, we provide evidence of HSC propensity to endosteal regions of Trabecular Bone Area (TBA). Independent of phenotypic definitions based on prospective isolation, functional studies indicate that human HSCs residing in the TBA of human and transplanted recipients had superior regenerative and self-renewal capacity and are molecularly distinct to those repopulating the Long Bone Area (LBA). Consistent with the non-cell-autonomous nature of HSC function, osteoblasts in the TBA possess unique characteristics and expressed a key network of factors including those involving Notch activity which could regulate TBA vs. LBA location of human HSCs in vivo. Our study illustrates that human-mouse xenografts provide a surrogate to indigenous human HSC in the BM, and demonstrates that BM architecture plays a critical role in defining functional properties of human HSCs.

overall_design: Total bone marrow cells were collected from NOD/SCID recipient adult mice. Osteoblast cells (OB) were sorted based on five paramater markers combination Lin- CD45- CD31- Sca1- CD51+ using a FACSAria II (BD). Total RNA from purified populations was extracted and amplified as described previously (Shojaei et al., 2005). Amplified-labeled RNA was hybridized to HG-U133Plus v2.0 chip.

first: Borhane

last: Guezguez

first: Clinton

middle: V

last: Campbell

first: Allison

last: Boyd

first: Francis

last: Karanu

first: Fanny

last: Casado

first: Christine

last: Di Cresce

first: Tony

middle: J

last: Collins

first: Zoya

last: Shapovalova

first: Anargyros

last: Xenocostas


title: Induction of the mouse germ cell fate by transcription factors in vitro

last: NAKAKI

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

overall_design: Refer to individual Series


title: Expression analysis of BM cells of ASXL-MT induced MDS mice

status: Public on Jul 31 2013

city: Tokyo

first: Daichi

last: Inoue

address: 4-6-1 Shirokanedai, Minato-ku

institute: Division of Cellular Therapy, Advanced Clinical Research Center, The Institute of Medical Science, The University of Tokyo

summary: Recurrent mutations in ASXL1 are found in various hematological malignancies and are associated with poor prognosis. In particular, ASXL1 mutations are frequently found in patients with hematological malignancies associated with myelodysplasia including myelodysplastic syndromes (MDS), and chronic myelomonocytic leukemia. Although loss-of-function ASXL1 mutations promote myeloid transformation, a large subset of ASXL1 mutations is thought to result in stable truncation of ASXL1. Here we demonstrate that C-terminal truncating ASXL1 mutations (ASXL1-MT) inhibit myeloid differentiation and induce MDS-like disease in mice, displaying all the features of human MDS including multi-lineage myelodysplasia, pancytopenia and occasional progression to overt leukemia. Concerning the molecular mechanisms, ASXL1-MT derepressed expression of Hoxa9 and miR-125a through inhibiting PRC2-mediated methylation of H3K27. miR-125a targeted expression of a surface receptor Clec5a, which was found to supports for myeloid differentiation. In addition, HOXA9 expression was high in MDS patients with ASXL1 mutations while Clec5a expression was generally low in MDS patients. Thus, ASXL1-MT induced MDS-like disease in mice via derepression of Hoxa9 and miR-125a, and Clec5a downregulation. Our data provide evidence for a novel axis of MDS pathogenesis (ASXL1 mutations-upregulation of HoxA9 and miR-125a-downregulation of Clec5a) and implicate both ASXL1 mutants and miR-125a as therapeutic targets in MDS.

overall_design: BM cells derived from mock-transplanted mice and ASXL1-MT transplanted mice were incubated with biotinylated antibodies for CD3e, B220, and TER-119, followed by incubation with streptavidin Micro Beads (Miltenyi Biotec). The marker-negative fraction was separated with LS Columns (Miltenyi Biotec). Using the sorted-BM cells, we compared the expression proliles between 3 sorted-BM cells with mock and 3 sorted-BM cells with ASXL1-MT. Total RNA was extracted by Trizol reagent (Invitrogen) according to the manufacturer’s protocol. Double-stranded cDNA was synthesized from 5 μg of total RNA with oligo (dT)24 T7 primer, amplified with T7 RNA polymerase up to approximately 50 μg of cRNA, and hybridized to Affymetrix Mouse Expression array 430A, which contains 45000 probe sets for 39000 transcripts and variants from over 34000 well-characterized mouse genes (Affymetrix). After washing and staining, the arrays were scanned on the GeneChip system confocal scanner (Affymetrix). The intensity for each feature of the array was captured with Affymetrix Microarray Suite (MAS) Version 5.0 software. Gene set enrichment analysis was performed by using Gene Ontology gene sets from the Molecular Signatures Database (http://www.broad.mit.edu/gsea/msigdb/).

first: Hiroyuki

last: Aburatani


title: Expression analysis of 32Dcl3 cells expressing ASXL-MT in the presence of  IL-3 or G-CSF

overall_design: Using 32Dcl3 cells transduced with pMYs-IG (mock) and pMYs-FLAG-ASXL1-MT-IG, we compared the expression profiles of 32Dcl3 cells with mock or ASXL1-MT under G-CSF stimulation at 4 time points, including 0hr (IL-3), 2hr, 6hr and 24hrs. Total RNA was extracted by Trizol reagent (Invitrogen) according to the manufacturer’s protocol. Double-stranded cDNA was synthesized from 5 μg of total RNA with oligo (dT)24 T7 primer, amplified with T7 RNA polymerase up to approximately 50 μg of cRNA, and hybridized to Affymetrix Mouse Expression array 430A, which contains 45000 probe sets for 39000 transcripts and variants from over 34000 well-characterized mouse genes (Affymetrix). After washing and staining, the arrays were scanned on the GeneChip system confocal scanner (Affymetrix). The intensity for each feature of the array was captured with Affymetrix Microarray Suite (MAS) Version 5.0 software. Gene set enrichment analysis was performed by using Gene Ontology gene sets from the Molecular Signatures Database (http://www.broad.mit.edu/gsea/msigdb/)


title: Gene expression in epithelial, EMT (epithelial-mesenchymal transition) and MET (mesenchymal-epithelial transition) cells

status: Public on Jul 26 2013

city: Worcester

first: cheng

last: chang

state: MA

address: 364 Plantation Street, LRB 470X

institute: Umass Medical School

summary:
NMuMG is an epithelial cell line that can be induced into EMT by TGF-β treatment or MET by TGF-β withdrawl. During EMT, several marker genes were downregulated/upregulated, which is consistent with its mesenchymal phenotype.
Transcription factors that are regulated during EMT and its reverse process MET are candidate genes for the regulations of the EMT marker genes.

overall_design: NMuMG cells treated with vehicle, TGF-β for 11 days, or 11days of TGF-β treatment followed by TGF-β withdrawl for another 13 days. RNA from these 3 conditions of NMuMG were extracted and subject to microarray analysis

first: Xiaofang

last: Yang

first: Cheng

last: Chang


title: Expression profiles for paediatric brain tumours

status: Public on Jul 29 2013

city: London

first: Denise

last: Sheer

address: Blizard Institute, 4 Newark Street

department: Neuroscience & Trauma

country: United Kingdom

institute: Barts & The London School of Medicine & Dentistry

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


title: Genome-wide expression of the epithelial layer cells of mice injected with Clostridium difficile Toxin A and B

status: Public on Jul 30 2013

city: Charlottesville

first: Kevin

middle: Michael

last: D'Auria

state: VA

address: 415 Lane Road, Room 2041

department: Biomedical Engineering

institute: University of Virginia

summary: Toxin A (TcdA) and Toxin B (TcdB), of the pathogen Clostridium difficile, are virulence factors that cause gross pathologic changes (e.g. inflammation, secretion, and diarrhea) in the infected host, yet the molecular and cellular pathways leading to observed host responses are poorly understood. To address this gap, TcdA and/or TcdB were injected into the ceca of mice and the genome-wide transcriptional response of epithelial layer cells was examined. Bioinformatic analysis of gene expression identified sets of cooperatively expressed genes. Further analysis of inflammation associated genes revealed dynamic chemokine responses.

overall_design: In total, 32 samples were analyzed (one microarray per mouse). The sample groups are separated by two factors: Toxin (TcdA, TcdB, TcdA+TcdB, or Sham injection) and endpoint (2, 6, or 16h). TcdA+B at 16h was not included, leaving 11 sample groups. Each sample group included biological triplicates, except TcdA+TcdB at 6h (one array) and Sham injection at 16h (four arrays).

first: Glynis

last: Kolling

first: Gina

last: Donato

first: Mary

middle: C

last: Gray

first: Cirle

middle: A

last: Warren

first: Erik

last: Hewlett

first: Jason

last: Papin


title: Gene expression in Fut8+/+ and Fut8-/- MEFs

city: Wako-shi

first: ayako

last: kurimoto

state: Saitama

address: Hirosawa

institute: RIKEN

summary: Effect of Fut8 deletion in MEF

overall_design: Fut8MEF was cultured in 10cm dish (WT,KO n=3). The MEFs were submitted this microarray analysis to compare the gene expression between Fut8+/+ and Fut8-/- MEFs.

first: Ayako

last: Kurimoto

first: Shinobu

last: Kitazume

first: Yasuhiko

last: Kizuka

first: Kazuki

last: Nakajima

first: Ritsuko

last: Oka

first: Reiko

last: Fujinawa

first: Hiroaki

last: Korekane

first: Yoshiki

last: Yamaguchi

first: Yoshinao

last: Wada

first: Naoyuki

last: Taniguchi


title: DNA damage-induced differentiation of NSC

status: Public on Jul 25 2013

city: Trieste

first: Paola

last: Roncaglia

state: TS

address: via Bonomea 265

department: Neurobiology

country: Italy

institute: SISSA/ISAS (International School for Advanced Studies)

summary:
Murine ES-derived neural stem cells (NSC) were not irradiated (ctrl) or irradiated with 10Gy and cultured for 7 days (irr).
The goal was to study the gene expression changes in NSC at d7 after irradiation.

overall_design: Total RNA was extracted from 4 ctrl and 4 irr samples (biological quadruplicates).

