title: Dexamethasone-stimulated DNA methylation of the epigenetic clock CpGs in peripheral blood

status: Public on Nov 03 2015

city: Munich

first: Janine

last: Arloth

address: Kraepelinstr. 2-10

country: Germany

institute: Max Planck Institute of Psychiatry

summary:
Whole-genome DNA methylation (baseline and following GR-stimulation with 1.5 mg dexamethasone p.o.) were analysed to identify glucocorticoid receptor (GR)-mediated changes in DNA methylation.
Lifetime stress accelerates epigenetic aging.

overall_design:
DNA methylation was assessed in whole blood at baseline and 3 hours after stimulation with the selective GR agonist dexamethasone (1.5 mg p.o.). Blood was collected in EDTA vacuum tubes prior to extraction. DNA methylation was interrogated for each sample using the HumanMethylation450 BeadChip (Illumina).

Supplementary files 'GSE74414_unmethylated_signals_353_CpG.txt', 'GSE74414_methylated_signals_353_CpG.txt', and 'GSE74414_detection.p.values_353_CpG.txt' include the raw data for the 353 CpGs used in the analysis in the associated manuscript.
Supplementary file 'GSE74414_beta_values_353_CpG.txt' includes the processed data for the 353 CpGs used in the analysis in the associated manuscript.

first: Elisabeth

last: Binder


title: Exposure of rat to a variety of toxicants, brain assayed by CodeLink microarray

status: Public on Aug 18 2014

city: Durham

first: Scott

last: Auerbach

state: North Carolina

address: 111 TW Alexander Drive

country: USA

institute: Division of the National Toxicology Program at NIEHS

summary: DrugMatrix is a comprehensive rat toxicogenomics database and analysis tool developed to facilitate the integration of toxicogenomics into hazard assessment.  Using the whole genome and a diverse set of compounds allows a comprehensive view of most pharmacological and toxicological questions and is applicable to other situations such as disease and development.

overall_design: Complete Drug Matrix dataset for rat brain. Approximately 600 different compounds were profiled in up to 8 different rat tissues by obtaining tissue samples from test compound-treated and vehicle control-treated rats in biological triplicates for gene expression analysis after 0.25, 1, 3, and 5 days of exposure with daily dosing. In a few studies (1.8%), 7 days of exposure was substituted for 5 days of exposure.  Samples were hybridized to CodeLink RU1 10K rat arrays (Amersham Biosciences).


title: Exposure of rat to a variety of toxicants, bone marrow assayed by CodeLink microarray

overall_design: Complete Drug Matrix dataset for rat bone marrow. Approximately 600 different compounds were profiled in up to 8 different rat tissues by obtaining tissue samples from test compound-treated and vehicle control-treated rats in biological triplicates for gene expression analysis after 0.25, 1, 3, and 5 days of exposure with daily dosing. In a few studies (1.8%), 7 days of exposure was substituted for 5 days of exposure.  Samples were hybridized to CodeLink RU1 10K rat arrays (Amersham Biosciences).


title: Exposure of rat hepatocytes to a variety of toxicants, assayed by CodeLink microarray.

overall_design: Complete Drug Matrix dataset for rat hepatocytes. Approximately 600 different compounds were profiled in up to 8 different rat tissues by obtaining tissue samples from test compound-treated and vehicle control-treated rats in biological triplicates for gene expression analysis after 0.25, 1, 3, and 5 days of exposure with daily dosing. In a few studies (1.8%), 7 days of exposure was substituted for 5 days of exposure.  Samples were hybridized to CodeLink RU1 10K rat arrays (Amersham Biosciences).


title: Exposure of rat to a variety of toxicants, heart assayed by Affymetrix microarray

status: Public on May 27 2014

overall_design: Complete Drug Matrix dataset for rat heart. Approximately 600 different compounds were profiled in up to 7 different rat tissues by obtaining tissue samples from test compound-treated and vehicle control-treated rats in biological triplicates for gene expression analysis after 0.25, 1, 3, and 5 days of exposure with daily dosing. In a few studies (1.8%), 7 days of exposure was substituted for 5 days of exposure.  Samples were hybridized to whole genome RG230_2.0 GeneChip arrays (Affymetrix, CA).