first: Leonid

last: Schneider

first: Fabrizio

last: d'Adda di Fagagna


title: Expression data from renal cortex of ICR-derived Glomerulonephritis (ICGN) mice and ICR mice

city: Osaka

first: Kotaro

last: Tamura

address: 2-1-6, Kashima, Yodogawa-ku

institute: Astellas Pharma Inc.

summary: ICR-derived glomerulonephritis (ICGN) mice is a novel inbred strain of mice with a hereditary nephrotic syndrome. Deletion mutation of tensin 2 (Tns2), a focal adhesion molecule, has been suggested to be responsible for nephrotic syndrome in ICGN mice, however, existence of other associative factors has been suggested. To identify additional associative factors and to better understand onset mechanism of nephrotic syndrome in ICGN mice, comprehensive gene expression analysis using DNA microarray was conducted. Immune-related pathways were markedly altered in ICGN mice kidney as compared with ICR mice. Furthermore, gene expression level of complement component 1, s subcomponent (C1s), whose human homologue has been reported to associate with lupus nephritis, was markedly low in ICGN mice kidney.

overall_design: RNA from renal cortex of 4- and 8-week-old ICGN and ICR mice was extracted and processed for hybridization on Affymetrix microarrays (N=3).

first: Kozue

last: Uchio-Yamada


title: Otitis Media Impact on Middle Ear

status: Public on Jul 23 2013

city: Portland

first: Carol

middle: J.

last: MacArthur

state: OR

address: 3181 SW Sam Jackson Park Rd

department: Otolaryngology

institute: Oregon Health and Science University

summary:
Objective: Otitis media is known to alter expression of cytokine and other genes in the mouse middle ear and inner ear. However, whole mouse genome studies of gene expression in otitis media have not previously been undertaken. Ninety-nine percent of mouse genes are shared in the human, so these studies are relevant to the human condition.
Methods: To assess inflammation-driven processes in the mouse ear, gene chip analyses were conducted on mice treated with trans-tympanic heat-killed Hemophilus influenza using untreated mice as controls. Middle and inner ear tissues were separately harvested at 6 hours, RNA extracted, and samples for each treatment processed on the Affymetrix 430 2.0 Gene Chip for expression of its 34,000 genes.
Results:  Statistical analysis of gene expression compared to control mice showed significant alteration of gene expression in 2,355 genes, 11% of the genes tested and 8% of the mouse genome.    Significant middle and inner ear upregulation (fold change >1.5, p<0.05) was seen in 1,081 and 599 genes respectively.  Significant middle and inner ear downregulation (fold change <0.67, p<0.05) was seen in 978 and 287 genes respectively. While otitis media is widely believed to be an exclusively middle ear process with little impact on the inner ear, the inner ear changes noted in this study were numerous and discrete from the middle ear responses. This suggests that the inner ear does indeed respond to otitis media and that its response is a distinctive process.  Numerous new genes, previously not studied, are found to be affected by inflammation in the ear.
Conclusion: Whole genome analysis via gene chip allows simultaneous examination of expression of hundreds of gene families influenced by inflammation in the middle ear.  Discovery of new gene families affected by inflammation may lead to new approaches to the study and treatment of otitis media.

overall_design: There are 8 control samples and 9 samples trans-tympanically injected with H flu 10e9 for 6 hours.  Each sample is from a single animal.

first: Fran

last: Hausman

first: Beth

last: Kempton

first: Dongseok

last: Choi

first: Dennis

middle: R

last: Trune


title: Otitis Media Impact on Inner Ear

overall_design: There are 6 control samples and 8 samples trans-tympanically injected with H flu 10e9 for 6 hours.  Each sample is a pool of 4 animals


title: Microarray gene expression profiling of transgenic mice with myocardium-specific over-expression of fatty acid synthase (FASN)

city: Zurich

first: Ursula

last: Quitterer

address: Winterthurerstrasse 190

department: Molecular Pharmacology

country: Switzerland

institute: ETH Zurich

summary: The fatty acid synthase (FASN) is the major fat synthesizing enzyme. FASN is an indispensable enzyme because mice with genetic deletion of Fasn are not viable. Apart from its physiological function, previous studies indicated that FASN could also exert a pathophysiological role, in the heart, because patients with heart failure showed up-reguation of FASN. To investigate the in vivo function of FASN up-regulation in the heart, we generated mice with myocardium-specific expression of FASN under control of the alpha-MHC promoter. Two different founder lines were generated with high and low FASN over-expression. Microarray gene expression profiling of heart tissue was performed of heart tissue from transgenic mice with high and low FASN expression

overall_design: Microarray gene expression profiling was performed with heart tissue isolated from three study groups: (i) Transgenic mice with high cardiac FASN expression, (ii) transgenic mice with low cardiac FASN expression, and (iii) B6 control mice.

first: Joshua

last: Abd Alla


title: ZNF365 promotes stability of fragile sites and telomeres

city: New york

first: Jihye

last: Paik

state: NY

address: 1300 York Ave.

department: Pathology

institute: Weill Cornell Medical College

summary: Critically short telomeres activate cellular senescence or apoptosis, as mediated by the tumor suppressor p53, but in the absence of this checkpoint response, telomere dysfunction engenders chromosomal aberrations and cancer. Here, analysis of p53-regulated genes activated in the setting of telomere dysfunction identified Zfp365 (ZNF365 in humans) as a direct p53 target that promotes genome stability. Germline polymorphisms in the ZNF365 locus are associated with increased cancer risk, including those associated with telomere dysfunction.  On the mechanistic level,  ZNF365 suppresses expression of a subset of common fragile sites (CFS) including telomeres.  In the absence of ZNF365, defective telomeres engage in aberrant recombination of telomere ends, leading to increased telomere sister chromatid exchange (T-SCE) and formation of anaphase DNA bridges, including ultra-fine DNA bridges (UFB), and ultimately increased cytokinesis failure and aneuploidy. Thus, the p53-ZNF365 axis contributes to genomic stability in the setting of telomere dysfunction.

overall_design: We expressed an inducible p53 allele encoding a p53-estrogen receptor fusion protein (p53ER) that becomes functional upon addition of 4-hydroxytamoxifen (4-OHT) in TKO cells. We chose a time point of 4 hours post-4-OHT induction to catalog potential direct targets.

first: Ji-hye


title: Expression data from GTF2i mutated ES cells

status: Public on Jul 12 2013

city: Barcelona

first: Victoria

last: Campuzano

address: Dr Aiguader, 88

department: CEXS

country: Spain

institute: Universitat Pompeu Fabra

summary: Data present the expression analysis of different mouse ES cell line with altered expression of GTF2I.

overall_design: We used microarrays to detail the global programme of gene expression underlying altered expression of GTF2I and identified distinct classes of deregulated genes

first: Maria

last: Segura-Puimedon

first: Cristina

last: Borralleras

first: Luis

last: Perez-Jurado


title: Translational activation of developmental mRNAs during neonatal mouse testis development

status: Public on Jul 27 2013

city: Greenville

first: Christopher

middle: B

last: Geyer

state: NC

address: 600 Moye Boulevard, Mail Stop 620

department: Anatomy and Cell Biology

institute: East Carolina University

summary:
The sequence of gene regulatory events that drive neonatal germ cell development in the mammalian testis is not yet clear. We assessed changes in mRNA utilization in the neonatal testis at 1 and 4 dpp, times when the testis contains quiescent gonocytes (1 dpp) and proliferating spermatogonia (4 dpp). There are not thought to be major changes in the nature or number of somatic cells over that interval.
We used microarrays to detail the global expression levels of mRNA distribution between non-translating mRNAs and efficiently translating mRNAs during testis development at 1 dpp and 4 dpp

overall_design: Extracts of mouse testes from 1 dpp and 4 dpp CD-1 mice were fractionated over a sucrose gradient in triplicate. Gradients were fractionated using an ISCO gradient fractionation system equipped with a UA-6 detector. The position of the 80S peak defined the boundary between translating and non-translating mRNAs.  Pooled non-polysomal (non-translating; fractions 1-3) and heavy polysomal (efficiently translating, fractions 7-13) RNAs were isolated from sucrose gradient fractions for hybridization on Affymetrix 420 2.0 microarrays.

first: Chappell

last: Vesna

first: Geyer

last: Christopher


title: Otitis Media Impact on Ear


title: Expression data from neurospheres derived from the neocortex, striatum and subventricular zones of the adult mouse brain

status: Public on Oct 01 2013

city: Cincinnati

first: Masato

last: Nakafuku

state: OH

address: 3333 Burnet Avenue

department: Developmental Biology

institute: Cincinnati Children's Hospital Medical Center

summary:
Differential gene expression profiles of neurospheres derived from different regions of the adult brain.
In this dataset, we include data on triplicated biological samples from each of the following brain regions: neocortex, striatum, and subventricular zone. We also include  duplicated data on neurospheres derived from the dorsal and ventralforebrain neural tubes and one spinal cord of E14.5 mouse embryos for comparison.

overall_design: Fourteen samples were analyzed in total. To compare the expression profiles across the samples, Affymetrix GeneChip Mouse Genome 430 2.0 Array Platform (total 41,170 probes) was used, and the data were analyzed using Silicon Genetics GeneSpring Software GX7.3.1. The data was normalized to median settings across the entire probe set and samples, and transcripts that are expressed across triplicated samples at levels two-fold or higher than the rest of the samples were considered as significantly enriched in particular biological samples. Comparisons between adult and embryonic samples also identified genes enriched in adult brain-derived samples.

first: Andrew

last: Grande


title: Cyclodextrin protects podocytes in diabetic kidney disease.