title: Gene expression profiling of 5 pea aphid morphs

status: Public on Jun 04 2014

city: Lincoln

first: Swapna

middle: R.

last: Purandare

state: Nebraska

address: 348 Manter Hall

department: Biological Sciences

institute: University of Nebraska-Lincoln

type: Expression profiling by high throughput sequencing

summary:
Purpose: Identify differentially expressed genes between 5 pea aphid morphs
Methods: Collected whole bodies of 30 adult aphids of each of the five pea morphs and three clones (total of 15 samples)

overall_design: 5 pea aphid morphs * 3 genotypes = 15 samples

middle: R

first: Jennifer

middle: A

last: Brisson


title: Gene-expression profiles of ovarian cancer regarding its microenvironment

status: Public on Mar 04 2014

city: Kyoto

first: Kaoru

last: Abiko

address: 54 Shogoin Kawaharacho, Sakyo-ku

department: Department of Gynecology and Obstetrics

country: Japan

institute: Kyoto University Graduate School of Medicine

summary: PD-L1 suppresses host immunity and promotes tumor growth. We investigated how IFN-γ regulates PD-L1 in the ovarian cancer microenvironment.  In clinical samples, the number of stromal CTLs in peritoneally disseminated tumors was correlated with PD-L1 expression on the tumor cells, and the lymphocyte number was significantly related to the IFN-γ signature score. In mouse models, PD-L1 was induced in peritoneal disseminated tumors, where lymphocytes were prominent, but not in subcutaneous tumors. Depleting IFNGR1 resulted in lower PD-L1 expression and longer survival in peritoneal dissemination model. Injection of IFN-γ into subcutaneous tumors increased PD-L1 expression and tumor size, and PD-L1 depletion abrogated tumor growth. These data suggest that IFN-γ works as a tumor progressor through PD-L1 induction. The source of IFN-γ in ovarian cancer microenvironment and its biological effect to the tumor cells is unclear. The immortalized human ovarian surface epithelial cell line, HOSE-E7/hTERT (HOSE) was treated with IFN-γ and expression microarray analysis was performed, and probes showing significantly higher values in IFN-γ-added group were termed “IFN-γ signature genes (295 probes)”.  We then applied this signature to our ovarian cancer microarray data, which included 75 ovarian cancer clinical samples, by means of ss-GSEA. IFN-γ signature score was strongly correlated to the number of infiltrating CD4-positive or CD8-positive lymphocytes in the tumors. These data suggest that the IFN-γ in the ovarian cancer microenvironment is derived from lymphocytes, and an IFN-γ-rich microenvironment is strongly correlated to a lymphocyte-rich microenvironment.

overall_design: Genome-wide transcriptional changes in human ovarian cancer tissue were observed in different tumor immunological microenvironment.

first: K

first: N

last: Matsumura


title: in vitro differentiated Th0, Th17, and Tr1 cells

status: Public on Mar 20 2014

first: Thomas

last: Korn

address: Ismaninger Str. 22

department: Neurology

institute: TU Munich, Klinikum rechts der Isar

summary:
Gene expression profiling of in vitro differentiated murine Th cell subsets. Flow cytometrically sorted naive Th cells (CD4+ CD44- Foxp3-) were polyclonally stimulated in vitro for 3 days using 4 µg/ml plate-bound antibody to CD3 (145-2C11) and 2 µg/ml soluble antibody to CD28 (PV-1).
Th0 cells were cultured in the absence of exogenous cytokines. Th17 cells were differentiated with 50 ng/ml IL-6 plus 0.5 ng/ml TGF-β. Tr-1 cells were differentiated with 100 ng/ml IL-27 plus 0.5 ng/ml TGF-β.

overall_design: Five biological replicates per Th subset (Th0, Th17, Tr1)

first: Sylvia

last: Heink

first: Christina

last: Heinemann


title: Exposure of rat to a variety of toxicants, kidney assayed by CodeLink microarray

overall_design: Complete Drug Matrix dataset for rat kidney. Approximately 600 different compounds were profiled in up to 8 different rat tissues by obtaining tissue samples from test compound-treated and vehicle control-treated rats in biological triplicates for gene expression analysis after 0.25, 1, 3, and 5 days of exposure with daily dosing. In a few studies (1.8%), 7 days of exposure was substituted for 5 days of exposure.  Samples were hybridized to CodeLink RU1 10K rat arrays (Amersham Biosciences).


title: The role of nitric oxide synthase activity in connection with induced resistance against low-dose hyper-radiosensitivity

status: Public on Apr 15 2013

city: Oslo

first: Nina

middle: Frederike Jeppesen

last: Edin

address: Sem Sælandsvei 24

department: Physics

country: Norway

institute: University of Oslo

summary: The cells harvested for microarray analysis were high-dose rate (HDR) irradiated, low-dose rate (LDR) irradiated or unirradiated T-47D cells. The HDR-irradiated cells were harvested 24h after a dose of 0.3 Gy at 35 Gy/h, a time where hyper-radiosensitivity (HRS) had returned. The HRS-deficient LDR-irradiated cells were harvested 2 months after a dose of 0.3 Gy at 0.3 Gy/h.

overall_design: LDR-irradiated vs. Control (unirradiated) contains 4 biological replicates. HDR- vs. LDR-irradiated contains 3 biological replicates. HDR-irradiated vs. Control contains 4 biological replicates.

middle: J

first: Joe

last: Sandvik

first: Hilde

middle: S

last: Vollan

first: Katharina

last: Reger

first: Agnes

last: Görlach

first: Erik

middle: O

last: Pettersen


title: Transcriptome and marker frequency analysis of E. coli (control vs. Trimethoprim) and S. pneumoniae (control vs. HPUra/Kanamycin)

status: Public on Apr 10 2014

city: Groningen

first: Jelle

last: Slager

address: Nijenborgh 7

department: Molecular Genetics

country: Netherlands

institute: University of Groningen

type: Genome variation profiling by high throughput sequencing

summary: We show that treatment with HPUra (for S. pneumoniae) and trimethoprim (for E. coli) leads to a skewed gene dosage profile (increase around the origin of replication), which is also propagated to the transcriptome level. Kanamycin, however, does not have this effect. In case of S. pneumoniae this shift in gene dosage distribution leads to the population-wide activation of competence.

sample_organism:
Escherichia coli
Streptococcus pneumoniae

overall_design: Pairwise comparison of untreated and antibiotic-treated cells (either RNA-seq or DNA-seq). It was performed with deep sequencing, using an Illumina HiSeq 2000 machine with 100 nt paired-end reads. Control (E. coli and S. pneumoniae), HPUra- (S. pneumoniae) and Trimethoprim-treated (E. coli) samples were analysed from duplicate samples, while other conditions were from single samples.

first: J

first: M

last: Kjos

first: L

last: Attaiech

middle: W

last: Veening


title: Individual array-based gene expression patterns generated using total RNA prepared from whole blood of 991 participants of the SHIP-TREND cohort

status: Public on Aug 29 2013

city: Greifswald

first: Uwe

last: Völker

address: Friedrich-Ludwig-Jahn-Str. 15A

department: Interfakultäres Institut für Genetik und Funktionelle Genomforschung

summary:
The data set comprises individual array-based genome-wide gene expression data of 991 participants of the SHIP-TREND cohort generated using RNA prepared from whole blood.
*** Due to privacy concerns, the SNP and phenotype data is not available with unrestricted access. Individuals wishing to obtain this data for research purposes may request access directly from the submitter (contact info below). ***

overall_design: Total RNA was prepared from whole-blood samples from 991 individuals belonging to the epidemiological SHIP-TREND cohort. Individual mRNA profiles were generated using the Illumina HumanHT-12 v3 Expression BeadChip.


title: NOD2-dependent licensing of the microbiota predispose to transmissible inflammation and tumorigenesis in the colon.