status: Public on Jul 11 2013

city: Miami

first: Sandra

last: Merscher-Gomez

address: 1580 NW 10th Avenue

department: Medicine

institute: University of Miami

first: Johanna

last: Guzman

first: Markku

last: Lehto

first: Robier

last: Aguillon-Prada

first: Armando

last: Mendez

first: Mariann

last: Lassenius

first: Carol

last: Forsblom

first: TaeHyun

last: Yoo

last: Pedigo

first: Rodrigo

last: Villarreal

first: Dony

last: Maiguel

first: Kevin

last: Johnson

first: Ronald

last: Goldberg

first: Viji

last: Nair

first: Ann

last: Randolph

first: Matthias

last: Kretzler

first: Robert

middle: G

last: Nelson

first: George

middle: W

last: Burke III

first: Per-Henrik

last: Groop

first: Alessia

last: Fornoni


title: Expression data from (mouse) normal lung fibroblasts and carcinoma-associated fibroblasts

status: Public on Jul 10 2013

city: Palo Alto

first: Dedeepya

last: Vaka

address: 265 Campus Drive

department: Pediatrics

institute: Stanford

summary:
Cancer-associated fibroblasts (CAFs) have been reported to support tumor progression by a variety of mechanisms. However, their role in the progression of non-small cell lung cancer (NSCLC) remains poorly defined. In addition, the extent to which specific proteins secreted by CAFs contribute directly to tumor growth is unclear. To study the role of CAFs in NSCLC, a cross-species functional characterization of mouse and human lung CAFs was performed, including gene expression analysis comparing normal mouse lung fibroblasts (NFs) and mouse lung CAFs to seek for differentially-expressed secreted proteins.
Gene expression microarrays were used to identify transcriptomic changes between NFs and CAFs that may contribute to their different tumor-enhancing capacity.

overall_design: NFs and CAFs were grown in vitro for RNA extraction and hybridization on mouse 430_2 Affymetrix microarrays

first: Alejandro

last: Sweet-Cordero

first: Silvestre

last: Vicent


title: Sox11 loss-of-function mutant cortex at E17.5

city: Biddeford

first: Lei

last: Lei

state: ME

address: 11 Hills Beach Road

department: Biology

institute: University of New England

summary:
Expression profiling of cortex from embryonic day (E) 17.5 telencephalon of Sox11(+/+) and Sox11(-/-) mouse embryos. Sox11 is implicated in regulating proliferation, neuronal migration and differentiation.
We used microarray to identify genes that were differentially expressed in the cortex in the wild type and Sox11 knockout embryos at E17.5.

overall_design: To uncover the molecular mechanisms undelying the function of Sox11 in cortical development, we conducted microarray analysis of E17.5 cortices from wild type and Sox11(-/-) mice. Total RNA was isolated from the cortex of one wild type embryo and one Sox11(-/-) littermate at E17.5. cRNA probe synthesis, hybridization, scanning, and data collection were performed following the manufacturer's instruction.


title: Cyclin D1 determines estrogen depependent signaling in mouse mammary gland.

status: Public on Jul 16 2013

first: Mathew

middle: Casimiro

last: Casimiro

state: United States

address: 233 South 10th St, Rm 1035

department: 233 South 10th St, Rm 1035

institute: Thomas Jefferson University

summary: Ovariectomized virgin Ccnd1-/- and Ccnd1+/+ mice (5 weeks of age) were allowed to recuperate for 2 weeks. The mice were assigned to either replacement pellets containing E2 (0.75 mg, 60-day release) or pellet containing placebo. Mice were sacrificed at day 7 after pellet implantation. RNA extracted from mammary glands (3 each group) was labeled and used to probe Affymetrix 430_2.0 arrays.

overall_design: Six separate control Ccnd1+/+ C57BL/6 were compared to six Ccnd1-/- C57BL/6 mice. 3 mice in each group treated with placebo and three mice treated with E2

first: Richard

last: Pestell


title: Expression data analysis of murine pulmonary cryptococcosis induced by C. gattii

status: Public on Jul 08 2013

city: Yokohama,

first: Yoichiro

last: Okubo

state: Kanagawa

address: 2-3-2, Nakao, Asahi-Ku

institute: Kanagawa Cancer Center

summary: Our previous investigation indicated that high-virulence C. gattii (C. gattii TIMM 4097) tend to reside in the alveoli, whereas low-virulence C. gattii (C. gattii TIMM 4903) tend to be washed out from the alveoli and move into the central side of the respiratory system. To test this hypothesis, we performed microarray assay.

overall_design: C. gattii TIMM 4097 and C. gattii TIMM 4903 were prepared for the study. The mice were anesthetized and the spore suspension was intratracheally injected into each mouse. Mice were sacrificed 15 days after the infection and then examined. Lung of the mice infected with C. gattii TIMM 4097 and C. gattii TIMM 4903 and normal controls were obtained (n=3, respectively. RNA targets preparation was performed according to the manufacturer's protocol using GeneChip(R) 3' IVT Express Kit (Affymetrix). One hundred nanograms of total RNA were converted into double-stranded cDNA template for transcription. In vitro transcription synthesized amplified RNA (aRNA) and incorporated a biotin-conjugated nucleotide. After purification and fragmentation of aRNA, 12.5 ug of them was hybridized to GeneChip(R) Mouse Genome 430 2.0 Array (Affymetrix).The Probe Array was scanned using a GeneChip(R) Scanner 3000 7G

first: Y

first: N

last: Tochigi

first: M

last: Wakayama

last: Shinozaki

first: H

last: Nakayama

first: K

last: Shimodaira

last: Makimura

last: Shibuya


title: Expression profile of melanoma cells following p300 HAT inhibition

city: Boston

first: Rhoda

last: Alani

address: 609 Albany Street, Suite 6J

department: Dermatology

institute: Boston University School of Medicine

summary:
Epigenetic events, including covalent post-translational modification of histones, have frequently been demonstrated to play critical roles in tumor development and progression. The transcriptional coactivator, p300/CBP, possesses both histone acetyltransferase (HAT) activity as well as scaffolding properties that directly influence transcriptional activation of targeted genes.  We have used a recently reported small molecule inhibitor of p300 HAT activity, C646, to explore the specific contribution of p300/CBP HAT activity to tumor development and progression.  We find that C646 inhibits the growth of lineage-specific tumor cell lines including human melanomas through direct transcriptional regulation of cell cycle regulatory proteins.  Further evaluation of the p300 HAT transcriptome in human melanoma cells using comprehensive gene expression profiling reveals that p300 HAT activity globally promotes cell cycle progression, nucleosome assembly, and the DNA damage checkpoint through direct transcriptional regulatory mechanisms.  Additionally, C646 promotes sensitivity to DNA damaging agents leading to enhanced apoptosis of melanoma cells following combination treatment with cisplatin. Together our data suggest that p300 HAT activity regulates critical growth regulatory pathways in tumors and may serve as a novel therapeutic target for melanoma and other malignancies by promoting cellular responses to DNA damaging agents.
Keywords: p300, small molecule inhibitor, melanoma

overall_design: WM35 cells grown under normal culture conditions were treated for 6 and 24 hours with compound C646 to block p300 HAT activity. A vehicle control (DMSO) was included at each time point. RNA was extracted from all 4 samples using the Qiagen RNeasy kit. RNA quality check, labeling, hybridization, initial data processing and analysis was performed by the JHMI Microarray Core Facility. Affymetrix GeneChip Human Exon 1.0 ST Array was used for this study.

first: Gai

last: Yan

first: Philip

last: Cole

first: Sean

middle: D

last: Taverna

first: Mark

middle: S

last: Eller

first: David

last: Meyers

first: Courtney

last: Elm

first: Cecilia

last: Larocca

first: Beverley

last: Dancy

first: Erin

last: Bowers

first: Lisa

last: Lareau


title: Cyclodextrin protects podocytes in diabetic kidney disease [HumanWG-6 v3.0 array]

first: Sandra

last: Merscher-Gomez

summary: Analysis of gene expression changes in differentiated human podocytes treated with the serum from patients with (DKD+) or without (DKD-) diabetic kidney disease when compared to normal subjects (C). The hypothesis is that the three groups can be distinghed by their differential gene expression pattern. The results obtained revealed important information regarding differences in gene expression in human podocytes treated with the serum from patients with (DKD+) or without (DKD-) diabetic kidney disease when compared to normal subjects (C).

overall_design: Human podocytes were contacted with the serum from patients with diabetes and kidney disease (DKD+) or without kidney disease (DKD-) and compared to normal human podocytes contacted with serum from patients without diabetes (C).

first: Johanna

last: Guzman

first: Markku

last: Lehto

first: Robier

last: Aguillon-Prada

first: Armando

last: Mendez

first: Mariann

middle: I

last: Lassenius

first: Carol

last: Forsblom

first: TaeHyun

last: Yoo

first: Christopher

last: Pedigo

first: Rodrigo

last: Villarreal

first: Dony

last: Maiguel

first: Kevin

last: Johnson

first: Ronald

last: Goldberg

first: Viji

last: Nair

first: Ann

last: Randolph

first: Matthias

last: Kretzler

first: Robert

last: Nelson

first: George

last: Burke III

first: Per-Henrik

last: Groop

first: Alessia

last: Fornoni


title: Integrative genomics of gene regulation by estrogen receptors and and coregulators [ChIP-seq]

status: Public on Jul 05 2013

city: Urbana

first: Zeynep

last: Madak Erdogan

state: IL

address: 1201 S Goodwin Ave

department: FSHN

institute: UIUC

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The closely related transcription factors (TFs), estrogen receptors ERα and ERβ, regulate divergent gene expression programs and proliferative outcomes in breast cancer. Utilizing MCF-7 breast cancer cells with ERα, ERβ, or both receptors as a model system to define the basis of differing response specification by related TFs, we show that these TFs and their key coregulators, SRC3 and RIP140, generate overlapping as well as unique chromatin-binding and transcription-regulating modules. Cistrome and transcriptome analyses and use of clustering algorithms delineated 11 clusters representing different chromatin-bound receptor and coregulator assemblies that could be functionally associated through enrichment analysis with distinct patterns of gene regulation and preferential coregulator usage, RIP140 with ERβ and SRC3 with ERα. The receptors modified each other’s transcriptional effect, and ERβ countered the proliferative drive of ERα through several novel mechanisms associated with specific binding site clusters. Our findings delineate distinct TF-coregulator assemblies that function as control nodes specifying precise patterns of gene regulation, proliferation, and metabolism, as exemplified by two of the most important nuclear hormone receptors in human breast cancer.

overall_design: Examination of Estrogen Receptors alpha and beta and their coregulators SRC3 and RIP140 in different cell types

last: Erdogan

first: Benita

last: Katzenellenbogen


title: Transcriptional Profiling of Neuronal APP/APLP2 Double-Conditional Knockout Mice.

city: Houston

first: Baiping

last: Wang

state: TX

address: One Baylor Plaza

department: HCOA

institute: Baylor College of Medicine

summary: Gene expression analysis of 2-month-old APP/APLP2 double-conditional Knockout (N-dCKO) mice and littermate APLP2 knockout controls, APP knockout and wildtype controls.

overall_design: Mouse hippocampus were dissected for RNA extraction and hybridization on Affymetrix microarrays.


title: Integrative genomics of gene regulation by estrogen receptors and and coregulators

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

overall_design: Refer to individual Series


title: Identification of genes modulated by JIB-04 in lung cancer cells

city: Dallas

first: Elisabeth

last: Martinez

address: 6000 Harry Hines Blvd

department: Department of Pharmacology

institute: UT Southwestern Medical Center

summary:
JIB-04 is an inhibitor of Jumonji histone demethylases identified through a cell based screen that measures the reactivation of an epigenetically silenced transgene.
The active JIB-04 E-isomer shows selectivity for cancer vs. normal cells affecting both transcriptional patterns and cell viability in a cancer specific manner.

overall_design: H358 lung cancer cells or the patient matched HCC4017 (cancer) vs. HBEC30KT (immortalized normal) lung cell pair were treated with DMSO vehicle or 500nM E-isomer or 500 nM Z-isomer of JIB-04 for 4 h or 24 h and RNA extracted.

first: Jianjun

last: Chang


title: Dissecting primary (translation independent) from secondary (translation dependent) IFN-mediated differential gene expression

status: Public on Jul 04 2013

city: Cambridge

first: Lars

last: Dölken

state: Cambridgeshire

address: Addenbrookes Hospital, Hills Road

institute: University of Cambridge

summary: NIH-3T3 cells were pretreated for 15 min with either DMSO (mock) or cycloheximide followed by addition of either mock, 100 U/ml IFNalpha or 100 U/ml IFNgamma for 1h. During the last 30 min, 500 µM 4-thiouridine was added to cell culture medium. Total cellular RNA was isolated using Trizol reagent and nascent RNA was purified as described (Dölken et al. RNA 2008) . Three replicates of nascent RNA were analyzed by Affymetrix Mouse Gene ST 1.0 arrays

overall_design: Primary (translation independent) from secondary (translation dependent) IFN-mediated differential gene expression were studied in NIH-3T3 fibroblasts by studying studying differential gene expression in presence and absence of Cycloheximide (CHX). In addition, the effect of 75 min CHX during the last 30 min of treatment was studied in nascent RNA.

first: Mirko

last: Trilling

first: Nicolas

last: Bellora

first: Caroline

last: Friedel

first: Paul

last: Dickinson

first: Olivia

last: Prazeres da Costa

first: Zsolt

last: Ruzsics

first: Peter

last: Ghazal

first: Ulrich

middle: H

last: Koszinowski

first: Mar

last: Alba


title: Stump project-- mRNA basal layer keratinocytes; Volar versus non-volar acral skin gene expression

status: Public on Jul 03 2013

city: Baltimore

first: Luis

middle: Andres

last: Garza

state: MD

address: 1550 Orleans St. Suite 204 CRBII Koch

institute: Johns Hopkins School of Medicine

summary: We were interested in defining the gene signature of volar skin.

overall_design: Punch biopsies of skin were split into epidermis and dermis after dispase treatment. Epidermis was trypsinized and sorted for alpha 6 integrin positive basal layer keratinocytes  We collected RNA from basal layer keratinocytes  of soles and backs of feet and submitted for Affymetrix Exon arrays. 2 replicates of each site from distinct human donors were included; total of 4 samples analyzed


title: Stump project -- mRNA fibroblasts; Volar versus non-volar acral skin gene expression

overall_design: Dermal fibroblasts were expanded from punch biopsies of skin. We collected RNA from fibroblasts  of palms, backs of hand, soles and backs of feet and  submitted for Affymetrix Exon arrays. 3 replicates of each site from distinct human donors were included; because of 1 failed sample(Palm_rep2), total of 11 samples analyzed


title: Stump project-- mRNA dermis; Volar versus non-volar acral skin gene expression

overall_design: Punch biopsies of skin were split into epidermis and dermis after dispase treatment. We collected RNA from dermis  of palms, backs of hand, soles and backs of feet and  submitted for Affymetrix Exon arrays. 3 replicates of each site from distinct human donors were included; total of 12 samples analyzed


title: Induced Cdx2 binding in progenitor motor neurons and its effect on H3K27me3 chromatin domains [Affymetrix]

city: University Park

first: Shaun

last: Mahony

state: PA

address: 404 South Frear Bldg

department: Biochemistry & Molecular Biology

institute: Penn State University

summary: We aim to understand the role that Cdx2 plays in specifying the rostro-caudal identity of differentiating motor neurons. We find that expressing Cdx2 in combination with FGF signaling is sufficient to produce motor neurons with a more caudal identity. ChIP-seq analysis of Cdx2 finds that it binds extensively throughout the Hox regions in progenitor motor neurons. Analysis of polycomb-associated chromatin over Hox regions in the subsequently generated motor neurons finds that Cdx2 binding corresponds to chromatin domains encompassing de-repressed caudal Hox genes. These results suggest a direct role for Cdx2 in specifying caudal motor neuron identity.

overall_design: Expression studies: Affymetrix arrays are used to profile gene expression in ES cells, RA/Hh-derived Day 5 motor neurons, and RA/Hh-derived motor neurons that have also been exposed to Dox (to activate iCdx2) and FGF.

first: Esteban

middle: O

last: Mazzoni

first: Carolyn

last: Morrison

first: David

middle: K

last: Gifford

first: Hynek

last: Wichterle


title: Laser Capture Microdissection isolation of preovulatory granulosa cells from WT and bERKO ovaries

city: RTP

first: NIEHS

last: Microarray Core

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

summary:
Determining the spatial and temporal expression of genes involved in the ovulatory pathway is critical for the understanding of the role of each estrogen receptor in the modulation of folliculogenesis and ovulation. Estrogen receptor (ER) β is highly expressed in ovarian granulosa cells and mice lacking ERβ (βERKO) are subfertile due to inefficient ovulation.  Previous work has focused on isolated granulosa cells or cultured follicles and while informative, provides confounding results due to the heterogeneous cell types present including granulosa, theca and oocytes and exposure to in vitro conditions.  Herein, we isolated preovulatory granulosa cells from WT and ERβ-null mice using laser capture microdissection to examine the genomic transcriptional response downstream of PMSG (mimicking FSH) and PMSG/hCG (mimicking LH) stimulation.  This allows for a direct comparison of in vivo granulosa cells at the same stage of development from both WT and ERβ-null ovaries. ERβ-null granulosa cells showed altered expression of genes known to be regulated by FSH (Akap12 and Runx2) as well as not previously reported (Arnt2 and Pou5f1) in WT granulosa cells. Our analysis also identified 304 genes not previously associated with ERβ in granulosa cells.  LH responsive genes including Abcb1b and Fam110c show reduced expression in ERβ-null granulosa cells; however novel genes including Rassf2 and Megf10 were also identified as being downstream of LH signaling in granulosa cells.  Collectively, our data suggests that granulosa cells from ERβ-null ovaries may not be appropriately differentiated and are unable to respond properly to gonadotropin stimulation
We used microarray to compare the gene expression profiles of wiltype (WT) and Erb-null (bERKO) preovulatory granulosa cells as they respond to either PMSG or PMSG+hCG treatments.

overall_design: Laser microdissection was used to collect a purified population of granulosa cells only from preovulatory follicles. We chose to compre the response to PMSG or PMSG+hCG of granulosa cells collected from either WT and bERKO preovulatory follicles. We chose to collect cells 48h after mice were treated with PMSG to compare the gene expression profile ot preovulatory granulosa cells. We also studied the response of these cells to LH (or hCG) as we collected cells 4h after mice were treated with hCG (peak of transcriptional response to hCG).

first: April

last: Binder

first: Karina

middle: F

last: Rodriguez

first: Katherine

middle: J

last: Hamilton

first: Patricia

last: Stockton

first: Casey

middle: E

last: Reed

first: Kenneth

last: Korach


title: Stump project -- mRNA epidermis; Volar versus non-volar acral skin gene expression

overall_design: Punch biopsies of skin were split into epidermis and dermis after dispase treatment. We collected RNA from epidermis  of palms, backs of hand, soles and backs of feet and  submitted for Affymetrix Exon arrays. 3 replicates of each site from distinct human donors were included; total of 12 samples analyzed

middle: A


title: Expression data from genetically engineered mouse models (GEMMs)

status: Public on Jul 02 2013

city: San Diego

last: Belmont

state: CA

address: 10724 Science Center Drive

institute: Pfizer Inc

summary:
3 Cell lines from Apc, p53 (AP) GEMMs were compared to 12 cell lines from Apc, Kras, p53 (AKP) GEMMs.
Mouse 430 2.0 arrays were used to determine genomic expression differences between the two genotypes (AP and AKP).