status: Public on Jan 02 2013

city: Lille

first: David

last: Hot

address: 1 rue du professeur Calmette

department: Center for Infection and Immunity of Lille

country: France

institute: Institut Pasteur de Lille

summary: Instability in the composition of gut bacterial communities, referred as dysbiosis, has been associated with important human intestinal disorders such as Crohn’s disease and colorectal cancer. Here, we show that dysbiosis coupled to Nod2 or Rip2 deficiency suffices to cause an increased risk for intestinal inflammation and colitis-associated carcinogenesis in mice. Aggravated epithelial lesions and dysplasia upon chemical-induced injury associated with loss of Nod2 or Rip2 can be prevented by antibiotics or anti-IL6R treatment. Nod2-mediated risk for intestinal inflammation and colitis-associated tumorigenesis is communicable through maternally-transmitted microbiota even to wild-type hosts. Disease progression was identified to drive complex NOD2-dependent changes of the colonic-associated microbiota. Reciprocal microbiota transplantation rescues the vulnerability of Nod2-deficient mice to colonic injury. Altogether, our results unveil an unexpected function for NOD2 in shaping a protective assembly of gut microbial communities, providing a rationale for intentional manipulation of genotype-dependent dysbiosis as a causative therapeutic principle in chronic intestinal inflammation.

overall_design: Analysis used RNA extracted from colonic mucosa of untreated, antibiotics-treated or metronidazole-treated C57Bl/6J and Nod2-deficient mice in CAC model. Direct comparisons were performed as follow: C57Bl/6J untreated mice vs Nod2-deficient untreated mice, C57Bl/6J antibiotics-treated mice vs Nod2-deficient antibiotics-treated mice, C57Bl/6J metronidazole-treated mice vs Nod2-deficient metronidazole-treated mice, C57Bl/6J untreated mice vs C57Bl/6J antibiotics-treated mice, C57Bl/6J untreated mice vs C57Bl/6J metronidazole-treated mice, Nod2-deficient untreated mice vs Nod2-deficient antibiotics-treated mice, Nod2-deficient untreated mice vs Nod2-deficient metronidazole-treated mice. Indirect comparisons with control data were made across multiple arrays with raw data pulled from different channels for data analysis.

first: Aurelie

last: Couturier

first: Mathias

last: Chamaillard

first: Ludovic

last: Huot


title: Exposure of rat to a variety of toxicants, thigh muscle assayed by Affymetrix microarray

first: Scott

last: Auerbach

overall_design: Complete Drug Matrix dataset for rat thigh muscle. Approximately 600 different compounds were profiled in up to 7 different rat tissues by obtaining tissue samples from test compound-treated and vehicle control-treated rats in biological triplicates for gene expression analysis after 0.25, 1, 3, and 5 days of exposure with daily dosing. In a few studies (1.8%), 7 days of exposure was substituted for 5 days of exposure.  Samples were hybridized to whole genome RG230_2.0 rat GeneChip arrays (Affymetrix, CA).


title: Gene expression profiling in anchorage-independent melanoma A375 cells

status: Public on Dec 13 2012

city: New Taipei City

first: Shaochen

last: Lee

address: 510 Zhongzheng Rd., Xinzhuang Dist.

department: School of Medicine

country: Taiwan

institute: FuJen Catholic University

summary: Analysis of gene expression and compare the significant changed genes with associated phenotypes

overall_design: Total RNA extracted from adherent and suspension culture of A375 cells

first: ShaoChen


title: Exposure of rat to a variety of toxicants, liver assayed by Codelink microarray

overall_design: Complete Drug Matrix dataset for rat liver. Approximately 600 different compounds were profiled in up to 7 different rat tissues by obtaining tissue samples from test compound-treated and vehicle control-treated rats in biological triplicates for gene expression analysis after 0.25, 1, 3, and 5 days of exposure with daily dosing. In a few studies (1.8%), 7 days of exposure was substituted for 5 days of exposure.  Samples were hybridized to single-channel CodeLink RU1 arrays.