overall_design: RNA was extracted from 3 AP and 10 AKP cell lines using the Qiagen RNEasy kit, and hybridized to individual Affymetrix mouse 430 2.0 chips as per manufacturer's instructions

first: Tao

last: Xie


title: ChIp-Chip using RNAP II, CREB C/EBPb and cJun antibody in undifferentiated or differentiated keratinocytes

status: Public on Jul 01 2013

city: Chapel Hill

first: Julian

last: Rozenberg

address: Brinkhous-Bullitt Bldg., CB#7525

department: Pathology and Lab Medicine

institute: University Of North Carolina

type: Genome binding/occupancy profiling by genome tiling array


title: Distinct signal transduction pathways downstream of the (P)RR revealed by microarray and ChIP-chip analyses

city: Berlin

first: Daniela

last: Zaade

address: Hessische Straße 3-4

department: Center for Cardiovascular Research

country: Germany

institute: Charité


title: ChIp-Chip using RNAP II, CREB C/EBPb and cJun antibody in undifferentiated or differentiated keratinocytes (expression)

summary:
Combinatorial recruitment of CREB, C/EBPb and Jun determines activation of promoters upon keratinocyte differentiation
Chromatin immunoprecipitation (ChIP) of RNAP II, CREB C/EBPb and cJun in undifferentiated or differentiated keratinocytes demonstrate recruitment of RNAP II to promoters bound by combination of specific transcription factors. Analysis of mRNA expression data from contrl keratinocytes or keratinovtyes where binding of transcription factors is disrupted demonstrate functional requirements for ceratin class of promoters

overall_design: comparison of undifferentiated and differentated keratinocytes using mRNA expression data

last: Rozenbereg

first: Charles

last: Vinson


title: Gene-expression profiles of primary cultures of cortical neurons and astrocytes.

city: Barcelona

first: Joan Marc

last: Servitja

state: Catalonia

address: Rosselló, 153

institute: IDIBAPS

summary: We used microarrays to compare the global programme of gene expression in primary cultures of neurons and astrocytes. These data sets were compared to the expression profiles of other tissues, including pancreatic islets, in order to identify a specific neuroendocrine program in pancreatic islets.

overall_design: Neurons and astrocytes were isolated from brain cortex and cultured in vitro for 7 and 20 days respectively. RNA was extracted and hybridized on Affymetrix microarrays. Two biological samples from neurons and astrocytes were analyzed.

first: J-M

first: A

last: Moreno-Asso


title: Regulation of Mouse Lens Development and Gene Expression by Krüppel-Like Factor 4

city: Pittsburgh

first: Stephen

middle: Alan Kenneth

last: Harvey

address: 203 Lothrop St

department: Ophthalmology

institute: University of Pittsburgh School of Medicine

summary:
Conditional disruption of Klf4 in the ectoderm-derived tissues of the eye results in defective cornea, conjunctiva and the lens.
Expression of Klf4 is first detected in the embryonic day-12 (E12) mouse lens, peaks at E16, and declines thereafter.
Lenses from Mice which were conditional null for Klf4 (Klf4CN) were characterized by morphology and transcriptome.

overall_design: Wild type and Klf4-conditional null mouse lens gene expression at  embryonic day 16.5 (E16.5) and postnatal day 56 (PN56) was surveyed using Affymetrix mouse whole genome 430 2 arrays.

first: Divya

last: Gupta

first: Doreswamy

last: Kenchegowda

first: Sudha

last: Swamynathan

first: Shivalingappa


title: Expression data from adult Myeloerythroid Progenitors (MP) Hes1-GFP positive and adult Myeloerythroid Progenitors (MP) Hes1-GFP negative

city: Paris

first: Camille

last: Lobry

address: 16 rue de la Grange aux Belles

department: IRSL Inserm U944 / CNRS UMR7212

country: France

institute: Inserm

summary: Notch signaling defines a conserved, fundamental pathway, responsible for determination in metazoan development and is widely recognized as an essential component of lineage specific differentiation and stem cell self-renewal in many tissues including the hematopoietic system. Until recently, the majority of studies in the hematopoietic system focused on Notch signaling in lymphocyte differentiation and knowledge of individual Notch receptor roles in early hematopoiesis has been limited due to a paucity of genetic tools available  To fate-map Notch receptor expression and pathway activity in the hematopoietic system we used tamoxifen-inducible CreER knock-in mice for individual Notch receptors in combination to a novel Notch reporter strain (Hes1GFP) and a conditional gain of function allele of Notch2 receptor (Rosa-lsl-ICN2).

overall_design: Bone marrow lineage negative, cKit+, Sca1- cells were sorted from Hes-GFP mice for RNA extraction and hybridization on Affymetrix microarrays

first: Philmo

last: Oh

first: Iannis

last: Aifantis


title: Expression data from NcGFP ki/+, NcGFP ki/ki and wt (W4) ES cells

city: Freiburg

first: Marc

middle: P.

last: Stemmler

address: Stuebeweg 51

department: Molecular Embryology

institute: Max-Planck Institute of Immunobiology and Epigenetics

summary:
We generated a gene replacement allele of the E-cadherin locus that express an N-cadherin-GFP fusion in ES cells. Expression profiles of homozygous and heterozygous knock-in ES cells were analyzed in comparison to wt ES cells.
The GEO Samples were compared to published data of E-cadherin knock-out ES cells (ArrayExpress, accession number E-MEXP-2836). The comparison data are linked below.

overall_design: RNA was extracted from two independent experiments per genotype, data analysis was performed using the R/Bioconductor Limma software. Quality of the data set was controlled by the simpleaffy package and normalized by quantile normalization with the GCRMA alogrithm.

first: M

middle: P

first: H

last: Alotaibi


title: Expression data from monocyte-derived macrophages after stimulation with mock, LPS, PolyI:C and P3C.

city: Nijmegen

first: Marloes

last: Vissers

address: Geert Grooteplein Zuid 10

department: Department of Pediatrics

country: Netherlands

institute: Radboud university medical center

summary: Pre-stimulation of MDMs with LPS (signals via MyD88 and TRIF dependent pathways) and PolyI:C (signals via a TRIF dependent pathway) leads to a reduced viral infection. In contrast, pre-stimulation with P3C (signals via MyD88 dependent pathway) does not lead to a reduced viral infection. This microarray was performed to find genes that are specifically upregulated in LPS and PolyI:C stimulated MDMs but not P3C stimulated MDMs. So to give us leads into the mechanism involved in the reduction of viral infection.

overall_design: MDMs of four different donors were stimulated for 4h with mock, LPS, PolyI:C or P3C. RNA was isolated and gene expression of these cells was assessed. Gene expression of LPS, PolyI:C and P3C stimulated MDMs was compared to mock.

first: D

last: Diavatopoulos


title: Expression data from E13.5 Fetal Liver LSK Hes1-GFP positive and E13.5 Fetal Liver LSK Hes1-GFP negative

overall_design: E13.5 Foetal Liver lineage negative, cKit+, Sca1+ cells were sorted from Hes-GFP mice for RNA extraction and hybridization on Affymetrix microarrays


title: Transcriptome Profile of Gα12-depleted OSCC cells

city: Zhunan, Miaoli County

first: Shiou-Ling

last: Jian

address: 35 Keyan Road

department: Institute of Molecular and Genomic Medicine

country: Taiwan

institute: National Health Research Institutes

summary: The elevation of guanine nucleotide binding protein alpha 12 (Gα12) expression is highly associated with tumor invasiveness in several human cancers. We used an siRNA strategy to deplete Gα12 in oral squamous cell carcinoma (OSCC) cells and analyze the transcriptome profile by the Affymetrix Human Exon 1.0 ST platform.

overall_design:
Transcriptome analysis of total RNA samples from OSCC cells.
We analyzed OSCC cell samples using the Affymetrix Human Exon 1.0 ST platform. Array data was processed by the Affymetrix Exon Array Computational Tool. No technical replicates were performed.

first: Jyh

middle: L

last: Juang

first: Shiou

first: Shu

last: Nien


title: Expression data from fresh and cultured islets at different glucose concentrations

first: Joan Marc

summary:
β-cell identity is determined by tightly regulated transcriptional networks that are modulated by extracellular cues, thereby ensuring β-cell adaptation to the organism’s insulin demands. We have observed in pancreatic islets that stimulatory glucose concentrations induced a gene profile that was similar to that of freshly isolated islets, indicating that glucose-elicited cues are involved in maintaining β-cell identity. Low glucose induces the expression of ubiquitous genes involved in stress responses, nutrient sensing, and organelle biogenesis. By contrast, stimulatory glucose concentrations activate genes with a more restricted expression pattern (β- and neuronal- cell identity). Consistently, glucose-induced genes are globally reduced in islets deficient with Hnf1a (MODY3), characterized by a deficient glucose metabolism. Of interest, a cell cycle gene module was the most enriched among the variable genes between intermediate and stimulatory glucose concentrations. Glucose regulation of the islet transcriptome was unexpectedly broadly maintained in islets from aged mice. However, the cell cycle gene module is selectively lost in old islets and the glucose activation of this module is not recovered even in the absence of the cell cycle inhibitor p16.
We used microarrays to detail the global programme of gene expression regulated by glucose in young and aged pancreatic islets as well as freshly-isolated islets.

overall_design: Pancreatic islets from young and old mice were isolated and cultured at different glucose concentrations for RNA extraction and hybridization on Affymetrix microarrays. Islets were cultured at 3mM (G3), 5.5mM (G5), 11mM (G11) and 16mM (G16). Freshly-isolated islets (F) were also processed for RNA extraction . We also assessed the dynamic glucose regulation of gene expression at different time-points after an overnight at 3mM (T0):  after 1h at 11mM (T1) and after 4h (T4).

first: J-M

first: A


title: Expression data after irradiating mMSCs for 2 hours with broadband terahertz source

city: Los Alamos

first: Boian

last: Alexandrov

state: NM

address: Bikini Atoll Road

department: Theoretical Division

institute: LANL

summary: We report that terahertz (THz) irradiation of mouse mesenchymal stem cells with a pulsed broadband (centered at 10 THz) source, or a single-frequency, 2.52 THz, (SF) laser source, both with weak average power (<1mW/cm2), results in specific heterogenic changes in gene expression. The insignificant differential expression of heat shock and stress related genes as well as our temperature measurements imply a non-thermal response. The microarray survey and RT-PCR experiments demonstrate that at different irradiation conditions distinct groups of genes are activated. Stem cells irradiated for 12 hours with the broadband THz source exhibit an accelerated differentiation toward adipose phenotype, while the 2-hour (broadband or SF) irradiation affects genes transcriptionally active in pluripotent stem cells. Phenotypic and gene expression differences suggest that the THz effect depends on irradiation parameters such as duration and type of THz source, and on the level of stem cell differentiation. Computer simulations of the core promoters of two pluripotency markers reveal association between gene upregulation and propensity for DNA breathing. We propose that THz radiation has potential for non-contact control of cellular gene expression.