title: Bronchial airway gene expression reflects a COPD-associated field of injury that changes with disease severity and is reversible with therapy

status: Public on Mar 22 2013

city: Boston

first: Katrina

last: Steiling

state: MA

address: 72 East Concord Street, E-631

department: Medicine

institute: Boston Univeristy School of Medicine

summary: RNA was isolated from bronchial brushings obtained from current and former smokers with and without COPD. mRNA expression was profiled using Affymetrix Human Gene 1.0 ST Arrays.

overall_design: RNA isolated from bronchial brushings was processed and hybridized to Affymetrix Human Gene 1.0 ST Arrays. A total of 269 arrays from 267 subjects were hybridized. Data from the 269 microarrays were used for RMA normalization. Data from 238 subjects was used in the analysis to determine the association of gene expression with COPD-related phenotypes.

first: Avrum

last: Spira


title: Transcriptomic analysis of host response to mouse-adapted SARS virus in wild type, STAT1 -/-, and IFNAR1 -/- mouse genetic backgrounds

status: Public on Feb 22 2012

city: Seattle

first: Michael

last: Katze

state: WA

address: Rosen Building 960 Republican St.

department: Microbiology

institute: University of Washington

summary: The mechanisms by which pulmonary lesions and fibrosis are generated during SARS-CoV infection are not known. Using high-throughput mRNA profiling, we examined the transcriptional response of wild-type (WT), type I interferon receptor knockout (IFNAR1−/−), and STAT1 knockout (STAT1−/−) mice infected with a recombinant mouse-adapted SARS-CoV (rMA15) to better understand the contribution of specific gene expression changes to disease progression.

overall_design: Ten week old 129S6/SvEv wild-type, STAT1−/− (Taconic Farms, Germantown, NY), and IFNAR1−/− mice bred on a 129SvEv background  were anesthetized with a ketamine and infected intranasally with either phosphate-buffered saline (PBS) alone (Invitrogen, Carlsbad, CA) or 1 × 10^5 PFU rMA15-PBS. Mice were euthanized and left lungs were harvested from individual mice (a total of 3 infected mice from each strain) at days 2, 5, and 9 postinfection (dpi) for microarray analyses. Lung samples were taken from mock-infected animals from each of the strains at 5 dpi.

first: Gregory

last: Zornetzer

first: Matthew

middle: B

last: Frieman

first: Elizabeth

last: Rosenzweig

first: Marcus

last: Korth

first: Carly

last: Page

first: Ralph

last: Baric

middle: G


title: Exposure of rat to a variety of toxicants, kidney assayed by Affymetrix microarray

overall_design: Complete Drug Matrix dataset for rat kidney. Approximately 600 different compounds were profiled in up to 7 different rat tissues by obtaining tissue samples from test compound-treated and vehicle control-treated rats in biological triplicates for gene expression analysis after 0.25, 1, 3, and 5 days of exposure with daily dosing. In a few studies (1.8%), 7 days of exposure was substituted for 5 days of exposure.  Samples were hybridized to whole genome RG230_2.0 rat GeneChip (Affymetrix, CA).


title: Gene-expression profiles of ascites-cytology-positive ovarian cancer

status: Public on Jul 10 2012

first: Kaoru

last: Abiko

summary: Ovarian cancer often progresses by disseminating to the peritoneal cavity, but how the tumor cells evade host immunity during this process is poorly understood. Programmed cell death 1 ligand 1 (PD-L1) is known to suppress immune system and to be an unfavorable prognostic factor in ovarian cancer. The purpose of this study was to elucidate the function of PD-L1 in peritoneal dissemination. Positive cytology in ascites was a significant poor prognostic factor in ovarian cancer. Microarray profiles of cytology-positive cases showed significant correlations with Gene Ontology terms related to immune system process. Microarray and immunohistochemistry in human ovarian cancer revealed significant correlation between PD-L1 expression and positive cytology. PD-L1 expression on mouse ovarian cancer cells was induced upon encountering lymphocytes in the course of peritoneal spread in vivo and upon co-culturing with lymphocytes in vitro. Tumor cell lysis by CTLs was attenuated when PD-L1 was overexpressed and promoted when it was silenced. PD-L1 overexpression also inhibited gathering and degranulation of CTLs. In mouse ovarian cancer dissemination models, depleting PD-L1 expression on tumor cells resulted in inhibited tumor growth in the peritoneal cavity and prolonged survival. Restoring immune function by inhibiting immune-suppressive factors such as PD-L1 may be a promising therapeutic strategy for peritoneal dissemination.