overall_design: Growing in petri dish mouse mesenchymal stem cell cultures are irradiated for 2 hours with pulsed ultrafast (35 fs) broadband (centered at ~10 THz) source. Three independent biological experiments were conducted. In each experiment, a control mMSC culture was placed adjacent to the irradiated sample, and the temperature was kept at 26-27ºC for both the control and the irradiated sample. Immediately after completing the irradiation, total RNA was extracted from the irradiated sample and the control, and microarrays were used to identify differential changes in gene expression between the irradiated sample and its respective control. In each experiment, the mMSC cultures were synchronized to be at the same differentiation time point immediately before the irradiation.

first: Lisa

last: Phipps

first: Ludmil

first: Layla

last: Booshehri

first: Anna

last: Erat

first: Janice

last: Zabolotni

first: Charles

last: Mielke

first: Hou-Tong

last: Chen

first: George

last: Rodriguez

first: Jennifer

last: Martinez

first: Kim

last: Rasmussen

first: Alan

last: Bishop

first: Anny

last: Usheva


title: Runx1 deficiency effect on MLL-ENL cells

status: Public on Jun 30 2013

city: Cincinnati

first: Susumu

last: Goyama

state: Ohio

address: 3333 Burnet Avenue

institute: Cincinnati Children's Hospital Medical Center

summary: To identify the target genes of Runx1 in MLL fusion leukemia, we performed microarray analysis using control and Runx1-deficient MLL-ENL leukemia cells.

overall_design: Runx1 intact and excised  bone marrow cells were transduced with MLL-ENL and transplanted into congenic mice. Leukemic cells were harvested from moribund mice, and gene expression was compared using 3 independent leukemia cells for each genotype.

first: Nahoko

last: Nishimoto

first: Shunya

last: Arai

first: Masahiro

last: Nakagawa

first: Mineo

last: Kurokawa


title: Expression data after irradiating mMSCs for 2 hours with single frequency terahertz laser source

first: Boian

last: Alexandrov

overall_design: Growing in petri dish mouse mesenchymal stem cell cultures are irradiated for 2 hours with a single-frequency (2.52 THz) CW laser source. Three independent biological experiments were conducted. In each experiment, a control mMSC culture was placed adjacent to the irradiated sample, and the temperature was kept at 26-27ºC for both the control and the irradiated sample. Immediately after completing the irradiation, total RNA was extracted from the irradiated sample and the control, and microarrays were used to identify differential changes in gene expression between the irradiated sample and its respective control. In each experiment, the mMSC cultures were synchronized to be at the same differentiation time point immediately before the irradiation.

first: Lisa


title: Expression profiling of 275 lung cancer specimens

first: Luc

last: Girard

address: 5323 Harry Hines Blvd

department: Hamon Center for Therapeutic Oncology Research

summary: From ~1,700 non-small cell lung cancer specimens collected at the MD Anderson Cancer Center over the years 1997 to 2005, we selected 914 tumors with detailed clinical and pathological information. We extracted RNA and DNA from frozen tissues using histology quality control from 700 cases. RNA was examined for quality using Agilent Bioanalyzer and RNA integrity number (RIN) was obtained for all specimens. A final selection of 275 tumor specimens was based on the following criteria: 1) Select mainly adenocarcinomas (n = 183) and squamous carcinomas (n = 80); 2) Tissue material contains at least 70% tumor by section examination; 3) within the tumor section, there should be at least 30% tumor cells (as opposed to stromal cells); 4) RIN should be at least 4.0 (range 0 - 10). Various profiling experiments were then performed including mRNA expression (this study), miRNA profiling, aCGH (Agilent), Reverse-phase protein array (RPPA), mutation analysis of 20 genes (Sequenom) and MS-MALDI-TOFF analysis.

overall_design: 275 lung cancer specimens collected at the MD Anderson Cancer Center were profiled on Illumina WG6-V3 expression arrays. Detailed clinico-pathological information were also collected.

first: Ignacio

last: Wistuba

first: John

middle: V

last: Heymach

last: Minna


title: Expression data after irradiating mMSCs for 12 hours with broadband terahertz source

overall_design: Growing in petri dish mouse mesenchymal stem cell cultures are irradiated for 12 hours with pulsed ultrafast (35 fs) broadband (centered at ~10 THz) source. Three independent biological experiments were conducted. In each experiment, a control mMSC culture was placed adjacent to the irradiated sample, and the temperature was kept at 26-27ºC for both the control and the irradiated sample. Immediately after completing the irradiation, total RNA was extracted from the irradiated sample and the control, and microarrays were used to identify differential changes in gene expression between the irradiated sample and its respective control. In each experiment, the mMSC cultures were synchronized to be at the same differentiation time point immediately before the irradiation.

last: Phipps

first: Ludmil

first: Layla

last: Booshehri

first: Anna

last: Erat

first: Janice

last: Zabolotni

first: Charles

last: Mielke


title: In Vivo Mapping of Notch Pathway Activity in Normal and Stress Hematopoiesis

first: Camille

last: Lobry

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

overall_design: Refer to individual Series

first: Philmo

last: Oh

first: Iannis

last: Aifantis


title: Whole genome expression data comparison between WT and Cebpg-/- MEFs.

city: FREDERICK

first: Peter

last: Johnson

address: 1050 Boyles St

department: Center for Cancer Research

institute: National Cancer Institute

summary: C/EBPβ is an important regulator of oncogene-induced senescence (OIS). Here we show that C/EBPγ, a heterodimeric partner of C/EBPβ whose biological functions are not well understood, inhibits cellular senescence. Cebpg-/- MEFs proliferated poorly, entered senescence prematurely, and expressed a pro-inflammatory gene signature, including elevated levels of senescence-associated secretory phenotype (SASP) genes whose induction by oncogenic stress requires C/EBPβ. The senescence-suppressing activity of C/EBPγ required its ability to heterodimerize with C/EBPβ. Covalently linked C/EBPβ homodimers (β~β) inhibited the proliferation and tumorigenicity of RasV12-transformed NIH3T3 cells, activated SASP gene expression, and recruited the CBP co-activator in a Ras-dependent manner, whereas γ~β heterodimers lacked these capabilities and efficiently rescued proliferation of Cebpg-/- MEFs. C/EBPβ depletion partially restored growth of C/EBPγ-deficient cells, indicating that the increased levels of C/EBPβ homodimers in Cebpg-/- MEFs inhibit proliferation. The proliferative functions of C/EBPγ are not restricted to fibroblasts, as hematopoietic progenitors from Cebpg-/- bone marrow also displayed impaired growth. Furthermore, high CEBPG expression correlated with poorer clinical prognoses in several human cancers, and C/EBPγ depletion decreased proliferation and induced senescence in lung tumor cells. Our findings demonstrate that C/EBPγ neutralizes the cytostatic activity of C/EBPβ through heterodimerization, which prevents senescence and suppresses basal transcription of SASP genes.

overall_design: Mouse embryonic fibroblasts were isolated at E13.5 and propagated.  At passage 3 cells were plated with equal density and collected 48 hours later.

first: Christopher

last: Huggins


title: Changes in gene expression upon co-treatment of cells with Dex and E2

city: Bethesda

first: Songjoon

last: Baek

address: 41 Library Drive

department: CCR

institute: NCI / NIH

summary: We report changes in gene expression  upon co-treatment with Dex and E2 when compared to Dex or E2 treatments alone.

overall_design: We examine expression under four different treatments (unt, Dex, E2, and Dex + E2).

first: Tina

middle: B

last: Miranda

first: Gordon

last: Hager

first: Myong-Hee

last: Sung


title: Expression data after irradiating mMSCs

first: Boian

last: Alexandrov


title: Gene expression data of Lsd1fl/fl and Lsd1fl/fl Mx1Cre Gr1dim Mac1 granulocytic progenitor cells.

status: Public on Jun 25 2013

city: Boston

first: Marc

middle: A.

last: Kerenyi

state: Massachusetts

address: 1 Blackfan Street - Karp Research Building

department: Hematology / Oncology

institute: Boston Children's Hospital and Dana Farber Cancer Institute

summary: We discovered that mice with hematopoietic-specific deletion of Lsd1 lacked Gr-1+ Mac1+ neutrophilic granulocytes whereas the numbers of Gr-1dim Mac1+ granulocytic progenitor cells was increased. To determine the genes altered by Lsd1-loss, Gr-1dim Mac1+ granulocytic progenitor cells from Lsd1fl/fl and Lsd1fl/fl Mx1Cre mice were FACS-purified to be analyzed by gene expression profiling.

overall_design: Primary Gr-1dim Mac1+ granulocytic progenitor cells were isolated from the bone marrow of Lsd1fl/fl and Lsd1fl/fl Mx1Cre animals by FACS-sorting, one week after the final p(I:C) dose. Total RNA from three biological replicates per genotype was extracted and used to hybridize to Affymetrix expression arrays using the Mouse Genome 430 2.0 array platform.

first: Stuart

last: Orkin


title: Differential gene expression in the Lacrimal gland during development and onset of xerostomia in Sjögren’s syndrome-like disease of the C57BL/6.NOD-Aec1Aec2 mouse.

city: Gainesville

first: Ammon

last: Peck

state: FL

address: 1945 SW 16th Avenue

department: Department of Infectious Diseases & Pathology

institute: University of Florida

summary:
Recently, we reported the development of the C57BL/6.NOD-Aec1Aec2 mouse that carries two genetic intervals derived from the NOD mouse capable of conferring Sjögren’s syndrome (SjS)-like disease in SjS-non-susceptible C57BL/6 mice.
In an attempt to define the molecular bases underlying onset of stomatitis sicca (xerostomia) in this C57BL/6.NOD-Aec1Aec2 mouse model, we have carried out a study utilizing genomic microarray technology.