overall_design: Genome-wide transcriptional changes in human ovarian cancer tissue from ascites-cytology-positive or -negative patients.

first: Masaki

last: Mandai


title: Gene Expression Profiles in BA46 of Subjects with Schizophrenia and Matched Controls

status: Public on Mar 31 2010

city: La Jolla

middle: A.

last: Thomas

state: CA

address: 10550 N. Torrey Pines Rd

department: Molecular Biology

institute: The Scripps Research Institute

summary: Results from clinical and imaging studies provide evidence for changes in schizophrenia with disease progression, however, the underlying molecular differences that may occur at different stages of illness have not been investigated.  To test the hypothesis that the molecular basis for schizophrenia changes from early to chronic illness, we profiled genome-wide expression patterns in prefrontal cortex of schizophrenic subjects at different stages of illness, along with their age- and sex-matched controls.   Results show that gene expression profiles change dramatically depending on the stage of illness, whereby the greatest number and magnitude of gene expression differences were detected in subjects with short-term illness (≤ 4 years from diagnosis).   Comprehensive pathways analyses revealed that each defined stage of illness was associated with dysfunction in both distinct, as well as overlapping systems.  Short-term illness was particularly associated with disruptions in gene transcription, metal ion binding, RNA processing and vesicle-mediated transport.  In contrast, long-term illness was associated with inflammation, stimulus-response and immune functions.   We validated expression differences of 12 transcripts associated with these various functions by real-time PCR analysis.  While only four genes, SAMSN1, CDC42BPB, DSC2 and PTPRE, were consistently expressed across all groups, there was dysfunction in overlapping systems among all stages, including cellular signal transduction, lipid metabolism and protein localization.  Our results demonstrate that the molecular basis for schizophrenia changes from early to chronic stages, providing evidence for a changing nature of schizophrenia with disease progression.

overall_design:
N=30 subjects with schizophrenia and n=29 age- and sex-matched controls.  Age range = 18-81 years

'Cont-7' was determined to be an outlier and was removed from the publication analysis.

first: Sujatha

last: Narayan

first: Bin

last: Tang

first: Steven

last: Head

first: Timothy

last: Gilmartin

first: J

last: Sutcliffe

first: Brian

last: Dean


title: Exposure of rat to a variety of toxicants, liver assayed by Affymetrix microarray

first: Scott

last: Auerbach

overall_design: Complete Drug Matrix dataset for rat liver. Approximately 600 different compounds were profiled in up to 7 different rat tissues by obtaining tissue samples from test compound-treated and vehicle control-treated rats in biological triplicates for gene expression analysis after 00.25, 1, 3, and 5 days of exposure with daily dosing. In a few studies (1.8%), 7 days of exposure was substituted for 5 days of exposure.  Samples were hybridized to whole genome RG230_2.0 rat GeneChip arrays (Affymetrix, CA).


title: Coculture with lin-/c-kit+ Stem Cells leads to a Paracrine Mediated Inhibition of Apoptosis in Cardiomyocytes