overall_design: The present study was designed to define the changing gene expression profiles within the Lacrimal glands of C57BL/6.NOD-Aec1Aec2 mice at five time points representing a pre-disease stage (4 weeks), the early pre-clinical stage (8 weeks), the initial influx of leukocytes into the Lacrimal glands (12 weeks), the early clinical phase of autoimmunity (16 weeks), and the early onset of clinical SjSlike disease characterized by secretory dysfunction (20 weeks). The C57BL/6.NOD-Aec1Aec2 mouse is a model of primary SjS in which the Idd3 region of chromosome 3 and the Idd5 region of chromosome 1 derived from the NOD mouse were bred into the non-autoimmune C57BL/6 mouse, resulting in a SjS-like disease susceptibility that mimics both the pathophysiological characteristics and reduced secretory responses observed with NOD mice during development and onset of disease. This SjS-susceptible strain was designated C57BL/6.NOD-Aec1Aec2, where Aec1 corresponds to Idd3 (of chromosome 3) and Aec2 corresponds to Idd5 (of chromosome 1).

first: Cuong

middle: Q

last: Nguyen

first: Ashok

last: Sharma

first: Byung

last: Lee

first: Jin-Xiong

last: She

first: Richard

last: McIndoe


title: Histone Demethylase Lsd1 Represses Hematopoietic Stem and Progenitor Cell Signatures During Blood Cell Maturation.


title: Role for DNA methylation in response to Gata4 activation in embryonic stem cell-derived mesoderm

status: Public on Jun 24 2013

city: Kobe

first: Masaki

last: Okano

state: Hyogo

address: 2-2-3 Minatojima-Minamimachi, Chuo-ku

department: Center for Developmental Biology

institute: RIKEN

summary: During embryogenesis, many key transcription factors are used repeatedly, achieving different outcomes depending on cell type and developmental stage. The epigenetic modification of the genome functions as a memory of a cell’s developmental history, and it has been proposed that such modification shapes the cellular response to transcription factors. To investigate the role of DNA methylation in the response to transcription factor Gata4, we examined expression profiles of Dnmt3a-/-Dnmt3b-/- ES cell-derived mesoderm cells cultured for 4 days with or without Gata4 activation, as well as the wild-type counterparts, using Affymetrix microarrays.

overall_design: Wild-type and Dnmt3a-/-Dnmt3b-/- (DKO) ES cell clones stably expressing dexamethasone (Dex)-inducible Gata4 were generated by introducing an expression plasmid for Gata4 fused with the ligand-binding domain of the human glucocorticoid receptor (Gata4GR) driven by the CAG promoter, by electroporation. For mesoderm differentiation, 1 x 10^5 ES cells were plated on a type IV collagen-coated 10-cm dish and cultured for 4 days. Cultured cells were harvested and collected as single-cell suspensions using 0.25% trypsin-EDTA, followed by incubation in differentiation medium at 37˚C to allow cell-surface markers to recover. Flk1(+)/PDGFRalpha(+) double-positive (DP) cells, which are considered equivalent to the lateral plate mesoderm, were sorted by FACS-Aria (BD Biosciences). Sorted DP cells were further cultured on type IV collagen-coated culture dishes in the absence or presence of 100 nM Dex for 4 days. For reference data, primitive endoderm (PE) cells were directly differentiated from undifferentiated ES cells by addition 100 nM Dex in ES cell-maintenance medium.

first: Masaaki

last: Oda

first: Lars

middle: M

last: Jakt


title: Expression data from tumoral thymocytes and DP thymocytes expressing an activated form of b-catenin in mouse T cells

status: Public on Jun 21 2013

city: Illkirch

first: Peggy

last: Kirstetter

address: 1, rue Laurent Fries

department: Functional Genomic and Cancer

institute: Institut de Génétique et de Biologie Cellulaire et Moléculaire

summary:
To assess the importance of the Wnt pathway during T cell develoment, we generated a mouse line (R26-βcat) in which high levels of active β-catenin are maintained throughout T cell development. Young R26-βcat mice (6-week-old) show a differentiation block at the CD4+CD8+ DP stage. All R26-βcat mice develop T cell leukemias with a DP phenotype at 5-6 months of age.
To identify the molecular pathways involved in tumor development, we profiled the global gene expression of transformed and pre-transformed DP cells.

overall_design: Thymocytes from 6-week-old mice (with a normal sized thymus and a polyclonal thymocyte population) were used to define the pre-transformed transcriptome. RNA from control and pre-leukemic R26-βcat DP thymocytes as well as R26-βcat total tumor cells were extracted and used for transcriptome analysis.


title: Gene expression data of Lsd1fl/fl and Lsd1fl/fl Mx1Cre CD150+ CD48- lin- c-Kit+ Sca-1+ LT-HSCs

summary: We discovered that mice that lack Lsd1 in hematopoietic cells were exhibited increased frequencies of CD150+ CD48- lin- c-Kit+ Sca-1+ LT-HSCs, but completely lacked the lin- c-Kit+ Sca-1- myeloid progenitor compartment. To determine the genes altered by Lsd1-loss, CD150+ CD48- lin- c-Kit+ Sca-1+ LT-HSCs from Lsd1fl/fl and Lsd1fl/fl Mx1Cre mice were FACS-purified to be analyzed by gene expression profiling.

overall_design: Primary CD150+ CD48- lin- c-Kit+ Sca-1+ LT-HSCs were isolated by FACS-sorting, from the bone marrow of Lsd1fl/fl and Lsd1fl/fl Mx1Cre animals, one week after the final p(I:C) dose. Total RNA from three biological replicates per genotype was extracted with the RNeasy Micro Kit (QIAGEN), treated with DNaseI, reverse transcribed. RNA extracted from CD150+ CD48- lin- c-Kit+ Sca-1+ cells was amplified with the Ovation Pico WTA RNA Amplification System 2 (NuGEN Technologies). Single-stranded cDNA amplification products were purified using QIAquick PCR Purification Kit (QIAGEN) and labeled with the FL-Ovation cDNA Biotin Module V2 (NuGEN).   The Biotin-labeled cDNA was used to hybridize to Affymetrix expression arrays using the Mouse Genome 430 2.0 array platform.  Primary CD150+ CD48- lin- c-Kit+ Sca-1+ LT-HSCs were isolated by FACS-sorting, from the bone marrow of Lsd1fl/fl and Lsd1fl/fl Mx1Cre animals, one week after the final p(I:C) dose. Total RNA from three biological replicates per genotype was extracted with the RNeasy Micro Kit (QIAGEN), treated with DNaseI, reverse transcribed. RNA extracted from CD150+ CD48- lin- c-Kit+ Sca-1+ cells was amplified with the Ovation Pico WTA RNA Amplification System 2 (NuGEN Technologies). Single-stranded cDNA amplification products were purified using QIAquick PCR Purification Kit (QIAGEN) and labeled with the FL-Ovation cDNA Biotin Module V2 (NuGEN).   The Biotin-labeled cDNA was used to hybridize to Affymetrix expression arrays using the Mouse Genome 430 2.0 array platform.  Primary CD150+ CD48- lin- c-Kit+ Sca-1+ LT-HSCs were isolated by FACS-sorting, from the bone marrow of Lsd1fl/fl and Lsd1fl/fl Mx1Cre animals, one week after the final p(I:C) dose. Total RNA from three biological replicates per genotype was extracted with the RNeasy Micro Kit (QIAGEN), treated with DNaseI, reverse transcribed. RNA extracted from CD150+ CD48- lin- c-Kit+ Sca-1+ cells was amplified with the Ovation Pico WTA RNA Amplification System 2 (NuGEN Technologies). Single-stranded cDNA amplification products were purified using QIAquick PCR Purification Kit (QIAGEN) and labeled with the FL-Ovation cDNA Biotin Module V2 (NuGEN).   The Biotin-labeled cDNA was used to hybridize to Affymetrix expression arrays using the Mouse Genome 430 2.0 array platform.

middle: H


title: Chronic TNBS Colitis in the FN14 KO Mouse

status: Public on Jun 20 2013

city: Cambridge

first: Suzanne

last: Szak

state: MA

address: 14 Cambridge Ctr

department: Drug Discovery

institute: BiogenIdec, Inc.

summary: To test TWEAK/Fn14 pathway and relative agents in chronic TNBS colitis

overall_design: Chronic colitis was induced by rectal injection of TNBS with ethanol for 6 weeks in WT or FN14 KO BALB/c mice. Colons were harvested for gene profiling.

first: Aoi

last: Son

first: Tomoyuki

last: Oshio

first: Motomi

last: Yamazaki

first: Yuki

middle: I

last: Kawamura

first: Teruki

last: Hagiwara

first: Kyoko

last: Inagaki-Ohara

first: Toshihiko

last: Okada

first: Ping

last: Wu

first: Linda

middle: C

last: Burkly

first: Taeko

last: Dohi


title: Gene expression of 4, 5, and 6 days differentiated Flk1+ WT ES cells, and of 6 days differentiated Flk1+ Runx1-/- and Tal-1-/- ES cells

status: Public on Jun 18 2013

first: Pawel

last: Durek

address: Charitéplatz 1

institute: Deutsches Rheuma-Forschungszentrum

summary: In order to identify genes that are activated in differentiating WT ESCs, but are missing in Tal-1-/- and Runx1-/- ESCs, and which might be involved in the generation of definitive hematopoietic progenitors and their specification thereafter, we performed microarray analyses on purified Flk-1+ cells, differentiated from these ESCs for 4, 5, and 6 days “in vitro”.