status: Public on Jun 19 2012

city: Heidelberg

first: Constantin

last: Kuehl

address: INF 350

department: Cardiology

institute: Heidelberg Universityhospital

summary:
Background: Experimental studies have suggested that stem cells (SC) may exert their beneficial effects on the ischemic heart by paracrine activation of antiapoptotic pathways. In order to identify potential cardioprotective mediators, we performed a systematic analysis of the differential gene expression of lin-/c-kit+ SC after coculture with cardiomyocytes (CM).
Methods: SC were separated from murine bone marrow and labeled with the green fluorescent CFDA. SC were then cocultivated with neonatal rat ventricular CM (NRVCM).  After 48 h, we performed two cell sorting steps to generate a highly purified population of conditioned SC (>99%) and isolated the RNA. Next, we performed a genome-wide microarray analysis of cocultured vs. monocultured SC with Illumina Chips (Coculture n=3; Monoculture n=3). Our systematic analysis of differentially expressed genes focused on products that are secretable, membrane-bound and potentially involved in antiapoptotic signal transduction.
Results: Our analysis resulted in 3 genes (out of more than 1000 differentially regulated genes) that met the criteria mentioned above and which could also be confirmed by RT-PCR. We found CCL-12 (12x, p<0.05), MIF (2x, p<0.05) and connexin 40 (4.5x; p<0.05) upregulated in our coculture model. An ELISA of cell culture supernatants was performed to proof secretability of candidate genes and showed that supernatants of coculture experiments have higher CCL-12 concentrations than monoculture experiments (20 pg/ml vs. 4 pg/ml; p<0.01). Next, we stimulated NRVCM with concentrated coculture supernatants which resulted in a significantly higher phosphorylation of AKT (p<0.01). Finally, NRVCM were labeled with Annexin-V and apoptosis of NRVCM in a co- and monoculture was measured by FACS. Thereby, we observed a reduction in apoptotic NRVCM in the coculture model (12% vs. 25%; p<0.05).
Conclusion: Our results provide evidence that coculture of SC with NRVCM leads to an upregulation of antiapoptotic genes and a paracrine-mediated increase in the phosphorylation of AKT. This results in less apoptotis in cocultured NRVCM. We therefore conclude, that cell-cell interactions lead to a modified gene expression in SC that may in part explain the cardioprotective effects of stem cell therapy.

sample_organism:
Mus musculus
Rattus norvegicus

overall_design: We analysed six RNA samples extracted from three cocultures and three monocultures. Every sample represents an independant biological experiment, derived from individual preparations of cardiac myocytes and bone marrow stem cells.

first: Mark

last: Rosenberg

first: Matthias

last: Lutz

last: Kühl

first: Rainer

last: Will

first: Volker

last: Eckstein

first: Jutta

last: Krebs

first: Hugo

last: Katus

first: Norbert

last: Frey


title: Distinct DNA methylation profiles between adenocarcinoma and squamous cell carcinoma of human uterine cervix

status: Public on Mar 18 2009

city: San Diego

first: Yipeng

last: Wang

institute: Vaccine Research Institute of San Diego

summary: A microarray-based strategy using digestion with the methylation-sensitive restriction enzyme HpaII, ligation, and PCR, was performed to assess the DNA methylation status of promoter regions in Six human cervical adenocarcinomas (ACA) and four squamous cell carcinomas (SCC). Two array platforms were used; an array of 11,994 ~1.5kb PCR products from 10,445 promoter regions, and an array of 355,264 oligonucleotides for 18,212 HpaII fragments in 12,617 promoter regions. Loci near 21 genes showed significant differences between ACA and SCC. Real time PCR-based validation was performed on 13 loci using other nearby candidate methylation targets in the same promoter. Methylation patterns of eleven of these 13 linked loci concurred with the microarray results. Four loci were further studied using tissues from additional patients. Hyper-methylation of loci in PAK6 and NOGOR most strongly correlated with adenocarcinoma.

overall_design:
In this project, we investigated the promoter methylation status in human cervical adenocarcinoma (ACA) and squamous cell carcinoma (SCC) to identify genes with tumor type-specific promoter DNA methylation patterns. Six ACA and four SCC tissue specimens from bulky tumor masses (clinical stage Ib2- IIb) were selected to minimize contamination from normal tissues.
Another set of hybridizations was performed using an in situ synthesized high-resolution oligonucleotide microarray (NimbleGen Inc), to increase the reliability of the data. This chip was designed to cover the same promoters as the in-house microarray. Four pools of samples were used to reduce the number of arrays used. These pools consisted of two sets of three ACA samples (total of six ACA samples) and two sets of two SCC samples (total of four SCC samples).