overall_design: Gene-expression profiling of three biological replicates was performed at days 4, 5, and 6 during the differentiation process of WT J1 ESCs (9 samples), and at day 6 during the differentiation process of either Runx1-/- J1 or Tal-1-/- J1 ESCs (3 samples each). Total RNA was extracted using the RNeasy Mini kit (Qiagen). The integrity and amount of isolated RNA was assessed for each sample using an Agilent 2100 Bioanalyzer (Agilent, Waldbronn, Germany) and a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE). Complementary DNA was synthesized from 3-5 μg total RNA, using reagents recommended in the technical manual GeneChip Expression Analysis (Affymetrix, Santa Clara, CA). The in vitro transcription, necessary for the synthesis of biotinylated complementary RNA (cRNA) was performed using the Enzo RNA Transcript Labeling kit (Affymetrix). Fifteen micrograms of fragmented cRNA of each sample were hybridized to nine Mouse Genome 430-2 arrays (Affymetrix). Hybridization was performed in a Hybridization Oven 640, and chips were washed and stained in the Fluidics Station 400 (both Affymetrix), according to procedure 2 as described in the technical manual. Finally, the arrays were scanned with a GeneChip Scanner 3000 using the GCOS software, both Affymetrix. All relevant GCOS data of quality checked microarrays were analyzed with High Performance Chip Data Analysis (HPCDA, unpublished), using the BioRetis database (www.bioretis-analysis.de), as described and validated previously (55). Used query parameters for database filtering process was described earlier several times (56). For hierarchical cluster analysis, we used the program Genes@Work (57) with gene vectors for normalization and Pearson w/mean for similarity measure. As cluster type, we used center of mass.

first: Julia

last: Tornack

first: Katharina

last: Seiler

first: Andreas

last: Grützkau

first: Joachim

middle: R

last: Grün

first: Masafumi

last: Onodera

first: Fritz

last: Melchers

first: Motokazu

last: Tsuneto


title: Expression data from bone marrow macrophage derived from lean and obese mice after 1,4, and 24h exposition to P.gingivalis

status: Public on Jun 12 2013

city: boston

first: Salomon

last: Amar

state: ma

address: 650 albany street

department: perio-oral bio

institute: boston university

summary:
Obesity is a chronic inflammatory disease that weakens macrophage innate immune response to infections. Since M1 polarization is crucial during acute infectious diseases, we hypothesized that diet-induced obesity inhibits M1 polarization of macrophages in the response to bacterial infection.
Using a computational approach in conjunction with microarray data, we identified switching genes that may differentially control the behavior of response pathways in macrophages from lean and obese mice.

overall_design: Bone marrow macrophages (BMMΦ) from lean and obese mice were exposed to live Porphyromonas gingivalis (P. gingivalis) for three incubation times (1 h, 4 h and 24 h). cDNA from BMMΦ of lean and obese mice were hybridized on Affymetrix Mouse Genome 430 2.0 Arrays. Hybridization was performed on three replicates at each time point (18 arrays total).

first: Guilhem

last: Richard


title: Gene expression of in vitro cultivated preB cells before and after 8, 16 and 24 hours induction of miR-221

status: Public on Jun 05 2013

city: Berlin

summary: PreB cells were analyzed for differences in gene expression before and after the overexpression of miR-221. In order to dissect possible targets for the miR-221, gene expression profiles of preB cells un-induced or induced for the miR-221 expression after 8, 16 and 24 hours were compared. All induction time-points, e.g. after 8, 16 and 24 hours were compared to un-induced preB cells and to each other group.

overall_design:
Gene expression profiles of un-induced preB cells, preB cells induced for miR-221 expression after 8, 16, and 24 hours were analyzed using Affymetrix MG 430 2.0 whole genome arrays. Each time-point was performed in triplicates for un-induced preB cells and preB cells induced for miR-221 expression after 8, 16, and 24 hours (12 arrays in total). To obtain genes significantly downregulated upon induction of miR-221, the expression profiles of un-induced preB cells were compared to preB cells activated for 8, 16, or 24 h and were also compared to each other.
After total RNA extraction, reverse transcription, cDNA extraction, the biotinylated cRNA was transcribed, fragmented, and 15 µg cRNA hybridized in triplicates for each of the four groups to the 12 GeneChip arrays: Group1, un-induced preB cells, Group2, preB cells induced for miR-221 expression after 8h, Group3, preB cells induced for miR-221 expression after 16h, Group4, preB cells induced for miR-221 expression after 24h.

first: Marko

last: Knoll

first: Szandor

last: Simmons

first: Corinne

last: Bouquet


title: Atrial Identity Is Determined by A COUP-TFII Regulatory Network (RNA)

status: Public on Jun 07 2013

city: Houston

first: San-pin

address: 1 Baylor Plaza

institute: Baylor College of Medicine

summary:
Atria and ventricles exhibit distinct molecular profiles that produce structural and functional differences between the two cardiac compartments. However, factors that determine these differences remain largely undefined. Cardiomyocyte-specific COUP- TFII ablation produces ventricularized atria that exhibit ventricle-like action potentials, increased cardiomyocyte size, and development of extensive T-tubules.
We used microarrays to examine the molecular profile of cardiomyocyte-specific COUP-TFII knockout adult atria in comparison with that of normal atria.

overall_design: We extracted RNA from mutant right atria, control right atria and control ventricles from 2 months old adult mice, followed by gene expression profiling using Affymetrix microarrays.

first: Ming-Jer

last: Tsai

first: Sophia

middle: Y


title: Stump project-- mRNA whole tissue; Volar versus non-volar acral skin gene expression

city: Baltimore

first: Luis

middle: Andres

last: Garza

address: 1550 Orleans St. Suite 204 CRBII Koch

department: Dermatology

institute: Johns Hopkins School of Medicine

summary: We were interesed in defining the gene signautre of volar skin.

overall_design: Whole skin punch biopsies of palms, backs of hand, soles and backs of feet were submitted for Affymetrix Exon arrays. 4 replicates of each site from distinct human donors were included; total of 16 samples analyzed.


title: Expression of heat shock factor 1 (HSF1) knock down (KD) in hepatocellular carcinoma (HCC) cells results in characteristic changes in gene expression profiles.

city: Sapporo

first: Makoto

last: Chuma

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

department: Gastroenterology and Hepatology

institute: Hokkaido University

summary: Analysis of HSF1-down regulation of HCC cells at gene expression level. Results provide important information of genes involved in HSF1, such as liver proliferation, apoptosis, stress response, metabolism, these genes were up- or down-regulated.

overall_design: Total RNA obtained from HSF1-KD KYN2 (HCC) cells and HSF1-control KYN2 cells. To identify genes generally involved in HSF1 associated, we compared expression profiles between HSF1-KD KYN2 (HCC) cells and HSF1-control KYN2 cells by using Illumina HumanWG-6 BeadChip.

first: Kosuke

last: Tashiro


title: Expression data from adult Myeloerythroid Progenitors (MP) ICN2 positive and adult Myeloerythroid Progenitors (MP) ICN2 negative

city: Paris

first: Camille

last: Lobry

address: 16 rue de la Grange aux Belles

institute: Inserm

summary: Notch signaling defines a conserved, fundamental pathway, responsible for determination in metazoan development and is widely recognized as an essential component of lineage specific differentiation and stem cell self-renewal in many tissues including the hematopoietic system. Until recently, the majority of studies in the hematopoietic system focused on Notch signaling in lymphocyte differentiation and knowledge of individual Notch receptor roles in early hematopoiesis has been limited due to a paucity of genetic tools available  To fate-map Notch receptor expression and pathway activity in the hematopoietic system we used tamoxifen-inducible CreER knock-in mice for individual Notch receptors in combination to a novel Notch reporter strain (Hes1GFP) and a conditional gain of function allele of Notch2 receptor (Rosa-lsl-ICN2).

overall_design: Bone marrow lineage negative, cKit+, Sca1- cells were sorted from Rosa-lsl-ICN2 Mx1-cre+ mice or Mx1-cre+ littermates for RNA extraction and hybridization on Affymetrix microarrays

first: Philmo

last: Oh

first: Iannis

last: Aifantis


title: Expression data from pre-iPSCs with a control, histone methyltransferase or Cbx3 (HP1g) knockdown

city: Madison

first: Rupa

last: Sridharan

address: 2118 Wisconsin Institute for Discovery

institute: UW-Madison

summary:
Transition from  a partially reprogrammed pre-iPSC state to iPSC state can be achieved by modulating levels of histone modifying enzymes or proteins that can bind to histone modifications
We used microarrays to determine the gene expression profile of pre-iPSCs depleted for either 3 histone methyltransferases together or the HP1gamma protein

overall_design: pre-iPSCs were subjected to simultaneous siRNA mediated knockdown of Ehmt1, Ehmt2 and Setdb1- which is the 3XHMT sample  that mediate H3k9me2/me3 or Cbx3( HP1gamma) or control siRNA to luciferase

first: Kathrin

last: Plath


title: Profiling of FACs sorted subpopulations of iPS cells from cell surface marker profile

city: St Lucia

first: Sean

last: Grimmond

state: Q

address: Services Rd

department: Institute for Molecular Bioscience

country: Australia

institute: University of Queensland

summary:
Two independent induced pluripotent stem cell lines: ES4CL1 (derived from foreskin) and MR90C2 (derived from lung Fibroblast) were maintained on inactivated mouse embryonic fibroblast (MEF) feeder cells in the presence of ESC media containing DMEM, 20% knock-out serum replacement with 100ng/mL of bFGF.  7 days after seeding, cells were harvested in TrypLE Express and FACs sorted using antibodies detecting the presence of cell surface antigens GCTM-2 and CD9.
4 independent fractions were isolated after cell sorting: P4 (CD9-Negative, GCTM-2 Negative); P5 (CD9-Low, GCTM-2 Low); P6 (CD9-Medium, GCTM-2 medium) and P7 (CD9-High, GCTM-2 High).  Each individual experiment was performed in triplicate.

Keywords: cell type comparison

overall_design: Three consecutive passages of both ES4CL1 and MR90C2 cells were grown in standard conditions, FACs sorted cells collected, and total RNA isolated.   Microarray was performed on a total of 24 samples, (3 replicates of 4 FACs sorted populations from two independent cell lines).

first: Gabriel

last: Kolle


title: Expression data from adult LSK Hes1-GFP positive and adult LSK Hes1-GFP negative

department: IRSL Inserm U944 / CNRS UMR7212

overall_design: Bone marrow lineage negative, cKit+, Sca1+ cells were sorted from Hes-GFP mice for RNA extraction and hybridization on Affymetrix microarrays