first: Eun-Ju

last: Lee

first: Sang-Ho

last: Choi

first: Fred

last: Long

first: Michael

last: McClelland

first: Je-Ho


title: NOD2 transmissible microbiota predispose WT mice to inflammation

first: David

last: Hot

summary: Instability in the composition of gut bacterial communities, referred as dysbiosis, has been associated with important human intestinal disorders such as Crohn’s disease and colorectal cancer. Our data showed that Nod2-mediated risk of intestinal inflammation in colitis model is communicable to WT mice by cohousing. Here, we investigated if Nod2-deficient mice microbiota is able to change transcript profiles in Nod2-immunocompetent mice (C57Bl6/J mice) independently of colitis.

overall_design: Analysis used RNA extracted from colonic mucosa of C57Bl/6J mice co-housed with Nod2-deficient mice and C57Bl/6J mice alone. Direct comparisons of 4 biologicals replicates of C57Bl/6J mice cohoused with Nod2-deficient mice vs C57Bl/6J mice were performed.

first: Aurelie

last: Couturier

first: Mathias

last: Chamaillard

first: Ludovic

last: Huot


title: In vitro exposure of rat hepatocytes to a variety of toxicants, assayed by Affymetrix microarray

first: Scott

last: Auerbach

overall_design: Complete Drug Matrix dataset for primary rat hepatocytes.  Cells were exposed to toxicants in culture medium and harvested after 0.67 or 1 day.


title: Drug Matrix Data - Affymetrix Arrays

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

overall_design: Refer to individual Series


title: Exposure of rat to a variety of toxicants, heart assayed by CodeLink microarray

summary: DrugMatrix is a comprehensive rat toxicogenomics database and analysis tool developed to facilitate the integration of toxicogenomics into hazard assessment.  Using the whole genome and a diverse set of compounds allows a comprehensive view of most pharmacological and toxicological questions and is applicable to other situations such as disease and development.

overall_design: Complete Drug Matrix dataset for rat heart. Approximately 600 different compounds were profiled in up to 8 different rat tissues by obtaining tissue samples from test compound-treated and vehicle control-treated rats in biological triplicates for gene expression analysis after 0.25, 1, 3, and 5 days of exposure with daily dosing. In a few studies (1.8%), 7 days of exposure was substituted for 5 days of exposure.  Samples were hybridized to CodeLink RU1 10K rat arrays (Amersham Biosciences).


title: Drug Matrix Data - CodeLink Arrays


title: Dysregulated synaptic gene expression and axonal neuropathology in a human iPSC-based model of familial Parkinson's disease

status: Public on Apr 23 2017

first: Ioannis

last: Vlachos

address: 330 Brookline Ave

department: Pathology

institute: Beth Israel Deaconess Medical Center

summary: We generated de novo induced pluripotent stem cells (iPSCs) from two Parkinson’s Disease patients (PD) harboring the p.A53T mutation. iPSC-derived mutant neurons displayed disease-relevant phenotypes at basal conditions, including protein aggregation, compromised neuritic outgrowth and contorted axons with swollen varicosities containing αSyn and tau. We have performed RNA Sequencing (RNA-Seq) of neurons from PD patient and control samples. RNA sequencing has also been performed to neurons derived from HUES samples subjected to the same differentiation protocol as reference.

overall_design: We have performed RNA Sequencing (RNA-Seq) in neurons PD and control samples (two clones from each individual), along with HUES-derived neurons.

first: Georgia

last: Kouroupi

first: Era

last: Taoufik

first: Artemis

last: Hatzigeorgiou

first: Rebecca

last: Matsas


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 20mGy/day gamma-rays for 400 days

status: Public on Nov 03 2016

city: Rokkasho-mura,Kamikita-gun,

first: Keiji

last: OGURA

state: Aomori

address: Takahoko, Hacchasawa,

department: Department of Radiobiology

institute: Institute for Environmental Science

type: Genome variation profiling by genome tiling array